Phylogenomics and bioinformatics of SARS-CoV

Trends in Microbiology

Volumn 12, Issue 3, 2004, Pages 106-111

  Liò, Pietro ^a,b   Goldman, Nick ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 1; NUCLEOTIDE; RECEPTOR PROTEIN; RNA DIRECTED RNA POLYMERASE;

AMINO ACID SUBSTITUTION; BIOINFORMATICS; DRUG DESIGN; DRUG HALF LIFE; DRUG MANUFACTURE; EVOLUTION; GENE MUTATION; GENOMICS; HEPATITIS VIRUS; MEMBRANE FUSION; METHODOLOGY; NONHUMAN; PHYLOGENY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RECEPTOR BINDING; REVIEW; RNA SEQUENCE; SARS CORONAVIRUS; STATISTICAL SIGNIFICANCE; VIRUS MUTATION;

CORONAVIRIDAE; CORONAVIRUS; MURINAE; MURINE HEPATITIS VIRUS; PROKARYOTA; RNA VIRUSES; SARS CORONAVIRUS;

EID: 1542286204     PISSN: 0966842X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tim.2004.01.005     Document Type: Short Survey

References (37)

1. Whelan S., et al. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17:2001;262-272.
2. Marra M.A., et al. The genome sequence of the SARS-associated coronavirus. Science. 300:2003;1399-1404.
3. Rota P.A., et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 300:2003;1394-1399.
4. Butler P.J.G. Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed. Philos. Trans. R. Soc. Lond. B Biol. Sci. 354:1999;537-550.
5. Russell R.B., et al. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269:1997;423-439.
6. Thorne J.L., et al. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:1996;666-673.
7. Liò P., et al. Combining protein secondary structure prediction and evolutionary inference. Bioinformatics. 14:1998;726-733.
8. Liò P., Goldman N. Using protein structural information in evolutionary inference: transmembrane proteins. Mol. Biol. Evol. 16:1999;1696-1710.
9. Thompson J.D., et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
10. Rost B. Predict protein. Methods Enzymol. 266:1996;525-539.
11. McGuffin L.J., et al. The PSIPRED protein structure prediction server. Bioinformatics. 16:2000;404-405.
12. Altschul S.F., Koonin E.V. Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci. 23:1998;444-447.
13. Ballesteros M.L., et al. Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism. Virology. 227:1997;378-388.
14. Godet M., et al. Major receptor-binding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein. J. Virol. 68:1994;8008-8016.
15. Sanchez C.M., et al. Targeted recombination demonstrates that the spike gene of transmissible gastroenteritis coronavirus is a determinant of its enteric tropism and virulence. J. Virol. 73:1999;7607-7618.
16. Bonavia A., et al. Identification of a receptor binding domain of the spike glycoprotein of human coronavirus HCoV-229E. J. Virol. 77:2003;2530-2538.
17. Zelus B.D., et al. Conformational changes in the spike glycoprotein of murine coronavirus are induced at 37°C either by soluble murine CEACAM1 receptors or by pH 8. J. Virol. 77:2003;830-840.
18. Cavanagh D. The coronavirus surface glycoprotein. Siddell S.G. The Coronaviridae. 1995;73-115 Plenum Press.
19. Benbacer L., et al. Interspecies aminopeptidase-N chimeras reveal species-specific receptor recognition by canine coronavirus, feline infectious peritonitis virus, and transmissible gastroenteritis virus. J. Virol. 71:1997;734-737.
20. Anand K., et al. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 300:2003;1763-1767.
21. Schwegmann-Wessels C., et al. Binding of transmissible gastroenteritis coronavirus to cell surface sialoglycoproteins. J. Virol. 76:2002;6037-6043.
22. Krempl C., et al. Characterization of the sialic acid binding activity of transmissible gastroenteritis coronavirus by analysis of haemagglutination- deficient mutants. J. Gen. Virol. 81:2000;489-496.
23. Krempl C., et al. Point mutations in the S protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus. J. Virol. 71:1997;3285-3287.
24. Zhang J. Severe acute respiratory syndrome and its lesions in digestive system. World J. Gastroenterol. 9:2003;1135-1138.
25. Chang K.W., et al. Coronavirus-induced membrane fusion requires the cysteine-rich domain in the spike protein. Virology. 269:2000;212-224.
26. Derdeyn C.A., et al. Sensitivity of human immunodeficiency virus type 1 to fusion inhibitors targeted to the gp41 first heptad repeat involves distinct regions of gp41 and is consistently modulated by gp120 interactions with the coreceptor. J. Virol. 75:2001;8605-8614.
27. Kliger Y., Levanon E.Y. Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy. BMC Microbiol. 3:2003;20-30.
28. Frank A.C., Lobry J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene. 238:1999;65-77.
29. Huynen M.A., et al. Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure. J. Mol. Evol. 34:1992;280-291.
30. Karlin S., et al. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32:1998;185-225.
31. Karlin S., Mrazek J. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. U. S. A. 94:1997;10227-10232.
32. Narayanan K., et al. Nucleocapsid-independent specific viral RNA packaging via viral envelope protein and viral RNA signal. J. Virol. 77:2003;2922-2927.
33. Qin L., et al. Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis. Acta Pharmacol. Sin. 24:2003;489-496.
34. Burch C.L., Chao L. Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature. 406:2000;625-628.
35. Chao L. Evolution of sex and the molecular clock in RNA viruses. Gene. 205:1997;301-308.
36. Ericsson T.A., et al. Identification of receptors for pig endogenous retrovirus. Proc. Natl. Acad. Sci. U. S. A. 100:2003;6759-6764.
37. Nielsen R., Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:1998;929-936.