Molecular Advances in Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV)

Chow, Ken Yan Ching; Hon, Chung Chau; Hui, Raymond Kin Hi; Wong, Raymond Tsz Yeung; Yip, Chi Wai; Zeng, Fanya; Leung, Frederick Chi Ching

Snijder et al (22 ) conducted an extensive phylogenetic analysis concerning the replicase gene of the SARS-CoV by using torovirus as an outgroup. These authors criticized the phylogram construction based on different SARS-CoV proteins as unconvincing, and suggested the possibility that the SARS-CoV can be clustered into an existing group. As the structural and other accessory genes can either be gained or lost throughout the evolutionary process and in view of their low level of conservation, the author decided to target the replicase gene to perform the phylogenetic analysis. For this reason, the phylogenetic relationship was reconstructed through a rooted tree. The construction of the phylogram was done with the fused replicase gene with manual adjustment and exclusion of poorly conserved region. The resulting tree reveals that the gene was mostly related to group 2 coronaviruses and was assigned as a subgroup 2b. The author further pointed out that the SARS-CoV contains homologues of domains that are unique for group 2 coronaviruses, in the region of nsp1 and nsp3 (PL2 PRO ), in addition to the differences in the sequence and arrangements of the 3 -located ORFs, and the lack of antigenic cross-reactivity do not contradict their conclusion, as such a phenomenon was also observed in group 1 coronaviruses.