Date of origin of the SARS coronavirus strains

We propose a mathematical model to estimate the evolution rate of the SARS coronavirus genome and the time of the last common ancestor of the sequenced SARS strains. Under some common assumptions and justifiable simplifications, a few simple equations incorporating the evolution rate (K) and time of the last common ancestor of the strains (T0) can be deduced. We then implemented the least square method to estimate K and T0 from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results.Based on 6 strains with accurate dates of host death, we estimated the time of the last common ancestor to be about August or September 2002, and the evolution rate to be about 0.16 base/day, that is, the SARS coronavirus would on average change a base every seven days. We validated our method by dividing the strains into two groups, which coincided with the results from comparative genomics.The applied method is simple to implement and avoid the difficulty and subjectivity of choosing the root of phylogenetic tree. Based on 6 strains with accurate date of host death, we estimated a time of the last common ancestor, which is coincident with epidemic investigations, and an evolution rate in the same range as that reported for the HIV-1 virus.A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world, affecting over 8,000 individuals in 32 countries[1,2]. In response to this outbreak, a global network of international collaborating laboratories was immediately sponsored and established by World Health Organization (WHO) to facilitate the identification of the causative agent of SARS. By now the putative pathogen of SARS has been identified, by experimental proof and by Koch's postulates, as a new coronavirus, a single positive-strand RNA virus [3-5]]. The whole genome of SARS coronavirus was first sequenced by the British Columbia Centre for Disease Control (CDC) in Canada