Isolation and complete nucleotide sequence of the measles virus IMB-1 strain in China

The complete nucleotide sequence of the measles virus strain IMB-1, which was isolated in China, was determined. As in other measles viruses, its genome is 15,894 nucleotides in length and encodes six proteins. The full-length nucleotide sequence of the IMB-1 isolate differed from vaccine strains (including wild-type Edmonston strain) by 4%–5% at the nucleotide sequence level. This isolate has amino acid variations over the full genome, including in the hemagglutinin and fusion genes. This report is the first to describe the full-length genome of a genotype H1 strain and provide an overview of the diversity of genetic characteristics of a circulating measles virus.     

A comparison of complete genome sequences of a rabies virus chinese isolate SH06 with the vaccine strains

In this study, we determined the complete nucleotide and deduced amino acid sequence of a primary isolate of rabies virus (SH06) obtained from the brain of a rabid dog. The overall length of the genome was 11 924 nucleotides. Comparison of the genomic sequence showed the homology of SH06 at nucleotide level with full-length genomes of reference vaccine strains ranged from 82.2% with the PV strain to 86.9% with the CTN strain. A full-length genome-based phylogenetic analysis was performed with sequences available from GenBank. Phylogenetic analysis of the complete genome sequences indicated that the SH06 exhibited the highest homology with rabies street virus BD06 and CTN vaccine strain originated from China.     

水稻瘤矮病毒基因组S9片段的基因结构特征

应用RT-PCR技术克隆了水稻瘤矮病毒(RGDV)中国广东信宜分离物(RGDV-C)的基因组S9片段,测定了全序列并进行了生物信息学分析。结果表明,RGDV-C S9片段全长共有1202bp(登录号AY556483),含有一个长的开放阅读框,这一开放阅读框编码一个由323个氨基酸残基组成的多肽,推测分子量约35.6kDa,与泰国分离物(RGDV-T)的全序列相比,它们的核苷酸长度相等,核苷酸同源性为98.1%,氨基酸同源性为98.5%。RGDV S9片段编码的Pns9蛋白在植物呼肠孤病毒属内未发现同源蛋白,其功能尚待确定。利用NCBI的BLAST查找与比较,发现Pns9与伯氏疏螺旋体(Borrelia burgdorferi)ATP依赖的Clp蛋白水解酶组分[ATP-dependent Clp prote-ase proteolytic component(clpP-1)]有21.8%的氨基酸序列同源性。     

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 complete coding sequence of a European isolate of GB-C/hepatitis G virus

We determined the full-length coding sequence of a GB-C/hepatitis G (GBV-C/HGV) virus isolate (AUQ) obtained from a French blood donor. The genome of AUQ strain contains a long open reading frame encoding 2842 amino acid residues. Comparison with the 33 complete genome sequences so far available from the databases indicates that the full-length sequence of GBV-C/HGV AUQ showed 9.0-14.1% nucleotide sequence divergence but only 1.6-5.3% at the amino acid level. Analysis of the potential cleavage sites of the polyprotein found that they were remarkably conserved among all sequences. Although phylogenetic studies based on partial genomic sequences suggested a clusterization according to the geographical origin, analysis based on full-length polyprotein did not provide similar conclusions.     

Genetic diversity within human erythroviruses: identification of three genotypes

B19 virus is a human virus belonging to the genus Erythrovirus: The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of B19 virus. To date, the V9 isolate remains the unique representative of a new variant in the genus Erythrovirus, and its taxonomic position is unclear. We report here the isolation of 11 V9-related viruses. A prospective study conducted in France between 1999 and 2001 indicates that V9-related viruses actually circulate at a significant frequency (11.4%) along with B19 viruses. Analysis of the nearly full-length genome sequence of one V9-related isolate (D91.1) indicates that the D91.1 sequence clusters together with but is notably distant from the V9 sequence (5.3% divergence) and is distantly related to B19 virus sequences (13.8 to 14.2% divergence). Additional phylogenetic analysis of partial sequences from the V9-related isolates combined with erythrovirus sequences available in GenBank indicates that the erythrovirus group is more diverse than thought previously and can be divided into three well-individualized genotypes, with B19 viruses corresponding to genotype 1 and V9-related viruses being distributed into genotypes 2 and 3.     

FMDV OH99株基因组全序列的测定及其基因特征研究

采用RT-PCR方法对FMDV OH99株基因组全序列进行了分子克隆与测序。结果表明OH99株基因组全基因组序列长8040nt,其中5’NCR长1026nt,前导蛋白(L)编码区长603nt。该毒株结构蛋白与非结构蛋白编码区的核苷酸序列为6318nt,3’NCR长93nt,其后是poly(A)尾巴,测序结果表明该结构至少含有56个A。应用分子生物学软件,将OH99株与其它参考毒株进行了序列比较,并对其基因特征、推导的氨基酸序列进行了研究分析。结果显示,在分类地位上OH99株归属于O型FMDV,与OTY TW／97具有较高的同源性,而与其他参考毒株的差异性比较大,而且在基因组功能未知区域和3A编码区域具有两处明显的基因片段缺失现象,其中3A编码区缺失30nt,与OTY TW/97株相同,但功能未知区域的缺失状况与OTY TW／97稍有差异。根据VP1基因序列,对OH99株与参考毒株进行了系统发生树分析,分析结果表明OH99株与0TY TW／97株在同一基因型内,其遗传关系最近,而与其毒株遗传关系较远。     

小RNA深度测序技术分析西瓜花叶病毒蜀葵分离物

蜀葵病毒病害的发生对其生长造成严重影响,明确蜀葵病毒病害的种类及变异进化对蜀葵病毒病害的防治具有重要意义。利用小RNA深度测序技术对具有明显脉明、花叶症状的蜀葵叶片进行鉴定。结果发现,感病蜀葵被西瓜花叶病毒(Watermelon mosaic virus, WMV)、锦葵脉明病毒(Mala vein cleaning virus, MVCV)和一种新的RNA病毒[暂命名为蜀葵病毒1号(Althaea rosea virus1, ArV1)]所侵染。为进一步明确WMV蜀葵分离物(WMV-Tg)的进化关系,对病毒WMV-Tg全基因组进行扩增,获得全长为10 046个核苷酸序列(nt)。序列分析结果显示,WMV-Tg与已报道的WMV分离物基因组核苷酸序列的同源性为83.3%～90.2%。系统进化关系表明,WMV-Tg与WMV-Pg聚为一簇,亲缘关系最近。对蜀葵WMV-Tg来源的小RNA(WMV-derived small interfering RNAs, WMV-vsiRNAs)的长度分布、5′碱基偏好性、极性分布以及热点区分布的分析,有助于加深对WMV-vsiRNAs的了解,并为进一步研究病毒来源的小RNA(virus-derived small interfering RNAs, vsiRNAs)在抗病毒防御中的功能,以及为蜀葵病毒病的防治奠定理论基础。     

西瓜花叶病毒中国分离株全基因组核苷酸序列测定

西瓜花叶病毒(Watermelon mosaic virus,WMV)是马铃薯Y病毒属(Potyvirus)成员,主要危害西瓜和甜瓜,引起花叶病。在田间,该病害主要由蚜虫以非持久性方式传播。西瓜和甜瓜花叶病在国内陕西、山东、云南、辽宁、山西、新疆、河南和黑龙江等地广泛发生[1-6]。从20世纪80年代中期开始发生,逐渐上升为普遍发生的主要病害。我国大部分地区因西瓜和甜瓜病毒病造成的损失为30%~50%,甚至会绝产,西瓜花叶病毒已经成为制约西瓜和甜瓜高产稳产最主要的因素之一[7]。到目前为止,多数工作集中在对西瓜和甜瓜病毒病的鉴定,在分子生物学上仅限于对CP基因…     

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.     

猪繁殖与呼吸综合征病毒HB-1(sh)/2002株全基因组分子特征分析

猪繁殖与呼吸综合征病毒(porcine reproductive and respiratory syndrome virus,PRRSV)可引起妊娠母猪流产,早产,产死胎、弱胎、木乃伊胎及仔猪和肥育猪的呼吸道症状.最先于20世纪80年代末期爆发于美国和欧洲一些国家,随后很快传至全世界,给世界养猪业造成了巨大的损失.我国在1995年底爆发该病,之后蔓延到我国很多省份.1996年郭宝清、杨汉春等分别从疑似PRRS的病例中分离出PRRSV[1,2].     

mRNA sequence and deduced amino acid sequence of the mumps virus small hydrophobic protein gene.

The mRNA of a putative small hydrophobic protein (SH) of mumps virus was identified in mumps virus-infected Vero cells, and its complete nucleotide sequence was determined by sequencing the genomic RNA and cDNA clones and partial sequencing of mRNA. The SH mRNA is 310 nucleotides long excluding the poly(A) and contains a single open reading frame encoding a protein of 57 amino acids with a calculated molecular weight of 6,719. The predicted protein is highly hydrophobic and contains a stretch of 25 hydrophobic amino acids near the amino terminus which could act as a membrane anchor region. There is no homology between the putative SH protein of mumps virus and the SH protein of simian virus 5, even though the SH genes are located in the same locus in the corresponding genome. One interesting observation is that the hydrophobic domain of simian virus 5 SH protein is at the carboxyl terminus, whereas that of mumps virus putative SH protein is near the amino terminus.     

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.     

Full sequence analysis of the original Sapporo virus

In this study, the full-length genome sequence of the prototype of sapovirus, namely Sapporo virus (SV82), was identified. Sapporo virus RNA was extracted from a fecal sample, amplified by RT-PCR and the PCR products sequenced directly and analyzed. Sequence analysis showed that Sapporo virus consists of 7433 nucleotides and has three open reading frames. The Sapporo strain shows 91.7% nucleotide sequence identity to the Manchester virus. Phylogenic analysis has also revealed the closeness of Sapporo virus to other sapovirus/genogroup I strains. Basic information on the evolutionary history of sapovirus analysis is provided here.     

Computational reconstruction of Bole1a, a representative synthetic hepatitis C virus subtype 1a genome

Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.     

First Report of a Strain of Alternanthera yellow vein virus Infecting Eclipta prostrate (L.) L. (Compositae) in China

In 2005, Eclipta prostrata plants exhibiting yellow vein symptoms were observed in Guangzhou, Guangdong province, China. A virus isolate G8 was cloned from a symptomatic plant. The complete nucleotide sequence of G8 DNA-A was determined to be 2745 nucleotides, which had typical characteristics of Begomovirus genome organization. The comparison of complete nucleotide sequence of DNA-A showed that isolate G8 shared the highest sequence identity with Alternanthera yellow vein virus (AlYVV) isolates G38 and Hn51 at 95.9% and 94.3%, respectively. These results show that G8 infecting E. prostrata in Guangdong is a strain of AlYVV.