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The Genome Sequence of the SARS-Associated Coronavirus
Marco A. Marra,1*Steven J. M. Jones,1Caroline R. Astell,1Robert A. Holt,1Angela Brooks-Wilson,1Yaron S. N. Butterfield,1Jaswinder Khattra,1Jennifer K. Asano,1Sarah A. Barber,1Susanna Y. Chan,1Alison Cloutier,1Shaun M. Coughlin,1Doug Freeman,1Noreen Girn,1Obi L. Griffith,1Stephen R. Leach,1Michael Mayo,1Helen McDonald,1Stephen B. Montgomery,1Pawan K. Pandoh,1Anca S. Petrescu,1A. Gordon Robertson,1Jacqueline E. Schein,1Asim Siddiqui,1Duane E. Smailus,1Jeff M. Stott,1George S. Yang,1Francis Plummer,2Anton Andonov,2Harvey Artsob,2Nathalie Bastien,2Kathy Bernard,2Timothy F. Booth,2Donnie Bowness,2Martin Czub,2Michael Drebot,2Lisa Fernando,2Ramon Flick,2Michael Garbutt,2Michael Gray,2Allen Grolla,2Steven Jones,2Heinz Feldmann,2Adrienne Meyers,2Amin Kabani,2Yan Li,2Susan Normand,2Ute Stroher,2Graham A. Tipples,2Shaun Tyler,2Robert Vogrig,2Diane Ward,2Brynn Watson,2Robert C. Brunham,3Mel Krajden,3Martin Petric,3Danuta M. Skowronski,3Chris Upton,4Rachel L. Roper4
We sequenced the 29,751-base genome of the severe acute respiratorysyndrome (SARS)–associated coronavirus known as the Tor2isolate. The genome sequence reveals that this coronavirus isonly moderately related to other known coronaviruses, includingtwo human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogeneticanalysis of the predicted viral proteins indicates that thevirus does not closely resemble any of the three previouslyknown groups of coronaviruses. The genome sequence will aidin the diagnosis of SARS virus infection in humans and potentialanimal hosts (using polymerase chain reaction and immunologicaltests), in the development of antivirals (including neutralizingantibodies), and in the identification of putative epitopesfor vaccine development.
1 British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada. 2 National Microbiology Laboratory, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada. 3 British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada. 4 Department of Biochemistry and Microbiology, University of Victoria, Post Office Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada.
* To whom correspondence should be addressed. E-mail: mmarra{at}bccgsc.ca
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7a Protein of Severe Acute Respiratory Syndrome Coronavirus Inhibits Cellular Protein Synthesis and Activates p38 Mitogen-Activated Protein Kinase.
S. A. Kopecky-Bromberg, L. Martinez-Sobrido, and P. Palese (2006)
J. Virol.
80, 785-793
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Evaluation of Affymetrix Severe Acute Respiratory Syndrome Resequencing GeneChips in Characterization of the Genomes of Two Strains of Coronavirus Infecting Humans.
I. M. Sulaiman, X. Liu, M. Frace, N. Sulaiman, M. Olsen-Rasmussen, E. Neuhaus, P. A. Rota, and R. M. Wohlhueter (2006)
Appl. Envir. Microbiol.
72, 207-211
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Severe Acute Respiratory Syndrome Coronavirus 3a Protein Is Released in Membranous Structures from 3a Protein-Expressing Cells and Infected Cells.
C. Huang, K. Narayanan, N. Ito, C. J. Peters, and S. Makino (2006)
J. Virol.
80, 210-217
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Expression of Hemagglutinin Esterase Protein from Recombinant Mouse Hepatitis Virus Enhances Neurovirulence.
L. Kazi, A. Lissenberg, R. Watson, R. J. de Groot, and S. R. Weiss (2005)
J. Virol.
79, 15064-15073
|Abstract »|Full Text »|PDF »
Severe Acute Respiratory Syndrome Coronavirus Infection of Human Ciliated Airway Epithelia: Role of Ciliated Cells in Viral Spread in the Conducting Airways of the Lungs.
A. C. Sims, R. S. Baric, B. Yount, S. E. Burkett, P. L. Collins, and R. J. Pickles (2005)
J. Virol.
79, 15511-15524
|Abstract »|Full Text »|PDF »
Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus.
S. R. Weiss and S. Navas-Martin (2005)
Microbiol. Mol. Biol. Rev.
69, 635-664
|Abstract »|Full Text »|PDF »
Subcellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein.
J. You, B. K. Dove, L. Enjuanes, M. L. DeDiego, E. Alvarez, G. Howell, P. Heinen, M. Zambon, and J. A. Hiscox (2005)
J. Gen. Virol.
86, 3303-3310
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ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia.
H. P. Jia, D. C. Look, L. Shi, M. Hickey, L. Pewe, J. Netland, M. Farzan, C. Wohlford-Lenane, S. Perlman, and P. B. McCray Jr (2005)
J. Virol.
79, 14614-14621
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Severe Acute Respiratory Syndrome Coronavirus Group-Specific Open Reading Frames Encode Nonessential Functions for Replication in Cell Cultures and Mice.
B. Yount, R. S. Roberts, A. C. Sims, D. Deming, M. B. Frieman, J. Sparks, M. R. Denison, N. Davis, and R. S. Baric (2005)
J. Virol.
79, 14909-14922
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Assembly of Severe Acute Respiratory Syndrome Coronavirus RNA Packaging Signal into Virus-Like Particles Is Nucleocapsid Dependent.
P.-K. Hsieh, S. C. Chang, C.-C. Huang, T.-T. Lee, C.-W. Hsiao, Y.-H. Kou, I-Y. Chen, C.-K. Chang, T.-H. Huang, and M.-F. Chang (2005)
J. Virol.
79, 13848-13855
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Severe Acute Respiratory Syndrome Coronavirus Fails To Activate Cytokine-Mediated Innate Immune Responses in Cultured Human Monocyte-Derived Dendritic Cells.
T. Ziegler, S. Matikainen, E. Ronkko, P. Osterlund, M. Sillanpaa, J. Siren, R. Fagerlund, M. Immonen, K. Melen, and I. Julkunen (2005)
J. Virol.
79, 13800-13805
|Abstract »|Full Text »|PDF »
Molecular Diagnosis of Severe Acute Respiratory Syndrome: The State of the Art.
Experience of using convalescent plasma for severe acute respiratory syndrome among healthcare workers in a Taiwan hospital.
K.-M. Yeh, T.-S. Chiueh, L. K. Siu, J.-C. Lin, P. K. S. Chan, M.-Y. Peng, H.-L. Wan, J.-H. Chen, B.-S. Hu, C.-L. Perng, et al. (2005)
J. Antimicrob. Chemother.
56, 919-922
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Bats Are Natural Reservoirs of SARS-Like Coronaviruses.
W. Li, Z. Shi, M. Yu, W. Ren, C. Smith, J. H. Epstein, H. Wang, G. Crameri, Z. Hu, H. Zhang, et al. (2005)
Science
310, 676-679
|Abstract »|Full Text »|PDF »
Scalable Transcriptional Analysis Routine--Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics.
E. P. Garcia, L. A. Dowding, L. W. Stanton, and V. I. Slepnev (2005)
J. Mol. Diagn.
7, 444-454
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Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus.
S. P. Yip, S. S. T. To, P. H.M. Leung, T. S. Cheung, P. K.C. Cheng, and W. W.L. Lim (2005)
Clin. Chem.
51, 1885-1888
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Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats.
S. K. P. Lau, P. C. Y. Woo, K. S. M. Li, Y. Huang, H.-W. Tsoi, B. H. L. Wong, S. S. Y. Wong, S.-Y. Leung, K.-H. Chan, and K.-Y. Yuen (2005)
PNAS
102, 14040-14045
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Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor.
Molecular Evolution Analysis and Geographic Investigation of Severe Acute Respiratory Syndrome Coronavirus-Like Virus in Palm Civets at an Animal Market and on Farms.
B. Kan, M. Wang, H. Jing, H. Xu, X. Jiang, M. Yan, W. Liang, H. Zheng, K. Wan, Q. Liu, et al. (2005)
J. Virol.
79, 11892-11900
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Mechanism of the Maturation Process of SARS-CoV 3CL Protease.
M.-F. Hsu, C.-J. Kuo, K.-T. Chang, H.-C. Chang, C.-C. Chou, T.-P. Ko, H.-L. Shr, G.-G. Chang, A. H.-J. Wang, and P.-H. Liang (2005)
J. Biol. Chem.
280, 31257-31266
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The Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein Is Phosphorylated and Localizes in the Cytoplasm by 14-3-3-Mediated Translocation.
M. Surjit, R. Kumar, R. N. Mishra, M. K. Reddy, V. T. K. Chow, and S. K. Lal (2005)
J. Virol.
79, 11476-11486
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Protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection.
S. Matsuyama, M. Ujike, S. Morikawa, M. Tashiro, and F. Taguchi (2005)
PNAS
102, 12543-12547
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Identification of Two Critical Amino Acid Residues of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Its Variation in Zoonotic Tropism Transition via a Double Substitution Strategy.
X.-X. Qu, P. Hao, X.-J. Song, S.-M. Jiang, Y.-X. Liu, P.-G. Wang, X. Rao, H.-D. Song, S.-Y. Wang, Y. Zuo, et al. (2005)
J. Biol. Chem.
280, 29588-29595
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Identification of Immunodominant Epitopes on the Membrane Protein of the Severe Acute Respiratory Syndrome-Associated Coronavirus.
Y. He, Y. Zhou, P. Siddiqui, J. Niu, and S. Jiang (2005)
J. Clin. Microbiol.
43, 3718-3726
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Vesicular stomatitis virus pseudotyped with severe acute respiratory syndrome coronavirus spike protein.
S. Fukushi, T. Mizutani, M. Saijo, S. Matsuyama, N. Miyajima, F. Taguchi, S. Itamura, I. Kurane, and S. Morikawa (2005)
J. Gen. Virol.
86, 2269-2274
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Inhibition, Escape, and Attenuated Growth of Severe Acute Respiratory Syndrome Coronavirus Treated with Antisense Morpholino Oligomers.
B. W. Neuman, D. A. Stein, A. D. Kroeker, M. J. Churchill, A. M. Kim, P. Kuhn, P. Dawson, H. M. Moulton, R. K. Bestwick, P. L. Iversen, et al. (2005)
J. Virol.
79, 9665-9676
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The Severe Acute Respiratory Syndrome Coronavirus 3a Protein Up-Regulates Expression of Fibrinogen in Lung Epithelial Cells.
Y.-J. Tan, P.-Y. Tham, D. Z. L. Chan, C.-F. Chou, S. Shen, B. C. Fielding, T. H. P. Tan, S. G. Lim, and W. Hong (2005)
J. Virol.
79, 10083-10087
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