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…     

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).     

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．     

There is the second virus that causes tobacco leaf curl disease (not TbLCV-CHI) in the field

Sequence analysis of virus isolation DNA of tobacco leaf curl disease shows that there is the second geminivirus (not Chinese Tobacco Leaf Curl Virus, TbLCV-CHI) that causes tobacco leaf curl disease in the field in the Guangxi Zhuang Autonomous Region, China. This virus DNA-A contains 2 734 nt. Large intergenic region (LIR) contains 269 nt, the virus sense strand contains 2 open reading frames (ORFs): AV1 (115 aa) and AV2 (coat protein gene, CP, 256 aa), and the complementary sense strand contains 4 ORFs: AC1 (replicase gene, 361 aa), AC2 (transactivator, 134 aa), AC3 (134 aa) and AC4 (97 aa). The virus belongs to one kind of subgroup III geminiviruses from old world, and could be the Chinese tomato yellow leaf curl virus (TYLCV-CHI).     

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…     

Genome sequencing and characterization analysis of a Beijing isolate of chicken coronavirus infectious bronchitis virus

Avian infectious bronchitis virus (AIBV) is classified as a member of the genus coronavirus in the family coronaviridae. The enveloped virus has a positive-sense, single-stranded RNA genome of approximately 28 kilo-bases,which has a 5‘ cap structure and 3‘ polyadenylation tract.The complete genome sequence of infectious bronchitis virus (IBV), Beijing isolate, was determined by cloning sequencing and primer walking. The whole genome is 27733 nucleotides in length, has ten open reading frames:5′-orfla-orflab-s-3a-3b-e-m- 6a-6b-n-3′. Alignments of the genome sequence of IBV Beijing isolate with those of two AIBV strains and one SARS coronavirus were performed respectively. The genome sequence of IBV Beijing isolate compared with that of the IBV strain LX4 (uncompleted, 19440 bp in size) was 91.2% similarity. However, the full-length genome sequence of IBV Beijing isolate was 85.2% identity to that of IBV Strain Beaudette, and was only 50.8% homology to that of SARS coronavirus. The results showed that the genome of IBV has remarkable variation. And IBV Beijing isolate is not closely related to SARS coronavirus. Phylogenetic analyses based on the whole genome sequence, S protein, M protein and N protein, also showed that AIBV Bering isolate is lone virus in group Ⅲ and is distant from SARS coronavirus. In conclusion, this study will contribute to the studies of diagnosis and diseases control on IBV in China.     

Cloning and characterization of <Emphasis Type="Italic">UL</Emphasis>34 gene of pseudorabies virus HB isolate

In this study, China isolate HB of pseudorabies virus (PRV) was confirmed and genotypically characterized by amplifying and sequencing of partial UL34, a conservative gene involved in the egress of nucleocapsids from the nucleus, for phylogenetic analysis. The open reading frame (orf) of UL34 of PRV HB isolate is composed of 786 nucleotides, which encoded 262 amino acids. In addition, a potential transmembrane domain (241-260 aa) and 11 potential phosphorylation sites were also found in the UL34 of PRV HB isolate. Multiple amino acids alignment indicated that UL34 proteins of PRV strains derived from different geographic origins were highly conservative, but some mutations were also found. Phylogenetic analysis based on UL34 protein indicated that PRV HB strain was evolutionarily distinct from other recent China strains sequenced so far, forming a single clade within the phylogeny. Moreover, PRV HB isolate had close evolutionary relationship with BoHV-1 and BoHV-5 within the Alphaherpesvirinae. Taken together, these results indicated that PRV strains were in the progress of evolution. This study has expanded the knowledge of genetic profiles of PRV strains.     

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).     

Coat protein gene and 3′ non-coding region of tobacco mosaic virus and tomato mosaic virus are associated with viral pathogenesis in Nicotiana tabacum

The camellia isolate of tomato mosaic virus (ToMV-TL) can induce local necrotic lesions on the inoculated leaves in Nicotiana tabacum, whereas the broad bean isolate of tobacco mosaic virus (TMV-B) produces the mosaic symptom on systemic leaves. To examine viral determinant for differential infection phenotype in N. tabacum, the coat protein gene and the 3′ non-coding region of TMV was replaced with that of ToMV, the chimeric virus induced similar local necrotic lesions to that induced by ToMV. The results indicate that the coat protein gene and the 3′ non-coding region of TMV and ToMV influence the virus-induced pathogenesis in N. tabacum.     

感染番茄抗病品种的番茄黄化曲叶病毒的基因变异分析

近几年来,生产中发现一些番茄抗病品种在不同环境条件下或应用几年后出现感病现象。为了解不同抗病品种中番茄黄化曲叶病毒(tomato yellow leafcurl virus,TYLCV)基因变异的情况,对5个感染TYLCV的番茄抗病品种进行了TYLCV全长基因克隆和序列测定。扩增结果显示,5个样品携带的TYLCV基因组长度均为2 781 bp,且均编码6个功能蛋白。基因组序列比较发现,这5个分离物与TYLCV-Israel株系同源性达到99%以上;通过功能蛋白比对发现,复制增强因子AC3蛋白存在变异,同世界各地报道的TYLCV-Israel株系典型分离物的AC3蛋白存在7处氨基酸差异的位点。分析结果表明,这五个病毒分离物均属于TYLCV-Israel株系,其AC3蛋白的氨基酸序列变异程度均不显著,并没有产生新的病毒株系。     

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…     

Isolation and identification of a novel coronavirus from wild bird

A novel coronavirus strain was isolated from laryngotracheal swab of wild partridge and designated as partridge/GD/S14/2003 (S14). Its whole genomic sequence was obtained (GenBank Accession number: AY646283) through RT-PCR amplification, cloning, nucleotide sequencing, and analysis by the DNASTAR program. To investigate the origin of the virus, we further analyzed the nucleotide sequences of the main structural proteins, and compared those with other available virus isolates. Our results showed that the highest nucleotide homologies between the S1 gene of S14 strain and those of nephrogenic-type strains JX1-99 and TJ2-96 were 94.6% and 93.4%, respectively. In addition, a relatively high genetic identity, 85% and 84.3%, respectively, was detected between S1 gene of S14 and those of strains QXIBV and LX4. The results suggested that the S14 strain may be originated from or related to nephrogenic-type and proventriculus-type infectious bronchitis virus (IBV). The highest nucleotide homology between the S2 gene of S14 strain and those of QXIBV and LX4 was 85% and 84.3%, respectively and all of them belonged to group II coronaviruses. The highest nucleotide homology between the M gene of S14 strain and those of strains SAIB20 and GD6-98 was 90.6% and 90.2%, respectively by which S14 belonged to group III. Although they displayed high level of genetic identity in S1 and S2 gene, there was lower homology of M coding sequences between S14 and BJ, and between S14 and QXIBV strains. Phylogenetic analysis of N gene indicated that group I strains might evolve from RNA recombination between strain H52 and Gray; while group II strains from strain H120 and D1466. S14 strain had the highest N gene homology with strain QXIBV which was 95.7%, thus classified as a group III member. Strains SAIB20 and GD6-98 which were closely related to the M gene of S14 strain belonged to group I and IV, respectively. A possible role of partridge S14 strain may play in the process of coronavirus evolution is discussed.     

SARS冠状病毒基因组复制酶起始结合位点的预测

严重急性呼吸综合征(Severe Acute Respiratory Syndrome,SARS)传染性强,死亡率高,给全世界约30个国家造成了巨大损失．其病原体为SARS冠状病毒(Severe acute Respiratory Syndrome Associated Coronavirus,SARS—CoV),是冠状病毒(Coronavirus)的新变异种．作者以“最大信息量”理论和方法为基础,使用结合位点搜寻软件等生物信息学方法,对冠状病毒基因组的3’非翻译区(Untranslated Regions,UTRs)进行分析,预测出了2株SARS—CoV(来自北京的SARSBJ01和浙江的SARSZJ01)以及其他38株冠状病毒株的复制酶起始结合位点(Replicase initial binding sites,RIBS)．在该预测结果中,不难发现,这些RIBS的序列与前人的研究成果有很大的相似之处,与公认的冠状病毒的顺式作用元件极为相似的基序也存在其中,而且其预测的二级结构与鼠肝炎病毒MHV基因组的某些蛋白结合位点类似．因此,预测的RIBS在病毒的复制中可能起重要作用．     

流感分子病毒学研究进展

流感病毒繁殖周期很短,基因结构又非常简单,病毒RNA分成8个独立的片段。每个基因片段编码一个蛋白,有利于宿主发生双重感染后不同毒株之间基因交换重组。流感病毒为了自身生存,适应外界环境,频繁发生变异。每次新亚型出现,都引起世界性大流行。人类与流感病毒将长期共存。     

Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia

A highly pathogenic avian influenza virus, H5N1, caused disease outbreaks in poultry in China and seven other east Asian countries between late 2003 and early 2004; the same virus was fatal to humans in Thailand and Vietnam. Here we demonstrate a series of genetic reassortment events traceable to the precursor of the H5N1 viruses that caused the initial human outbreak in Hong Kong in 1997 (refs 2-4) and subsequent avian outbreaks in 2001 and 2002 (refs 5, 6). These events gave rise to a dominant H5N1 genotype (Z) in chickens and ducks that was responsible for the regional outbreak in 2003-04. Our findings indicate that domestic ducks in southern China had a central role in the generation and maintenance of this virus, and that wild birds may have contributed to the increasingly wide spread of the virus in Asia. Our results suggest that H5N1 viruses with pandemic potential have become endemic in the region and are not easily eradicable. These developments pose a threat to public and veterinary health in the region and potentially the world, and suggest that long-term control measures are required.     

甲/戊型肝炎病毒重组抗原基因的克隆及表达

 将甲肝病毒vp1编码基因(aa 24~171)和戊型肝炎病毒ORF2基因(aa 431~615)通过一段编码柔性甘氨酸链(Gly4 Ser Gly4)的基因片断连接,获得编码HAV/HEV融合蛋白基因(AEAg342).将该融合基因插入质粒pBV220,构建表达质粒pBV220-AEAg342.将pBV220-AEAg342转化入大肠杆菌BL21中进行表达,表达量约占菌体总量的20%,经离子交换层析纯化,目的蛋白纯度达90%以上.Western blot证实该蛋白能与甲肝及戊肝患者阳性血清发生特异性反映,为进一步开发双价疫苗和联合诊断试剂奠定了一定基础.     

Cloning and Characterization of UL34 Gene of Pseudorabies Virus HB Isolate

In this study, China isolate HB of pseudorabies virus(PRV) was confirmed and genotypically characterized by amplifying and sequencing of partial UL34, a conservative gene involved in the egress of nucleocapsids from the nucleus, for phylogenetic analysis. The open reading frame(orf) of UL34 of PRV HB isolate is composed of 786 nucleotides, which encoded 262 amino acids. In addition, a potential transmembrane domain(241-260 aa) and 11 potential phosphorylation sites were also found in the UL34 of PRV HB isolate. Multiple amino acids alignment indicated that UL34 proteins of PRV strains derived from different geographic origins were highly conservative, but some mutations were also found. Phylogenetic analysis based on UL34 protein indicated that PRV HB strain was evolutionarily distinct from other recent China strains sequenced so far, forming a single clade within the phylogeny. Moreover, PRV HB isolate had close evolutionary relationship with Bo HV-1 and Bo HV-5 within the Alphaherpesvirinae. Taken together, these results indicated that PRV strains were in the progress of evolution. This study has expanded the knowledge of genetic profiles of PRV strains.     

2001年春季临安、昆明和香港臭氧垂直分布特征的对比分析

利用2001年3月到4月上旬在中国临安、昆明和香港特别行政区进行臭氧探测获得的资料,对这3个地点的臭氧垂直分布特征进行了分析与对比,发现3个地点的臭氧分布特征既有相同点,也有不同点。其主要不同点有,最大臭氧分压和所处高度不同;临安10～16km高度的臭氧浓度远远大于昆明与香港;在对流层低层,香港有一特别突出的高臭氧浓度层,昆明次之;临安对流层的中上层没有像昆明和香港出现的臭氧低值区现象。根据NCEP分析资料给出的2001年3月的背景大气环流特征表明不同的大气环流有不同的臭氧垂直分布特征,临安地区易受北方冷气团的影响,昆明和香港则受低纬度暖湿气团影响较大;对流层高层的副热带急流对3个地点臭氧垂直分布也有不同的影响。     

Biological function of HIV-1 transmembrane protein gp41──A study on a putative cellular receptor of gp41

Since 1992, the study of biological functions of HIV-1 gp41 has made great progress. Experimental evidence from several research groups demonstrated that gp41 has a putative cellular receptor. A recombinant soluble gp41 (aa539-684) and gp41 immunosuppressive peptide (aa583-599) could bind to human B lymphocytes and monocytes, but weakly bind to T lymphocytes. It was found that gp41 contains two cellular binding sites (aa583-599 and 641-675). GP41 could selectively inhibit cell proliferation of human T, B lymphocytes and monocytes, enhance human MHC class Ⅰ, Ⅱ and ICAM-1 molecule expression on cell surface. Gp41 binding proteins and a monoclonal antibody against the first binding site could inhibit this modulation effect. Amino acid sequence homology exists between gp41 and human type Ⅰ interferons, and the homologous region is located in the first binding site on gp41 and in the receptor binding site on type Ⅰ interferons. Studies in other groups indicate that both binding sites in gp41 may be associated with HIV infection of cells. Peptides containing two binding sites could respectively inhibit HIV infection of cells. A monoclonal antibody recognizing the second binding site could neutralize lab-strains and recently separated strains of HIV-1. Besides, antibodies against two regions (homologous with gp41 binding sites) of SIV transmembrane protein gp32 could protect macaques from SIV infection. These results suggest that the study of gp41 binding sites and cellular receptor could contribute to understanding the mechanism of HIV infection and to developing HIV vaccine and anti-HIV drugs.