Research Article

Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome

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Science  30 May 2003:
Vol. 300, Issue 5624, pp. 1394-1399
DOI: 10.1126/science.1085952
  • Fig. 1.

    Genome organization and mRNA mapping of SARS-CoV. (A) Overall organization of the 29,727-nt SARS-CoV genomic RNA. The 72-nt leader sequence is represented by a small orange square at the 5′ terminus of the genome and the subgenomic mRNAs (below). Predicted ORFs 1a and 1b, encoding the nonstructural polyproteins, and those encoding the S, E, M, and N structural proteins are indicated. The vertical position of the boxes indicates the phase of the reading frame. (B) Expanded view of the structural protein coding region and predicted mRNA transcripts. Known structural protein coding regions (blue boxes) and reading frames X1 to X5, encoding potential nonstructural proteins longer than 50 amino acids (gray boxes), are indicated. Lengths and map locations of the 3′-coterminal mRNAs, as predicted by identification of conserved transcription-regulating sequences, are indicated. (C) Northern blot analysis of SARS-CoV mRNAs. Poly(A)+ RNA was separated on a formaldehyde-agarose gel, transferred to a nylon membrane, and hybridized with a digoxigenin-labeled riboprobe overlapping the 3′ untranslated region. Signals were visualized by chemiluminescence. Sizes of the SARS-CoV mRNAs were calculated by interpolation from a log-linear fit of those of the molecular mass marker. Lane 1, SARS-CoV mRNA; lane 2, Vero E6 cell mRNA; lane 3, molecular mass marker (sizes in kilobases).

  • Fig. 2.

    Phylogenetic analysis and pairwise identities of coronavirus proteins. Predicted amino acid sequences of SARS-CoV proteins were compared with those from reference viruses representing each species in the three groups of coronaviruses for which complete genomic sequence information was available [group 1(G1): human coronavirus 229E (HCoV-229E), af304460; porcine epidemic diarrhea virus (PEDV), af353511; transmissible gastroenteritis virus (TGEV), aj271965. Group 2 (G2): bovine coronavirus (BCoV), af220295; murine hepatitis virus (MHV), af201929. Group 3 (G3): infectious bronchitis virus (IBV), m95169]. Sequences for representative strains of other coronavirus species, for which partial sequence information was available, were included for some of the structural protein comparisons [group 1: canine coronavirus (CCoV), d13096; feline coronavirus (FCoV), ay204704; porcine respiratory coronavirus (PRCoV), z24675. Group 2: human coronavirus OC43 (HCoV-OC43), m76373, l14643, m93390; porcine hemagglutinating encephalomyelitis virus (HEV), ay078417; rat coronavirus (RtCoV), af207551]. (A) Sequence alignments and neighbor-joining trees were generated by the use of ClustalX 1.83 with the Gonnet protein comparison matrix. The resulting trees were adjusted for final output with treetool 2.0.1. (B) Uncorrected pairwise distances were calculated from the aligned sequences with the Distances program from the Wisconsin Sequence Analysis Package, version 10.2 (Accelrys, Burlington, MA). Distances were converted to percent identity by subtracting from 100. aa, amino acid.

  • Fig. 3.

    Conserved motifs in coronavirus S proteins. Alignment of the C-terminal region of the SARS-CoV and reference coronavirus S proteins was generated with ClustalX 1.83. Residues that match the SARS-CoV sequence exactly are boxed. The membrane-spanning domain and cytoplasmic tails are delineated with arrows. The amino acid sequence Y(V/I)KWPW(Y/W)VWL (26) is a conserved motif in all three coronavirus groups. The cysteine-rich region, which overlaps the membrane-spanning region and the cytoplasmic region, is also found in all coronavirus groups.

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  • Abstract
    Full Text
    Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome
    Paul A. Rota, M. Steven Oberste, Stephan S. Monroe, W. Allan Nix, Ray Campagnoli, Joseph P. Icenogle, Silvia Peñaranda, Bettina Bankamp, Kaija Maher, Min-hsin Chen, Suxiong Tong, Azaibi Tamin, Luis Lowe, Michael Frace, Joseph L. DeRisi, Qi Chen, David Wang, Dean D. Erdman, Teresa C. T. Peret, Cara Burns, Thomas G. Ksiazek, Pierre E. Rollin, Anthony Sanchez, Stephanie Liffick, Brian Holloway, Josef Limor, Karen McCaustland, Melissa Olsen- Rassmussen, Ron Fouchier, Stephan Günther, Albert D. M. E. Osterhaus, Christian Drosten, Mark A. Pallansch, Larry J. Anderson, William J. Bellini

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    Materials and Methods
    Figs. S1 to S4
    Tables S1 to S3
    References

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