A complete sequence and comparative analysis of a SARS-associated virus （Isolate BJO1）

The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-assoclated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs.We report the complete genome sequence and comparative analysis of an isolate (B J01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 20RFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host.Two amino acid changes have been detected in the M protein,which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).     

A common function for polyoma virus large-T and papillomavirus E1 proteins?

Nucleotide sequencing has revealed a common genetic organization for three papillomaviruses: BPV-1 (bovine papillomavirus type 1), HPV-1 (human papillomavirus type 1a) and HPV-6 (human papillomavirus type 6b). Several open reading frames, corresponding to as yet uncharacterized proteins, were observed in these genomes in the region that is required for oncogenic transformation by BPV-1 and for plasmidial maintenance of its genome. The longest of these frames, E1, is also the most conserved between the three viruses; we have compared the amino acid sequence of its putative product ('E1 protein') with those of the large-T proteins of three polyoma viruses and report here significant homologies in their carboxy-terminal halves, extending for over 200 amino acids. Moreover, similar secondary structures were predicted in this region, especially in two blocks of homologous residues, which correspond in the large-T proteins of polyoma and simian virus 40 (SV40) viruses to sites involved in the ATPase and nucleotide-binding activities. These observations suggest that the papillomavirus E1 proteins might have a function in common with the polyoma virus large-T proteins (which are required for the initiation of viral DNA replication). As it was suggested recently that the E1 gene product is involved in maintaining the BPV-1 genome as a plasmid in transformed cells, we speculate that the structural features conserved in these otherwise very different viruses are general characteristics of eukaryotic proteins involved in the control of DNA replication.     

Characterization of the 1918 influenza virus polymerase genes

The influenza A viral heterotrimeric polymerase complex (PA, PB1, PB2) is known to be involved in many aspects of viral replication and to interact with host factors, thereby having a role in host specificity. The polymerase protein sequences from the 1918 human influenza virus differ from avian consensus sequences at only a small number of amino acids, consistent with the hypothesis that they were derived from an avian source shortly before the pandemic. However, when compared to avian sequences, the nucleotide sequences of the 1918 polymerase genes have more synonymous differences than expected, suggesting evolutionary distance from known avian strains. Here we present sequence and phylogenetic analyses of the complete genome of the 1918 influenza virus, and propose that the 1918 virus was not a reassortant virus (like those of the 1957 and 1968 pandemics), but more likely an entirely avian-like virus that adapted to humans. These data support prior phylogenetic studies suggesting that the 1918 virus was derived from an avian source. A total of ten amino acid changes in the polymerase proteins consistently differentiate the 1918 and subsequent human influenza virus sequences from avian virus sequences. Notably, a number of the same changes have been found in recently circulating, highly pathogenic H5N1 viruses that have caused illness and death in humans and are feared to be the precursors of a new influenza pandemic. The sequence changes identified here may be important in the adaptation of influenza viruses to humans.     

Bioinformatic Analysis of Putative Gene Products Encoded in SARS—HCoV Genome

The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus named as SARS-HCoV. Using bioinformatic methods, we have performed a detailed domain search. In addition to the viral structure proteins, we have found that several putative polypeptides share sequence similarity to known domains or proteins. This study may provide a basis for future studies on the infection and replication process of this notorious virus.     

Protein Subcellular Localization Prediction and Genomic Polymorphism Analysis of the SARS Coronavirus

Introduction In March 2003, a novel coronavirus (CoV) was dis-covered in association with the outbreak of severe acute respiratory syndrome (SARS)[1-3]. The complete genome sequence of several SARS-CoV isolates was soon determined and characterized[4,5]. Comparison of variant SARS-CoV genome sequences has identified certain genetic signatures that can be used to trace sources of infection[6]. Vaccines are now being devel-oped and molecular modeling has suggested that modi-fied rhinovir…     

Bioinformatics analysis of SARS-Cov M protein provides information for vaccine development

Severalmonthsago ,anoutbreakofsevereacuterespiratorysyndrome (SARS )startedtospreadaroundtheworld .Asofthiswriting (May 14 ,2 0 0 3) ,morethan 75 0 0 personshavebeeninfectedinasmanyas 2 9countries[1] .The pathogencausingSARShasalreadybeenidentifiedtobeSARS Covbyanumberoflaboratoriesworldwide[2 ,3] .Severedis easesinanimals ,suchasthediseasescausedbyporcinetransmissiblegastroenteritisvirus (TGEV ) ,murinehepatitisvirus (MHV)andporcinehemagglu tinatingencephalomyelitisvirus (PHEV ) ,ha…     

引起人非典型性肺炎的冠状病毒基因组与其它冠状病毒基因组的初步比较

一种在世界范围内突然爆发的致命流行病——急性呼吸窘迫综合症(SARS)击倒了数干人，一种全新的冠状病毒被认为是其病原．5个SARS相关冠状病毒的全基因组序列已经完成．我们进行了SARS相关冠状病毒和其它冠状病毒的基因组进化分析和序列比较，结果显示：1．SARS相关冠状病毒不直接来自于任何已知的冠状病毒；2．E蛋白的基因可能是在近期从其它病毒横向转移到SARS病毒中来的；3．Sl和S2基因发生了较大范围的缺失或插入突变．这些基因横向转移和突变改变了SARS相关病毒的表面结构和抗原性，极有可能是导致其获得侵染人类细胞的主要原因．     

SARS冠状病毒及相关病毒的分子系统学分析

根据SARS冠状病毒及其相关病毒的基因组核酸序列和3种不同蛋白质序列，应用最大简约法和最小进化法重建系统发育树；并对SARS冠状病毒的11个推测蛋白质(ORF)做BLAST分析。结果表明，SARS冠状病毒和鼠肝炎病毒——牛冠状病毒分支构成姊妹群。其单系群性质得到强有力的统计学支持。这暗示了SARS的爆发可能源自种间屏障的突破事件，该病毒天然宿主可能为猪、牛或鼠。SARS冠状病毒与已知的人冠状病毒分属冠状病毒科的不同分支，因此致病机制可能有很大不同。3个基因的系统树分支格局的一致性表明：SARS冠状病毒这3个主要基因与其他冠状病毒间不存在重组，但全部11个ORF的BLAST分析却认为其基因组上一些小的区段可能与其他病毒存在重组。     

啤酒花潜隐病毒新疆分离物的全基因组序列分析

对新疆啤酒花上获得的HpLV分离物HpLV-XJ进行了全长克隆和基因组序列分析。结果显示:HpLV-XJ的全基因组序列为8612个核苷酸(nt)(不包括poly A),含有6个开放阅读框(ORF),分别编码224 kDa(ORF1)、25kDa(ORF2)、11 kDa(ORF3)、7 kDa(ORF4)、34 kDa(ORF5)、和12 kDa(ORF6)蛋白。序列相似性分析结果表明,HpLV-XJ与HpLV(GenBank:AB032469)序列相似性达98.5%,6个开放阅读框的核苷酸序列相似性分别为98.3%、99.0%、97.6%、96.7%、99.5%和98.4%;由此推导的氨基酸序列相似性分别为98.6%、98.7%、97.2%、95.0%、99.4%和98.1%,各个基因的核苷酸序列和蛋白的氨基酸之间存在着一定的差异。     

Spike protein homology between the SARS-associated virus and murine hepatitis virus implies existence of a putative receptor-binding region

Coronavirus has been determined to be the cause of the recent outbreak of severe acute respiratory syndrome (SARS). Human coronavirus 229E had been studied well and its receptor-binding domain was restricted to aa417-547 of S protein. However, this region has no homology with the newly separated SARS-associated virus (Hong Kong isolate CUHK-W1). Then we analyzed the phyiogenesis of S1 subunit of the coronavirus spike protein (SARS-associatedvirus, Hong Kong isolate CUHK-W1). Interestingly, thehighest homology between murine hepatitis virus (MHV)and SARS-associated coronavirus was found. And the important sites (aa62-65 and aa214-216) on the spike proteinof MHV with receptor-binding capacity were highly conservative in comparison with the newly separated SARS-associated virus (the corresponding sites are aa51-54 and aa195-197). These results from bioinformatics analysis mighthelp us to study the receptor-binding sites of SARS-associated virus and the mechanism of the virus entry into the target cell, and design antiviral drugs and potent vaccines.     

双链RNA技术在果树病毒研究中的应用

含ＲＮＡ基因组的植物病毒在复制时会产生双链ＲＮＡ（ｄｓＲＮＡ）。本文介绍了用ＣＦ－１１纤维素粉提取ｄｓＲＮＡ的步骤,并列举了ｄｓＲＮＡ在果树病毒研究中的应用,其主要应用有：１）果树病毒病及病原鉴定;２）病毒分化株系的鉴定;３）以ｄｓＲＮＡ为中介对病毒核酸序列进行测定;４）探针制备和ｃＤＮＡ克隆的获得;５）用于检测病毒卫星ＲＮＡ和亚基因组ＲＮＡ;６）侵染性测定和制备抗血清等方面的研究。     

Nucleotide sequence and formation of the transforming gene of a mouse sarcoma virus

The complete nucleotide sequence of the transforming gene of a mouse sarcoma virus has been determined. It codes for a protein of 374 amino acids. The nucleotide sequence of the junctions between a murine leukaemia virus and cellular sequences leading to the formation of the viral transforming gene have also been elucidated. The viral transforming sequence and its cellular homologue share an uninterrupted stretch of 1,159 nucleotides, with few base substitutions. The predicted amino acid sequence of the mouse sarcoma virus transforming gene was found to share considerable homology with the proposed amino acid sequence of the avian sarcoma virus oncogene (src) product.     

Tobacco curly shoot virus iso-lated in Yunnan is a distinct species of Begomovirus

Virus isolate Y1 was obtained from tobacco showing curly shoot symptoms in Baoshan, Yunnan Province. Whitefly transmission test and virion morphology observation showed that it is a begomovirus. In reactions with 14 monoclonal antibodies raised against begomoviruses, Y1 was readily differentiated from begomoviruses reported in China, Pakistan and India. The complete nucleotide sequence of DNA-A was determined, it contains 2746 nucleotides, with two ORFs in virion-sense DNA and four ORFs in complementary-sense DNA. Comparisons with total DNA-A, intergenic region and deduced amino acid sequences of individual ORFs showed that Y1 is a distinct Begomovirus species, for which the name Tobacco curly shoot virus (TCSV) is proposed. The total DNA-A of TCSV is most closely related to that of Tomato leaf curl virus from India (85% sequence identity). In contrast, the deduced coat protein of TCSV is most like that of Cotton leaf curl virus 72b isolate from Pakistan (98% amino acid sequence identity).     

Complete nucleotide sequence and genomic organization of Periplaneta fuliginosa densonucleosis virus

We have cloned the replicative form of thePeriplaneta fuliginosa densonucleosis virus (PfDNV) genome and determined its complete sequence. The sequence has 5 454 nucleotides (nt), the genome consists of an internal unique sequence flanked by inverted terminal repeats (201 nt). The first 122 nt at the 5′ end and the terminal 122 nt at the 3′ end of both plus and minus strands can fold into a typical hairpin structure. The genome contains seven major open reading frames (ORFs). The plus strand has 4 ORFs occupying the 5′ half of the plus strand, whereas the others span the 5′ half of the minus strand. Two potential promoters were found at map units (m.u.) 3 and 97. Computer analysis of sequence homologies with other parvoviruses suggests that the plus strand ofPf DNV encodes very likely the nonstructural proteins and the minus strand probably encodes the structural proteins.     

Molecular characterization of H1N1 influenza A viruses from human cases in North America

Subtypes of H1N1 influenza virus can be found in humans in North America, while they are also associated with the infection of swine. Characterization of the genotypes of viral strains in human populations is important to understand the source and distribution of viral strains. Genomic and protein sequences of 10 isolates of the 2009 outbreak of influenza A （H1N1） virus in North America were obtained from GenBank database. To characterize the genotypes of these viruses, phylogenetic trees of genes PB2, PB1, PA, HA, NP, NA, NS and M were constructed by Phylip3.67 program and N-Linked glycosylation sites of HA, NA, PB2, NS1 and M2 proteins were analyzed online by NetNGlyc1.0 program. Phylogenetic analysis indicated that these isolates are virtually identical but may be recombinant viruses because their genomic fragments come from different viruses. The isolates also contain a characteristic lowly pathogenic amino acid motif at their HA cleavage sites （IPSIQSR↓GL）, and an E residue at position 627 of the PB2 protein which shows its high affinity to humans. The homologous model of M proteins showed that the viruses had obtained the ability of anti-amantadine due to the mutation at the drug-sensitive site, while sequence analysis of NA proteins indicated that the viruses are still susceptible to the neuraminidase inhibitor drug （i.e. oseltamivir and zanamivir） because no mutations have been observed. Our results strongly suggested that the viruses responsible for the 2009 outbreaks of influenza A （H1N1） virus have the ability to cross species barriers to infect human and mammalian animals based on molecular analysis. These findings may further facilitate the therapy and prevention of possible transmission from North America to other countries.     

Molecular characterization of<Emphasis Type="Italic">Tomato yellow leaf curl China</Emphasis> virus and its satellite DNA isolated from tobacco

Virus isolates, Y8, Y36 and Y38, were obtained from tobacco plants showing leaf curl symptoms in Honghe,Yunnan Province. In reactions with 14 monoclonal antibodies raised against Begomoviras particles, Y8, Y36 and Y38 had similar antigenic reaction in TAS-ELISA as Tomato yellow leaf carl China virus (TYLCCNV). The complete DNA-A nueleotide sequences of Y8, Y36 and Y38 were determined and they contain 2727, 2730 and 2730 nueleotides, respectively. Each of the DNA-A sequences has a typical Begomovirus genome organization encoding 60RFs with 20RFs[AVI(CP) and AV2] in virion-sense DNA and 40RFs (AC1 to AC4) in complementary-sense DNA. Comparisons with total DNA-A, intergenie region and deduced amino acid sequences of individual ORFs show that Y8, Y36 and Y38 are isolates of TYLCCNV. Satellite DNA molecules (DNAβ) were found to be associated with Y8, Y36 and Y38, which consist of 1338, 1339 and 1338 nucleotides, respectively. Comparisons show that these DNAβ molecules share 98%--99% sequence identities on nucleotide level and have a common ORF (designated C1) encoding 126 amino acids on the complementary strand.     

Myristic acid is coupled to a structural protein of polyoma virus and SV40

In the lytic cycle of papova viruses, both uncoating of the viral genome after infection and assembly of functional virions take place in the cell nucleus. The mechanisms by which newly internalized virions are targeted to the nucleus and viral DNA encapsidated into particles are poorly understood. Although the major capsid protein VP1 is involved in endocytosis, and largely defines virion structure, the functions of the minor proteins VP2 and VP3 have remained obscure. Here we show that VP2 from both polyoma virus and simian virus 40 (SV40) is covalently linked to myristic acid; this is the first report of a myristylated protein in the nucleus and of a fatty acid being important in the structure of a nonenveloped virus. We consider the implications of this unusual modification on encapsidation and suggest that VP2 may be a scaffolding protein for virion assembly.