Genome sequence variation analysis of two SARS coronavirus isolates after passage in Vero cell culture

SARS coronavirus is an RNA virus whose replication is error-prone, which provides possibility for escape of host defenses, and even leads to evolution of new viral strains during the passage or the transmission. Lots of variations have been detected among different SARS-CoV strains. And a study on these variations is helpful for development of efficient vaccine. Moreover, the test of nucleic acid characterization and genetic stability of SARS-CoV is important in the research of inactivated vaccine. The whole genome sequences of two SARS coronavirus strains after passage in Vero cell culture were determined and were compared with those of early passages, respectively. Results showed that both SAPS coronavirus strains have high genetic stability, although nearly 10 generations were passed. Four nucleotide variations were observed between the second passage and the llth passage of Sinol strain for identification of SARS inactivated vaccine. Moreover, only one nucleotide was different between the third passage and the 10th passage of Sino3 strain for SARS inactivated vaccine. Therefore, this study suggested it was possible to develop inactivated vaccine against SARS-CoV in the future.     

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.     

SARS冠状病毒的基因组结构与药物治疗

介绍了SAPS冠状病毒的基因组结构及其作用机制的最新研究进展，探讨了抗SARS病毒药物的研制。     

重组SARS冠状病毒S蛋白的原核表达研究

目的克隆表达SARS冠状病毒的主要结构蛋白(S蛋白)。方法合成SARS冠状病毒S蛋白特异性基因片断并克隆入pET32a原核表达载体,转化BL21菌,经IPTG诱导高效表达得到重组S蛋白,并通过W estern印迹对重组蛋白质进行鉴定。结果重组蛋白质经镍柱亲和层析得到了部分纯化,免疫动物后得到SARS病毒的多克隆抗体。结论经E lisa检测,表达的重组S蛋白基本具备检测病人血清中抗SARS病毒IgG和IgM的能力,可进一步用于S蛋白功能研究与SARS诊断试剂盒的研制。     

Dissection of SARS Coronavirus Spike Protein into Discrete Folded Fragments

Introduction Severe acute respiratory syndrome coronavirus (SARS-CoV), which is the causative agent of the atypical pneumonia, was first identified in the fall of 2002 to be a previously unknown member of the family of coronaviruses[1]. The rapid transmis…     

SARS相关冠状病毒刺突糖蛋白的研究(综述)

概述了SARS—CoV的S蛋白的结构及功能相关研究。严重急性呼吸综合症相关的冠状病毒(SARS-CoV)引起2003年我国南方非典型肺炎爆发流行,波及多个国家和地区。目前全球许多学对SARS-CoV进行了广泛的研究,发现S蛋白是病毒表面的主要蛋白,它构成冠状病毒科特征性的冠状样结构,在严重急性呼吸综合症的发病机制起着关键性作用,可介导表达相关受体的宿主细胞感染。现已鉴定出SARS-CoV的S蛋白相关受体,同时它在抗病毒感染中是一个关键靶蛋白。     

Molecular phylogeny of coronaviruses including human SARS-CoV

The outbreak of SARS sets an urgent task to reveal the origin of human SARS-CoV, i.e. its relation to other known species of coronavirus, and to trace the genetic variation in the spreading process of SARS. Partial answer to the problem may be obtained from phylogenetic analy-sis of available genomes. We call a phylogenetic tree of different species of coronavirus including the human SARS-Cov a CoV Tree and that of different isolates of SARS-CoV a SARS Tree. CoV trees have been c…     

用计算流体力学方法研究非典型肺炎病毒颗粒的分布

通过分析非典型肺炎（SARS）病毒颗粒在空气中随气流绕过建筑物后的运动过程和分布情况,研究了病毒颗粒在空气中的扩散、聚集和分布情况,得到了病毒颗粒在空气中的动态流型、相关的影响区范围以及主要扩散方向．提供了在受到病毒污染的建筑物后面设置有效隔离带的计算流体力学（CFD）研究数据,给出了一种建筑物群位置合理排列的CFD研究方法．     

SARS冠状病毒N蛋白的表达及二级结构预测分析

通过RT-PCR获得SARS冠状病毒N蛋白基因，分别克隆到原核表达载体pET21a，pET32a和pGEX-4T-1中，将3种重组质粒pET2la-N，pET32a-N和pGEX-4T-1-N分别转化大肠杆菌BL21(DE3)，经IPTG诱导，细菌中分别表达出约46kD的重组N蛋白、约60kD的6xHis-N融合蛋白和约70kD的GST-N融合蛋白，表达量分别达总蛋白的45％、40％和30％．进一步的分析表明：6xHis-N融合蛋白在大肠杆菌中为可溶性表达，该可溶性组分占细菌裂解液的70％左右，且能被6xHis抗体所识别．用蛋白分析软件对N蛋白进行了序列分析和二级结构预测．SARS冠状病毒N蛋白在大肠杆菌中的高效可溶性表达，有助于进一步结晶后进行X射线晶体衍射分析其结构与功能．     

A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

Severe Acute Respiratory Syndrome (SARS) is a newly identified infectious disease[1—5]. The global outbreak of SARS has been threatening the health of people worldwide and has killed 353 people and infected more than 5462 in 27 countries, as reported by WHO on April 29, 2003 (http://www.who.int/csr/sarscountry/en). Although it has been recognized that a variant of virus from the family of coronavirus might be the candidate pathogen of SARS[1—5], its identity as the unique pathogen sti…     

Genome organization and phylogenetic tree analysis of Garlic virus E, a new member of genus Allexivirus

The complete sequence of an Allexivirus isolated from garlic plants in Yuhang City, Zhejiang Province, China had been determined. The single-strand, positive RNA genome was 8451 nucleotides in length excluding poly(A) tail. The genome organization of this virus was similar to that of the other Allexiviruses but only with 62.8%-64.8% nucleotide acid identities. The amino acid sequences of proteins encoded by ORF1-6 shared 67.6%-78.5%, 55.4%-66.2%, 56.7%- 66.4%, 40.3%-55.6%, 66.3%-79.7% and 52.2%- 68.8% identities with those of the others respectively. The homology range between it and the other Allexiviruses was similar to that between the other distinct species in this genus. A more comprehensive comparison using all available CP amino acid sequences showed that it shared only 63.9%- 79.8% amino acids identical with the others. Therefore, it had been considered as a new member of the genus, named as garlic virus E (GarV-E). Phylogenetic analysis confirmed GarV-E as a distinct member and the correct names and classification of some members of genus Allexivirus were also discussed.     

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…     

Genome organization and phylogenetic tree analysis of Garlic virus E, a new member of genus Allexivirus

The complete sequence of an Allexivirus isolated from garlic plants in Yuhang City, Zhejiang Province, China had been determined. The single-strand, positive RNA genome was 8451 nucleotides in length excluding poly(A) tail. The genome organization of this virus was similar to that of the other Allexiviruses but only with 62.8%–64.8% nucleotide acid identities. The amino acid sequences of proteins encoded by ORF1-6 shared 67.6%–78.5%, 55.4%–66.2%, 56.7%–66.4%,40.3%–55.6%,66.3%–79.7%and 52.2%–68.8% identities with those of the others respectively. The homology range between it and the other Allexiviruses was similar to that between the other distinct species in this genus. A more comprehensive comparison using all available CP amino acid sequences showed that it shared only 63.9%–79.8% amino acids identical with the others. Therefore, it had been considered as a new member of the genus, named as garlic virus E (GarV-E). Phylogenetic analysis confirmed GarV-E as a distinct member and the correct names and classification of some members of genus Allexivirus were also discussed.     

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).