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. 2004 Mar;4(1):15-9.
doi: 10.1016/j.meegid.2003.10.001.

Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV

Michael J Stanhope  1 , James R Brown, Heather Amrine-Madsen
Affiliations

Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV

Michael J Stanhope et al. Infect Genet Evol. 2004 Mar.

Abstract

The origins and evolutionary history of the Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS-CoV) remain an issue of uncertainty and debate. Based on evolutionary analyses of coronavirus DNA sequences, encompassing an approximately 13kb stretch of the SARS-TOR2 genome, we provide evidence that SARS-CoV has a recombinant history with lineages of types I and III coronavirus. We identified a minimum of five recombinant regions ranging from 83 to 863bp in length and including the polymerase, nsp9, nsp10, and nsp14. Our results are consistent with a hypothesis of viral host jumping events, concomitant with the reassortment of bird and mammalian coronaviruses, a scenario analogous to earlier outbreaks of influenzae.

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Figures

Fig. 1
Fig. 1
Examples and summary of recombinational analyses. Sequence identifications are as follows: 229E (human): AF304460; PEDV, porcine epidemic diarrhea virus: AF353511; TGEV, porcine transmissible gastroenteritis virus: AJ271965; AIBV-LX4, Avian infectious bronchitis virus-LX4: AY223860; AIBV, Avian infectious bronchitis virus: M95169; SARS-TOR2: AY274119; MHV-ML10, Murine hepatitis virus-ML-10: AF208067; MHV, Murine hepatitis virus: M55148; MHV-2, Murine hepatitis virus strain 2: AF201929; BCov-Quebec, Bovine coronavirus Quebec: AF220295; BCov-LUN, Bovine coronavirus-LUN: AF391542. (a) the control topology with Bayesian (Huelsenbeck and Ronquist, 2001) posterior probabilities (1.0 for all nodes) and ML (Swofford, 2002) bootstrap values; branch lengths drawn proportional to the amount of sequence change. (b) a tree resulting from one of the PLATO detected anomalous zones, implicating a recombination event involving SARS-CoV and the group III lineage; ML bootstrap and Bayesian posterior probabilities are indicated for both recombination events involving SARS-CoV with the group III lineage, corresponding with the red numbers in d. (c) A tree resulting from a recombinational zone implicating genetic exchange involving SARS-CoV and the group I lineage; ML bootstrap and Bayesian posterior probabilities are indicated for all three recombination events involving SARS-CoV with the group I lineage, corresponding with the blue numbers in (d). (d) A schematic of the recombination and non-recombination events identified in the SARS-TOR2 genome between position 7349 and 20,969.
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