MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Virus Genes' source. Mon, 06 Feb 2012 09:32:24 +0100 http://www.medworm.com/index.php?rid=5654685&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv31w3k4j86xw5772%2F Abstract  The H5N1 HPAI virus has brought heavy loss to poultry industry. Although, there exists limited human-to-human transmission, it poses potential serious risks to public health. HA is responsible for receptor-binding and membrane-fusion and contains the host receptor-binding sites and major epitopes for neutralizing antibodies. To investigate molecular adaption of HPAI H5N1 viruses, we performed a phylogenetic analysis of HA sequences with 240 HPAI virus strains isolated from human. The topology of the tree reveals overall clustering of strains in four major clusters based on geographic location, and shows antigenic diversity of HA of human H5N1 isolates co-circulating in Asia, Africa, and Europe. The four clusters possess distinct features within the cleavage site a... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5654685 Fri, 27 Jan 2012 17:53:08 +0100 5654685 http://www.medworm.com/index.php?rid=5654686&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fl558661824175425%2F Abstract  The genome of Banana bunchy top virus (BBTV) consists of six segments of single-stranded DNA of approximately 1 kb in length. We identified and sequenced the complete genomes of two BBTV isolates, one with and one without satellite DNA, from Haikou, Hainan, China. The Haikou-2 isolate contains six genomic segments and an additional satellite DNA while the Haikou-4 isolate contains only six genomic segments. Typical of other babuviruses, each genomic segment encodes a single open reading frame and contains the highly conserved stem-loop and major common regions. Phylogenetic analysis of the two Haikou isolates together with existing sequence records in GenBank confirmed the grouping of BBTV into two large groups and further refined the geographical distribution... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5654686 Fri, 27 Jan 2012 17:53:07 +0100 5654686 http://www.medworm.com/index.php?rid=5642407&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ffnl4172671288142%2F This study showed “a” determinant S gene mutations in HBV infected people with HBsAg positivity in Golestan Province-Iran. The rate of mutation in our study was 95%. Collectively, the results of this project exhibited that most of mutations were clustered in CD4 + antigenic epitopes. Content Type Journal ArticlePages 1-6DOI 10.1007/s11262-012-0715-zAuthors Abdolvahab Moradi, Infectious Diseases Research Centre, Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, IranSareh Zhand, Infectious Diseases Research Centre, Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, IranAmir Ghaemi, Infectious Diseases Research Centre, Department of Microbiology, School of Medicine, Golestan University o... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5642407 Tue, 24 Jan 2012 18:14:42 +0100 5642407 http://www.medworm.com/index.php?rid=5642408&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fj452m786u5562472%2F Abstract  The porcine epidemic diarrhoea virus (PEDV), a member of the Coronaviridae family, causes acute diarrhoea and dehydration in pigs. Although it was first identified in Europe, it has become increasingly problematic in many Asian countries, including Korea, China, Japan, the Philippines, and Thailand. The economic impacts of the PEDV are substantial, given that it results in significant morbidity and mortality in neonatal piglets and is associated with increased costs related to vaccination and disinfection. Recently, progress has been made in understanding the molecular epidemiology of PEDV, thereby leading to the development of new vaccines. In the current review, we first describe the molecular and genetic characteristics of the PEDV. Then we discuss its molecula... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5642408 Tue, 24 Jan 2012 07:16:23 +0100 5642408 http://www.medworm.com/index.php?rid=5623721&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F16277513317n50p1%2F Abstract  Influenza A viruses infect a large number of mammals and birds resulting in sporadic infections, seasonal epidemics, epizootics and pandemics. The segmented genome of the virus encodes 10 or 11 proteins depending on the strain. The neuraminidase, non-structural 1 and the PB1-F2 proteins are known to be variable in their length due to very specific deletions, truncations and elongations. This review presents an update on what is currently known about these three proteins and discusses their length variations in relation to virulence and host adaptation in addition to identifying possible areas of future research. Content Type Journal ArticlePages 1-11DOI 10.1007/s11262-012-0714-0Authors William G. Dundon, OIE/FAO and National Reference Laboratory for Avian Inf... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5623721 Fri, 20 Jan 2012 07:46:44 +0100 5623721 http://www.medworm.com/index.php?rid=5623722&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fw51603523p083678%2F We report the complete genome sequence of one, and partial sequences of three other Indian isolates of BTV-9. Evolutionary relationships with segment-2 and -6 sequences of BTV isolates around the world, deduced using four different phylogenetic analyses and a similarity programme, show that BTV-9 (Eastern), BTV-9 (Western), and BTV-5 form a triad of equidistant, genetically distinct groups of viruses. The Indian BTV-9 isolates were closely related to Mediterranean and European BTV-9 isolates (Eastern topotype) based on segment-2 and -6 sequences. By contrast, segment-5 analyses clustered the Indian BTV-9 isolates with South African BTV-3 reference strain (98% identity), which belongs to one of the Western types. These results have implications on BTV origin and movement, genotyping, ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5623722 Thu, 19 Jan 2012 06:56:07 +0100 5623722 http://www.medworm.com/index.php?rid=5615643&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F857337t52v34l039%2F Abstract  Nine avian influenza A viruses (AIVs), H1N2 (n = 2) and H1N3 (n = 7), were isolated from domestic ducks in live poultry markets in Zhejiang Province, Eastern China, in 2011. All viruses were characterized by whole genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that the viruses clustered in the Eurasian lineage of influenza A viruses. The hemagglutinin cleavage site of all viruses displayed features of a monobasic cleavage site. Although there was no evidence of re-assortment in subtype H1 AIVs among the avian species and mammalian hosts in this study, continued surveillance is needed considering the important role of the domestic duck in the dissemination and ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5615643 Wed, 18 Jan 2012 06:59:20 +0100 5615643 http://www.medworm.com/index.php?rid=5615642&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fg965hx6376k82u47%2F Abstract  We developed a new cell culture drug assay system (AH1R), in which genome-length hepatitis C virus (HCV) RNA (AH1 strain of genotype 1b derived from a patient with acute hepatitis C) efficiently replicates. By comparing the AH1R system with the OR6 assay system that we developed previously (O strain of genotype 1b derived from an HCV-positive blood donor), we demonstrated that the anti-HCV profiles of reagents including interferon-γ and cyclosporine A significantly differed between these assay systems. Furthermore, we found unexpectedly that rolipram, an anti-inflammatory drug, showed anti-HCV activity in the AH1R assay but not in the OR6 assay, suggesting that the anti-HCV activity of rolipram differs depending on the HCV strain. Taken together, these results su... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5615642 Wed, 18 Jan 2012 06:59:20 +0100 5615642 http://www.medworm.com/index.php?rid=5590872&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh6792274285w2646%2F Abstract  Recent outbreaks of orf in China have been attributed to a novel strain of Orf virus (ORFV) designated ORFV-Jilin. Currently, monoclonal antibodies (Mabs) have not yet been developed against this specific pathogen even though such entities could have potential applications regarding the diagnosis and characterization of ORFV-Jilin. Therefore, the current study was undertaken to generate Mab against the immunodominant ORFV059 protein of this virus. For this purpose, the ORFV-Jilin ORFV059 protein was expressed in Escherichia coli and subsequently used as an antigen to immunize mice and for the initial screening of hybridomas prepared from the mice for their ability to produce anti-ORFV059 protein Mabs via an indirect ELISA. Ten, positive hybridomas were identified i... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5590872 Wed, 11 Jan 2012 17:52:29 +0100 5590872 http://www.medworm.com/index.php?rid=5590873&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F1360218416482113%2F Abstract  Recombination is a major driver of diversification of geminiviruses and is believed to be, for a large part, responsible for the present taxonomic structure of the family Geminiviridae. Examples of recent intergeneric recombination between viruses of the genera Begomovirus and Mastrevirus remain to be identified. Here, we show that one of the prerequisites for begomovirus–mastrevirus intergeneric recombination, co-infection of a single plant, does occur. The lack of reported recombination between viruses of these two genera may suggest that there are constraints to viable intergeneric recombinant viruses being produced, possibly due to the extreme genetic distances between extant begomo- and mastreviruses. Content Type Journal ArticlePages 1-3DOI 10.1007/s112... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5590873 Wed, 11 Jan 2012 17:52:27 +0100 5590873 http://www.medworm.com/index.php?rid=5590874&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F43614434434m38n1%2F Abstract  Rice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), I... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5590874 Tue, 10 Jan 2012 17:00:22 +0100 5590874 http://www.medworm.com/index.php?rid=5575506&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F802m987hr17t8445%2F Abstract  The eight gene segments of avian influenza virus (AIV) reassort frequently and rapidly to generate novel genotypes and subtypes that are transmissible to a broad range of hosts. There is evidence that AIV can have a restricted host range and can segregate in space and time. Host–virus relationships at the species, geographic, and spatial scales have not been fully defined for AIV populations of the Pacific Flyway, particularly among the diverse waterfowl that occupy the Flyway in Alaska and California. Using the sequence analysis program Bayesian Tip-association Significance testing (BaTS) created for analysis of phylogeny–trait associations, we determined whether the genetic structure of Pacific Flyway AIVs sampled between 2006 and 2008 was influenced by the ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5575506 Thu, 05 Jan 2012 17:01:00 +0100 5575506 http://www.medworm.com/index.php?rid=5575507&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ff102q3723mj51388%2F Abstract  The existence of four dengue serotypes is associated with a phenomenon called “Antibody-Dependent Enhancement” that has been suggested to cause a severe form of dengue hemorrhagic fever and shock syndrome. To study the evolutionary event that drove the serotype separation, we employed the maximum likelihood approach by focusing on the Premembrane (prM) and Envelop (E) genes. We showed that the separation of dengue serotypes had been dominantly under purifying selection. In spite of the strong selective constraint, one codon of prM gene and twelve codons of E gene were detected to be under positive selection. This indicates that the E protein might have been under a stronger positive pressure than the PrM protein. The codons under positive selection were identifi... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5575507 Thu, 05 Jan 2012 17:00:59 +0100 5575507 http://www.medworm.com/index.php?rid=5567087&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F4p8322116q042225%2F In this study, molecular detection and genetic analysis of a partial VP2 gene region of CPVs from domestic cats living in Turkey between 2006 and 2010 was performed by PCR amplification and sequence analysis. The results indicated that CPV-2a, CPV-2c, and FPLV were circulating in vaccinated and unvaccinated cats. This is the first description of molecular characterization of CPVs in domestic cats from Turkey. Content Type Journal ArticlePages 1-8DOI 10.1007/s11262-011-0703-8Authors Dilek Muz, Department of Virology, Faculty of Veterinary Medicine, Mustafa Kemal University, Antakya, Hatay, TurkeyT. Çiğdem Oğuzoğlu, Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, TurkeyM. Özkan Timurkan, Department of Virology, Faculty of Veterinary Medicine,... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5567087 Fri, 30 Dec 2011 06:48:23 +0100 5567087 http://www.medworm.com/index.php?rid=5548743&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp4337455815lk128%2F Abstract  Isolates of the A(H1N1)pdm2009 virus were first identified in asymptomatic swine in Jiangsu province, China in January 2010, indicating that the virus has retro-infected swine after circulating through humans in mainland China. The purpose of this study was to determine whether the avian-origin European H1N1 swine influenza virus (SIV) and the A(H1N1)pdm2009 virus are cocirculating in swine in Jiangsu province of China. From May 2010 to May 2011, 1,030 nasal swab samples were collected from healthy swine in Jiangsu province of China and were tested for influenza A H1N1 using reverse transcription-PCR. Fragments of the complete genomes of viruses from the samples that were positive for influenza A H1N1 were sequenced and analysed. A total of 32 avian-origin Europea... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5548743 Sat, 24 Dec 2011 16:45:39 +0100 5548743 http://www.medworm.com/index.php?rid=5519552&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy10lm7148132724j%2F Abstract  Kaposi’s sarcoma-associated herpesvirus ORF30-33 locus encodes four genes with unknown functions. We performed transcriptional mapping of these genes. Northern-hybridization, 5′- and 3′-rapid amplification of cDNA ends, and DNA sequencing identified four transcripts of 3.7, 3.6, 2.7, and 1.4 kb, none of which has alternative splicing. While all transcripts have the same termination site, their start sites vary. All transcripts are not expressed or only weakly expressed in latent cells but can be chemically induced. The 3.7 and 3.6 kb transcripts contain all four genes and are sensitive to cycloheximide (CH) but resistant to phosphonoacetic acid (PAA), indicating that they are early lytic transcripts. The 2.7 kb transcript contains ORF32 and OR... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519552 Fri, 16 Dec 2011 16:54:28 +0100 5519552 http://www.medworm.com/index.php?rid=5519555&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F96p65l5612805857%2F Abstract  Yellow mosaic disease causes severe yield loss in grain legumes in Indian subcontinent and south east Asia. The disease is caused by two virus species, Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV). They have genome organization typical of Old World begomoviruses, the unique feature being the presence of an open reading frame (ORF) AV2 upstream of coat protein gene. In order to elucidate its function, ORF AV2 of blackgram isolate, Mungbean yellow mosaic India virus-[India:New Delhi:Blackgram 3:1991] MYMIV-[IN:ND:Bg3:91] and cowpea isolate, Mungbean yellow mosaic India virus-[India:New Delhi:Cowpea7:1998] MYMIV-[IN:ND:Cp7:98], respectively, were over expressed in Escherichia coli in fusion with maltose binding protein (MBP). The... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519555 Thu, 15 Dec 2011 16:48:14 +0100 5519555 http://www.medworm.com/index.php?rid=5519554&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fr536318q0007l240%2F Abstract  Human noroviruses (NoVs) of the Caliciviridae family are a major cause of epidemic gastroenteritis. The NoV genus is genetically diverse and recombination of viral RNA is known to depend upon various immunological and intracellular constraints that may allow the emergence of viable recombinants. In the present study, we report the development of a broadly reactive RT-PCR assay, which allowed the characterization of strain A6 at molecular level, established its genetic relationship at the sub-genogroup level and classified A6 strain at the sub-genotype level. The detection was carried out initially by enzyme-linked immunosorbent assay (ELISA) and the subsequent detection and molecular characterization of NoV strain was achieved by reverse transcription-PCR and seque... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519554 Thu, 15 Dec 2011 16:48:14 +0100 5519554 http://www.medworm.com/index.php?rid=5519553&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fam63v64550646327%2F Abstract  Human cosavirus (HCoSV) is a newly discovered virus in Picornaviridae family. At present it is not clear whether HCoSV is associated with diseases, including gastroenteritis in humans, as epidemiological data is limited. Epidemiological surveillance of HCoSV was conducted on 150 fecal specimens collected from children and 150 samples from adults with diarrhea in Thailand by RT-PCR screening. HCoSV was found in a single adult specimen and not in any of the fecal specimens from children. This represents the first report of HCoSV infection in patients with diarrhea in Thailand. Extensive epidemiological surveillance of novel viruses associated with diarrhea in other populations may provide a better understanding of the distribution, genetic diversity, and association ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519553 Thu, 15 Dec 2011 16:48:14 +0100 5519553 http://www.medworm.com/index.php?rid=5519556&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fq43767g722837455%2F Abstract   Gallid herpesvirus-1 (GaHV-1), commonly named infectious laryngotracheitis (ILT) virus, causes the respiratory disease in chickens known as ILT. The molecular determinants associated with differences in pathogenicity of GaHV-1 strains are not completely understood, and a comparison of genomic sequences of isolates that belong to different genotypes could help identify genes involved in virulence. Dideoxy sequencing, 454 pyrosequencing and Illumina sequencing-by-synthesis were used to determine the nucleotide sequences of four genotypes of virulent strains from GaHV-1 groups I–VI. Three hundred and twenty-five open reading frames (ORFs) were compared with those of the recently sequenced genome of the Serva vaccine strain. Only four ORFs, ORF C, UL37, ICP4 and US... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519556 Thu, 15 Dec 2011 16:48:13 +0100 5519556 http://www.medworm.com/index.php?rid=5519557&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fg798403v63g45l3x%2F Abstract  A rapid method for detection, discrimination and quantification of wheat and barley strains of wheat dwarf virus (WDV) was successfully developed. The sensitivity of quantification of the wheat and barley strains of WDV ranged from an average of 1.2 × 107–1.2 × 102 and from an average of 1.4 × 107–1.4 × 104 copies of viral genome, respectively. These standard serial dilutions were applied to plant and vector tissues for virus titer calculations. Both strains of WDV were clearly discriminated by specific probes and melting curve analysis. Both TaqMan® and SYBR® Green technologies provided accurate and reliable methods for monitoring, detection, discrimination, and quantification of WDV. Content Type Journal Articl... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5519557 Thu, 15 Dec 2011 16:48:12 +0100 5519557 http://www.medworm.com/index.php?rid=5510698&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe7343903284376l7%2F Abstract  Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Similar motifs are also present in other RNA viruses. Two fecal specimens and 18 litter extracts collected from chickens and turkeys yielded RT-PCR products. BLAST search and phylogenetic analysis revealed that all amplicons represented picornaviruses that clustered into two major groups. Four chicken and one turkey samples yielded 250 bp amplicons with 84–91% nucleotide identity to the recently described turkey hepatitis viruses, while 280 and 283 bp amplicons o... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5510698 Mon, 12 Dec 2011 17:14:34 +0100 5510698 http://www.medworm.com/index.php?rid=5481655&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fc656352547957n70%2F Abstract  Ribgrass mosaic virus (RMV) has severely decreased the production and lowered quality of Chinese cabbage co-infected with Turnip mosaic virus (63.4%) in Korea. The complete genome sequence of RMV isolated from Brassica rapa ssp. pekinensis was determined. The full genome consisted of 6,304 nucleotides and showed sequence identities of 91.5–94.2% with the corresponding genome of other RMV strains. Full-length cDNA of RMV-Br was amplified by RT-PCR with a 5′-end primer harboring a T7 promoter sequence and a 3′-end RMV specific primer. Subsequently, the full-length cDNA was cloned into plasmid vectors. Capped transcripts synthesized from the cDNA clone were highly infectious and caused characteristic symptoms in B. rapa ssp. pekinensis and several indicator plant... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5481655 Mon, 05 Dec 2011 17:43:36 +0100 5481655 http://www.medworm.com/index.php?rid=5453114&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F51742743155508h2%2F Abstract  Porcine circovirus 2 (PCV2) is a small circular single-stranded DNA virus that causes postweaning multisystemic wasting syndrome in pigs. We obtained an infectious clone, derived from PCV2 strain 1147 (size 1,767 bp), with a 60 bp insertion in the cap–rep intergenic region at the 3′ end of the rep. In vitro propagation and sequencing of virus showed mixed sequence for the cap–rep intergenic region. Cloning of this region of virus from the passages 2 and 20 showed deletions of various size of the 60 bp insertion. Viruses from the passage 20 showed deletions of the 60 bp insertion and had extra (+1 to +5) or less (−1 or −2) bp in the intergenic region as compared to 1,147. These findings suggest that insertion of a 60-bp DNA sequence at th... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5453114 Thu, 24 Nov 2011 17:44:55 +0100 5453114 http://www.medworm.com/index.php?rid=5453115&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fr321251k37132321%2F Abstract  Porcine kobuvirus is a new candidate species of the genus Kobuvirus in the family Picornaviridae, and information is still limited. The identification of porcine kobuvirus has been performed by the sequence analyses of the 3D region of the viruses. Therefore, the purpose of this study was to characterize the molecular properties of VP1 nucleotide sequences of the porcine kobuviruses isolated from porcine stool samples in Japan during 2009 and Thailand between 2006 and 2008. In addition, previous identification of a unique porcine kobuvirus; Japanese H023/2009/JP, which is a bovine kobuvirus-like strain based on sequence analysis of the 3D region, was also included in this study. All of the strains were amplified by the VP1-specific primer pair: the amplicons were s... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5453115 Tue, 22 Nov 2011 17:59:06 +0100 5453115 http://www.medworm.com/index.php?rid=5446409&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ft1r77k678861430v%2F Abstract  Tomato yellow leaf curl virus (TYLCV) and Ageratum yellow vein betasatellite (AYVB) are members of the genus Begomovirus (family Geminiviridae). TYLCV and AYVB have been found in Japan over the last 15 years, and are associated with tomato leaf curl and the tomato yellow leaf curl diseases (TYLCD). AYVB is also associated with some monopartite begomoviruses. We have cloned both TYLCV and AYVB and demonstrated that TYLCV can trans-replicate with AYVB in Nicotiana benthamiana and tomato plants. A mixed infection of TYLCV and AYVB induced more severe symptoms of upward leaf curl, stunting, vein thickening, and swelling compared with TYLCV infection alone. The symptoms induced by infection of AYVB included a rise in abnormal cell proliferation, and pigmentation aro... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5446409 Mon, 21 Nov 2011 18:04:59 +0100 5446409 http://www.medworm.com/index.php?rid=5436138&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fb21180714p75q302%2F Abstract  The Sofjin strain is one of the first isolates of tick-borne encephalitis virus and, due to its wide distribution in virus collections, it has become the reference strain. Until now, GenBank has recorded several sequences associated with the Sofjin strain that have significant differences between each other. We have sequenced the complete genome of the Sofjin strain from a virus collection and a genome fragment of the two vaccine Sofjin strains. According to phylogenetic analysis, we concluded that the GenBank sequences belong to three independent groups of Sofjin strains of the Far Eastern subtype. Their genetic differences are not a result of microevolution associated with numerous passages. Retrospective analysis of the peculiarities of origin and distribution ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5436138 Fri, 18 Nov 2011 06:58:05 +0100 5436138 http://www.medworm.com/index.php?rid=5426980&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F8u050787110435j2%2F In conclusion, full genome sequence analysis of circulating enteroviral strains is a prerequisite to understand the complexity of enterovirus evolution. Content Type Journal ArticlePages 1-10DOI 10.1007/s11262-011-0688-3Authors Zaharoula Kyriakopoulou, Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos & Aeolou Str., Larissa, 41 221 GreeceVaia Pliaka, Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos & Aeolou Str., Larissa, 41 221 GreeceDimitris Tsakogiannis, Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos & Aeolou Str., Larissa, 41 221 GreeceIrina G. A. Ruether, Department of Biochemistry & Biotechnology, University of Thessaly, 26 Ploutonos & Aeolou Str., Larissa, 41 221 GreeceDimitris K... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5426980 Wed, 16 Nov 2011 16:48:11 +0100 5426980 http://www.medworm.com/index.php?rid=5426982&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fj717k4mu161j5v77%2F Abstract  Since 2003, a new viral disease of eggplant (Solanum melongena L.) has been spreading in fields in the Jordan and Arava Valleys, Israel. The symptoms of this disease include mild leaf mottling and varying degrees of fruit distortion. This disease can be transmitted by mechanical sap inoculation, as well as by the whitefly Bemisia tabaci (Homoptera, Aleyrodidae) and has been tentatively named eggplant mild leaf mottle virus (EMLMV). Our study aimed to determine the complete sequence and genome organization of EMLMV. The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by ds-cDNA synthesis or PCR amplification. The ssRNA genome of EMLMV includes 9,280 nucleotides... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5426982 Tue, 15 Nov 2011 16:48:15 +0100 5426982 http://www.medworm.com/index.php?rid=5426981&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ft65411650722u321%2F This study investigated genetic variations in eight major genes (hemagglutinin, HA; neuraminidase, NA; matrix protein, MP; non-structural protein, NS; nucleoprotein, NP; polymerase, PA; PA basic protein 1, PB1; and PA basic protein 2, PB2) of the influenza A virus subtype H3N2 (A/H3N2) to determine the evolutionary pattern in codon bias. A total of 6,881 sequences isolated between 1993 and 2010 were used. The relative synonymous codon usage (RSCU) and G+C% content at the three codon positions were analyzed by calculating the codon substitution patterns were analyzed by calculating the percentage of synonymously substituted codons (SSCs) and that of codons substituted to the same codon within each synonymous codon group (EMC) between 1993 and subsequent years. In the multivariate analy... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5426981 Tue, 15 Nov 2011 16:48:15 +0100 5426981 http://www.medworm.com/index.php?rid=5415584&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp02v0774j5423328%2F Abstract  Nine avian influenza viruses (AIV), H5N1 subtype, were isolated from dead poultry in the Karachi region of Pakistan from 2006 to 2008. The intravenous pathogenicity indices and HA protein cleavage sites of all nine viruses were consistent with highly pathogenic AIV. Based on phylogenetic analysis of the HA genes, these isolates belong to clade 2.2 and both the HA and NA are closely related to each other (nucleotide identities above 99.0%) and to other Middle Eastern H5N1 AIV isolates (nucleotide identities above 98.0%). The phylogenetic data suggest that the virus in both epornitics of H5N1 HPAIV in commercial poultry in the Karachi region of Pakistan between 2006 and 2008 were from a very closely related source, however, there is inadequate epidemiological data t... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5415584 Mon, 14 Nov 2011 16:57:12 +0100 5415584 http://www.medworm.com/index.php?rid=5394474&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh887q55758552785%2F Abstract  Since the 1980s, the Japanese encephalitis virus (JEV) variants with slightly short variable regions (VR) of the 3′ non-translated region (NTR) have been found; however, the implications of these short VR remain unclear. We recently identified two novel types of short VR (5 and 9 nt shorter than that of major group of genotype I JEV strains) of genotype I JEV isolates. To elucidate the impact of these short VR on the replication and virulence of JEV, we generated five recombinant JEV viruses: M41-d5 and M41-d9 have deletions in the VR that correspond to those observed in some recent JEV isolates, M41-d5d9 has both the 5- and 9-nt deletions in the VR, M41-d27 has a large deletion that encompasses both the 5- and 9-nt deletion regions, and M41-a13 has a 13-nt... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5394474 Sat, 05 Nov 2011 17:10:31 +0100 5394474 http://www.medworm.com/index.php?rid=5394475&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh603650u74l70607%2F Abstract  Encephalomyocarditis virus (EMCV) could infect many host species and cause acute myocarditis and sudden death in pre-weaned piglets. It was necessary to develop new antiviral strategies for the treatment of the virus infection. Here, four plasmids expressing shRNA (small hairpin RNA) targeted to 1D or 3AB protein genes of EMCV were constructed and their inhibition efficiency on the replication of EMCV was evaluated in both BHK21 cells and mice. The results showed that three out of those four shRNA constructs could significantly inhibit EMCV replication in BHK21 cells on the levels of viral RNA and protein. Moreover, it was found that the shRNAs could suppress significantly the load of EMCV in the brain tissue of the mice pretreated with the constructs for 6–24&n... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5394475 Thu, 03 Nov 2011 16:56:46 +0100 5394475 http://www.medworm.com/index.php?rid=5372172&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F760171207666t354%2F In this study, we found that Syk, a downstream molecule of ITAM, interacts with the wild-type (WT) CVB3 VP0 protein, but not with the mutant CVB3 VP0 (called YYFF), and that an inhibitor of Syk reduced the growth of CVB3. The WT CVB3 activated nuclear factor kappa B (NF-κB), a protein activated by ITAM, and eventually induced the production of interleukin-6 (IL-6)—one of the proinflammatory cytokines induced by NF-κB—in macrophages. However, the YYFF form did not. In addition, viral VP2 protein may be dependent on the phosphorylation of an ITAM-like region that affected the activation of NF-κB. Taken together, these results suggest that the ITAM-like sequences in CVB3 VP2 can not only affect viral structure but also act as signals in pathogenesis. Content Type Journal Art... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5372172 Fri, 28 Oct 2011 17:23:51 +0100 5372172 http://www.medworm.com/index.php?rid=5353706&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv3744t2p6j182275%2F Abstract  The variability in the nucleotide (nt) and amino acid (aa) sequences of the coat protein (CP) of Cymbidium mosaic virus (CymMV), which naturally infects orchids worldwide, was investigated. The CP genes of 55 CymMV isolates originating from different locations in Korea were amplified using RT-PCR and sequenced. The encoded CP consists of 223 aa. The CP sequences of the Korean isolates were compared with those of previously published CymMV isolates originating from different countries at both nt and aa levels. The Korean isolates shared 74.9–98.3 and 52.7–100% CP homology with CymMV isolates from other countries at the nt and aa levels, respectively. No particular region of variability could be found in either grouping of viruses. In the deduced CymMV CP aa seq... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5353706 Fri, 21 Oct 2011 05:47:15 +0100 5353706 http://www.medworm.com/index.php?rid=5342110&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F3027835282t3212t%2F Abstract  Japanese quince, ornamental and wild pear symptomless samples were infected with Apple stem pitting virus (ASPV). Identification of ASPV was achieved by different PCR assays that amplified either the RNA polymerase or coat protein gene regions. For further confirmation, 312 bp amplicons within the polymerase gene were sequenced and compared with previously published ASPV sequences and additional sequences of isolates from ancient Italian cultivars. Comparison of the partial sequences isolated from wild/ornamental hosts and from cultivated species revealed significant divergence levels. Among the wild/ornamental isolates, the PCT88 isolate from Pyrus calleryana was the most divergent, having an amino acid deletion and incorporating a unique stretch of amino acid... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5342110 Mon, 17 Oct 2011 16:03:34 +0100 5342110 http://www.medworm.com/index.php?rid=5320116&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fcl104108r4103278%2F Abstract   Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus. The large intergenic region (LIGR) of RTBV having a single transcriptional promoter produces more than genome length pregenomic RNA (pgRNA) which directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis of LIGR, the 11 RTBV isolates sequenced so far were compared with respect to structural organization of promoter and pgRNA 5′-leader. The results revealed only 74.90% identity at LIGR between ‘Southeast Asian’ (SEA) and ‘South Asian’ (SA) isolates of RTBV indicating considerable variation between two groups which was also reflected during analysis of promoter and leader sequence. The predicted promoter region of SA isolates exhibi... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5320116 Tue, 11 Oct 2011 15:52:40 +0100 5320116 http://www.medworm.com/index.php?rid=5309491&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F83167627717061g5%2F In this study, we determined the complete sequence of the genomic DNA of a Polish isolate of Blueberry red ringspot virus (BRRSV24) and compared it with a Czech (Darrow 5), and the US isolates of the virus and those of other Caulimoviridae family. The genomic DNA of BRRSV24 consists of 8,265 nucleotides and encodes eight open reading frames (ORFs). The sequence homologies of the eight ORFs of BRRSV24 were from 95 to 98% in respect of Darrow 5 and from 91 to 98% in respect of the US isolates at the amino acid level. This high level of amino acid sequence identity within the coding regions among the Czech, the US and Polish BRRSV isolates is suggestive of their common origin. Content Type Journal ArticlePages 1-3DOI 10.1007/s11262-011-0679-4Authors E. Kalinowska, Faculty of Horticu... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5309491 Mon, 10 Oct 2011 15:01:43 +0100 5309491 http://www.medworm.com/index.php?rid=5300906&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F808v1p8118l076v7%2F Abstract   Xanthium strumarium is a common weed that often shows symptoms typical of begomovirus infection, such as leaf curling and vein thickening. The virus complex isolated from the weed consisted of two begomoviruses along with a betasatellite and an alphasatellite. The first begomovirus was shown to be an isolate of Cotton leaf curl Burewala virus, a new recombinant begomovirus species that is associated with resistance breaking in previously resistant cotton varieties in Pakistan, whereas the second was shown to be an isolate of Tomato leaf curl Gujarat virus (ToLCGV), a begomovirus previously reported to be bipartite. However, there was no evidence for the presence of the second genomic component, DNA B, of ToLCGV in X. strumarium. The betasatellite was shown to be a... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5300906 Tue, 04 Oct 2011 05:56:16 +0100 5300906 http://www.medworm.com/index.php?rid=5280054&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fkx2p0v13pt26056r%2F Abstract  The recognition of a common source norovirus outbreak is supported by finding identical norovirus sequences in patients. Norovirus sequencing has been established in many (national) public health laboratories and academic centers, but often partial and different genome sequences are used. Therefore, agreement on a target sequence of sufficient diversity to resolve links between outbreaks is crucial. Although harmonization of laboratory methods is one of the keystone activities of networks that have the aim to identify common source norovirus outbreaks, this has proven difficult to accomplish, particularly in the international context. Here, we aimed at providing a method enabling identification of the genomic region informative of a common source norovirus outbrea... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5280054 Fri, 30 Sep 2011 05:54:09 +0100 5280054 http://www.medworm.com/index.php?rid=5280053&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fu20158592w30426q%2F In this study, EHV-4 gG deletion mutant has been generated by using bacterial artificial chromosome technology to investigate the role of gG in viral pathogenesis. Our findings reported here revealed no significant difference between parental EHV-4 and gG-negative strain in their replication cycle in cell culture. Furthermore, virus titers and plaque formation were comparable in both viruses. It is noteworthy that these findings disagree with the previously published study describing gG deletion in another EHV-4 strain. Content Type Journal ArticlePages 1-3DOI 10.1007/s11262-011-0677-6Authors Walid Azab, Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, EgyptAbuelyazeed El-Sheikh, Department of Virology, Faculty of Veterinary Medicine, Zagazig ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5280053 Fri, 30 Sep 2011 05:54:09 +0100 5280053 http://www.medworm.com/index.php?rid=5280055&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F34q473p2458l0455%2F In this study, 33 NDV isolates, which included NDVs recovered from LBMs in Nigeria, during active surveillance from 2007 to 2008 and viruses recovered from outbreaks in backyard and commercial chicken farms within the same period were analysed. Based on determination of the F0 cleavage site amino acid sequence and phylogenetic analysis, the isolates were classified as virulent; 16 strains were identified as sub-lineage 5g and 17 as sub-lineage 5f. Interestingly, 13 strains from the 5f group formed a distinct cluster that was not identified by other groups in similar studies. The close genetic similarities identified, provided evidence for the first time of the epidemiological link between the viruses circulating in the LBMs and those recovered from outbreaks in backyard and commerci... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5280055 Fri, 30 Sep 2011 05:54:08 +0100 5280055 http://www.medworm.com/index.php?rid=5280056&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F175t441165622h47%2F Abstract  Porcine reproductive and respiratory syndrome (PRRS) is a swine disease of major economic importance that causes reproductive and respiratory problems in pigs. PRRSV strains are divided into European (Type 1) and North-American (Type 2) genotypes. Within the European PRRSV genotype, three subtypes have been delineated. Full genome sequences for North American and European subtype 1 strains have been described. Here, the first complete genomic characterization of a European subtype 3 strain (Lena) is described. Amplification of Orf1a and Orf1b fragments was achieved using a set of degenerate oligonucleotides. Using RT-PCR with Lena-specific primers, the full length sequence (15001 nt) was obtained. Alignment of Lena with European subtype 1 reference strain Lel... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5280056 Tue, 27 Sep 2011 05:48:46 +0100 5280056 http://www.medworm.com/index.php?rid=5256145&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fq4852190725m4106%2F Abstract  The Ibusuki (IB) strain of the East Asian Passiflora virus (EAPV) causes mottling of fruit when it infects passionfruit, but not malformation or woodiness, unlike the Amami-O-shima (AO) strain, and the host range for these two strains are different. We determined the complete nucleotide sequence of the IB strain, and a comparison with that of the AO strain revealed the great diversity of the 5′-terminal region of the IB strain’s genome (5′ UTR and P1 gene). The involvement of these regions in the different symptoms on fruit and host range was suggested. The neighbor-joining tree constructed using the nucleotide sequences of coat protein gene of eight EAPV isolates including those from abroad showed the independent position of the IB strain, and that construct... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5256145 Fri, 23 Sep 2011 15:51:52 +0100 5256145 http://www.medworm.com/index.php?rid=5256146&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fpq787286q54q80xg%2F Abstract  Hepatopancreatic parvovirus (HPV) of shrimp is distributed worldwide and the entire genome of Thailand and Indian strains (PmDNV) and one Australian strain (PmergDNV) have now been reported. The complete nucleotide sequence of a HPV strain isolated from the fleshy prawn Fenneropenaeus chinensis in Korea (FcDNV) was determined and compared to previously reported sequences. The entire genome of FcDNV contains 6,336 nucleotides, with 40% G+C content, which is the biggest of the known HPV strains. The HPV genome has three open reading frames (ORFs) with a slight overlap between the first and second ORFs. The three ORFs encode the NS2 and NS1 proteins and VP that consist of 425, 578, and 820 amino acids, respectively. Among the three proteins, the NS1 protein shows the h... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5256146 Fri, 23 Sep 2011 15:51:50 +0100 5256146 http://www.medworm.com/index.php?rid=5256147&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F7153px748vp52126%2F Abstract  To counteract plant antiviral defense based on RNA silencing, many viruses express proteins that inhibit this mechanism at different levels. The genome of Citrus leaf blotch virus (CLBV) encodes a 227-kDa protein involved in replication, a 40-kDa movement protein (MP), and a 41-kDa coat protein (CP). To determine if any of these proteins might have RNA silencing suppressor activities, we have used Agrobacterium-mediated transient assays in the green fluorescent protein (GFP)-expressing Nicotiana benthamiana line 16c. Only CLBV MP was able to suppress intracellular GFP silencing induced by expression of either single- or double-stranded (ds) GFP RNA, but not cell-to-cell or long distance spread of the silencing signal. The MP suppressor activity was weak compared to ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5256147 Fri, 23 Sep 2011 15:51:49 +0100 5256147 http://www.medworm.com/index.php?rid=5256148&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe4715t68r0132k74%2F Abstract  Hepatitis C virus nonstructural protein, NS4A, is a small protein comprising of about 54 amino acids. Despite its small size, it plays key role in many viral and cellular functions. The most important of which is its role as the co-factor of viral serine protease and helicase (NS3). Our study examines the phylogenetic and structural analysis of this coding region after isolation from Pakistani HCV patient samples. Phylogenetic analysis of the gene revealed that Pakistani 3a HCV strains do not show significant divergence from those reported from the rest of the world. The findings of this study also depict that NS4A sequence is conserved within genotypes, whereas it shows variations among different genotypes. While predicting the tertiary structure of the protein t... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5256148 Fri, 23 Sep 2011 15:51:48 +0100 5256148 http://www.medworm.com/index.php?rid=5244735&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fak6254t14725h725%2F This study provides a comprehensive genetic characterization of a novel FMDV isolate of the Mya-98 lineage. Content Type Journal ArticlePages 1-9DOI 10.1007/s11262-011-0670-0Authors Haixue Zheng, State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 ChinaJijun He, State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 ChinaJianhong Guo, State Key Laboratory o... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5244735 Mon, 19 Sep 2011 15:40:33 +0100 5244735 http://www.medworm.com/index.php?rid=5231300&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F2j34k306w4kt55n0%2F Content Type Journal ArticleCategory ErratumPages 1-1DOI 10.1007/s11262-011-0671-zAuthors G. B. Manjunatha Reddy, Division of Animal Health, Central Institute for Research on Goats (CIRG), Makhdoom, Farah, Mathura, 281122 UP, IndiaR. Singh, Center for Animal Disease Research and Diagnosis, Indian Veterinary Research Institute, Izatnagar, 243122 UP, IndiaR. P. Singh, Division of Biological Product, Indian Veterinary Research Institute, Izatnagar, 243122 UP, IndiaK. P. Singh, Center for Animal Disease Research and Diagnosis, Indian Veterinary Research Institute, Izatnagar, 243122 UP, IndiaP. K. Gupta, Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, 243122 UP, IndiaAnita Mahadevan, Department of Neuropathology, National Institute of Mental Health and Neu... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5231300 Fri, 16 Sep 2011 05:50:32 +0100 5231300 http://www.medworm.com/index.php?rid=5231299&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fj8513366611lxgt4%2F Abstract  Pigeon circoviruses (PiCV) had been identified worldwide and are responsible for immune suppression and a variety of diseases collectively referred to as young pigeon disease syndrome. Samples from racing pigeons were collected throughout Hungary and analyzed for the presence of PiCV by polymerase chain reaction. The capsid protein coding gene was amplified from ten PiCVs of different origins, and compared with known PiCV sequences. The results indicated that PiCV was highly variable, the viruses formed five distinct genetic groups. Differences of the 3′ end of the gene suggested the possibility of genetic recombination among these groups. Content Type Journal ArticlePages 1-5DOI 10.1007/s11262-011-0669-6Authors Attila Cságola, Department of Microbiology ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5231299 Fri, 16 Sep 2011 05:50:32 +0100 5231299 http://www.medworm.com/index.php?rid=5216618&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fa2g3125552v00562%2F Abstract  The complete genomic sequences of a Chinese ASPV isolates KL1 and KL9 were determined from ten overlapping cDNA clones. The genomes of both isolates were 9265 nucleotides excluding the poly (A) tail and contained five open reading frames (ORFs). The identities between two complete genomes were 92.5% at nt level. Multiple alignment of the amino acid sequences showed that 110 aa variations between two genomic sequences and the variable domains mainly distributed in 5′-terminal of ORF1, ORF3, and ORF5, respectively. Two complete genomic sequences shared 71.4–77.3% identities with other ASPV isolates at nt level. Phylogenetic relationship analysis of the coat protein genes revealed that ASPV isolates had high variables and formed three groups. All ASPV isolates fr... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5216618 Sat, 10 Sep 2011 15:46:38 +0100 5216618 http://www.medworm.com/index.php?rid=5216620&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fm87q2446707220k1%2F Abstract  It is well documented that baculovirus populations contain many genotypic variants, but little is known about the degree of genetic variation in specific baculovirus genes. Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying genetic variation in nucleopolyhedrovirus genes. Next generation sequencing (NGS) was used to identify single-nucleotide polymorphisms (SNPs) within a core baculovirus gene (DNA polymerase) and two core lepidopteran-specific baculovirus genes (dbp1 and me53) in HearNPV populations. Analysis of the NGS data identified 60 SNPs within the 3063 bp DNA polymerase gene, 13 SNPs within the 972 bp dbp1 gene, and 25 SNPs within the 1080 bp me53 gene. Depending on the gene, between 31 and 35% of the SNP... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5216620 Sat, 10 Sep 2011 06:01:57 +0100 5216620 http://www.medworm.com/index.php?rid=5216619&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fm70241k24m73r637%2F Abstract  Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. The attenuated viruses did not cause any clinical signs of disease and had lower replication rates than the pathogenic viruses of the sam... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5216619 Sat, 10 Sep 2011 06:01:57 +0100 5216619 http://www.medworm.com/index.php?rid=5216621&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy2g8845777w13g5q%2F Abstract  In spring 2009, one strain of H5N1 clade 2.3.2 virus was isolated from wild swans in Shanghai, indicating the importance of the wild swan in the ecology of this highly pathogenic avian influenza virus (HPAIV) in Eastern China. Pathogenicity experiments conducted in this study indicated that the virus was highly pathogenic for chickens but lowly pathogenic for mammalian hosts, as evidenced by reduced infection of mice. The analysis of complete genome sequences and genetic evolution showed that A/Swan/Shanghai/10/09 (SW/SH/09) may be derived from the strain A/silky chicken/Shantou/475/2004 (CK/ST/04), which is homologous to the influenza viruses isolated from chicken, duck, pika, little egret, swan, mandarin duck and bar-headed goose in China Hunan, China Qinghai, M... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5216621 Fri, 09 Sep 2011 05:49:36 +0100 5216621 http://www.medworm.com/index.php?rid=5189767&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp012132414065217%2F Abstract  In 1993, a virus causing red mosaic and leaf distortion has been isolated from black bryony (Tamus communis) in Italy. Based on particle properties and serology, the virus was assigned to the genus Potexvirus and named Tamus red mosaic virus (TRMV), pending a genome sequence. The original Italian TRMV isolate was submitted to the DSMZ plant virus collection (PV-0397). To confirm the taxonomic status of the virus, the entire genome sequence was determined comprising 6,495 nucleotides excluding the poly(A)-tail. Five putative open reading frames (ORFs) in an arrangement typical for potexviruses were predicted. TRMV is closely related to but distinct from Clover yellow mosaic virus and Allium virus X. In addition to previous morphological and serological characterizatio... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5189767 Wed, 31 Aug 2011 15:56:31 +0100 5189767 http://www.medworm.com/index.php?rid=5189766&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy08711550j880420%2F In this study, the nucleotide sequences of the coat protein gene of worldwide ToMV isolates were analyzed to estimate the genetic structure and diversity of this virus and the involved evolutionary forces. The phylogenetic analysis showed three clades with high bootstrap support: Clade I contained three ToMV isolates from Brazil collected from pepper, Clade II comprised one Brazilian ToMV isolate from pepper, and Clade III was composed of ToMV isolates collected from different plant hosts (pepper, tomato, eggplant, lilac, camellia, dogwood, red spruce, etc.) and water (from melting ice, lakes and streams) from different countries: USA, Brazil, Korea, Germany, Spain, Denmark (Greenland), China, Taiwan, Malaysia, Iran, and Kazakhstan. With the exception of Brazil, nucleotide diversity ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5189766 Wed, 31 Aug 2011 15:56:31 +0100 5189766 http://www.medworm.com/index.php?rid=5189768&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe2112w0021u29076%2F Abstract  The genomic RNA of a novel chicken astrovirus was determined. The full length sequence is 7520 nucleotides and encodes three open reading frames (1a, 1b, 2) for three proteins. The genomic organization was similar to other astroviruses with two exceptions. The open reading frame of the RNA-dependent RNA polymerase contains its own start codon which is different from other astroviruses described to date, providing evidence for a replication mechanism different than what has previously been described for astroviruses. Furthermore, the stem-loop structure located at the potential ribosomal frameshift signal described for other astroviruses has been shown to be a hairpin structure for the novel chicken astrovirus. Phylogenic analysis of the full length sequence reveal... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5189768 Tue, 30 Aug 2011 15:59:32 +0100 5189768 http://www.medworm.com/index.php?rid=5189769&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fewr7733716106459%2F Abstract  Bats have great potential as reservoirs for emerging viruses such as severe acute respiratory syndrome-coronavirus. In this study, bat coronaviruses (BtCoVs) were detected by RT-PCR from intestinal and fecal specimens of Miniopterus fuliginosus breeding colonies in Wakayama Prefecture caves, where we previously identified bat betaherpesvirus 2. Two primer sets were used for the detection of BtCoV: one was for the RNA-dependent RNA polymerase (RdRp) region and the other was for the spike (S) protein region. Eleven and 73% of intestinal and fecal specimens, respectively, were positive for RdRp region, and 2 and 40% of those were positive for S protein region. Sequencing and phylogenetic analysis showed that the detected BtCoV belonged to the group 1 (alpha) coronavir... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5189769 Mon, 29 Aug 2011 16:00:26 +0100 5189769 http://www.medworm.com/index.php?rid=5153407&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F5882012733401464%2F Abstract  In order to investigate the genetic heterogeneity of small ruminant lentivirus (SRLV) isolates in Italy, 55 clinical samples collected between 1998 and 2010 were analysed. The phylogenetic study was based on analysis of gag–pol sequences. Our findings revealed that the SRLVs belonged to the subtype A9 (n = 3, sheep), B1 (n = 5, goat), B2 (n = 3, sheep) and E2 (n = 5, goat). Interestingly, 39 isolates from both sheep and goat, significantly differed from all the other SRLVs previously described and formed two separate clusters within genotypes A and B tentatively named A11 (n = 27, goat and sheep) and B3 (n = 12, goat and sheep), which have never been shown before. These results revealed a marked diversity a... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153407 Fri, 19 Aug 2011 16:01:52 +0100 5153407 http://www.medworm.com/index.php?rid=5153406&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fm45373tvu74q8590%2F Abstract  The continuous emergence of new strains of canine parvovirus (CPV), poorly protected by current vaccination, is a concern among breeders, veterinarians, and dog owners around the world. Therefore, the understanding of the genetic variation in emerging CPV strains is crucial for the design of disease control strategies, including vaccines. In this paper, we obtained the sequences of the full-length gene encoding for the main capsid protein (VP2) of 11 canine parvovirus type 2 (CPV-2) Argentine representative field strains, selected from a total of 75 positive samples studied in our laboratory in the last 9 years. A comparative sequence analysis was performed on 9 CPV-2c, one CPV-2a, and one CPV-2b Argentine strains with respect to international strains reported... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153406 Fri, 19 Aug 2011 16:01:52 +0100 5153406 http://www.medworm.com/index.php?rid=5153409&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe1585qlv41q517q1%2F Abstract  In January 2009, an H4N2 subtype of avian influenza virus [A/duck/Hunan/8-19/2009 (H4N2)] was isolated from domestic ducks in Dongting Lake wetland. The whole genome of the virus was sequenced and the results indicated that multiple gene segments of the virus had a high homology with viruses isolated from wild waterfowl, which indicated that the virus was probably transmitted from wild waterfowl to domestic ducks. Phylogenetic analysis revealed that the each gene belonged to the Eurasian lineage of avian influenza viruses, but genetic reassortment occurs between viruses of different subtypes. Content Type Journal ArticlePages 1-8DOI 10.1007/s11262-011-0658-9Authors Hongbo Zhang, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153409 Fri, 19 Aug 2011 05:49:13 +0100 5153409 http://www.medworm.com/index.php?rid=5153408&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ff01vuq4585091h13%2F Abstract  Transgenic tobacco plants expressing fused, tandem, inverted-repeat, double-stranded RNAs derived either from the three viruses [potato virus Y (PVY), potato virus A (PVA), and potato leafroll virus (PLRV)] or the five viruses [PVY, PVA, PLRV as well as tobacco rattle virus (TRV), and potato mop-top virus (PMTV)] were generated in this study to examine whether resistance could be achieved against these three viruses or five viruses, respectively, in the same plant. The transgenic lines were engineered to produce 600- or 1000-bp inverted hairpin transcripts with an intron, in two orientations each, which were processed to silencing–inducing RNAs (siRNAs). Fewer lines were regenerated from the transformants with either 1000-bp inverted hairpin transcripts, or a se... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153408 Fri, 19 Aug 2011 05:49:13 +0100 5153408 http://www.medworm.com/index.php?rid=5153410&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe66320q8340t1223%2F Abstract   Vernonia yellow vein virus (VeYVV) is a distinct monopartite begomovirus associated with a satellite DNA β. After constructing dimers of both DNA A and DNA β in binary vectors, a number of infection methods were attempted. However, only a modified stem-prick method produced up to 83% infection in the natural host Vernonia cinerea, thus, fulfilling the Koch’s postulate. The presence of the viral DNA in the agroinfected plants was confirmed by rolling circle amplification (RCA), followed by Southern hybridization. DNA β induces typical symptoms of Vernonia yellow vein disease (VeYVD) when co-agroinoculated with the begomovirus to Vernonia and also leads to the accumulation of DNA A systemically. VeYVV represents a new member of the emerging group of monopartit... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153410 Thu, 18 Aug 2011 06:03:14 +0100 5153410 http://www.medworm.com/index.php?rid=5153411&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fk48q635262616522%2F Abstract   Chilli ringspot virus (ChiRSV), a novel potyvirus, was recently found in Hainan, China with high prevalence. The genomic sequence of the ChiRSV-HN/14 isolate was determined by sequencing overlapping cDNA segments generated by reverse transcription polymerase chain reaction with degenerate and/or specific primers. ChiRSV genome (GenBank Acc. no. JN008909) comprised of 9,571 nucleotides (nt) excluding the 3′-terminal poly (A) tail and contained a large open reading frame of 9,240 nt encoding a large polyprotein of 3,079 amino acids with predicted Mr of 349.1 kDa. A small, overlapping PIPO coding region was also found to span from nt 2,913 to 3,095, with a capacity to encode a peptide of 60 amino acids. ChiRSV shares sequence identities of only 48.5–65... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5153411 Wed, 17 Aug 2011 05:55:43 +0100 5153411 http://www.medworm.com/index.php?rid=5136752&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F68715t7023255076%2F Abstract  Mungbean yellow mosaic geminivirus (MYMV) causes severe yellow mosaic disease in blackgram, mungbean, Frenchbean, pigeonpea, soybean and mothbean. We attempted to induce resistance against this virus using the transcriptional activator protein gene deleted in the C-terminal activation domain (TrAP-∆AD) and Agrobacterium tumefaciens virE2. MYMV is known to replicate in agroinoculated tobacco leaf discs. Three transgenic tobacco plants which harboured a truncated MYMV transcriptional activator protein gene and two tobacco plants transformed with the octopine type A. tumefaciens virE2 gene were agroinoculated with an A. tumefaciens strain which harboured the partial dimers of both DNA A and DNA B of MYMV. The level of viral DNA accumulation in leaf discs of trans... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5136752 Sat, 13 Aug 2011 06:05:32 +0100 5136752 http://www.medworm.com/index.php?rid=5136753&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fd800877p70672427%2F Abstract  As part of our ongoing surveillance program, 40 field strains of avian infectious bronchitis virus (IBV) were isolated from dead or diseased chicken flocks in different areas of China between 2009 and 2010. S1 glycoprotein genes of these strains were sequenced and analyzed with 38 strains published in GenBank. S1 genes of these isolated strains and the vaccine strains showed nucleotide homologies ranging from 65.2 to 82% and amino acid homologies ranging from 58.4 to 81.9%. Meanwhile, Chinese IBV strains isolated in this study, which were mainly nephropathogenic, could be separated into six variant lineages (CH I–CH VI), and current vaccine strains used in China formed Mass variant lineage that is evolutionarily distant from Chinese isolates. Moreover, CK/CH/GD/... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5136753 Sat, 13 Aug 2011 06:05:31 +0100 5136753 http://www.medworm.com/index.php?rid=5115591&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fpr57657724757607%2F In this study, we have designed siRNA from the most conserved regions of viral coat protein (AV1) and replicase (AC1) genes retrieved from different isolates of geminiviruses infecting papaya (PLCV), and tomato (TLCV & TLCV, Northern India), so as to give a broad spectrum resistance and efficient silencing as it is highly homology-dependent strategy. Software siRNA finder (Ambion) was used on the selected conserved sequences in order to select only those putative siRNA oligonucleotides which fulfill all the basic criteria required as per the algorithm. Finally, a cross search using BLAST was performed to confirm that the designed siRNAs do not have any homology to plant genome sequences. The putative siRNA sequences thus designed to target essential genes of geminiviruses and introdu... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5115591 Sat, 06 Aug 2011 05:46:59 +0100 5115591 http://www.medworm.com/index.php?rid=5115590&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fpv846066j3p86255%2F Abstract  Novel porcine parvoviruses showing the genetic characteristics of bocaviruses have recently been identified. The first such porcine bocavirus (PoBoV1), described as boca-like virus (PBo-likeV), was discovered in PMWS affected pigs in Sweden. Later, several other bocaviruses with divergent genomes were reported under various names in domestic pigs. This is the first report of the presence of bocaviruses in European wild boars. 842 wild boar samples originating from the Western region of Romania (Transylvania) were collected during the 2006/2007 and the 2010/2011 hunting seasons and tested for the presence of PoBoV1 by polymerase chain reaction and sequencing. The results showed 12.94% (109/842) overall positivity, with an increasing prevalence from the 2006/2007 (9... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5115590 Sat, 06 Aug 2011 05:46:59 +0100 5115590 http://www.medworm.com/index.php?rid=5101785&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fj706667060rtw0g1%2F Abstract  In silico analysis of three Penaeus stylirostris densovirus (PstDNV) promoters, designated P2, P11, and P61, revealed sequence motifs including the TATA box, downstream promoter element (DPE), GC- and A-rich regions, inverted repeat, activation sequence-1 like (ASL) box, and a conserved guanosine (G) at +24. To delineate the regulatory role of these motifs on promoter activity, deletion constructs were made in a promoter assay vector, pGL3 Basic, that contains a luciferase reporter gene. Luciferase assay showed that P2 had the highest promoter activity followed by P11 and P61 in Sf9 cells. The deletions of inverted repeat, DPE, and GC-rich regions in P2 had the highest negative impact on this promoter. Deletions of DPE, G at the +24, and ASL box in P11 had the high... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5101785 Tue, 02 Aug 2011 16:01:05 +0100 5101785 http://www.medworm.com/index.php?rid=5084500&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F6777748555768927%2F In this study, the mcp gene of LCDV and the cyt b gene of the host fish were selected as molecular markers, and the phylogenetic relationships between LCDV and its host were analyzed. The 25 LCDV isolates examined in this study were attributed to seven LCDV genotypes: genotype I (LCDV-1), genotype II (LCDV-cn, etc.), genotype III (LCDV-rf), genotype IV (LCDV-rc and LCDV-sb), genotype V (LCDV-cb), genotype VI (LCDV-tl), and genotype VII (LCDV-sa). Genotype VII is a new genotype. LCDV1 was found to have differentiated first, followed by LCDV-rf; then LCDV-tl; LCDV-cb; and then LCDV-sa; and by LCDV-rc and LCDV-sb; and finally by LCDV-cn, LCDV-C, and LCDV-jf. From the host evolutionary perspective, Rachycentron canadum was found to have differentiated first, followed by Trichogaster leeri... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5084500 Fri, 29 Jul 2011 16:06:55 +0100 5084500 http://www.medworm.com/index.php?rid=5075053&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F75152056878t642t%2F Abstract  A new isolate of Rice tungro bacilliform virus (RTBV) was collected from Chinsura, West Bengal, India. The full genome was sequenced and deposited to GenBank designating the new one as Chinsura isolate. The four open reading frames (ORFs) of the new isolate were compared with those of previously reported ‘South-east Asian’ (SEA) and ‘South Asian’ (SA) isolates emphasizing the ORF3, which is the largest and functionally most important gene of RTBV. In the ORFs, Chinsura isolate shared 90.0–100.0% identity at amino acid level with SA isolates, but only 58.76–88.63% identity with SEA isolates for the same. Similarly, the amino acid identity of ORFs between SEA and SA isolates ranged from 58.77 to 88.64, whereas within each group the corresponding value was... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5075053 Wed, 27 Jul 2011 15:49:18 +0100 5075053 http://www.medworm.com/index.php?rid=5075054&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F2625m4q41543ug72%2F In this study, a total of 116 stool specimens were collected from pigs of different ages in three pig farms of Shanghai in China during 2010. Forty-five (38.8%) stool specimens were positive for porcine kobuvirus using reverse transcriptase-polymerase chain reaction (RT-PCR). The prevalence rate of porcine kobuvirus in the three pig farms which are located in Minhang District, Qingpu District and Fengxian District was 46.7%(21/45), 35.1%(13/37), and 32.4%(11/34), respectively. We demonstrated that porcine kobuvirus infections are existent in certain domestic pigs in Shanghai and high prevalence of this virus was found in the piglets under the age of 6 weeks and in pigs with diarrhea in Shanghai. Twenty-seven representative strains of porcine kobuvirus detected in this study were r... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5075054 Tue, 26 Jul 2011 05:50:56 +0100 5075054 http://www.medworm.com/index.php?rid=5075055&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh33xw2752xk22pk0%2F Abstract  The main aim of the present study were to investigate sequence diversity in the Meq gene of Marek’s disease viruses (MDV) isolated in China and to determine the most prevalent MDV strains. The 19 MDV strains were isolated from dead or diseased chickens from different chicken farms in China during 2006–2008, and the Meq gene was sequenced from each of these strains. Sequence analysis showed that all of the isolates contained an open reading frame of 1020 nucleotides, which encoded a 339 amino acid peptide. Compared with reference MDV strains, 12 of the 19 MDV isolates possessed two amino acid substitutions, (T → A) at position 139 and (P → R) at position 176, one isolate shared sequence similarity with the attenuated strain CVI988, and fiv... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5075055 Tue, 26 Jul 2011 05:50:55 +0100 5075055 http://www.medworm.com/index.php?rid=5060894&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy816134rl360n817%2F Abstract   Sugarcane mosaic virus (SCMV) is the most prevalent virus causing maize dwarf mosaic disease in northern China. A SCMV isolate, BD8, was obtained from the maize showing dwarf and mosaic symptoms in Baoding, China. The complete genomic sequence of BD8 is 9,576 nucleotides (nt) excluding the poly(A) tail. It contains one single open reading frame of 9,192 nt and encodes a large polyprotein of 3,063 amino acids (aa), flanked by a 5′-untranslated region (UTR) of 148 nt and a 3′-UTR of 236 nt. The entire genomic sequence of BD8 shares identities of 79.1–80.8% with those of other 13 SCMV isolates available in the GenBank at nt level, while their CP genes share identities of 76.9–82.6 and 82.8–86.9% at nt and aa levels, respectively. Phylog... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5060894 Thu, 21 Jul 2011 17:55:48 +0100 5060894 http://www.medworm.com/index.php?rid=5046563&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe27663172j62225w%2F We report a novel reovirus (MRV-HLJ/2007) isolated from swine in Heilongjiang Province, China. Genome sequence analysis indicated a close genetic relationship between MRV-HLJ/2007 and strain SC-A, which was isolated from swine in 2006 in Sichuan, China. Although phylogenetic analysis indicated that MRV-HLJ/2007 may have originated from the SC-A strain, the M2 and S3 genes differ between these strains. Phylogenetic analysis also showed that, except for differences in the S1 gene, MRV-HLJ/2007 and SC-A are closely related to a reovirus that infects humans. These findings suggest that MRV-HLJ/2007 might be a novel reovirus strain circulating in China. Content Type Journal ArticlePages 1-8DOI 10.1007/s11262-011-0642-4Authors Chaofan Zhang, Division of Swine Infectious Diseases, Sta... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5046563 Thu, 14 Jul 2011 16:56:34 +0100 5046563 http://www.medworm.com/index.php?rid=5034560&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F5k28hx6x60126681%2F Abstract  Human cytomegalovirus (HCMV) RL13 gene is a member of the RL11 gene family. To study the expression kinetics and transcript structures of the gene, screening of cDNA library, Northern blot, 3′ and 5′ RACE analyses were performed with a low-passaged clinical strain. The results showed that the RL13 gene was mainly transcribed in the late expression phase with at least seven forms of transcripts of 3628, 3114, 2515–2443, 1737, 1240, 1029 and 846 nt, respectively. All these transcripts were unspliced with an identical 3′ terminal and the same typical polyA signal “AATAAA”. Except for the transcript of 846 nt, RL13 open reading frames (ORFs) were 909 bp and completely identical in all of the transcripts. The sequence of the RL13 ORF in the examined cl... Virus Genes journals http://www.medworm.com/rss/comments.php?id=5034560 Wed, 13 Jul 2011 06:13:27 +0100 5034560 http://www.medworm.com/index.php?rid=4996753&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F96g321l723r28u71%2F Abstract  The baculovirus Condylorrhiza vestigialis multiple nucleopolyhedrovirus (CoveMNPV), isolated from C. vestigialis infected larvae in Paraná (Brazil), was identified in our laboratory. A full-length clone was obtained from the CoveMNPV genome, of the gene that encodes the homolog to baculoviral p74, essential for oral infectivity which was then sequenced and characterized. The CoveMNPV p74 gene (GenBank accession number EU919397) contains an ORF of 1935 bp that encodes a deduced protein of 73.61 kDa. The phylogenetic affiliations of the CoveMNPV gene were determined by a heuristic search of 40 aligned baculovirus p74 nucleotide sequences using maximum parsimony (PAUP 4.0b4a). The phylogenetic analysis placed CoveMNPV within lepidopteran nucleopolyhedrovirus... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4996753 Thu, 30 Jun 2011 17:47:08 +0100 4996753 http://www.medworm.com/index.php?rid=4996754&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F8725274q6273g778%2F In this study, an L segment sequence of 9,040 bp from a new tospovirus (family Bunyaviridae) naturally infecting bean (Phaseolus vulgaris L.) plants was characterized. It encodes the largest RdRp gene known yet for this genus, with deduced 2932aa and a molecular mass of approximately 336 kDa. A Lysine-rich C-terminal extension was found, which apart from our isolate, was only recognized in another recently discovered tospovirus infecting Fabaceae, Soybean vein necrosis associated virus (SVNaV). Due to its distinct biological features and L protein-based phylogenetic analysis showing an almost equidistant position in comparison to Eurasian and American Tospovirus groups, as well as the clustering with SVNaV, we suggest the tentative name Bean necrotic mosaic virus for this uni... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4996754 Thu, 30 Jun 2011 17:47:05 +0100 4996754 http://www.medworm.com/index.php?rid=4973890&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fj146812771054778%2F Abstract  During 2008–2009, fifteen field infectious bronchitis viruses (IBVs) were isolated from commercial chicken farms in Thailand. After sequencing of the complete S1 gene, phylogenetic analysis was performed and this found that the Thai IBV isolates were divided into three distinct groups, unique to Thailand (group I), QX-like IBV (group II), and Massachusetts type (group III). This finding indicated that the recent Thai IBVs evolved separately and that at least three groups of viruses are circulating in Thailand. The recombination analysis of the S1 gene demonstrated that the 5′-terminus of the group I was similar to isolate THA001 which was unique to Thailand, isolated in 1998 whereas the 3′-terminus was similar to the group II. Moreover, the analysis of the S... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4973890 Sat, 25 Jun 2011 15:54:18 +0100 4973890 http://www.medworm.com/index.php?rid=4973891&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F5rn1601386262210%2F Abstract  The incidence of measles in China has increased over the last decade. To evaluate the genetic variation of measles strains, 16 measles wild-type virus strains were isolated from 14 vaccinated cases and 2 nonvaccinated cases in Jilin Province during 2005–2006, and their nucleoprotein (N) and hemagglutinin (H) genes were amplified by RT-PCR. The amplified products were sequenced and compared with the Edmonston virus and the existing vaccine strains (Changchun-47 and Shanghai-191). The results showed that the variation rate between the vaccine and wild-type strains was 9.8–12.0% in the N gene and 5.9–6.9% in the H gene, respectively. In addition, cross-neutralization assays revealed that although sera obtained from infants following primary vaccination effectiv... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4973891 Thu, 23 Jun 2011 16:30:35 +0100 4973891 http://www.medworm.com/index.php?rid=4973892&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fl5t652881x8477q4%2F Abstract  The spike (S) protein is a key structural protein of coronaviruses including, the porcine transmissible gastroenteritis virus (TGEV). The S protein is a type I membrane glycoprotein located in the viral envelope and is responsible for mediating the binding of viral particles to specific cell receptors and therefore specific cell types. It is also an important immune target for the host in neutralizing the virus. Four antigenic sites A, B, C, and D that reside near the N-terminal domain have been defined in the S protein. Of these, the region encoding antigenic sites A and to a lesser extent D, herein defined as S-AD, are most critical in eliciting host neutralizing antibodies. Herein, we enzymatically amplified, cloned, and expressed the S-AD fragment from TGEV in... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4973892 Thu, 23 Jun 2011 16:30:34 +0100 4973892 http://www.medworm.com/index.php?rid=4966369&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ff2q1765514n41053%2F Abstract  Pepper (Capsicum annuum L.) contains a range of endogenous dsRNA molecules resembling the genomes of cryptoviruses. In this work, we have completed the molecular characterization of Pepper cryptic virus 1 (PCV-1) from cv “Jalapeño M” and generated complete genomic sequences of another cryptovirus from cv “Hungarian Wax” designated Pepper cryptic virus 2 (PCV-2). The two viruses share limited identical amino acid content in both genomic segments and appear phylogenetically closer to cryptoviruses reported from other crops (i.e. Raphanus sativus cryptic virus 3, Black raspberry cryptic virus) than to each other. Two sets of virus-specific primers were successfully used in RT-PCR tests for the simultaneous and discriminative detection of these two viruses in ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4966369 Tue, 21 Jun 2011 20:56:53 +0100 4966369 http://www.medworm.com/index.php?rid=4950543&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F5m4r435801v18036%2F Abstract  Twenty-four avian influenza viruses were collected from poultry farms in three different governorates in Egypt during the years 2006–2009 and genetically characterized. All the isolates were confirmed to be type A and subtype H5 influenza virus by chromatographic strip test and hemagglutination inhibition assay. The sequence and phylogenetic data revealed that all Egyptian isolates cluster together and belong to subclade 2.2.1 of the H5N1 virus of Eurasian origin. Within the clade, Egyptian isolates were classified into three major groups (A, B, and C) based on genetic similarity and chronology of the isolation. The majority of the recent isolates belonged to subgroup A. Interestingly, four strains, which were isolated from the same farm with two of the samples ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4950543 Wed, 15 Jun 2011 05:47:16 +0100 4950543 http://www.medworm.com/index.php?rid=4930474&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fg18343k36278558k%2F In this study, the complete genome sequence of a Newcastle disease virus (NDV) isolate collected from an outbreak in 1995 in chickens was fully characterized and compared with other NDV sequences. The genome was found to be 15,192 nucleotides long and to consist of six genes in the order 3′-NP-P-M-F-HN-L-5′, similar to other avian paramyxoviruses type-I. However, a six-nucleotide insertion was observed in the 5′ non-coding regions of the nucleoprotein (NP) gene, a feature that is unique to some NDV isolates. The isolate shows the amino acid sequence 112RRQKRF117 at the cleavage site of the F protein, which is identical to a known motif for virulent pathotypes of NDV. The phylogenetic analysis of the coding region of the F gene indicated that this isolate belongs to genotype VI, ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4930474 Sun, 12 Jun 2011 06:03:04 +0100 4930474 http://www.medworm.com/index.php?rid=4930475&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ft571n7x4433801m6%2F Abstract  Leaf curl disease of tobacco (TbLCD) is endemic in India. A monopartite Begomovirus, a betasatellite and an alphasatellite were found associated with the disease in Pusa, Bihar. The DNA-A of the Begomovirus associated with TbLCD in Pusa, Bihar was found to comprise of 2707 nt with a typical Old World begomovirus-like genome organization. The full-length sequence of DNA-A [HQ180391] showed that the Pusa isolate is a newly described member of the genus Begomovirus, as it had <89% sequence homology with DNA-A of all the known begomoviruses. The isolate is tentatively named as Tobacco leaf curl Pusa virus [India:Pusa:2010]. The betasatellite (HQ180395) associated with TbLCD in Pusa was identified as a variant of Tomato leaf curl Bangladesh betasatellite [IN:Raj:0... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4930475 Sat, 11 Jun 2011 06:37:35 +0100 4930475 http://www.medworm.com/index.php?rid=4918924&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fc41162235702x10r%2F Abstract  A rare genotype G6P[9] was identified in two human group A rotavirus strains designated as KF14 and KF17, that were detected in stool specimens from children with diarrhea in Japan. VP7 gene sequences of these two strains were identical and genetically closely related to G6 human rotavirus strains reported in European countries and the United States. To our knowledge, this is the first report of detection of a G6 human rotavirus in Japan. For further genetic analysis to elucidate the origin of the G6 rotavirus, nearly full-length sequences of all 11 RNA segments were determined for the KF17 strain. The complete genomic constellation of KF17 was determined as G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, a novel genotype constellation for human rotavirus. Phylogenetic analys... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4918924 Wed, 08 Jun 2011 15:46:55 +0100 4918924 http://www.medworm.com/index.php?rid=4918925&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F9470036312052002%2F Abstract  Norovirus (NoV) is the major etiological agent causing foodborne and waterborne outbreaks worldwide. We developed a novel duplex real-time quantitative RT-PCR assay designed for the simultaneous detection of and discrimination between NoV genogroups GI and GII, by targeting the short junction region between ORF1 and ORF2, with sensitivity and efficiency comparable to those of each simplex RT-PCR assay. This new duplex assay was evaluated against clinical stool (n = 82) and environmental (groundwater or surface water, n = 60) specimens from South Korea, and the results were compared with those of conventional RT-PCR (cRT-PCR) assays. The duplex assay detected more positive samples than did the cRT-PCR for both clinical (74 vs. 71) and, more striki... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4918925 Sat, 04 Jun 2011 06:02:54 +0100 4918925 http://www.medworm.com/index.php?rid=4918926&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fq07181wg82162x32%2F Abstract  Classical swine fever virus (CSFV) causes a highly contagious disease that leads to significant economic losses in the pig industry worldwide. However, there is a paucity of knowledge on the accurate genotyping of CSFV isolates in south China. This study genotyped the E2 gene of 14 CSFV strains isolated during 2008–2010 from domestic pigs in different districts of south China. Phylogenetic analyses revealed that all of the 14 CSFV isolates were clustered into genetic subgroup 1.1. This contrasts with most parts of China, where group 2 isolates are predominant. Furthermore, the positive selection pressures acting on the Erns and E2 envelope protein genes of CSFV were assessed and a site-by-site analysis of the dN/dS ratio was performed to identify specific codons ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4918926 Sat, 04 Jun 2011 06:02:53 +0100 4918926 http://www.medworm.com/index.php?rid=4918927&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F03v30610p4v48j67%2F In this study, partial viral genomic nucleotide sequences were determined using the rapid determination system of viral nucleic acid sequences (RDV) ver. 3.1, which we recently developed for discovering novel viruses. Phylogenetic analysis of VP1 and 3A proteins and their encoding nucleotide sequences of enteroviruses and sapeloviruses indicated that the isolated virus was closely related to porcine sapelovirus. RT-PCR detected viral sequences in six of 48 wild boar fecal samples. Content Type Journal ArticlePages 1-6DOI 10.1007/s11262-011-0628-2Authors Masako Abe, The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 JapanNaoto Ito, The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193 JapanKou... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4918927 Sat, 04 Jun 2011 06:02:51 +0100 4918927 http://www.medworm.com/index.php?rid=4918928&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp70h86505033w486%2F In this study, we characterized the rinderpest virus (RPV) Fusan strain cattle type (B), which is the most classical isolate in Asia, by complete genomic sequence analysis and compared it with its lapinized Nakamura III (L) strain. The transversion rates of the M, F, and H genes were higher than those of other genes. In contrast, the deduced amino acid (aa) substitution rates of the P, C, and V genes were higher than those of other genes, although their transversion rates were not higher. The characteristic nucleotide (nt) or aa residues of the cattle-virulent B and Kabete ‘O’ strains were observed in the P/C/V, M, and L genes. According to these results, we speculate that nt/aa substitution in the P/C/V genes is one of the key determinants for the difference in the pathogenicity... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4918928 Sat, 04 Jun 2011 06:02:50 +0100 4918928 http://www.medworm.com/index.php?rid=4900151&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fu3284n18v51653j3%2F In this study using wild type and ‘knockout’ mouse embryonic fibroblasts (MEFs), we showed that two of the eIF2α kinases, PERK and GCN2, were not responsible for translational regulation under physiological and a higher apoptotic doses of H2O2 (100 μM). However, a differential translational response was observed at a lower apoptotic dose of H2O2 (50 μM) between Perk+/+ and Perk−/− MEFs but not that between Gcn2+/+ and Gcn2−/− MEFs, suggesting that PERK may play a role in translational up-regulation under oxidative stress. Our results also suggest that PERK mediates such an effect via an eIF2-independent pathway. This is in contrast to the canonical role of PERK on translational inhibition under stress conditions via phosphorylation of eIF2α. When tested for th... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4900151 Fri, 03 Jun 2011 06:00:02 +0100 4900151 http://www.medworm.com/index.php?rid=4900152&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fx357h24020728481%2F In this study, the DNA methylation profiles of five CpG sites located within the promoter/enhancer regions and nine CpG sites located within the early and late coding regions of the replicating BKV genome were investigated. BKV genomic DNA from mature virions and from the early and late phases of replicating BKV were examined for DNA methylation by bisulfite sequencing that covered 14 CpG sites. Our results showed that none of the examined BKV DNA from the various different stages of replication was methylated. This is the first report to analyze the methylation of BKV genomic DNA during viral replication. The results seem to indicate that methylation is not involved in regulation of BKV replication. Content Type Journal ArticlePages 1-7DOI 10.1007/s11262-011-0627-3Authors Chi-... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4900152 Mon, 30 May 2011 16:58:05 +0100 4900152 http://www.medworm.com/index.php?rid=4900154&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fg035471716730263%2F Abstract  Comparative complete genome analysis of 17 serotype A Indian field isolates representing different genotypes and sub-lineages is presented in this report. Overall 79% of amino acids were invariant in the coding region. Chunk deletion of nucleotide was observed in S and L fragment of 5′-UTR. More variability which is comparable to that of capsid coding region was found in L and 3A region. Functional motifs and residues critical for virus biology were conserved most. Polyprotein cleavage sites accepted few changes. Many sites were detected to be under positive selection in L, P1, 2C, 3A, 3C, and 3D region and of which some are functionally important and antigenically critical. Genotype/lineage specific signature residues could be identified which implies evolution... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4900154 Sat, 21 May 2011 23:05:25 +0100 4900154 http://www.medworm.com/index.php?rid=4900153&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F1621780517766748%2F In this study, we compared BV infectivity of S1 and T3 in B. mori larvae and cultured cells. Larval bioassays by intrahemocoelic BV injection revealed that the median lethal dose of S1’s BV was approximately three times lower than that of T3. In addition, S1 produced more BVs and occlusion bodies (OBs) in the hemolymph of B. mori larvae compared with T3. Furthermore, we observed that the locomotion was enhanced earlier and the median lethal time was shorter in S1-infected larvae compared with those in T3-infected larvae. Western blot analysis of S1- and T3-infected BmN cells revealed that expression of late and very late gene products in S1-infected cells was higher than that in T3-infected cells. Collectively, these results clearly show that S1’s BV infectivity is higher than tha... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4900153 Sat, 21 May 2011 23:05:25 +0100 4900153 http://www.medworm.com/index.php?rid=4900155&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy3r1h52335221086%2F Abstract  A new, widespread disease was recently observed in soybean in the United States. The disease, named Soybean vein necrosis, is manifested by intraveinal chlorosis and necrosis, and has been found in almost all of the 50 fields visited over a period of 3 years in the midwest and midsouth part of the United States. A virus was isolated from symptomatic material, and detection protocols were developed. More than 150 symptomatic specimens collected from seven US States were tested, and all were found positive for the virus unlike 75 asymptomatic samples, revealing the absolute association between virus and disease. Protein pairwise comparisons coupled with phylogenetic analyses indicate that the virus is a new member of the genus Tospovirus. Content Type Jou... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4900155 Sat, 21 May 2011 23:05:23 +0100 4900155 http://www.medworm.com/index.php?rid=4860010&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F60661803621l16u1%2F Abstract  Triple-reassortant (TR) H3N2 swine influenza viruses (SIV) are a major cause of respiratory disease in swine worldwide, causing considerable morbidity and mortality. Continuous surveillance of circulating SIV strains is imperative for effective control and prediction of new emerging strains with interspecies transmission potential. The current study characterized SIV isolates from commercial swine population in USA (2006–2007). Nine isolates were completely sequenced, and the molecular evolution of all gene segments was analyzed. Phylogenetic analysis of the nine H3N2 viruses indicated that these strains belonged to cluster-IV of the human/swine/avian TR genotype, grouping with H3N2 viruses of turkey origin, while forming a separate sub-lineage from those of hum... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4860010 Fri, 20 May 2011 16:03:46 +0100 4860010 http://www.medworm.com/index.php?rid=4851672&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh32871375673371k%2F Abstract   Puumala virus (PUUV) is the predominant hantavirus species in Germany causing large numbers of mild to moderate cases of haemorrhagic fever with renal syndrome (HFRS). During an outbreak in South-East Germany in 2004 a novel PUUV subtype designated Bavaria was identified as the causative agent of HFRS in humans [1]. Here we present a molecular characterization of this PUUV strain by investigating novel partial and almost entire nucleocapsid (N) protein-encoding small (S-) segment sequences and partial medium (M-) segment sequences from bank voles (Myodes glareolus) trapped in Lower Bavaria during 2004 and 2005. Phylogenetic analyses confirmed their classification as subtype Bavaria, which is further subdivided into four geographical clusters. The entire N protein,... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4851672 Thu, 19 May 2011 16:36:32 +0100 4851672 http://www.medworm.com/index.php?rid=4838140&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fd4680h4944453g05%2F Abstract  Two hundred forty potato samples with one or more symptoms of leaf mosaic, distortion, mottling and yellowing were collected between 2005 and 2008 from seven Iranian provinces. Forty-four of these samples tested positive with double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) using a Potato virus S (PVS) polyclonal antibody. Of these 12 isolates of PVS were selected based on the geographical location for biological and molecular characterization. The full coat protein (CP) and 11K genes from 12 PVS isolates were PCR amplified, cloned and sequenced. All 12 PVS isolates showed mosaic symptoms on Nicotiana debneyii and N. tabacum cv. Whiteburly and local lesion on Chenopodium amaranticolor, C. quinoa and C. album. The Iranian isolates share between... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4838140 Thu, 12 May 2011 17:22:56 +0100 4838140 http://www.medworm.com/index.php?rid=4818623&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F1x2q056625747150%2F In this study, we further maintained the 83P-5 in Vero cells up to the 100th passage and analyzed changes in the spike (S), membrane (M), and nucleocapsid (N) gene sequences and pathogenicity of the virus at the 34th, 61st, and 100th passage levels. Sequence analyses revealed a strong selection for the S gene of 83P-5 in Vero cells, and virtually all mutations occurring at the 34th and 61st passages had been carried over to the 100th-passaged virus. In contrast, the viral M and N genes showed a strong conservation during the serial passage. Pigs experimentally infected with the 34th- or 61st-passaged virus, but not the 100th-passaged virus, exhibited diarrhea, indicating an attenuation of the 83P-5 at the 100th passage. Interestingly, S protein of the attenuated 100th-passaged 83P-5 ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4818623 Wed, 11 May 2011 06:26:56 +0100 4818623 http://www.medworm.com/index.php?rid=4818624&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fg66212477247413w%2F Abstract  Velvet bean [Mucuna pruriens (L.) DC] is one of the most important medicinal plants. It is used to treat many ailments, but is widely used for the treatment especially for Parkinson’s disease because of the presence of 3,4-dihydroxyphenylalanine (l-dopa) in it. It was noticed in last 5 years that the plants in the field showed severe mosaic, downward curling of the leaves, stunting, etc. This is consistently observed over the years in India. The disease was transmitted by whiteflies and by grafting and the causal agent was found to be a bipartite begomovirus. The whole genome was amplified by rolling circle amplification (RCA) using ϕ-29 DNA polymerase and characterized. DNA-A and DNA-B shared a 124-nucleotide (nt) long highly conserved (98%) common region ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4818624 Tue, 10 May 2011 06:02:04 +0100 4818624 http://www.medworm.com/index.php?rid=4818625&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp7254x252646w56n%2F Abstract  It is well known that scrapie is a fatal, neurodegenerative disease in sheep and goat, which belongs to the group of transmissible spongiform encephalopathies (TSEs) or prion diseases. It has been confirmed that the polymorphisms of prion protein gene (PRNP) at codons 136, 154, and 171 have strong relationship with scrapie in sheep. In the present study, nine polymorphisms of PRNP at codons 136, 154, and 171 and other six loci (at codons 101, 112, 127, 137, 138, and 152) were detected in 180 Chinese Hu sheep. All the alleles at codons 136, 154, and 171 have been identified and resulted in three new genotypes. The frequencies of predominant alleles were 85% (A136), 99.40% (R154), and 37.78% (Q171), respectively. The predominant haplotype ARQ has a relatively high f... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4818625 Tue, 10 May 2011 06:02:02 +0100 4818625 http://www.medworm.com/index.php?rid=4787139&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp76867311v47qk42%2F This study analysed the NS gene of 31 isolates from Kenya in order to obtain a more detailed knowledge about the genetic variation of NS gene of 2009 influenza A (H1N1) isolates from Kenya. A comparison with the vaccine strain and viruses isolated elsewhere in Africa was also made. The amino acid sequences of the non-structural protein, NS1 of the viruses from this study and the vaccine strain revealed 18 differences. Conversely, the nuclear export protein (NEP) of the isolates in this study had 11 differences from the vaccine strain. Analysis of the NS1 protein showed only one fixed amino acid change I123V which is one of the characteristics of clade 7 viruses. In the NEP, the amino acid at position 77 was the most mutable with 9 (39%) of all mutations seen in this protein. A mutati... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4787139 Mon, 02 May 2011 15:00:44 +0100 4787139 http://www.medworm.com/index.php?rid=4787138&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy16l60m5k307kp09%2F Abstract   Cowpea chlorotic mottle virus (CCMV, family Bromoviridae) is found worldwide and has been used as a model virus for a long time, but no data is available about the genetic diversity of field isolates. Recently, two new field isolates (Car1 and Car2) of CCMV obtained from cowpea showed distinct phenotypic symptoms when inoculated to cowpea. CCMV-Car1 induced severe mosaic and interveinal chlorosis, while CCMV-Car2 produced mild mottling and leaf rolling. Both isolates produced asymptomatic infection in Nicotiana benthamiana. The complete genome of both isolates was amplified by reverse transcription-polymerase chain reaction using specific primers against the CCMV sequences available in the GenBank database, cloned and sequenced. Both nucleotide and amino acid sequ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4787138 Mon, 02 May 2011 15:00:44 +0100 4787138 http://www.medworm.com/index.php?rid=4779037&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ft2580h3548677452%2F Abstract  The aim of this study is to investigate the profile of ovine PrP gene by amino acid polymorphism at codons 136, 141, 154, and 171 for determining the genetic predisposition to the Scrapie disease for the tribal sheep and rams, with different numbers and distribution in Bulgaria. Three hundred twenty four animals originating from 41 tribal herds comprising eight breeds were included in the study. DNA was isolated from blood samples specifically amplified by PCR and sequenced. The alignments of codons 136, 141, 154, and 171 were determined. Based on the sequencing, it was established that Bulgarian breeds belong to the second and third risk groups, those with low and moderate risk of Scrapie disease. Establishment of 11 genotypes in Synthetic Population Bulgarian Mi... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4779037 Fri, 29 Apr 2011 15:47:27 +0100 4779037 http://www.medworm.com/index.php?rid=4779038&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fa6108m48w8273711%2F In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649–7663 nucleotides. These isolates share identities of 96.4–97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1–3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNAmet-binding site is also present in the 935-bp inte... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4779038 Fri, 29 Apr 2011 15:47:26 +0100 4779038 http://www.medworm.com/index.php?rid=4752114&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fh228v175k4j43l24%2F Content Type Journal ArticlePages 1-1DOI 10.1007/s11262-011-0606-8Authors Jamil A. Hashmi, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P. O. Box 577, Jhang Road, Faisalabad, PakistanYusuf Zafar, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P. O. Box 577, Jhang Road, Faisalabad, PakistanMuhammad Arshad, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P. O. Box 577, Jhang Road, Faisalabad, PakistanShahid Mansoor, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P. O. Box 577, Jhang Road, Faisalabad, PakistanShaheen Asad, Agricultural Biotechnology Di... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4752114 Thu, 21 Apr 2011 18:00:26 +0100 4752114 http://www.medworm.com/index.php?rid=4744506&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fx02442t6738l38r3%2F Abstract  Neuraminidase (NA) gene of avian influenza viruses isolated from Live Bird Markets (LBMs) on the east coast of the United States was sequenced and analyzed for mutations associated with antiviral resistance. In total, 189 isolates collected from 1994 to 2005 were used in this study. Full length sequences of the NA gene were obtained from 183 of the 189 isolates. Four different lengths of NA gene were observed; 40 isolates had full length (about 1400 nt), 132 isolates had a deletion of 48 nt, 10 isolates had a deletion of 66 nt, and one isolate had a deletion of 72 nt. Amino acid analysis of the sequence data showed point mutations distributed throughout the gene length. None of these deletions was in the catalytic region and most of the mutations were observed in ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4744506 Wed, 20 Apr 2011 06:06:15 +0100 4744506 http://www.medworm.com/index.php?rid=4744507&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fm6608003g61m5j50%2F In this study, we introduced mutations into the meq gene and used dual luciferase reporter assays to analyze the transcriptional activities of the resulting Meq proteins to determine whether distinct mutations in Meq could be responsible for differences in transcriptional activity among MDV strains. A proline-to-alanine substitution at position 217, the second position of one of the proline direct repeats in the transactivation domain, enhanced the transactivation activity of Meq. In addition, we found that two substitutions at positions 283 and 320 affected transactivation activity. These results suggest that the distinct diversity of and point mutations in the Meq proteins are responsible for differences in transactivation activity among MDV strains. Content Type Journal Artic... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4744507 Tue, 19 Apr 2011 07:15:45 +0100 4744507 http://www.medworm.com/index.php?rid=4730818&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fa5271u865jp56390%2F Abstract  In California, a novel closterovirus was detected in “Redglobe” grapevine, associated with graft incompatibility and given a trivial name “Grapevine rootstock stem lesion associated virus (GRSLaV).” The biological properties of the putative virus were ascertained when asymptomatic yet infected Redglobe scion buds were graft-inoculated onto test plants of Cabernet Sauvignon propagated on 18 different rootstocks. It proved lethal on test plants growing on rootstocks 1616C, 5BB, 5C, 3309C, and 1103 P, whereas latent infections occurred on the remaining scion-rootstock combinations. In contrast, GLRaV-2 type (type strain) produced only typical leafroll symptoms. In a different experiment, GLRaV-2 type was successfully sap-transmitted to N. benthamiana, whereas ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4730818 Tue, 12 Apr 2011 21:34:50 +0100 4730818 http://www.medworm.com/index.php?rid=4730819&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fd32w885h39551n31%2F Abstract  The presence of Cucumber mosaic virus (CMV) satellite RNA dramatically changes symptoms on some hosts. A satellite RNA present in a strain of CMV (PepY-CMV) that induced chlorosis in pepper (Capsicum annuum) was shown to induce chlorosis in pepper in combination with another strain (Fny-CMV) that by itself induced a green mosaic symptom. The location of sequences within the PepY satellite RNA (PepY-satRNA) of CMV that conferred the ability to induce chlorosis on pepper plants were analyzed by exchanging sequence domains between cDNA clones of PepY-satRNA and an attenuated mosaic satellite RNA (Paf-satRNA), as well as site-directed mutagenesis of various clusters of the 22-nt sequence differences between the two satellite RNAs in the delimited central domain. The s... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4730819 Tue, 12 Apr 2011 05:58:35 +0100 4730819 http://www.medworm.com/index.php?rid=4708221&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fr0q1871630w30kw5%2F Abstract  A severe yellow vein mosaic disease was noticed on several Jatropha gossypifolia plants growing nearby agriculture fields at Lucknow, India. Diseased plants exhibited yellow vein mosaic, leaf deformation, vein swelling and stunting. A population of whiteflies (Bemisia tabaci) was also noticed in the vicinities; therefore, begomovirus infection was suspected. To confirm begomovirus association, total DNA was isolated from symptomatic leaf samples and subjected to PCR using DNA-A, DNA-B and DNA-β-specific primers. DNA-A and DNA-β was successfully amplified but several attempts failed to amplify DNA-B indicating monopartite nature of the begomovirus. The sequence analysis of amplicons revealed the presence of 2757 nucleotides of DNA-A genome (EU727086) and 1315 n... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4708221 Fri, 08 Apr 2011 20:56:46 +0100 4708221 http://www.medworm.com/index.php?rid=4708222&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F9x5u6014jh26x0k3%2F Abstract  Foot-and-mouth disease (FMD) is endemic in mainland Southeast Asia where up to seven genetically distinct viral lineages co-circulate (O/SEA/Mya-98, O/SEA/Cam-94, O/ME-SA/PanAsia, O/ME-SA/PanAsia-2, O/CATHAY, A/ASIA/Sea-97, and serotype Asia 1). The aim of this study was to analyse the sequence variability between representative complete genomes for these seven lineages. The genome sequences varied from 8130 to 8192 nucleotides in length and shared nucleotide identities ranging from 91.8 to 78.9%. Broad-scale differences such as block and codon deletions observed in these genomes paralleled features that have been reported previously for other FMDV sequences from Southeast Asia. Comparison between these sequences revealed the presence of 2501 variant sites which w... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4708222 Fri, 08 Apr 2011 20:56:45 +0100 4708222 http://www.medworm.com/index.php?rid=4681690&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fe16l43m1w8445014%2F Abstract  A live-attenuated dengue-2 virus strain S16803 vaccine candidate that is immunogenic and safe in humans was derived by 50 passages in primary dog kidney (PDK) cells. To identify mutations associated with attenuation of the dengue-2 PDK50 vaccine strain, we determined the nucleotide changes that arose during PDK passage of the dengue-2 virus. Thirteen mutations distinguished the PDK50 virus from low-passage parent resulting in amino acid substitutions in the premembrane (E89G), envelope (E202K, N203D), nonstructural proteins NS1 (A43T), NS2A (L181F), NS2B (I26V), and NS4B (I/T108T, L112F). In addition, the PDK50 virus contained a C to T change of nucleotide 57 in the 5′ non-coding region and four silent mutations of nucleotides 591, 987, 6471, and 8907. An infect... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4681690 Sun, 03 Apr 2011 05:45:54 +0100 4681690 http://www.medworm.com/index.php?rid=4681691&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F6432443rm60t1r72%2F Abstract  The complete genome sequences were determined for avian paramyxovirus type 2 (APMV-2) strains F8 and NK isolated from chickens in China. Both strains had a genome of 14,904 nucleotides (nt) in length, which followed the “rule of six”. Each genome consisted of six genes in the order 3′-N-P-M-F-HN-L-5′, with a 55-nt leader at the 3′ end and a 154-nt trailer at the 5′ end. Sequence alignment and phylogenetic analysis showed that APMV-2 strains F8 and NK shared the highest sequence identity with APMV-2 prototype strain Yucaipa, being classified in the same subgroup as strains Yucaipa, England and Kenya, while strain Bangor represented another subgroup of APMV-2. Among the APMVs, APMV-2 strains F8 and NK exhibited a closer evolutionary relationship with APM... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4681691 Sat, 02 Apr 2011 05:49:44 +0100 4681691 http://www.medworm.com/index.php?rid=4681692&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fm0px762817722324%2F This study investigated the prevalence of sapovirus infections in children with acute gastroenteritis in Monastir region, Tunisia, from January 2003 to April 2007. Sapovirus was characterized by sequence and phylogenetic analyses of the partial polymerase gene. From 788 fecal specimens tested, 6 (0.8%) were positive for sapovirus, of these, 4 (66.7%) were monoinfections. All sapovirus positive samples were detected in outpatient, contrary to norovirus which was significantly more frequent in hospitalized children than in outpatients (14.5 vs. 9.5%, P = 0.03). The mean age of children with sapovirus infections was 11 ± 5.56 months (range 6–19 months). Sapovirus isolates were detected in March and between September and December 2003. Fever, vomiting, abd... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4681692 Sat, 02 Apr 2011 05:49:43 +0100 4681692 http://www.medworm.com/index.php?rid=4681693&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv80j60122n867516%2F Abstract  Avian influenza viruses A/turkey/Almaty/535/04 (H11N9) and A/herring gull/Atyrau/2186/07 (H11N2) isolated in Kazakhstan were characterized as low pathogenic in biological and genetic studies. Putative glycosylation sites were identical to the putative sites in published H11, N2, and N9 isolates sequences. Compared with published data no additional basic amino acid residues were found in the hemagglutinin (HA) cleavage site of these Kazakhstan strains. Phylogenetic analysis revealed a rare case of Eurasian-American reassortment in the HA gene of A/herring gull/Atyrau/2186/07 (H11N2) virus and significant sequence difference of the HA and the neuraminidase genes of the virus A/turkey/Almaty/535/04 (H11N9) from the previously published GenBank viruses. Content Ty... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4681693 Sat, 02 Apr 2011 05:49:42 +0100 4681693 http://www.medworm.com/index.php?rid=4675217&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fn43517537085ln78%2F In this study to know the dynamics of rabies virus, a total of 41 rabies positive brain samples from dogs, cats, domestic animals, wildlife, and humans from 11 states were subjected to RT-PCR amplification of N gene between nucleotide N521-N1262 (742 bp) and P gene between nucleotide P239-P750 (512 bp). The N gene could be amplified from 30, while P gene from 41 samples, using specific sets of primers. The N gene-based phylogenetic analysis indicated that all Indian virus isolates are genetically closely related with a single cluster under arctic/arctic-like viruses. However, two distinct clusters were realized in P gene-based phylogeny viz., Rabies virus isolates of Punjab and Rabies virus isolates of remaining parts of India (other than Punjab). All the Indian rabies viru... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4675217 Thu, 31 Mar 2011 07:22:37 +0100 4675217 http://www.medworm.com/index.php?rid=4651047&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fn80596x77m61114l%2F Abstract  The complete nucleotide sequence of Cymbidium mosaic virus (CymMV) isolated from vanilla in Hainan province, China was determined for the first time. It comprised 6,224 nucleotides; sequence analysis suggested that the isolate we obtained was a member of the genus Potexvirus, and its sequence shared 86.67–96.61% identities with previously reported sequences. Phylogenetic analysis suggested that CymMV from vanilla fragrans was clustered into subgroup A and the isolates in this subgroup displayed little regional difference. Content Type Journal ArticlePages 1-4DOI 10.1007/s11262-011-0592-xAuthors Zhen He, State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4651047 Fri, 25 Mar 2011 18:55:17 +0100 4651047 http://www.medworm.com/index.php?rid=4651048&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fmp5l23304r474373%2F Abstract  For the past 10 years, endemic swine influenza H1 viruses in Thailand have been characterized as reassortants of swine virus genes from swine influenza viruses (SIV) in US and European pigs. Here the authors report the emergence of a novel reassorted H1N1 (rH1N1) virus consisted of human, avian, and swine virus genes from the pandemic H1N1 2009 (pH1N1) virus with a neuraminidase (NA) gene from a Thai swine H1N1 (ThH1N1) isolate. The rH1N1 virus was detected in nursery pigs during a respiratory disease outbreak in central Thailand in early 2010. The rH1N1 virus was repeatedly isolated from infected pigs, suggesting that it can transmit efficiently among the pig population. The appearance of rH1N1 virus in the field occurred within months of the introduction of... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4651048 Fri, 25 Mar 2011 18:55:16 +0100 4651048 http://www.medworm.com/index.php?rid=4614283&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fr261623726170568%2F Content Type Journal ArticlePages 1-1DOI 10.1007/s11262-011-0598-4Authors Seyyed Mahmoud Ebrahimi, Department of Biotechnology, Razi Vaccine and Serum Research Institute (RVSRI), P.O. Box 31975/148, Karaj, Tehran, IranMajid Tebianian, Department of Biotechnology, Razi Vaccine and Serum Research Institute (RVSRI), P.O. Box 31975/148, Karaj, Tehran, Iran Journal Virus GenesOnline ISSN 1572-994XPrint ISSN 0920-8569 (Source: Virus Genes) Virus Genes journals http://www.medworm.com/rss/comments.php?id=4614283 Thu, 17 Mar 2011 18:16:31 +0100 4614283 http://www.medworm.com/index.php?rid=4589138&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F66u6x4208875320q%2F Abstract  The envelope proteins of classical swine fever virus (CSFV) mediate the binding of CSFV to cell surface molecules and allow CSFV subsequent to enter host cells. However, the proteins binding to host cells and their binding sequences are uncertain. The results showed that the protein E1, E2, and Erns were displayed on the surfaces of T7 phages. The E2 and Erns phage clones showed high binding affinity to host cells, in which the E2 phage clone interacted more specifically with host cells than with other cells, while the Erns phage clone interacted with all tested cells. A 30-mer phage displaying peptide library was constructed and screened against immobilized host cells, in which each peptide was overlapped 10aa to another peptide and spanned all amino acid sequenc... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4589138 Sat, 12 Mar 2011 16:53:09 +0100 4589138 http://www.medworm.com/index.php?rid=4589139&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv88k3u5417v3r67u%2F Abstract  The P3 protein encoded by Shallot yellow stripe virus onion isolate (SYSV-O) interacted in the Yeast Two-hybrid (Y2H) system and in co-immunoprecipitation (Co-IP) assays with the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) protein that is encoded by the rbcL gene of its onion host. Dissection analysis by Y2H showed that the main part of SYSV P3 (amino acids 1–390) and onion RbcL (amino acids 1–137) were responsible for the interaction. The P3 proteins encoded by Onion yellow dwarf virus (OYDV), Soybean mosaic virus Pinellia isolate (SMV-P), and Turnip mosaic virus (TuMV) also interacted with RbcL, suggesting that a P3/RbcL interaction might exist generally for potyviruses. An interaction between P3 of these potyviruses and the ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4589139 Sat, 12 Mar 2011 16:53:08 +0100 4589139 http://www.medworm.com/index.php?rid=4580371&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F70q3258037393851%2F Abstract  Fecal samples (n = 107) were collected from cattle with ascertained or suspected diarrheal disease on Korean farms during 2008–2010. Of these, 37 samples tested positive for bovine kobuvirus. The 37 positive samples came from 32 cattle that exhibited diarrhea and five cattle that were non-diarrhetic. The majority of the virus-positive feces samples were from calves under 1 month of age (n = 25). Nine of the 37 cattle infected with bovine kobuvirus were confirmed to have a co-infection with other viruses including bovine rotavirus (n = 3), bovine coronavirus (n = 1), bovine viral diarrhea virus (n = 1), and both bovine coronavirus and bovine viral diarrhea virus (n = 4). A neighbor-joining tree grouped... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4580371 Fri, 11 Mar 2011 18:08:05 +0100 4580371 http://www.medworm.com/index.php?rid=4580372&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fw127554203u63j37%2F In this study, we show that transfection of PK-15 cells with a plasmid expressing the Lpro of FMDV, in the absence of other FMDV proteins, inhibited dsRNA-induced RANTES transcription and promoter activity. Promoter mutagenesis experiments revealed that the interferon-stimulated response element (ISRE) was important for the ability of Lpro to inhibit dsRNA-induced RANTES promoter activity. Furthermore, over-expression of Lpro also inhibited IRF-3/7-mediated RANTES activation. Screening Lpro mutants indicated that catalytic activity and a SAP (for SAF-A/B, Acinus, and PIAS) domain of Lpro were required to suppress dsRNA-induced RANTES transcription. Content Type Journal ArticlePages 1-6DOI 10.1007/s11262-011-0590-zAuthors Dang Wang, Division of Animal Infectious Diseases, State Key... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4580372 Fri, 11 Mar 2011 18:08:04 +0100 4580372 http://www.medworm.com/index.php?rid=4580373&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F521737648hp503q3%2F Abstract  The incidence of watermelon chlorotic stunt disease and the molecular characterization of the Jordanian isolate of Watermelon chlorotic stunt virus (WmCSV-[JO]) are described in this study. Symptomatic leaf samples obtained from watermelon (Citrullus lanatus Thunb.), melon (Cucumis melo L.), squash (Cucurbita pepo), cucumber (Cucumis sativus L.), and bottle gourd (Lagenaria siceraria) plants were tested for WmCSV-[JO] infection by PCR. The virus could be detected in 8 melon and 87 watermelon samples obtained from Ghor Assafi (southern part of Jordan Valley). Three samples collected from Mafraq (eastern part of Jordan) were found mixed infected with WmCSV-[JO] and Squash leaf curl virus. The full-length DNA-A and DNA-B genomes of WmCSV-[JO] were amplified, and sequence... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4580373 Fri, 11 Mar 2011 18:08:02 +0100 4580373 http://www.medworm.com/index.php?rid=4558351&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F1xj447335n75q54p%2F Abstract  Yellow mosaic disease in grain legumes in Indian subcontinent is caused by two important virus species viz. Mungbean yellow mosaic virus (MYMV) and Mungbean yellow mosaic India virus (MYMIV), belonging to the genus Begomovirus of the family Geminiviridae. The genomic components of a begomovirus causing yellow mosaic disease in blackgram in southern India were cloned and sequenced. Nucleotide sequence comparison of DNA A component shows the virus isolate to be a variant of Mungbean yellow mosaic virus:–(MYMV-[IN:Vam:05]). However, DNA B component of the present virus isolate has greater similarity (92%) to Mungbean yellow mosaic India virus. Agroinoculations of the viral clones produced typical yellow mosaic symptoms in blackgram and mungbean, severe leaf curl and st... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4558351 Sat, 05 Mar 2011 16:49:52 +0100 4558351 http://www.medworm.com/index.php?rid=4558350&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F9325036578320x82%2F Abstract  The Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus with enveloped, rod-shaped virions. Its genome is 127,615 bp in size and contains 139 predicted protein-coding open reading frames (ORFs). In-depth genome sequence comparisons revealed a varying number of shared gene homologues, not only with other nudiviruses (NVs) and baculoviruses, but also with other arthropod-specific large dsDNA viruses, including the so-called Monodon baculovirus (MBV), the salivary gland hypertrophy viruses (SGHVs) and white spot syndrome virus (WSSV). Nudivirus genomes contain 20 baculovirus core gene homologues associated with transcription (p47, lef-8, lef-9, lef-4, vlf-1, and lef-5), replication (dnapol and helicase), virus structure (p74, pif-1, pif-2, pif-3, 19kda/pif-4, odv... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4558350 Sat, 05 Mar 2011 16:49:52 +0100 4558350 http://www.medworm.com/index.php?rid=4558352&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv03806645733121x%2F Abstract  Three discrete regions of the African swine fever virus (ASFV) were analysed in the genomes of a wide range of isolates collected from wild and domestic pigs in Sardinia, over a 31-year period (1978–2009). The analysis was conducted by genotyping based on sequence data from three single copy ASF genes. The E183L gene encoding the structural protein p54 and part of the gene encoding the p72 protein were used to delineate genotypes, before intra-genotypic resolution of viral relationships by analysis of tetramer amino acid repeats within the hypervariable central variable region (CVR) of the B602L gene. The data revealed that these isolates did not show significant variation in their p72 and p54 sequence when compared between different isolates showing a remarkable... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4558352 Fri, 04 Mar 2011 11:02:04 +0100 4558352 http://www.medworm.com/index.php?rid=4558353&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F52536p8lr24p0421%2F In this study, a total of three strains of NoV and 37 strains of SaV were detected in 567 porcine fecal samples by RT-PCR, corresponding detection rates of 0.5 and 6.5%, respectively. Phylogenetic analyses were conducted using amino acid sequences of the partial RNA-dependent RNA polymerase (RdRp) and complete capsid proteins of both viruses to determine their genogroups. Analysis with the RdRp sequences indicated that all three NoV strains HW41, DG32, and DO35 detected in this study were classified into genogroup II (GII). A further analysis with the complete capsid sequence demonstrated that the DO35 strain belonged to subgenotype b in GII-21 (GII-21b) along with the SW918 strain. A total of 26 strains out of 27 strains that were selected from the 37 porcine SaVs were classified in... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4558353 Thu, 03 Mar 2011 08:47:04 +0100 4558353 http://www.medworm.com/index.php?rid=4511012&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fy687r18g87716764%2F Abstract  Chickpea stunt disease (CSD) across southern Asia, the Middle East and North Africa is caused by a number of viruses that include single-stranded DNA viruses of the genus Mastrevirus (family Geminiviridae). Despite the importance of CSD in reducing chickpea and lentil production, until recently little was known of the nature of the pathogens causing the disease. Sequence characterisation of virus isolates from Sudan and Pakistan showed the viruses concerned to potentially be new mastrevirus species related to Bean yellow dwarf virus (BeYDV), a virus known to occur in both southern Africa and southern Asia. Here we have determined the complete nucleotide sequence of a mastrevirus associated with CSD in Syria. This virus represents a proposed new species, closely rela... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4511012 Mon, 21 Feb 2011 17:04:28 +0100 4511012 http://www.medworm.com/index.php?rid=4511013&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F708633541765wg18%2F Abstract  Researchers reported that co-cultivating the JM/102W strain of Marek’s disease virus (MDV) with reticuloendotheliosis virus (REV) resulted in an REV long terminal repeat (LTR) being inserted into the internal repeat short (IRS) region of JM/102W. When the resulting recombinant virus was serially passed in cell culture, the initial LTR was duplicated and a second LTR spontaneously appeared in the terminal repeat short (TRS) region of the MDV genome. The virus, designated RM1, was significantly attenuated but still induced severe bursal and thymic atrophy (Isfort et al. PNAS 89:991–995). To determine whether the altered phenotype was due solely to the LTR, we cloned the LTR from the RM1 IRS region and inserted it into the IRS region of a very virulent bacterial ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4511013 Mon, 21 Feb 2011 17:04:26 +0100 4511013 http://www.medworm.com/index.php?rid=4511014&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fb111712207k106x6%2F Abstract  Marek’s disease virus (MDV), an oncogenic alphaherpesvirus, induces a rapid onset T-cell lymphoma and demyelinating disease in chickens. Since the 1970s the disease has been controlled through mass vaccination with herpesvirus of turkeys [meleagrid herpesvirus type 1 (MeHV-1)]. Over time this vaccine’s efficacy decreased, and in the 1980s a bivalent vaccine consisting of MeHV-1 and a non-oncogenic gallid herpesvirus type 3 (GaHV-3) strain known as SB-1 was introduced. The complete DNA sequence (165,994 bp) of this GaHV-3 strain was determined using 454 pyrosequencing. A total of 524 open reading frames (ORFs) were examined for homology to protein sequences present in GenBank using BLAST (E-values <0.9). Of the 128 ORF hits, 75 ORFs showed homology to we... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4511014 Sat, 19 Feb 2011 18:24:23 +0100 4511014 http://www.medworm.com/index.php?rid=4500774&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fw46xr44404587382%2F Abstract  The complete genome sequences of two isolates A/chicken/Egypt/CL6/07 (CL6/07) and A/duck/Egypt/D2br10/07 (D2br10/07) of highly pathogenic avian influenza virus (HPAI) H5N1 isolated at the beginning of 2007 outbreak in Egypt were determined and compared with all Egyptian HPAI H5N1 sequences available in the GenBank. Sequence analysis utilizing the RNA from the original tissue homogenate showed amino acid substitutions in seven of the viral segments in both samples. Interestingly, these changes were different between the CL6/07 and D2br10/07 when compared to other Egyptian isolates. Moreover, phylogenetic analysis showed independent sub-clustering of the two viruses within the Egyptian sequences signifying a possible differential adaptation in the two hosts. Further... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4500774 Thu, 17 Feb 2011 07:05:01 +0100 4500774 http://www.medworm.com/index.php?rid=4493817&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Frtn400405786x468%2F Abstract  Several important biological processes are performed by distinct functional domains found on replication-associated protein (Rep) encoded by AC1 of geminiviruses. Two truncated forms of replicase (tAC1) gene, capable of expressing only the N-terminal 669 bp (5′AC1) and C-terminal 783 bp (3′AC1) nucleotides cloned under transcriptional control of the CaMV35S were introduced into cotton (Gossypium hirsutum L.) using LBA4404 strain of Agrobacterium tumefaciens to make use of an interference strategy for impairing cotton leaf curl virus (CLCuV) infection in transgenic cotton. Compared with nontransformed control, we observed that transgenic cotton plants overexpressing either N-terminal (5′AC1) or C-terminal (3′AC1) sequences confer resistance to CLCu... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4493817 Wed, 16 Feb 2011 07:03:55 +0100 4493817 http://www.medworm.com/index.php?rid=4488039&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fw12936w2m6026671%2F In conclusion, these strains had distant genetic relationship with each other and with other EV96 strains. Content Type Journal ArticlePages 1-8DOI 10.1007/s11262-011-0584-xAuthors Aiqiang Xu, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012 People’s Republic of ChinaZexin Tao, Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014 People’s Republic of ChinaHaiyan Wang, Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014 People’s Republic of ChinaYong Zhang, WHO WPRO Regional Polio Reference Laboratory and State ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4488039 Mon, 14 Feb 2011 07:03:33 +0100 4488039 http://www.medworm.com/index.php?rid=4488040&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F53853957xl315236%2F Abstract  Determination of the transcription level of cellular prion protein (PrPC) is essential for understanding its role in organisms and revealing mechanism of susceptibility and resistance to scrapie. However, the expression of prion protein (PrP) mRNA in sheep has not been quantified in great detail in digestive tract which is important during scrapie spread through oral route. Herein, we report on measurement of sheep PrP mRNA using absolute quantitative real-time RT-PCR. Total RNA was isolated from five different regions of the central nervous system (CNS), four regions of lymphoid system, eleven regions of digestive tract, and two reproductive organ tissues of eight sheep of two different genotypes (ARR/ARQ and ARH/ARQ) and PrP mRNA was quantified by real-time RT-PC... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4488040 Mon, 14 Feb 2011 07:03:32 +0100 4488040 http://www.medworm.com/index.php?rid=4488043&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F48m44w45847l2307%2F Abstract  A begomovirus associated with yellow mosaic disease in Rhynchosia minima, a common weed was cloned and sequenced. The virus has a bipartite genome, of which DNA-A is 2727 nucleotide length, and DNA-B 2679 nucleotides, and has a typical Old World bipartite begomovirus genome organization. Sequence comparison to all other begomovirus sequences available in the database shows the virus isolated from R. minima to be distinct. Maximum identity of 84% was seen with an isolate of Velvet bean severe mosaic virus-(India: Lucknow:2009) VBSMV-(IN:Luc:09) (GeneBank Accession No. FN543425), while less than 73% identity was observed with any other legumovirus. The molecular data show that the virus identified here is a new species in the genus Begomovirus for which the name Rhync... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4488043 Mon, 14 Feb 2011 07:03:31 +0100 4488043 http://www.medworm.com/index.php?rid=4488042&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fcr2681w510m5q4q4%2F Abstract  Two double-stranded RNA (dsRNA) segments of a virus with a bipartite genome identified in fig (Ficus carica L.) and denoted Fig cryptic virus (FCV) were cloned and sequenced. Viral dsRNAs are 1696 bp (RNA-1) and 1415 bp (RNA-2) in size. RNA-1 contains a single ORF (1419 nt) potentially encoding a 54 kDa protein and comprising the conserved amino acid motifs of the RNA-dependent RNA polymerase (RdRp) domain of species of the genus Alphacryptovirus. Its full-length amino acid sequence has the highest identity with Raphanus sativus cryptic virus 2 (RsCV-2) (36%), Beet cryptic virus 3 (BCV-3) (36%) and Fragaria chiloensis cryptic virus (FCCV) (34%). RNA-2 has also a single ORF (1014 nt) coding for a polypeptide with a predicted molecular mass of ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4488042 Mon, 14 Feb 2011 07:03:31 +0100 4488042 http://www.medworm.com/index.php?rid=4488041&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fcll31403p14t2376%2F This study suggested that CSFV NS2 plays an important role in the inflammatory response and in persistent CSFV infection. These findings provide novel information on the function of the poorly characterized CSFV NS2. Content Type Journal ArticlePages 1-8DOI 10.1007/s11262-011-0582-zAuthors Qinghai Tang, College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi, 712100 People’s Republic of ChinaKangkang Guo, College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi, 712100 People’s Republic of ChinaKai Kang, College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi, 712100 People’s Republic of ChinaYanming Zhang, College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi, 712100 People’s Republic... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4488041 Mon, 14 Feb 2011 07:03:31 +0100 4488041 http://www.medworm.com/index.php?rid=4441534&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fv1823w8007613076%2F Abstract  The second matrix (M2) gene of avian metapneumovirus subgroup C (aMPV-C) contains two overlapping open reading frames (ORFs), encoding two putative proteins, M2-1 and M2-2. Both proteins are believed to be involved in viral RNA transcription or replication. To further characterize the function of the M2-2 protein in virus replication, the non-overlapping region of the M2-2 ORF was deleted from an infectious cDNA clone of the aMPV-C strain, and a viable virus was rescued by using reverse genetics technology. The recombinant virus, raMPV-C ΔM2-2, was characterized in vitro and in vivo. In Vero cells, raMPV-C ΔM2-2 replicated slightly less efficiently than the parental virus, 10-fold reduction at 48-h post-infection. The raMPV-C ΔM2-2 virus induced typica... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4441534 Thu, 03 Feb 2011 07:27:11 +0100 4441534 http://www.medworm.com/index.php?rid=4441533&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F59501547008k715k%2F In this study, suspected classical swine fever (CSF) samples from the Guangxi Province of China were obtained from pigs with acute CSF, aborted fetuses, newborn pigs that died at 1–2 days of age, tonsils of healthy pigs, and leukocytes of immunized sows during 2001–2009. About 92 of 775 samples were found to be positive by RT-PCR, and 41 isolates were obtained. Phylogenetic analysis was performed on the 31 isolates by sequencing the E2 gene, and the isolates were found to cluster into two groups: (1) isolates from aborted fetuses (except GXGZ02), deceased newborn baby pigs, tonsils of healthy pigs, and leukocytes of immunized sows belonged to group 1.1, along with vaccine strain, HCLV, and standard virulent strain, Shimen, of China, and (2) 20 isolates from pigs with acute CS... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4441533 Thu, 03 Feb 2011 07:27:11 +0100 4441533 http://www.medworm.com/index.php?rid=4441536&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F428606742v5084q8%2F Abstract  We determined for the first time the complete genome sequences of two Korean strains of the tick-borne encephalitis virus (TBEV), designated KrM 93 and KrM 213, isolated from the lung tissues of wild rodents in 2006. The genomes are 11,097 nucleotides (nt) in length and consist of a 132 nt 5′-noncoding region (NCR), a 10,245 nt open reading frame (ORF) containing 10 viral protein-coding regions (3,415 amino acids), and a 720 nt 3′-NCR. Compared with the 31 fully sequenced TBEV strains currently available, KrM 93 and KrM 213 show genomic nucleotide (and deduced amino acid) sequence divergences ranging from 1.8 (0.7) to 19.2 (26.6)% and 1.9 (0.8) to 19.3 (26.7)%, respectively. Phylogenetic and recombination analyses based on the complete genome sequenc... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4441536 Tue, 01 Feb 2011 08:46:59 +0100 4441536 http://www.medworm.com/index.php?rid=4441535&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fc8r5733kt8668823%2F In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). Six primers were designed to amplify the nucleocapsid (N) gene of PEDV. The optimization, sensitivity, and specificity of the RT-LAMP were investigated. The results showed that the optimal reaction condition for RT-LAMP amplifying PEDV N gene was achieved at 63°C for 50 min. The RT-LAMP assay was more sensitive than gel-based RT-PCR and enzyme-linked immunosorbent assay. It was capable of detecting PEDV from clinical samples and differentiating PEDV from Porcine transmissible gastroenteritis virus, Porcine rotavirus, Porcine pseudorabies virus, Porcine reproductive and respiratory syndrome virus, and Avian infectious bronchi... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4441535 Tue, 01 Feb 2011 08:46:59 +0100 4441535 http://www.medworm.com/index.php?rid=4427940&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fl5506737g64747vg%2F Abstract  Two unusual human rotavirus G12 strains, CAU195 and CAU214, were isolated from female pediatric diarrhea patients under 12 months of age in 2006 using a cell culture system and their full genome sequences were analyzed. The 11 gene segments of both Korean G12 strains were classified as G12-P[6]-R1-C1-M1-I1-A1-N1-T1-E1-H1 genotypes. Notably, the Korean strains were of the same genotypes as previously reported strains isolated from Bangladesh in 2003 (Dhaka12-03), from the United States in 2005–2006 (US6597), and from Germany in 2008 (GER126-08 and GER172-08), suggesting that closely related G12P[6] strains are persistent and widespread. Content Type Journal ArticlePages 1-6DOI 10.1007/s11262-011-0576-xAuthors Van Thai Than, Department of Microbiology a... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4427940 Sat, 29 Jan 2011 17:18:54 +0100 4427940 http://www.medworm.com/index.php?rid=4404326&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fk82m401654483364%2F Abstract  The influenza A virus subtypes H1N1, H1N2 and H3N2 are prevalent in pig populations worldwide. In the present study, two relatively uncommon swine influenza virus (SIV) H1N2 subtypes, isolated in Sweden in 2009 and 2010, were compared regarding their molecular composition and biological characteristics. The differences regarding markers purportedly related to pathogenicity, host adaptation or replication efficiency. They included a truncated PB1-F2 protein in the earlier isolate but a full length version in the more recent one; differences in the number of haemagglutinin glycosylation sites, including a characteristic human one; and a nuclear export protein with altered export signal. Of particular interest, the NS1 amino acid sequence of swine H1N2-2009 and 2010 ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4404326 Fri, 21 Jan 2011 15:23:16 +0100 4404326 http://www.medworm.com/index.php?rid=4381439&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F52810426h705715p%2F In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and dinucleotide were used to investigate codon usage pattern of each protein-coding gene and genome among 31 Newcastle disease virus (NDV) isolates. The result shows that the overall extent of codon usage bias in NDV is low (mean ENC = 56.15 > 40). The good correlation between the (C + G)12% and (G + C)3% suggests that the mutational pressure, rather than natural selection, is the main factor that determines the codon usage bias and base component in NDV. It is observed that synonymous codon usage pattern in NDV genes is gene function and geography specific, but not host specific. By contrasting synonymous codon usag... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4381439 Wed, 19 Jan 2011 16:58:59 +0100 4381439 http://www.medworm.com/index.php?rid=4381440&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Ft4276066j7654708%2F Abstract  Twenty-three CSFV isolates recovered from field outbreaks in various parts of India during 2006–2009 were used for genetic analysis in the NS5B region (409 nts). Seventeen of these were studied earlier [16] in the 5′UTR region. Phylogenetic analysis indicated the continued dominance of subgroup 1.1 strains in the country. Detailed analysis of a subgroup 2.2 virus indicated the plausible Chinese origin of this subgroup in India and provided indirect evidence of routes of CSFV movement within South East Asia region. Content Type Journal ArticlePages 1-5DOI 10.1007/s11262-011-0572-1Authors S. S. Patil, Project Directorate on Animal Disease Monitoring and Surveillance, HA Farm Post, Hebbal, Bangalore, 560024 IndiaD. Hemadri, Project Directorate on Animal Disea... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4381440 Tue, 18 Jan 2011 19:35:19 +0100 4381440 http://www.medworm.com/index.php?rid=4355165&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fc521628131xk070n%2F Abstract  Eight serum specimens collected from dengue patients in Guatemala and Honduras during the Central American epidemic of 2007 were analyzed. Virus identification and serotyping performed by a nested RT-PCR assay revealed two DENV-1 isolates from Guatemala, four DENV-2 isolates, two each from Guatemala and Honduras, and two DENV-4 isolates from Honduras. Viral genotyping determined by phylogenetic analysis of the complete envelope gene sequences demonstrated that the DENV-2 isolates from Guatemala and Honduras fell into the American/Asian Genotype III, and were most closely related to DENV-2/NI/BID-V2683-1999 isolated from a dengue case in Nicaragua in 1999; and the DENV-4 F07-076 isolate from Honduras belonged to genotype II, and was most closely related to DENV-4/U... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4355165 Fri, 14 Jan 2011 14:17:28 +0100 4355165 http://www.medworm.com/index.php?rid=4341762&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2F07664n6282373w63%2F Abstract  Poxviruses are complex in their nucleotide compositional features of the coding regions. The codon usages in Poxviruses are in accordance with their compositional bias. In the Poxviridae family, codon usage patterns and nucleotide compositional traits are widely divergent across species but some conservation was observed within a genus. Viruses from six Chordopox genera, i.e., Avipoxvirus, Capripoxvirus, Cervidpoxvirus, Orthopoxvirus, Suipoxvirus, Yatapoxvirus, and one Entomopox genus- Betaentomopoxvirus, and some unclassified Entomopoxvirus are significantly rich in AT composition. Four other Chordopox genera- Molluscipoxvirus, Orthopoxvirus, Parapoxvirus, and some unclassified Chordopoxvirus are dominated by the GC rich viruses. Poxviruses from these AT rich and GC ... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4341762 Mon, 10 Jan 2011 16:14:47 +0100 4341762 http://www.medworm.com/index.php?rid=4326699&cid=s_33279_50_f&fid=33279&url=http%3A%2F%2Fwww.springerlink.com%2Fcontent%2Fp744668512165695%2F Abstract  Integration of DNA copies in a host genome is a necessary stage in the life cycle of retroviruses and LTR-retrotransposons. There is still no clear understanding of integration specificity of retroelements into a target site. The selection of the target DNA is believed to potentially affect a number of factors such as transcriptional status, association with histones and other DNA-binding proteins, and DNA bending. The authors performed a comprehensive computer analysis of the integration specificity of Drosophila melanogaster LTR-retrotransposons and retroviruses including an analysis of the nucleotide composition of targets, terminal sequences of LTRs, and integrase sequences. A classification of LTR-retrotransposons based on the integration specificity was deve... Virus Genes journals http://www.medworm.com/rss/comments.php?id=4326699 Fri, 07 Jan 2011 14:49:49 +0100 4326699