1501
|
Yap YL, Zhang XW, Danchin A. Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling. BMC Bioinformatics 2003; 4:43. [PMID: 14499005 PMCID: PMC222961 DOI: 10.1186/1471-2105-4-43] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Accepted: 09/20/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.
Collapse
Affiliation(s)
- Yee Leng Yap
- HKU-Pasteur Research Centre, Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong
| | - Xue Wu Zhang
- HKU-Pasteur Research Centre, Dexter H.C. Man Building, 8 Sassoon Road Pokfulam, Hong Kong
| | - Antoine Danchin
- Institute Pasteur, Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
1502
|
Knudsen TB, Kledal TN, Andersen O, Eugen-Olsen J, Kristiansen TB. Severe acute respiratory syndrome--a new coronavirus from the Chinese dragon's lair. Scand J Immunol 2003; 58:277-84. [PMID: 12950672 PMCID: PMC7169508 DOI: 10.1046/j.1365-3083.2003.01302.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 05/22/2003] [Indexed: 11/22/2022]
Abstract
The recent identification of a novel clinical entity, the severe acute respiratory syndrome (SARS), the rapid subsequent spread and case fatality rates of 14-15% have prompted a massive international collaborative investigation facilitated by a network of laboratories established by the World Health Organization (WHO). As SARS has the potential of becoming the first pandemic of the new millennium, a global warning by the WHO was issued on 12 March 2003. The disease, which is believed to have its origin in the Chinese Guangdong province, spread from Hong Kong via international airports to its current worldwide distribution. The concerted efforts of a globally united scientific community have led to the independent isolation and identification of a novel coronavirus from SARS patients by several groups. The extraordinarily rapid isolation of a causative agent of this newly emerged infectious disease constitutes an unprecedented scientific achievement. The main scope of the article is to provide the clinician with an overview of the natural history, epidemiology and clinical characteristics of SARS. On the basis of the recently published viral genome and structural features common to the members of the coronavirus family, a model for host cell-virus interaction and possible targets for antiviral drugs are presented. The epidemiological consequences of introducing a novel pathogen in a previously unexposed population and the origin and evolution of a new and more pathogenic strain of coronavirus are discussed.
Collapse
Affiliation(s)
- T B Knudsen
- Department of Infectious Diseases, and Clinical Research Unit, Copenhagen University Hospitals Hvidovre, Copenhagen, Denmark.
| | | | | | | | | |
Collapse
|
1503
|
Hsueh PR, Hsiao CH, Yeh SH, Wang WK, Chen PJ, Wang JT, Chang SC, Kao CL, Yang PC. Microbiologic characteristics, serologic responses, and clinical manifestations in severe acute respiratory syndrome, Taiwan. Emerg Infect Dis 2003; 9:1163-7. [PMID: 14519257 PMCID: PMC3016775 DOI: 10.3201/eid0909.030367] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The genome of one Taiwanese severe acute respiratory syndrome-associated coronavirus (SARS-CoV) strain (TW1) was 29,729 nt in length. Viral RNA may persist for some time in patients who seroconvert, and some patients may lack an antibody response (immunoglobulin G) to SARS-CoV <21 days after illness onset. An upsurge of antibody response was associated with the aggravation of respiratory failure.
Collapse
Affiliation(s)
- Po-Ren Hsueh
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Cheng-Hsiang Hsiao
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Wei-Kung Wang
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Jer Chen
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jin-Town Wang
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shan-Chwen Chang
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chuan-Liang Kao
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pan-Chyr Yang
- National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | | |
Collapse
|
1504
|
Thiel V, Ivanov KA, Putics Á, Hertzig T, Schelle B, Bayer S, Weißbrich B, Snijder EJ, Rabenau H, Doerr HW, Gorbalenya AE, Ziebuhr J. Mechanisms and enzymes involved in SARS coronavirus genome expression. J Gen Virol 2003; 84:2305-2315. [PMID: 12917450 DOI: 10.1099/vir.0.19424-0] [Citation(s) in RCA: 660] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel coronavirus is the causative agent of the current epidemic of severe acute respiratory syndrome (SARS). Coronaviruses are exceptionally large RNA viruses and employ complex regulatory mechanisms to express their genomes. Here, we determined the sequence of SARS coronavirus (SARS-CoV), isolate Frankfurt 1, and characterized key RNA elements and protein functions involved in viral genome expression. Important regulatory mechanisms, such as the (discontinuous) synthesis of eight subgenomic mRNAs, ribosomal frameshifting and post-translational proteolytic processing, were addressed. Activities of three SARS coronavirus enzymes, the helicase and two cysteine proteinases, which are known to be critically involved in replication, transcription and/or post-translational polyprotein processing, were characterized. The availability of recombinant forms of key replicative enzymes of SARS coronavirus should pave the way for high-throughput screening approaches to identify candidate inhibitors in compound libraries.
Collapse
Affiliation(s)
- Volker Thiel
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Konstantin A Ivanov
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Ákos Putics
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Tobias Hertzig
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Barbara Schelle
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Sonja Bayer
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Benedikt Weißbrich
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Holger Rabenau
- Institute for Medical Virology, Johann Wolfgang Goethe University, Frankfurt (Main), Germany
| | - Hans Wilhelm Doerr
- Institute for Medical Virology, Johann Wolfgang Goethe University, Frankfurt (Main), Germany
| | - Alexander E Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| |
Collapse
|
1505
|
Rest JS, Mindell DP. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2003; 3:219-25. [PMID: 14522185 PMCID: PMC7129878 DOI: 10.1016/j.meegid.2003.08.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2003] [Revised: 07/21/2003] [Accepted: 08/04/2003] [Indexed: 11/29/2022]
Abstract
The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5' fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3' fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5' tree could be rejected for the 3' region, and the optimal 3' tree could be rejected for the 5' region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1-3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3' RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.
Collapse
Affiliation(s)
| | - David P Mindell
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA
| |
Collapse
|
1506
|
Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LLM, Guan Y, Rozanov M, Spaan WJM, Gorbalenya AE. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 2003; 331:991-1004. [PMID: 12927536 PMCID: PMC7159028 DOI: 10.1016/s0022-2836(03)00865-9] [Citation(s) in RCA: 942] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The genome organization and expression strategy of the newly identified severe acute respiratory syndrome coronavirus (SARS-CoV) were predicted using recently published genome sequences. Fourteen putative open reading frames were identified, 12 of which were predicted to be expressed from a nested set of eight subgenomic mRNAs. The synthesis of these mRNAs in SARS-CoV-infected cells was confirmed experimentally. The 4382- and 7073 amino acid residue SARS-CoV replicase polyproteins are predicted to be cleaved into 16 subunits by two viral proteinases (bringing the total number of SARS-CoV proteins to 28). A phylogenetic analysis of the replicase gene, using a distantly related torovirus as an outgroup, demonstrated that, despite a number of unique features, SARS-CoV is most closely related to group 2 coronaviruses. Distant homologs of cellular RNA processing enzymes were identified in group 2 coronaviruses, with four of them being conserved in SARS-CoV. These newly recognized viral enzymes place the mechanism of coronavirus RNA synthesis in a completely new perspective. Furthermore, together with previously described viral enzymes, they will be important targets for the design of antiviral strategies aimed at controlling the further spread of SARS-CoV.
Collapse
Key Words
- nidovirus
- genome organization
- subgenomic mrna synthesis
- replicase
- rna processing
- sars-cov, severe acute respiratory syndrome coronavirus
- orf, open reading frame
- sg, subgenomic
- bcov, bovine coronavirus
- etov, equine torovirus
- hcov, human coronavirus
- mhv, mouse hepatitis coronavirus
- pl1pro, papain-like proteinase 1
- ibv, avian infectious bronchitis coronavirus
- sud, sars-cov unique domain
- trs, transcription-regulating sequence
- xendou, poly(u)-specific endoribonuclease
- exon, 3′-to-5′ exonuclease
- 2′-o-mt, s-adenosylmethionine-dependent ribose 2′-o-methyltransferase
- adrp, adenosine diphosphate-ribose 1″-phosphatase
- cpd, cyclic phosphodiesterase
- snorna, small nucleolar rna
Collapse
Affiliation(s)
- Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Room L4-34, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
1507
|
Abstract
A mass outbreak of severe acute respiratory syndrome (SARS) in the Amoy Gardens housing complex in Hong Kong at the end of March, 2003, affected more than 300 residents in less than a month, and has epidemiologists all over the world puzzled about the mode of transmission of this new disease, which until then was thought to be transmitted solely by respiratory droplets. The source of the outbreak was later traced to an individual with SARS who spent two nights at Amoy Gardens. Official explanations failed to account for the large number of residents infected over a wide area within a short time. A powerful environmental mechanism that efficiently amplified and distributed the causal agent must have been at work to cause this outbreak. One such mechanism could be an animal vector, most probably roof rats, that was infected by the index patient and subsequently spread the disease to more than 150 households.
Collapse
Affiliation(s)
- Stephen K C Ng
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, USA.
| |
Collapse
|
1508
|
Hawkey PM, Bhagani S, Gillespie SH. Severe acute respiratory syndrome (SARS): breath-taking progress. J Med Microbiol 2003; 52:609-613. [PMID: 12867552 DOI: 10.1099/jmm.0.05321-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reports of a new severe respiratory disease, now defined as severe acute respiratory syndrome (SARS), began to emerge from Guangdong, in southern China, in late 2002. The condition came to international attention through an explosive outbreak in Hong Kong in March 2003. Cases appeared throughout South-East Asia and in Toronto, the spread of SARS being accelerated by international air travel. A global emergency was declared by the World Health Organization, bringing together an international team of epidemiologists, public health physicians and microbiologists to study and contain the disease. This response has enabled the nature of the infectious agent to be identified, its mode of transmission to be established and diagnostic tests to be created rapidly.
Collapse
Affiliation(s)
- Peter M Hawkey
- Public Health Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK 2Royal Free Hospital, Pond Street, London NW3 2QG, UK 3University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| | - Sanjay Bhagani
- Public Health Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK 2Royal Free Hospital, Pond Street, London NW3 2QG, UK 3University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| | - Stephen H Gillespie
- Public Health Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK 2Royal Free Hospital, Pond Street, London NW3 2QG, UK 3University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, UK
| |
Collapse
|
1509
|
Xu J, Hu J, Wang J, Han Y, Hu Y, Wen J, Li Y, Ji J, Ye J, Zhang Z, Wei W, Li S, Wang J, Wang J, Yu J, Yang H. Genome organization of the SARS-CoV. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:226-35. [PMID: 15629035 PMCID: PMC5172239 DOI: 10.1016/s1672-0229(03)01028-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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.
Collapse
Affiliation(s)
- Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianfei Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Wenzhou Medical College, Wenzhou 325003, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Zizhang Zhang
- College of Materials Science and Chemical Engineering, Yuquan Campus, Zhejiang University, Hangzhou 310027, China
| | - Wei Wei
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| |
Collapse
|
1510
|
Abstract
Severe acute respiratory syndrome (SARS) is caused by a novel coronavirus (SARS-CoV). Future research on the molecular virology of SARS-CoV will be important in the understanding of the epidemiology and the natural history of SARS. This will also facilitate the development of sensitive and accurate diagnostic tests, as well as vaccination and other therapeutics to combat SARS.
Collapse
Affiliation(s)
- Henry L Y Chan
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, 9/F Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong
| | | | | |
Collapse
|
1511
|
Meskauskas A, Harger JW, Jacobs KLM, Dinman JD. Decreased peptidyltransferase activity correlates with increased programmed -1 ribosomal frameshifting and viral maintenance defects in the yeast Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2003; 9:982-92. [PMID: 12869709 PMCID: PMC1240118 DOI: 10.1261/rna.2165803] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2002] [Accepted: 05/22/2003] [Indexed: 05/20/2023]
Abstract
Increased efficiencies of programmed -1 ribosomal frameshifting in yeast cells expressing mutant forms of ribosomal protein L3 are unable to maintain the dsRNA "Killer" virus. Here we demonstrate that changes in frameshifting and virus maintenance in these mutants correlates with decreased peptidyltransferase activities. The mutants did not affect Ty1-directed programmed +1 ribosomal frameshifting or nonsense-mediated mRNA decay. Independent experiments demonstrate similar programmed -1 ribosomal frameshifting specific defects in cells lacking ribosomal protein L41, which has previously been shown to result in peptidyltransferase defects in yeast. These findings are consistent with the hypothesis that decreased peptidyltransferase activity should result in longer ribosome pause times after the accommodation step of the elongation cycle, allowing more time for ribosomal slippage at programmed -1 ribosomal frameshift signals.
Collapse
Affiliation(s)
- Arturas Meskauskas
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | | | | | | |
Collapse
|
1512
|
Li S, Lin L, Wang H, Yin J, Ren Y, Zhao Z, Wen J, Zhou C, Zhang X, Li X, Wang J, Zhou Z, Liu J, Shao J, Lei T, Fang J, Xu N, Liu S. The epitope study on the SARS-CoV nucleocapsid protein. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:198-206. [PMID: 15629032 PMCID: PMC5172353 DOI: 10.1016/s1672-0229(03)01025-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleocapsid protein (N protein) has been found to be an antigenic protein in a number of coronaviruses. Whether the N protein in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is antigenic remains to be elucidated. Using Western blot and Enzyme-linked Immunosorbent Assay (ELISA), the recombinant N proteins and the synthesized peptides derived from the N protein were screened in sera from SARS patients. All patient sera in this study displayed strong positive immunoreactivities against the recombinant N proteins, whereas normal sera gave negative immunoresponses to these proteins, indicating that the N protein of SARS-CoV is an antigenic protein. Furthermore, the epitope sites in the N protein were determined by competition experiments, in which the recombinant proteins or the synthesized peptides competed against the SARS-CoV proteins to bind to the antibodies raised in SARS sera. One epitope site located at the C-terminus was confirmed as the most antigenic region in this protein. A detailed screening of peptide with ELISA demonstrated that the amino sequence from Codons 371 to 407 was the epitope site at the C-terminus of the N protein. Understanding of the epitope sites could be very significant for developing an effective diagnostic approach to SARS.
Collapse
|
1513
|
Drosten C, Preiser W, Günther S, Schmitz H, Doerr HW. Severe acute respiratory syndrome: identification of the etiological agent. Trends Mol Med 2003; 9:325-7. [PMID: 12928032 PMCID: PMC7128529 DOI: 10.1016/s1471-4914(03)00133-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The severe acute respiratory syndrome (SARS) emerged in late 2002 in southern China and rapidly spread to countries around the globe. Three research groups within a World Health Organization (WHO)-coordinated network have independently and simultaneously shown that a novel coronavirus is linked to SARS. A fourth group has completed the Koch's postulates by infecting monkeys with the agent. Sequencing of the complete genome was achieved only weeks after the first isolate of the virus became available.
Collapse
Affiliation(s)
- Christian Drosten
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Bernhard-Nocht Strasse 74, 20359 Hamburg, Germany.
| | | | | | | | | |
Collapse
|
1514
|
Liu G, Hu S, Hu Y, Chen P, Yin J, Wen J, Wang J, Lin L, Liu J, You B, Yin Y, Li S, Wang H, Ren Y, Ji J, Zhao X, Sun Y, Zhang X, Fang J, Wang J, Liu S, Yu J, Zhu H, Yang H. The C-terminal portion of the nucleocapsid protein demonstrates SARS-CoV antigenicity. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:193-7. [PMID: 15629031 PMCID: PMC5172413 DOI: 10.1016/s1672-0229(03)01024-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to develop clinical diagnostic tools for rapid detection of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) and to identify candidate proteins for vaccine development, the C-terminal portion of the nucleocapsid (NC) gene was amplified using RT-PCR from the SARS-CoV genome, cloned into a yeast expression vector (pEGH), and expressed as a glutathione S-transferase (GST) and Hisx6 double-tagged fusion protein under the control of an inducible promoter. Western analysis on the purified protein confirmed the expression and purification of the NC fusion proteins from yeast. To determine its antigenicity, the fusion protein was challenged with serum samples from SARS patients and normal controls. The NC fusion protein demonstrated high antigenicity with high specificity, and therefore, it should have great potential in designing clinical diagnostic tools and provide useful information for vaccine development.
Collapse
Affiliation(s)
- Guozhen Liu
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, China
| | - Shaohui Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Wenzhou Medical College, Wenzhou 325007, China
| | - Peng Chen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianning Yin
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jingqiang Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Liang Lin
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jinxiu Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Bo You
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Ye Yin
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Shuting Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Hao Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Ren
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaoqian Zhao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yongqiao Sun
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaowei Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianqiu Fang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Siqi Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Heng Zhu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Molecular, Cellular, and Developmental Biology, Yale University, CT 06520, U. S. A
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| |
Collapse
|
1515
|
Bi S, Qin E, Xu Z, Li W, Wang J, Hu Y, Liu Y, Duan S, Hu J, Han Y, Xu J, Li Y, Yi Y, Zhou Y, Lin W, Wen J, Xu H, Li R, Zhang Z, Sun H, Zhu J, Yu M, Fan B, Wu Q, Lin W, Tang L, Yang B, Li G, Peng W, Li W, Jiang T, Deng Y, Liu B, Shi J, Deng Y, Wei W, Liu H, Tong Z, Zhang F, Zhang Y, Wang C, Li Y, Ye J, Gan Y, Ji J, Li X, Tian X, Lu F, Tan G, Yang R, Liu B, Liu S, Li S, Wang J, Wang J, Cao W, Yu J, Dong X, Yang H. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:180-92. [PMID: 15629030 PMCID: PMC5172409 DOI: 10.1016/s1672-0229(03)01023-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
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 BJ01, BJ02, BJ03, and BJ04) 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 identified 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.
Collapse
Affiliation(s)
- Shengli Bi
- Center of Disease Control and Prevention, Beijing 100050, China
| | - E’de Qin
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Zuyuan Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Wei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Wenzhou Medical College, Wenzhou 325003, China
| | - Yong Liu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shumin Duan
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Jianfei Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yao Yi
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Yongdong Zhou
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Wei Lin
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Hong Xu
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Ruan Li
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Zizhang Zhang
- College of Materials Science and Chemical Engineering, Yuquan Campus, Zhejiang University, Hangzhou 310027, China
| | - Haiyan Sun
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jingui Zhu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Man Yu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Baochang Fan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Qingfa Wu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Lin
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Lin Tang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Bao’an Yang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Guoqing Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wenming Peng
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Wenjie Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Tao Jiang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Yajun Deng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Bohua Liu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jianping Shi
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yongqiang Deng
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Wei Wei
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Hong Liu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Zongzhong Tong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Feng Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yu Zhang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Cui’e Wang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Yuquan Li
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Yonghua Gan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaoyu Li
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiangjun Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Fushuang Lu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Gang Tan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Ruifu Yang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Bin Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Siqi Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Wuchun Cao
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Xiaoping Dong
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| |
Collapse
|
1516
|
Ren Y, Zhou Z, Liu J, Lin L, Li S, Wang H, Xia J, Zhao Z, Wen J, Zhou C, Wang J, Yin J, Xu N, Liu S. A strategy for searching antigenic regions in the SARS-CoV spike protein. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:207-15. [PMID: 15629033 PMCID: PMC5172407 DOI: 10.1016/s1672-0229(03)01026-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the face of the worldwide threat of severe acute respiratory syndrome (SARS) to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA), these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469-882 in the S protein, and one epitope site was located at Codons 599-620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis.
Collapse
|
1517
|
Chen LL, Ou HY, Zhang R, Zhang CT. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun 2003; 307:382-8. [PMID: 12859968 PMCID: PMC7134609 DOI: 10.1016/s0006-291x(03)01192-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5-6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (http://tubic.tju.edu.cn/sars/). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.
Collapse
Affiliation(s)
- Ling-Ling Chen
- Department of Physics, Tianjin University, Tianjin 300072, PR China
- Department of Biology, Shandong University of Technology, Zibo 255049, PR China
| | - Hong-Yu Ou
- Department of Physics, Tianjin University, Tianjin 300072, PR China
| | - Ren Zhang
- Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, PR China
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, PR China
- Corresponding author. Fax: +86-22-2740-2697
| |
Collapse
|
1518
|
Bioinformatics Analysis of SARS Proteins and Molecular Dynamics Simulated Structure of an Alpha-helix Motif. B KOREAN CHEM SOC 2003. [DOI: 10.5012/bkcs.2003.24.7.899] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
1519
|
|
1520
|
Abstract
It's less than four months since the World Health Organization issued global warnings about a mysterious and deadly form of pneumonia. Nature 's reporters pose key questions about the outbreak, and assess our preparedness to deal with future viral threats.
Collapse
|
1521
|
|
1522
|
Thomas PA. SEVERE ACUTE RESPIRATORY SYNDROME. Indian J Med Microbiol 2003. [PMID: 17643010 PMCID: PMC8112622 DOI: 10.1016/s0255-0857(21)03064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a form of atypical pneumonia that apparently originated in Guangdong Province of the People’s Republic of China in late 2002. This first came to the world’s attention in late February 2003, and has since spread worldwide. As of June 23rd 2003, the disease had been reported from 32 countries or regions globally, affecting 8459 people; 805 individuals (9.5 % of the total affected) have died of the disease. A novel coronavirus, the SARS-associated coronavirus (SARS-CoV) has been found in various specimens taken from patients with SARS. Although there has been rapid development of tests to detect SARS Co-V, these tests presently have certain limitations. Definitions of suspected, confirmed and probable cases have been formulated. Measures currently used for the management of patients with SARS include isolation, ribavirin, corticosteroid therapy and mechanical ventilation. Unfortunately, almost 10 % of affected patients succumb to their illness, underlying the need for developing more effective therapy. It remains to be seen how long it will take to bring this epidemic under control.
Collapse
|
1523
|
Sampathkumar P, Temesgen Z, Smith TF, Thompson RL. SARS: epidemiology, clinical presentation, management, and infection control measures. Mayo Clin Proc 2003; 78:882-90. [PMID: 12839084 PMCID: PMC7094524 DOI: 10.4065/78.7.882] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus. It appears to be spread primarily by large droplet transmission. There is no specific therapy, and management consists of supportive care. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS.
Collapse
Affiliation(s)
- Priya Sampathkumar
- Division of Infectious Diseases and Internal Medicine, Mayo Clinic, Rochester, Minn 55905, USA.
| | | | | | | |
Collapse
|
1524
|
|
1525
|
Riley S, Fraser C, Donnelly CA, Ghani AC, Abu-Raddad LJ, Hedley AJ, Leung GM, Ho LM, Lam TH, Thach TQ, Chau P, Chan KP, Lo SV, Leung PY, Tsang T, Ho W, Lee KH, Lau EMC, Ferguson NM, Anderson RM. Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions. Science 2003; 300:1961-6. [PMID: 12766206 DOI: 10.1126/science.1086478] [Citation(s) in RCA: 643] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present an analysis of the first 10 weeks of the severe acute respiratory syndrome (SARS) epidemic in Hong Kong. The epidemic to date has been characterized by two large clusters-initiated by two separate "super-spread" events (SSEs)-and by ongoing community transmission. By fitting a stochastic model to data on 1512 cases, including these clusters, we show that the etiological agent of SARS is moderately transmissible. Excluding SSEs, we estimate that 2.7 secondary infections were generated per case on average at the start of the epidemic, with a substantial contribution from hospital transmission. Transmission rates fell during the epidemic, primarily as a result of reductions in population contact rates and improved hospital infection control, but also because of more rapid hospital attendance by symptomatic individuals. As a result, the epidemic is now in decline, although continued vigilance is necessary for this to be maintained. Restrictions on longer range population movement are shown to be a potentially useful additional control measure in some contexts. We estimate that most currently infected persons are now hospitalized, which highlights the importance of control of nosocomial transmission.
Collapse
Affiliation(s)
- Steven Riley
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
1526
|
How and who does SARS kill? Nature 2003. [PMCID: PMC7095033 DOI: 10.1038/nature.2003.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
1527
|
Affiliation(s)
- Kathryn V Holmes
- University of Colorado Health Sciences Center, Department of Microbiology, Denver, Colorado 80262, USA.
| |
Collapse
|
1528
|
Nie QH, Luo XD, Hui WL. Advances in clinical diagnosis and treatment of severe acute respiratory syndrome. World J Gastroenterol 2003; 9:1139-43. [PMID: 12800213 PMCID: PMC4611773 DOI: 10.3748/wjg.v9.i6.1139] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2003] [Revised: 06/02/2003] [Accepted: 06/04/2003] [Indexed: 02/06/2023] Open
Abstract
It has been proved that severe acute respiratory syndrome (SARS) is caused by SARS-associated coronavirus, a novel coronavirus. SARS originated in Guangdong Province, the People's Republic of China at the end of 2002. At present, it has spread to more than 33 countries or regions all over the world and affected 8 360 people and killed 764 by May 31,2003. Identification of the SARS causative agent and development of a diagnostic test are important. Detecting disease in its early stage, understanding its pathways of transmission and implementing specific prevention measures for the disease are dependent upon swift progress. Due to the efforts of the WHO-led network of laboratories testing for SARS, tests for the novel coronavirus have been developed with unprecedented speed. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses. WHO established the definitions of suspected and confirmed and probable cases. But the laboratory tests and definitions are limited. Until now, the primary measures included isolation, ribavirin and corticosteroid therapy, mechanical ventilation, etc. Other therapies such as convalescent plasma are being explored. It is necessary to find more effective therapy. There still are many problems to be solved in the course of conquering SARS.
Collapse
Affiliation(s)
- Qing-He Nie
- The Chinese PLA Center of Diagnosis and Treatment for Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, Shaanxi Province, China.
| | | | | |
Collapse
|
1529
|
Zhang JZ. Severe acute respiratory syndrome and its lesions in digestive system. World J Gastroenterol 2003; 9:1135-8. [PMID: 12800212 PMCID: PMC4611772 DOI: 10.3748/wjg.v9.i6.1135] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Revised: 05/24/2003] [Accepted: 05/27/2003] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) is an infectious atypical pneumonia that has recently been recognized in the patients in 32 countries and regions. This brief review summarizes some of the initial etiologic findings, pathological description, and its lesions of digestive system caused by SARS virus. It is an attempt to draw gastroenterologists and hepatologists' attention to this fatal illness, especially when it manifests itself initially as digestive symptoms.
Collapse
Affiliation(s)
- Jian-Zhong Zhang
- Department of Pathology, 306 Hospital of PLA, Beijing 100101, China.
| |
Collapse
|
1530
|
LIN Y, SHEN X, YANG RF, LI YX, JI YY, HE YY, SHI MD, LU W, SHI TL, WANG J, WANG HX, JIANG HL, SHEN JH, XIE YH, WANG Y, PEI G, SHEN BF, WU JR, SUN B. Identification of an epitope of SARS-coronavirus nucleocapsid protein. Cell Res 2003; 13:141-5. [PMID: 12862314 PMCID: PMC7091728 DOI: 10.1038/sj.cr.7290158] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2003] [Revised: 06/01/2003] [Accepted: 06/01/2003] [Indexed: 12/17/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) is a major virion structural protein. In this study, two epitopes (N1 and N2) of the N protein of SARS-CoV were predicted by bioinformatics analysis. After immunization with two peptides, the peptides-specific antibodies were isolated from the immunized rabbits. The further experiments demonstrated that N1 peptide-induced polyclonal antibodies had a high affinity to bind to E. coli expressed N protein of SARS-CoV. Furthermore, it was confirmed that N1 peptide-specific IgG antibodies were detectable in the sera of severe acute respiratory syndrome (SARS) patients. The results indicated that an epitope of the N protein has been identified and N protein specific Abs were produced by peptide immunization, which will be usefull for the study of SARS-CoV.
Collapse
Affiliation(s)
- Ying LIN
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Xu SHEN
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Rui Fu YANG
- Institute of Microbiology and Epidemiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Yi Xue LI
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yong Yong JI
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - You Yu HE
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Mu De SHI
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Wei LU
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Tie Liu SHI
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jin WANG
- Institute of Microbiology and Epidemiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Hong Xia WANG
- Institute of Microbiology and Epidemiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Hua Liang JIANG
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jian Hua SHEN
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - You Hua XIE
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yuan WANG
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Gang PEI
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Bei Fen SHEN
- Institute of Microbiology and Epidemiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing, 100071 China
| | - Jia Rui WU
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Bing SUN
- Institute of Biochemistry and Cell Biology, Institute of Materia Medica, Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| |
Collapse
|
1531
|
Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TCT, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus ADME, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 2003; 300:1394-9. [PMID: 12730500 DOI: 10.1126/science.1085952] [Citation(s) in RCA: 1853] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.
Collapse
Affiliation(s)
- Paul A Rota
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
1532
|
Affiliation(s)
- Kathryn V Holmes
- Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, USA.
| | | |
Collapse
|
1533
|
|
1534
|
Wu Q, Zhang Y, Lü H, Wang J, He X, Liu Y, Ye C, Lin W, Hu J, Ji J, Xu J, Ye J, Hu Y, Chen W, Li S, Wang J, Wang J, Bi S, Yang H. The E protein is a multifunctional membrane protein of SARS-CoV. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:131-44. [PMID: 15626343 PMCID: PMC5172412 DOI: 10.1016/s1672-0229(03)01017-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The E (envelope) protein is the smallest structural protein in all coronaviruses and is the only viral structural protein in which no variation has been detected. We conducted genome sequencing and phylogenetic analyses of SARS-CoV. Based on genome sequencing, we predicted the E protein is a transmembrane (TM) protein characterized by a TM region with strong hydrophobicity and alpha-helix conformation. We identified a segment (NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH) in the carboxyl-terminal region of the E protein that appears to form three disulfide bonds with another segment of corresponding cysteines in the carboxyl-terminus of the S (spike) protein. These bonds point to a possible structural association between the E and S proteins. Our phylogenetic analyses of the E protein sequences in all published coronaviruses place SARS-CoV in an independent group in Coronaviridae and suggest a non-human animal origin.
Collapse
Affiliation(s)
- Qingfa Wu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yilin Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Hong Lü
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Ximiao He
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yong Liu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Chen Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Lin
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianfei Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wenjun Chen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Shengli Bi
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| |
Collapse
|
1535
|
Qin E, He X, Tian W, Liu Y, Li W, Wen J, Wang J, Fan B, Wu Q, Chang G, Cao W, Xu Z, Yang R, Wang J, Yu M, Li Y, Xu J, Si B, Hu Y, Peng W, Tang L, Jiang T, Shi J, Ji J, Zhang Y, Ye J, Wang C, Han Y, Zhou J, Deng Y, Li X, Hu J, Wang C, Yan C, Zhang Q, Bao J, Li G, Chen W, Fang L, Li C, Lei M, Li D, Tong W, Tian X, Wang J, Zhang B, Zhang H, Zhang Y, Zhao H, Zhang X, Li S, Cheng X, Zhang X, Liu B, Zeng C, Li S, Tan X, Liu S, Dong W, Wang J, Wong GKS, Yu J, Wang J, Zhu Q, Yang H. A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:101-7. [PMID: 15626340 PMCID: PMC5172408 DOI: 10.1016/s1672-0229(03)01014-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.
Collapse
Affiliation(s)
- E’de Qin
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Xionglei He
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yong Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Wei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jingqiang Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Baochang Fan
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Qingfa Wu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Guohui Chang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Wuchun Cao
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Zuyuan Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Ruifu Yang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Man Yu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Bingyin Si
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Wenming Peng
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Lin Tang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Tao Jiang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jianping Shi
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yu Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Cui’e Wang
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jun Zhou
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yajun Deng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xiaoyu Li
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Jianfei Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Caiping Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Chunxia Yan
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Qingrun Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jingyue Bao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Guoqing Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Weijun Chen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Lin Fang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Changfeng Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Meng Lei
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Dawei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Wei Tong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xiangjun Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jin Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Bo Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Haiqing Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Yilin Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Hui Zhao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xiaowei Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Shuangli Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xiaojie Cheng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xiuqing Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Bin Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Changqing Zeng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Xuehai Tan
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Siqi Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Wei Dong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Qingyu Zhu
- Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| |
Collapse
|
1536
|
Hu Y, Wen J, Tang L, Zhang H, Zhang X, Li Y, Wang J, Han Y, Li G, Shi J, Tian X, Jiang F, Zhao X, Wang J, Liu S, Zeng C, Wang J, Yang H. The M protein of SARS-CoV: basic structural and immunological properties. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:118-30. [PMID: 15626342 PMCID: PMC5172243 DOI: 10.1016/s1672-0229(03)01016-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We studied structural and immunological properties of the SARS-CoV M (membrane) protein, based on comparative analyses of sequence features, phylogenetic investigation, and experimental results. The M protein is predicted to contain a triple-spanning transmembrane (TM) region, a single N-glycosylation site near its N-terminus that is in the exterior of the virion, and a long C-terminal region in the interior. The M protein harbors a higher substitution rate (0.6% correlated to its size) among viral open reading frames (ORFs) from published data. The four substitutions detected in the M protein, which cause non-synonymous changes, can be classified into three types. One of them results in changes of pI (isoelectric point) and charge, affecting antigenicity. The second changes hydrophobicity of the TM region, and the third one relates to hydrophilicity of the interior structure. Phylogenetic tree building based on the variations of the M protein appears to support the non-human origin of SARS-CoV. To investigate its immunogenicity, we synthesized eight oligopeptides covering 69.2% of the entire ORF and screened them by using ELISA (enzyme-linked immunosorbent assay) with sera from SARS patients. The results confirmed our predictions on antigenic sites.
Collapse
Affiliation(s)
- Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Lin Tang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Haijun Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaowei Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Guoqing Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianping Shi
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiangjun Tian
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Feng Jiang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaoqian Zhao
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Siqi Liu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Changqing Zeng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| |
Collapse
|
1537
|
Li J, Luo C, Deng Y, Han Y, Tang L, Wang J, Ji J, Ye J, Jiang F, Xu Z, Tong W, Wei W, Zhang Q, Li S, Li W, Li H, Li Y, Dong W, Wang J, Bi S, Yang H. The structural characterization and antigenicity of the S protein of SARS-CoV. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:108-17. [PMID: 15626341 PMCID: PMC5172354 DOI: 10.1016/s1672-0229(03)01015-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The corona-like spikes or peplomers on the surface of the virion under electronic microscope are the most striking features of coronaviruses. The S (spike) protein is the largest structural protein, with 1,255 amino acids, in the viral genome. Its structure can be divided into three regions: a long N-terminal region in the exterior, a characteristic transmembrane (TM) region, and a short C-terminus in the interior of a virion. We detected fifteen substitutions of nucleotides by comparisons with the seventeen published SARS-CoV genome sequences, eight (53.3%) of which are non-synonymous mutations leading to amino acid alternations with predicted physiochemical changes. The possible antigenic determinants of the S protein are predicted, and the result is confirmed by ELISA (enzyme-linked immunosorbent assay) with synthesized peptides. Another profound finding is that three disulfide bonds are defined at the C-terminus with the N-terminus of the E (envelope) protein, based on the typical sequence and positions, thus establishing the structural connection with these two important structural proteins, if confirmed. Phylogenetic analysis reveals several conserved regions that might be potent drug targets.
Collapse
Affiliation(s)
- Jingxiang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Chunqing Luo
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yajun Deng
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Medical College, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Lin Tang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Fanbo Jiang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Zhao Xu
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Wei Tong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Wei
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Qingrun Zhang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Shengbin Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Medical College, Xi’an Jiaotong University, Xi’an 710049, China
| | - Wei Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Hongyan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yudong Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Wei Dong
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| | - Shengli Bi
- Center of Disease Control and Prevention, Beijing 100050, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University, Hangzhou 310008, China
| |
Collapse
|
1538
|
Krokhin O, Li Y, Andonov A, Feldmann H, Flick R, Jones S, Stroeher U, Bastien N, Dasuri KVN, Cheng K, Simonsen JN, Perreault H, Wilkins J, Ens W, Plummer F, Standing KG. Mass spectrometric characterization of proteins from the SARS virus: a preliminary report. Mol Cell Proteomics 2003; 2:346-56. [PMID: 12775768 PMCID: PMC7780042 DOI: 10.1074/mcp.m300048-mcp200] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A new coronavirus has been implicated as the causative agent of severe acute respiratory syndrome (SARS). We have used convalescent sera from several SARS patients to detect proteins in the culture supernatants from cells exposed to lavage another SARS patient. The most prominent protein in the supernatant was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a approximately 46-kDa species. This was found to be a novel nucleocapsid protein that matched almost exactly one predicted by an open reading frame in the recently published nucleotide sequence of the same virus isolate (>96% coverage). A second viral protein corresponding to the predicted approximately 139-kDa spike glycoprotein has also been examined by MALDI-TOF MS (42% coverage). After peptide N-glycosidase F digestion, 12 glycosylation sites in this protein were confirmed. The sugars attached to four of the sites were also identified. These results suggest that the nucleocapsid protein is a major immunogen that may be useful for early diagnostics, and that the spike glycoprotein may present a particularly attractive target for prophylactic intervention in combating SARS.
Collapse
Affiliation(s)
- Oleg Krokhin
- Department of Physics, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
1539
|
Zheng BJ, Guan Y, Tang Q, Cheng D, Xie FY, He ML, Chan KW, Wong KL, Lader E, Woodle MC, Lu PY, Li B, Zhong N. Prophylactic and Therapeutic Effects of Small Interfering Rna Targeting Sars-Coronavirus. Antivir Ther 2003. [DOI: 10.1177/135965350400900310] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives To identify and characterize the siRNA duplexes that are effective for inhibition of SARS-CoV infection and replication in the non-human primate cells. This in vitro study will serve as the foundation for development of novel anti-SARS therapeutics. Methods 48 siRNA sequences were designed for targeting regions throughout entire SARS-CoV genome RNA including open-reading frames for several key proteins. Chemically synthesized siRNA duplexes were transfected into foetal rhesus kidney (FRhK-4) cells prior to or after SARS-CoV infection. The inhibitory effects of the siRNAs were evaluated for reductions of intracellular viral genome copy number and viral titres in the cell culture medium measured by Q-RT-PCR and CPE-based titration, respectively. Four siRNA duplexes were found to achieve potent inhibition of SARS-CoV infection and replication. A prolonged prophylactic effect of siRNA duplexes with up to 90% inhibition that lasted for at least 72 h was observed. Combination of active siRNA duplexes targeting different regions of the viral genome resulted in therapeutic activity of up to 80% inhibition. Conclusion Chemically synthesized siRNA duplexes targeting SARS-CoV genomic RNA are potent agents for inhibition of the viral infection and replication. The location effects of siRNAs were revealed at both genome sequence and open-reading frame levels. The rapid development of siRNA-based SARS-CoV inhibitors marked a novel approach for combating newly emergent infectious diseases.
Collapse
Affiliation(s)
- Bo-jian Zheng
- Department of Microbiology, Institute of Molecular Biology, Department of Pathology, University of Hong Kong, Hong Kong, China
| | - Yi Guan
- Department of Microbiology, Institute of Molecular Biology, Department of Pathology, University of Hong Kong, Hong Kong, China
| | | | - Du Cheng
- Guangzhou Top Genomics, Ltd, Guangzhou, China
| | | | - Ming-Liang He
- Department of Microbiology, Institute of Molecular Biology, Department of Pathology, University of Hong Kong, Hong Kong, China
| | - Kwok-Wah Chan
- Department of Microbiology, Institute of Molecular Biology, Department of Pathology, University of Hong Kong, Hong Kong, China
| | - Kin-Ling Wong
- Department of Microbiology, Institute of Molecular Biology, Department of Pathology, University of Hong Kong, Hong Kong, China
| | - Eric Lader
- Qiagen Sciences, Inc., Germantown, Md., USA
| | | | | | - Baojian Li
- Guangzhou Top Genomics, Ltd, Guangzhou, China
- Biotechnology Research Center of Sun Yatsen University, and Key Laboratory of Gene Engineering of Ministry of Education of China, Department of Education of the State, Guangzhou, China
| | - Nanshan Zhong
- Guangzhou Institute of Respiratory Diseases, Guangzhou, China
| |
Collapse
|
1540
|
Qi Z, Hu Y, Li W, Chen Y, Zhang Z, Sun S, Lu H, Zhang J, Bu D, Ling L, Chen R. Phylogeny of SARS-CoV as inferred from complete genome comparison. CHINESE SCIENCE BULLETIN-CHINESE 2003; 48:1175-1178. [PMID: 32214702 PMCID: PMC7089017 DOI: 10.1007/bf03183930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 06/06/2003] [Indexed: 11/18/2022]
Abstract
SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS.
Collapse
Affiliation(s)
- Zhen Qi
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yu Hu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Wei Li
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China
| | - Yanjun Chen
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Zhihua Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shiwei Sun
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Hongchao Lu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Jingfen Zhang
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Dongbo Bu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Lunjiang Ling
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Runsheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China
| |
Collapse
|
1541
|
Lu Y, Chen Y. Spike protein homology between the SARS-associated virus and murine hepatitis virus implies existence of a putative receptor-binding region. CHINESE SCIENCE BULLETIN-CHINESE 2003; 48:1115-1117. [PMID: 32214699 PMCID: PMC7089281 DOI: 10.1007/bf03185764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Accepted: 05/15/2003] [Indexed: 11/16/2022]
Abstract
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 phylogenesis of S1 subunit of the coronavirus spike protein (SARS-associated virus, Hong Kong isolate CUHK-W1). Interestingly, the highest homology between murine hepatitis virus (MHV) and SARS-associated coronavirus was found. And the important sites (aa62-65 and aa214-216) on the spike protein of MHV with receptor-binding capacity were highly conservative in comparison with the newly separated SARS-associated virus (the corresponding sites are aa51-54 and aal95-197). These results from bioinformatics analysis might help 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.
Collapse
Affiliation(s)
- Yun Lu
- Laboratory of Immunology, Department of Biology, Tsinghua University, Protein Science Laboratory of Ministry of Education, 100084 Beijing, China
| | - Yinghua Chen
- Laboratory of Immunology, Department of Biology, Tsinghua University, Protein Science Laboratory of Ministry of Education, 100084 Beijing, China
| |
Collapse
|
1542
|
Liu S, Guo T, Ji X, Sun Z. Bioinformatical study on the proteomics and evolution of SARS-CoV. CHINESE SCIENCE BULLETIN-CHINESE 2003; 48:1277-1287. [PMID: 32214704 PMCID: PMC7089238 DOI: 10.1007/bf03184163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Accepted: 06/26/2003] [Indexed: 12/02/2022]
Abstract
A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome (SARS). For all the SARS-CoV associated proteins derivated from the SARS-CoV genome, the physiochemical properties such as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. The transmembrane segments and subcellular localization (SubLocation) prediction and conserved protein motifs search against database were employed to analyze the function of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrix calculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses were employed to identify the classification and phylogenetic relationship between SARS-CoV and other coronaviruses. The results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously known groups of coronviruses, but it is closer to Bo-CoV and MHV than to other coronaviruses. This study is in aid of experimental determination of SARS-CoV proteomics and the development of antiviral vaccine.
Collapse
Affiliation(s)
- Shuqun Liu
- Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, 100084 Beijing, China
| | - Tao Guo
- Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, 100084 Beijing, China
| | - Xinglai Ji
- Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, 100084 Beijing, China
| | - Zhirong Sun
- Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, 100084 Beijing, China
| |
Collapse
|
1543
|
Pareja Bezares A, Torán Mateos M. SARS: una nueva enfermedad desenmascarada. Aten Primaria 2003; 32:531-4. [PMID: 14651831 PMCID: PMC7130739 DOI: 10.1016/s0212-6567(03)70783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- A Pareja Bezares
- Médico epidemiólogo. Unidad de Epidemiología y Control de Infecciones. Hospital Son Llátzer. Palma de Mallorca. Baleares. España.
| | | |
Collapse
|
1544
|
Abstract
The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long-standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N-glycolylneuraminic acid (Neu5Gc), a cell-surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development.
Collapse
|
1545
|
Shi R, Ma W, Wu Q, Zhang B, Song Y, Guo Q, Xiao W, Wang Y, Zheng W. Design and application of 60mer oligonucleotide microarray in SARS coronavirus detection. CHINESE SCIENCE BULLETIN-CHINESE 2003; 48:1165-1169. [PMID: 32214700 PMCID: PMC7089259 DOI: 10.1007/bf03183928] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2003] [Accepted: 06/11/2003] [Indexed: 11/23/2022]
Abstract
The 60mer oligonucleotide microarray was designed and applied to detecting of SARS (severe acute respiratory syndrome) coronavirus. Thirty 60mer specific oligos were designed to cover the whole genome of the first submitted coronavirus strain, according to the sequence of TOR2 (GENEBANK Accession: AY274119). These primers were synthesized and printed into a microarray with 12 ×12 spots. RNAs were extracted from the throat swab and gargling fluid of SARS patients and reverse-transcripted into the double strand cDNAs. The cDNAs were prepared as restricted cDNA fragments by the restriction display (RD) technique and labeled by PCR with the Cy5-universal primer. The labeled samples were then applied to the oligo microarray for hybridization. The diagnostic capability of the microarray was evaluated after the washing and scanning steps. The scanning result showed that samples of SARS patients were hybridized with multiple SARS probes on the microarray, and there is no signal on the negative and blank controls. These results indicate that the genome of SARS coronavirus can be detected in parallel by the 60mer oligonucleotide microarray, which can improve the positive ratio of the diagnosis. The oligo microarray can also be used for monitoring the behavior of the virus genes in different stages of the disease status.
Collapse
Affiliation(s)
- Rong Shi
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Wenli Ma
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Qinghua Wu
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Bao Zhang
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Yanbin Song
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Qiuye Guo
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Weiwei Xiao
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Yan Wang
- Institute of Molecular Biology, First Military Medical University, 510515 Guangzhou, China
| | - Wenling Zheng
- Department of Medical Research, Guangzhou Liu Hua Qiao Hospital, 510010 Guangzhou, China
| |
Collapse
|