X病毒属6个成员中国分离物CP基因的克隆及同源性分析

根据Genbank报道的大蒜A病毒(GarVA)、大蒜B病毒(GarVB)、大蒜C病毒(GarVC)、大蒜D病毒(GarVD)、大蒜E病毒(GarVE)和大蒜X病毒(GarVX)的序列设计引物,克隆外壳蛋白(CP)基因、测序并进行同源性分析。结果表明,6种病毒CP基因分别由756、735、780、753、759和732核苷酸组成。氨基酸序列多重对齐比对结果表明,GarVC与GarVD同源性最低(57.69%),GarVB与GarVX同源性最高(87.70%);同属6种病毒CP基因在C端变异性大,N端保守。进化树显示Gar-VA、GarVE和GarVD成簇,GarVB和GarVX成簇,GarVC与其他5种病毒亲缘关系较远。本研究结果为预测6种病毒之间是否存在血清学交叉反应,在进行ELISA检测是否会相互干扰提供指导意义。     

Genome sequence of a reassortant strain of bluetongue virus serotype 23 from western India

The full genome sequence (19,177 bp) of an Indian strain (IND1988/02) of bluetongue virus (BTV) serotype 23 was determined. This virus was isolated from a sheep that had been killed during a severe bluetongue outbreak that occurred in Rahuri, Maharashtra State, western India, in 1988. Phylogenetic analyses of these data demonstrate that most of the genome segments from IND1988/02 belong to the major "eastern" BTV topotype. However, genome segment 5 belongs to the major "western" BTV topotype, demonstrating that IND1988/02 is a reassortant. This may help to explain the increased virulence that was seen during this outbreak in 1988. Genome segment 5 of IND1988/02 shows >99% sequence identity with some other BTV isolates from India (e.g., BTV-3 IND2003/08), providing further evidence of the existence and circulation of reassortant strains on the subcontinent.     

Serological Relationships Among the Over-expressed Coat Proteins of Allexiviruses

Coat protein genes of six members of the genus Allexivirus, Garlic viruses ‐A, ‐B, ‐C, ‐D, ‐E and ‐X, were over‐expressed in bacteria and used to prepare polyclonal antibodies. In western blot analysis, Garlic virus D (GarV‐D) and GarV‐E were closely related serologically and there were weaker relationships between some other pairs, particularly GarV‐E with GarV‐A, GarV‐X with GarV‐A, GarV‐X with GarV‐B and GarV‐X with GarV‐C. Sequence analysis suggested that there was no simple relationship between amino acid identity and serological properties.     

Complete genome sequence of an isolate of bluetongue virus serotype 2, demonstrating circulation of a Western topotype in southern India

Bluetongue virus serotype 2 (IND2003/02) was isolated in Tiruneveli City, Tamil Nadu State, India, and is stored in the Orbivirus Reference Collection at the Institute for Animal Health, Pirbright, United Kingdom. The entire genome of this isolate was sequenced, showing that it is composed of a total of 19,203 bp (all 10 genome segments). This is the first report of the entire genome sequence of a western strain of BTV-2 isolated in India, indicating that this virus has been introduced and is circulating in the region. These data will aid in the development of diagnostics and molecular epidemiology studies of BTV-2 in the subcontinent.     

中国烟草曲叶病毒广西株的初步研究

双生病毒 (Ｇｅｍｉｎｉｖｉｒｕｓ)是一种具有孪生颗粒形态的单链环状ＤＮＡ植物病毒[1] 。根据基因组结构特征及传播介体 ,双生病毒可分为三个亚组[1] :亚组Ⅰ双生病毒全部为叶蝉传播的单组份基因组病毒 ,基因组大小在 2 .6～ 2 .8ｋｂ之间 ,其代表病毒是玉米条纹病毒 (ＭＳＶ) ;亚组Ⅱ双生病毒是单组份基因组病毒 ,基因组大小在 2 .7～ 3.0ｋｂ之间 ;亚组Ⅲ双生病毒全部为粉虱 (Ｂｅｍｉｓｉａｔａｂａｃｉ)传播 ,基因组大小为 2 .5～ 2 .8ｋｂ ,除番茄曲叶病毒ＴＬＣＶ ＡＵＳ[2 ] 等几个病毒为单组份基因组外 ,大多数亚组Ⅲ双生病病毒…     

乙型脑炎病毒减毒中间株SA14—12—1—7基因组全序列的测定

本研究通过对乙型脑炎活疫苗减毒过程中间株SA14 12 1 7株进行全序列测定和分析 ,进一步了解乙脑活疫苗减毒及其稳定性的分子机制。根据已发表的SA14 14 2株及SA14 株的序列 ,设计 6对重叠引物 ,涵括整个乙脑病毒的基因组 ,通过RT PCR扩增出SA14 12 1 7株的各cDNA片段 ,分别克隆到pGEM T载体 ,转化至TG1受体菌中 ,挑取阳性克隆进行鉴定后测序。结果表明SA14 12 1 7株基因组全序列长 10 976个核苷酸 ,从 96到 10 394为一个长开放读码框 ,编码 3432个氨基酸。与野毒株SA14 和疫苗株SA14 14 2的核苷酸序列和氨基酸序列相比 ,同源性均在 99%以上 ,突变位点分散于各个区域 ,E区有 5个位点与疫苗株一致而与野毒株不同 ,3个位点与野毒株一致而与疫苗株不同 ,推测与其容易产生回复突变、恢复毒力有关。此外 ,NS3、NS5和 3′NTR的几个位点可能与病毒毒力稳定性相关。综上所述 ,乙脑病毒减毒中间株的基因组全序列基本类似于已发表的序列 ,若干突变位点影响病毒的弱毒性及毒力的稳定性。全序列的测定对于研究疫苗株的减毒机理具有重要意义     

Complete genome sequence of bluetongue virus serotype 9: implications for serotyping

The second complete genome of bluetongue virus serotype 9 (BTV-9) is presented in this report. The sequence analysis points to continued circulation in India of a mixed topotype virus apparently belonging to the BTV-9 serotype, and it raises questions about approaches for serotyping bluetongue viruses.     

Complete genome sequence of bluetongue virus serotype 16 of goat origin from India

In this article, we document the first complete genome sequence of an isolate of bluetongue virus serotype 16 (BTV16) from a goat in India. The virus was isolated from an in-contact goat from an animal farm in Chennai where clinical disease occurs in sheep. The total size of the genome is 19,185 bp. The information provided for full-length sequences of all 10 segments will help in understanding the geographical origin and transmission of the Indian isolate of BTV16 as well as its comparison with global isolates of BTV16 of sheep, cattle, and other host species origins.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3'-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3'-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3′-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3′-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Complete Genome Sequence of Newcastle Disease Virus Mesogenic Vaccine Strain R2B from India

Mesogenic vaccine strains of Newcastle disease virus (NDV) are widely used in many countries of Asia and Africa to control the Newcastle disease of poultry. In India, the mesogenic strain R2B was introduced in 1945; it protects adult chickens that have been preimmunized with a lentogenic vaccine virus and provides long-lasting immunity. In this article, we report the complete genome sequence of the hitherto unsequenced Indian vaccine virus strain R2B. The viral genome is 15,186 nucleotides in length and contains the polybasic amino acid motif in the fusion protein cleavage site, indicating that this vaccine strain has evolved from a virulent virus. Phylogenetic analysis of this mesogenic vaccine virus classified it with the viruses belonging to genotype III of the class cluster II of NDV.     

Complete nucleotide sequence of a mumps virus SP strain isolated in China

The complete nucleotide sequence of the mumps virus SP, which was isolated in China, was determined. As with other mumps viruses, its genome was 15 384 nucleotides (nts) in length and encoded seven proteins. The full-length nucleotide sequence of the SP isolate differed from other strains by 4%-6.8% at the nucleotide sequence level. Due to variations of amino acids over the full genome (including the HN and N genes), this isolate exhibited significant variations in the antigenic sites. This report is the first to describe the full-length genome of a genotype F strain and provide an overview of the diversity of genetic characteristics of a circulating mumps virus.     

Characterization, Genetic Diversity, and Evolutionary Link of Cucumber mosaic virus Strain New Delhi from India

The genome of Cucumber mosaic virus New Delhi strain (CMV-ND) from India, obtained from tomato, was completely sequenced and compared with full genome sequences of 14 known CMV strains from subgroups I and II, for their genetic diversity. Sequence analysis suggests CMV-ND shares maximum sequence identity at the nucleotide level with a CMV strain from Taiwan. Among all 15 strains of CMV, the encoded protein 2b is least conserved, whereas the coat protein (CP) is most conserved. Sequence identity values and phylogram results indicate that CMV-ND belongs to subgroup I. Based on the recombination detection program result, it appears that CMV is prone to recombination, and different RNA components of CMV-ND have evolved differently. Recombinational analysis of all 15 CMV strains detected maximum recombination breakpoints in RNA2; CP showed the least recombination sites.     

The Global Trade in Fresh Produce and the Vagility of Plant Viruses: A Case Study in Garlic

As cuisine becomes globalized, large volumes of fresh produce are traded internationally. The potential exists for pathogens infecting fresh produce to hitchhike to new locations and perhaps to establish there. It is difficult to identify them using traditional methods if pathogens are novel, scarce, and/or unexpected. In an attempt to overcome this limitation, we used high-throughput sequencing technology as a means of detecting all RNA viruses infecting garlic (Allium sativum L.) bulbs imported into Australia from China, the USA, Mexico, Argentina and Spain, and those growing in Australia. Bulbs tested were grown over multiple vegetative generations and all were stably infected with one or more viruses, including two species not previously recorded in Australia. Present in various combinations from 10 garlic bulbs were 41 virus isolates representing potyviruses (Onion yellow dwarf virus, Leek yellow stripe virus), carlaviruses (Shallot latent virus, Garlic common latent virus) and allexiviruses (Garlic virus A, B, C, D, and X), for which 19 complete and 22 partial genome sequences were obtained, including the first complete genome sequences of two isolates of GarVD. The most genetically distinct isolates of GarVA and GarVX described so far were identified from Mexico and Argentina, and possible scenarios explaining this are presented. The complete genome sequence of an isolate of the potexvirus Asparagus virus 3 (AV3) was obtained in Australia from wild garlic (A. vineale L.), a naturalized weed. This is first time AV3 has been identified from wild garlic and the first time it has been identified beyond China and Japan. The need for routine generic diagnosis and appropriate legislation to address the risks to primary production and wild plant communities from pathogens spread through the international trade in fresh produce is discussed.     

Genotypic and pathotypic characterization of Newcastle disease viruses from India

Newcastle disease virus (NDV) is an avian paramyxovirus that causes significant economic losses to the poultry industry in most parts of the world. The susceptibility of a wide variety of avian species coupled with synanthropic bird reservoirs has contributed to the vast genomic diversity of this virus as well as diagnostic failures. Since the first panzootic in 1926, Newcastle disease (ND) became enzootic in India with recurrent outbreaks in multiple avian species. The genetic characteristics of circulating strains in India, however, are largely unknown. To understand the nature of NDV genotypes in India, we characterized two representative strains isolated 13 years apart from a chicken and a pigeon by complete genome sequence analysis and pathotyping. The viruses were characterized as velogenic by pathogenicity indices devised to distinguish these strains. The genome length was 15,186 nucleotides (nt) and consisted of six non-overlapping genes, with conserved and complementary 3' leader and 5' trailer regions, conserved gene starts, gene stops, and intergenic sequences similar to those in avian paramyxovirus 1 (APMV-1) strains. Matrix gene sequence analysis grouped the pigeon isolate with APMV-1 strains. Phylogeny based on the fusion (F), and hemagglutinin (HN) genes and complete genome sequence grouped these viruses into genotype IV. Genotype IV strains are considered to have "died out" after the first panzootic (1926-1960) of ND. But, our results suggest that there is persistence of genotype IV strains in India.     

Cloning, restriction mapping and phylogenetic relationship of genomic components of MYMIV from Lablab purpureus

The present work describes cloning of genomic components of whitefly transmitted geminivirus infecting Lablab purpureus syn. Dolichos lablab (commonly known as Dolichos bean or Hyacinth bean). The genome characterization using PCR with geminiviral degenerate primers and DNA sequencing were used to describe the bipartite virus associated with yellow mosaic disease of Dolichos lablab. Full-length DNA-A and DNA-B clones were obtained. The DNA-A sequence analysis showed that the isolate was similar to other Mungbean yellow mosaic India virus (MYMIV) isolates reported earlier. The nucleotide sequence analysis of the full-length DNA-A of virus isolate revealed more than 97% homology with Mungbean yellow mosaic India virus-[Cowpea] (AF481865), while the DNA-B also showed >95% homology with MYMIV-[Cp] (AF503580) and MYMIV-[Sb] (AY049771). The phylogenetic analysis of present isolate showed close relationship to legume geminiviruses. The nucleotide sequence analysis showed presence of six open reading frames (ORFs) in DNA-A, with 2 ORFs aligned in sense and 4 ORFs in antisense orientation. Similarly, DNA-B contained two open reading frames (ORFs), one in sense and another in antisense orientation.     

The genome sequence of bluetongue virus type 10 from India: evidence for circulation of a western topotype vaccine strain

Bluetongue virus is the type species of the genus Orbivirus in the family Reoviridae. We report the first complete genome sequence of an isolate (IND2004/01) of bluetongue virus serotype 10 (BTV-10) from Andhra Pradesh, India. This isolate, which is stored in the Orbivirus Reference Collection (ORC) at IAH Pirbright, shows >99% nucleotide identity in all 10 genome segments with a vaccine strain of BTV-10 from the United States.     

蚕豆萎蔫病毒2号板蓝根分离株全基因组序列测定与分析

板蓝根(Isatidis Radix)病毒病害的发生已对其产量和品质造成了严重影响。因此,建立一套灵敏、快速、有效的板蓝根病毒病害检测手段十分重要。本研究利用双链RNA(double-stranded RNA,dsRNA)和非序列依赖PCR扩增(sequence-independent amplification,SIA)等技术对感病板蓝根进行鉴定,确定其被蚕豆萎蔫病毒2号(Broad bean wilt virus 2, BBWV2)所侵染。为明确BBWV2板蓝根分离物(BBWV2-IR)的进化关系,对其全基因组进行序列扩增与分析,获得其RNA1序列全长为5 955 bp,RNA2序列全长为3 602 bp,分别编码由1 870和1 064个氨基酸组成的多聚蛋白质。序列比对发现,BBWV2-IR RNA1与BBWV2-Am分离物的同源性最高,RNA2与BBWV2-SN分离物的同源性最高。全基因组变异情况分析表明,BBWV2-IR RNA1和RNA2分别与其同源性最高的株系存在多个氨基酸变异位点。系统进化分析表明,BBWV2-IR RNA1与BBWV2-Am RNA1聚为一簇,RNA2与BBWV2-SN RNA2聚为一簇,亲缘性最近。本研究获得了BBWV2板蓝根分离株的全基因组序列,并明确其在进化过程中的地位和区域变化情况,为进一步研究BBWV2-IR致病性变异提供一定的理论基础。     

Complete genome sequence of a peste des petits ruminants virus recovered from wild bharal in tibet, china

For the first time, here we announce the complete genome sequence of a field isolate of Peste des petits ruminants virus (PPRV) derived from macerated rectal tissue of a free living bharal (Pseudois nayaur) that displayed clinical disease consistent with severe infection with PPRV. Further, we compare the full genome of this isolate, termed PPRV Tibet/Bharal/2008, with previously available PPRV genomes, including those of virus isolates from domestic small ruminants local to the area where the reported isolate was collected. The current sequence is phylogenetically classified as a lineage IV virus, sharing high levels of sequence identity with previously described Tibetan PPRV isolates. Indeed, across the entire genome, only 26 nucleotide differences (0.16% nucleotide variation) and, consequently, 9 amino acid changes were present compared to sequences of locally derived viruses.     

Espirito Santo virus: a new birnavirus that replicates in insect cells

Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of Espirito Santo, Brazil, and amplified in insect cells. ESV was found to be dependent upon coinfection with a virulent strain of dengue-2 virus and to replicate in C6/36 insect cells but not in mammalian Vero cells. A sequence of the genome has been produced by de novo assembly and was not found to match to any known viral sequence. An incomplete match to the nucleotide sequence of the RNA-dependent RNA polymerase from Drosophila X virus (DXV), another birnavirus, could be detected. Mass spectrometry analysis of ESV proteins found no matches in the protein data banks. However, peptides recovered by mass spectrometry corresponded to the de novo-assembled sequence by BLAST analysis. The composition and three-dimensional structure of ESV are presented, and its sequence is compared to those of other members of the birnavirus family. Although the virus was found to belong to the family Birnaviridae, biochemical and sequence information for ESV differed from that of DXV, the representative species of the genus Entomobirnavirus. Thus, significant differences underscore the uniqueness of this infectious agent, and its relationship to the coinfecting virus is discussed.