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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 Structural Characterization and Antigenicity of the S Protein of SARS-CoV显示文摘The corona-like spikes or peplomers on the surface of the virion under electronicmicroscope are the most striking features of coronaviruses. The S (spike) proteinis the largest structural protein, with 1,255 amino acids, in the viral genome. Itsstructure can be divided into three regions: a long N-terminal region in the exte-rior, a characteristic transmembrane (TM) region, and a short C-terminus in theinterior of a virion. We detected fifteen substitutions of nucleotides by comparisonswith the seventeen published SARS-CoV genome sequences, eight (53.3%) of whichare non-synonymous mutations leading to amino acid alternations with predictedphysiochemical changes. The possible antigenic determinants of the S protein arepredicted, and the result is confirmed by ELISA (enzyme-linked immunosorbentassay) with synthesized peptides. Another profound finding is that three disulfidebonds are defined at the C-terminus with the N-terminus of the E (envelope) pro-tein, based on the typical sequence and positions, thus establishing the structuralconnection with these two important structural proteins, if confirmed. Phyloge-netic analysis reveals several conserved regions that might be potent drug targets. | JingxiangLi ChunqingLuo YajunDeng YujunHan LingTang JingWang JiaJi JiaYe FanboJiang ZhaoXu WeiTong WeiWei QingrunZhang ShengbinLi WeiLi HongyanLi YudongLi WeiDong JianWang ShengliBi HuanmingYaug | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 5 |
| 3 | A Statistical Approach Designed for Finding Mathematically Defined Repeats in Shotgun Data and Determining the Length Distribution of Clone-Inserts显示文摘The large amount of repeats, especially high copy repeats, in the genomes of higher animals and plants makes whole genome assembly (WGA) quite difficult. In order to solve this problem, we tried to identify repeats and mask them prior to assembly even at the stage of genome survey. It is known that repeats of different copy number have different probabilities of appearance in shotgun data, so based on this principle, we constructed a statistical model and inferred criteria for mathematically defined repeats (MDRs) at different shotgun coverages. According to these criteria, we developed software MDRmasker to identify and mask MDRs in shotgun data. With repeats masked prior to assembly, the speed of assembly was increased with lower error probability. In addition, clone-insert size affects the accuracy of repeat assembly and scaffold construction. We also designed length distribution of clone-inserts using our model. In our simulated genomes of human and rice, the length distribution of repeats is different, so their optimal length distributions of clone-inserts were not the same. Thus with optimal length distribution of clone-inserts, a given genome could be assembled better at lower coverage. | LanZhong KunlinZhang XiangangHuang PeixiangNi YujunHan KaiWang JunWang SonggangLi | 2003 | Genomics, Proteomics & Bioinformatics2003，1，1： | 1 |
| 4 | 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 |
| 5 | 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 |
| 6 | Evolution and Variation of the SARS-CoV Genome显示文摘Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARSCoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us. | JianfeiHu JingWang JingXu WeiLi YujunHan YanLi JiaJi JiaYe ZhaoXu ZizhangZhang WeiWei SonggangLi JunWang JianWang JunYu HuanmingYang | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 0 |
| 7 | Genome Organization of the SARS-CoV显示文摘Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves.Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions.The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs. | JingXu JianfeiHu JingWang YujunHan YongwuHu JieWen YanLi JiaJi JiaYe ZizhangZhang WeiWei SonggangLi JunWang JianWang JunYu HuanmingYang | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 0 |
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