Skip to main content
NCBI home page
Wiley - PMC COVID-19 Collection logoLink to Wiley - PMC COVID-19 Collection
. 2004 Sep 14;74(3):369–372. doi: 10.1002/jmv.20187

Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions

G Magiorkinis 1, E Magiorkinis 1, D Paraskevis 1,2, AM Vandamme 2, M Van Ranst 2, V Moulton 3, A Hatzakis 1,✉
PMCID: PMC7166499  PMID: 15368527

Abstract

The origin of the severe acute respiratory syndrome‐coronavirus (SARS‐CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS‐CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both. J. Med. Virol. 74:369–372, 2004. © 2004 Wiley‐Liss, Inc.

Keywords: SARS‐CoV, phylogenetic discordance, recombination, Bayesian scanning

REFERENCES

  1. Drosten C, Gunther S, Preiser W, van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RA, Berger A, Burguiere AM, Cinatl J, Eickmann M, Escriou N, Grywna K, Kramme S, Manuguerra JC, Muller S, Rickerts V, Sturmer M, Vieth S, Klenk HD, Osterhaus AD, Schmitz H, Doerr HW. 2003. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348: 1967–1976. [DOI] [PubMed] [Google Scholar]
  2. Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. 2003. Phylogeny of the SARS coronavirus. Science 302: 1504–1505. [DOI] [PubMed] [Google Scholar]
  3. Fu K, Baric RS. 1992. Evidence for variable rates of recombination in the MHV genome. Virology 189: 88–102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, Luo SW, Li PH, Zhang LJ, Guan YJ, Butt KM, Wong KL, Chan KW, Lim W, Shortridge KF, Yuen KY, Peiris JS, Poon LL. 2003. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 302: 276–278. [DOI] [PubMed] [Google Scholar]
  5. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755. [DOI] [PubMed] [Google Scholar]
  6. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348: 1953–1966. [DOI] [PubMed] [Google Scholar]
  7. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks‐Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, 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 GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. 2003. The genome sequence of the SARS‐associated coronavirus. Science 300: 1399–1404. [DOI] [PubMed] [Google Scholar]
  8. Muller T, Vingron M. 2000. Modeling amino acid replacement. J Comput Biol 7: 761–776. [DOI] [PubMed] [Google Scholar]
  9. Paraskevis D, Lemey P, Salemi M, Suchard M, Van der Peer Y, Vandamme A‐M. 2003. Analysis of the evolutionary relationships of HIV‐1 and SIVcpz sequences using Bayesian inference: Implications for the origin of HIV‐1. Mol Biol Evol 20: 1986–1996. [DOI] [PubMed] [Google Scholar]
  10. Poutanen SM, Low DE, Henry B, Finkelstein S, Rose D, Green K, Tellier R, Draker R, Adachi D, Ayers M, Chan AK, Skowronski DM, Salit I, Simor AE, Slutsky AS, Doyle PW, Krajden M, Petric M, Brunham RC, McGeer AJ. 2003. Identification of severe acute respiratory syndrome in Canada. N Engl J Med 348: 1995–2005. [DOI] [PubMed] [Google Scholar]
  11. Rest JS, Mindell DP. 2003. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host‐shifting. Infect Genet Evol 3: 219–225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen‐Rassmussen M, Fouchier R, Gunther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. 2003. Characterization of a novel Coronavirus associated with severe acute respiratory syndrome. Science 300: 1394–1399. [DOI] [PubMed] [Google Scholar]
  13. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE‐PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502–504. [DOI] [PubMed] [Google Scholar]
  14. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE. 2003. Unique and conserved features of genome and proteome of SARS‐coronavirus, an early split‐off from the coronavirus group 2 lineage. J Mol Biol 331: 991–1004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Stavrinides J, Guttman DS. 2004. Mosaic evolution of the severe acute respiratory syndrome coronavirus. J Virol 78: 76–82. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum‐likelihood approach. Mol Biol Evol 18: 691–699. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Medical Virology are provided here courtesy of Wiley

RESOURCES