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| 1 | A Genome Sequence of Novel SARS-CoV Isolates: the Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China显示文摘We report a complete genomic sequence of rare isolates (minor genotype) of theSARS-CoV from SARS patients in Guangdong, China, where the first few casesemerged. The most striking discovery from the isolate is an extra 29-nucleotidesequence located at the nucleotide positions between 27,863 and 27,864 (referredto the complete sequence of B J01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream ofthe N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29,suggests a significant genetic event and differentiates it from the previously re-ported genotype, the dominant form among all sequenced SARS-CoV isolates. A17-nt segment of this extra sequence is identical to a segment of the same size intwo human mRNA sequences that may interfere with viral genome replication andtranscription in the cytosol of the infected cells. It provides a new avenue for theexploration of the virus-host interaction in viral evolution, host pathogenesis, andvaccine development. | E‘deQin XiongleiHe WeiTian YongLiu WeiLi JieWen BingyinSi YongwuHu WenmingPeng LinTaug TaoJiang JianpingShi JiaJia YuZhang JiaYe Cui’eWang YujunHan JingqiangWang BaochangFan QingfaWu GuohuiChang WuchunCao ZuyuanXu RuifuYang JmgWang ManYu YanLi JingXu JunZhou YajumDeng XiaoyuLi JianfeiHu CaipingWang ChunxiaYan QingrunZhang JingyueBao GuoqingLi HaiqingZhang YilinZhang HuiZhao XiaoweiZhang ShuangliLi XiaoJieCheng XiuqingZhang BinLiu ChangqingZeng HuanmingYang WeijunChen LinFang ChangfengLi MengLei DaweiLi WeiTong XiangjunTian JianWang BoZhang SonggangLi XuehaiTan SiqiLiu WeiDong JunWang GaneKa-ShuWong JunYu QingyuZhu | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 6 |
| 2 | The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV显示文摘The Coronaviridae family is characterized by a nucleocapsid that is composed of thegenome RNA molecule in combination with the nucleoprotein (N protein) withina virion. The most striking physiochemical feature of the N protein of SARS-CoVis that it is a typical basic protein with a high predicted pI and high hydrophilicity,which is consistent with its function of binding to the ribophosphate backbone ofthe RNA molecule. The predicted high extent of phosphorylation of the N proteinon multiple candidate phosphorylation sites demonstrates that it would be relatedto important functions, such as RNA-binding and localization to the nucleolus ofhost cells. Subsequent study shows that there is an SR-rich region in the N proteinand this region might be involved in the protein-protein interaction. The abundantantigenic sites predicted in the N protein, as well as experimental evidence withsynthesized polypeptides, indicate that the N protein is one of the major antigensof the SARS-CoV. Compared with other viral structural proteins, the low variationrate of the N protein with regards to its size suggests its importance to the survivalof the virus. | JingqiangWang JiaJi JiaYe XiaoqianZhao JieWen WeiLi JianfeiHu DaweiLi MinSun HaipanZeng YongwuHu XiangjunTian XuehaiTan NingzhiXu ChangqingZeng JianWang ShengliBi HuanmingYang | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 3 |
| 3 | Complete Genome Sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04)显示文摘Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates B J01, B J02, B J03,and B J04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identifled from the BJ group, 32 are non-synonymous changes at the amino acid level.Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions. | ShengliBi E‘deQin ZuyuanXu WeiLi JingWang YongWuHu YongLiu ShuminDuan JianfeiHu YujunHan JingXu YanLi YaoYi YongdongZhou WeiLin1 JieWen HongXu RuanLi ZizhangZhang HaiyanSun JinguiZhu ManYu BaochangFan QingfaWu WeiLin2 LinTang Bao’anYang GuoqingLi WenmingPeng WenjieLi TaoJiang YajunDeng BohuaLiu JianpingShi YongqiangDeng WeiWei HongLiu ZongzhongTong FengZhang YuZhang Cui‘eWang YuquanLi JiaYe YonghuaGan JiaJi XiaoyuLi XiangjunTian FushuangLu GangTan RuifuYang BinLiu SiqiLiu SonggangLi JunWang JianWang WuchunCao JunYu XiaopingDong HuanmingYang | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 1 |
| 4 | The M Protein of SARS-CoV: Basic Structural and Immunological Properties显示文摘We studied structural and immunological properties of the SARS-CoV M (mem-brane) protein, based on comparative analyses of sequence features, phylogeneticinvestigation, and experimental results. The M protein is predicted to contain atriple-spanning transmembrane (TM) region, a single N-glycosylation site near itsN-terminus that is in the exterior of the virion, and a long C-terminal region inthe interior. The M protein harbors a higher substitution rate (0.6% correlated toits size) among viral open reading frames (ORFs) from published data. The foursubstitutions detected in the M protein, which cause non-synonymous changes,can be classified into three types. One of them results in changes of pI (isoelectricpoint) and charge, affecting antigenicity. The second changes hydrophobicity of theTM region, and the third one relates to hydrophilicity of the interior structure.Phylogenetic tree building based on the variations of the M protein appears tosupport the non-human origin of SARS-CoV. To investigate its immunogenicity,we synthesized eight oligopeptides covering 69.2% of the entire ORF and screenedthem by using ELISA (enzyme-linked immunosorbent assay) with sera from SARSpatients. The results confirmed our predictions on antigenic sites. | JunWang SiqiLiu ChangqingZeng JianWang HuanmingYang YongwuHu JieWen LinTang HaijunZhang XiaoweiZhang YahLi JingWang YujunHan GuoqingLi JianpingShi XiangjunTian FengJiang XiaoqianZhao | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 1 |
| 5 | The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04显示文摘The R (replicase) protein is the uniquely defined non-structural protein (NSP)responsible for RNA replication, mutation rate or fidelity, regulation of transcrip-tion in coronaviruses and many other ssRNA viruses. Based on our completegenome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China,we analyzed the structure and predicted functions of the R protein in comparisonwith 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF(open-reading frame) encodes for two major enzyme activities, RNA-dependentRNA polymerase (RdRp) and proteinase activities. The R polyprotein under-goes a complex proteolytic process to produce 15 function-related peptides. Ahydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identifiedwithin NSP1. The substitution rate of the R protein is close to the average ofthe SARS-CoV genome. The functional domains in all NSPs of the R proteingive different phylogenetic results that suggest their different mutation rate underselective pressure. Eleven highly conserved regions in RdRp and twelve cleavagesites by 3CLP (chymotrypsin-like protein) have been identified as potential drugtargets. Findings suggest that it is possible to obtain information about the phy-logeny of SARS-CoV, as well as potential tools for drug design, genotyping anddiagnostics of SARS. | HaiyanSun XiaoweiZhang JunZhow SonggangLi JunWang JianWang ShenghBi HuanmingYang ZuyuanXu HaiqingZhang XiangjunTian JiaJi WeiLi YahLi WeiTian LiftWang ZizhangZhang JingXu WeiWei JinguiZhu | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 0 |
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