SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting

Infection, Genetics and Evolution

Volumn 3, Issue 3, 2003, Pages 219-225

  Rest, Joshua S ^a   Mindell, David P ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Coronavirus; Host shift; Phylogeny; Recombination; RNA dependent RNA polymerase; SARS CoV Nidovirales; Severe acute respiratory syndrome

Indexed keywords

NUCLEOCAPSID PROTEIN; RNA DIRECTED RNA POLYMERASE; VIRUS PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTERIVIRUS; ARTICLE; BAYES THEOREM; CHICKEN; CLADISTICS; CONTROLLED STUDY; CORONAVIRUS; GENETIC RECOMBINATION; HOST; MAMMAL; MOUSE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; RAT; SARS CORONAVIRUS; TURKEY (BIRD); VIRUS NUCLEOCAPSID;

ANIMALS; BAYES THEOREM; CORONAVIRUS; HOST-PARASITE RELATIONS; HUMANS; MEMBRANE GLYCOPROTEINS; NUCLEOCAPSID; PHYLOGENY; RECOMBINATION, GENETIC; RNA REPLICASE; SARS VIRUS; VIRAL ENVELOPE PROTEINS;

ARTERIVIRIDAE; AVES; CORONAVIRIDAE; CORONAVIRUS; GALLUS GALLUS; MAMMALIA; NIDOVIRALES; PUFFINUS AURICULARIS; PUFFINUS PUFFINUS;

EID: 0141716995     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2003.08.001     Document Type: Article

References (29)

1. Bateman A. Birney E. Cerruti L. Durbin R. Etwiller L. Eddy S.R. Griffiths-Jones S. Howe K.L. Marshall M. Sonnhammer E.L. The Pfam protein families database Nucleic Acids Res. 30 2002 276-280
2. de Haan C.A. Volders H. Koetzner C.A. Masters P.S. Rottier P.J. Coronaviruses maintain viability despite dramatic rearrangements of the strictly conserved genome organization J. Virol. 76 2002 12491-12502
3. Decimo D. Philippe H. Hadchouel M. Tardieu M. Meunier-Rotival M. The gene encoding the nucleocapsid protein: sequence analysis in murine hepatitis virus type 3 and evolution in Coronaviridae Arch. Virol. 130 1993 279-288
4. Desdevises Y. Morand S. Jousson O. Legendre P. Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): the study of a complex host-parasite system Evolution 56 2002 2459-2471
5. Dimmic M.W. Rest J.S. Mindell D.P. Goldstein R.A. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny J. Mol. E 55 2002 65-73
6. Eddy S.R. Profile hidden Markov models Bioinformatics 14 1998 755-763
7. Huelsenbeck J.P. Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754-755
8. Jia W. Karaca K. Parrish C.R. Naqi S.A. A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Arch. Virol. 140 1995 259-271
9. Jonassen C.M. Jonassen T.O. Grinde B. A common RNA motif in the 3′ end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus J. Gen. Virol. 79 1998 715-718
10. Keeling P.J. Palmer J.D. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase Proc. Natl. Acad. Sci. U.S.A. 98 2001 10745-10750
11. Kirkwood J.K. Cunningham A.A. Hawkey C. Howlett J. Perrins C.M. Hematology of fledgling Manx shearwaters (Puffinus puffinus) with and without 'puffinosis' J. Wildl. Dis. 31 1995 96-98
12. Lai M.M. Coronavirus: organization, replication and expression of genome Annu. Rev. Microbiol. 44 1990 303-333
13. Lai M.M.C. Recombination in large RNA viruses: coronaviruses Semin. Virol. 7 1996 381-388
14. Marra M.A. Jones S.J. Astell C.R. Holt R.A. Brooks-Wilson A. Butterfield Y.S. Khattra J. Asano J.K. Barber S.A. Chan S.Y. Cloutier A. Coughlin S.M. Freeman D. Girn N. Griffith O.L. Leach S.R. Mayo M. McDonald H. Montgomery S.B. Pandoh P.K. Petrescu A.S. Robertson A.G. Schein J.E. Siddiqui A. Smailus D.E. Stott J.M. Yang G.S. Plummer F. Andonov A. Artsob H. Bastien N. Bernard K. Booth T.F. Bowness D. Czub M. Drebot M. Fernando L. Flick R. Garbutt M. Gray M. Grolla A. Jones S. Feldmann H. Meyers A. Kabani A. Li Y. Normand S. Stroher U. Tipples G.A. Tyler S. Vogrig R. Ward D. Watson B. Brunham R.C. Krajden M. Petric M. Skowronski D.M. Upton C. Roper R.L. The Genome sequence of the SARS-associated coronavirus Science 300 2003 1399-1404
15. Mau B. Newton M.A. Larget B. Bayesian phylogenetic inference via Markov chain Monte Carlo methods Biometrics 55 1999 1-12
16. Morris A. Marsden M. Halcrow K. Hughes E.S. Brettle R.P. Bell J.E. Simmonds P. Mosaic structure of the human immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: evidence for frequent in vivo recombination events in the evolution of regional populations J. Virol. 73 1999 8720-8731
17. Murphy W.J. Eizirik E. O'Brien S.J. Madsen O. Scally M. Douady C.J. Teeling E. Ryder O.A. Stanhope M.J. de Jong W.W. Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2001 2348-2351
18. Rest J.S. Mindell D.P. Retroids in archaea: phylogeny and lateral origins Mol. Biol. E 20 2003 1134-1142
19. Ronquist F. 2000 TreeFitter. Ver. 1.0. Software avialable via http://www.ebc.uu.se/systzoo/research/treefitter/treefitter.html. Uppsala University, Uppsala, Sweden.
20. Ronquist F. Liljeblad J. Evolution of the gall wasp-host plant association Evolution 55 2001 2503-2522
21. Rota P.A. Oberste M.S. Monroe S.S. Nix W.A. Campagnoli R. Icenogle J.P. Penaranda S. Bankamp B. Maher K. Chen M.H. Tong S. Tamin A. Lowe L. Frace M. DeRisi J.L. Chen Q. Wang D. Erdman D.D. Peret T.C. Burns C. Ksiazek T.G. Rollin P.E. Sanchez A. Liffick S. Holloway B. Limor J. McCaustland K. Olsen-Rasmussen M. Fouchier R. Gunther S. Osterhaus A.D. Drosten C. Pallansch M.A. Anderson L.J. Bellini W.J. Characterization of a novel coronavirus associated with severe acute respiratory syndrome Science 300 2003 1394-1399
22. Salminen M.O. Carr J.K. Burke D.S. McCutchan F.E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning AIDS Res. Hum. Retroviruses 11 1995 1423-1425
23. Shimodaira H. An approximately unbiased test of phylogenetic tree selection Syst. Biol. 51 2002 492-508
24. Shimodaira H. Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection Bioinformatics 17 2001 1246-1247
25. Siddell S.G. 1995 The Coronaviridae: an introduction. In: Siddell, S.G. (Ed.), The Coronaviridae: An Introduction. Plenum Press, New York, NY, pp. 1-10.
26. Sturman L.S. Holmes K.V. The molecular biology of coronaviruses Adv. Virus Res. 28 1983 35-112
27. Wang L. Junker D. Collisson E.W. Evidence of natural recombination with the S1 gene of infectious-bronchitis virus Virology 192 1993 710-716
28. Yang Z.H. PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci. 13 1997 555-556
29. Yang Z.H. Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method Mol. Biol. E 14 1997 717-724