Molecular evolution and multilocus sequence typing of 145 strains of SARS‐CoV

Abstract

In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventyfour of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into subgenotypes C1-C4 and T1-T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.

The human severe acute respiratory syndrome coronavirus (SARS-CoV) 8b protein is distinct from its counterpart in animal SARS-CoV and down-regulates the expression of the envelope protein in infected cells

“…Interestingly, the clustering of patients with different patterns of variations in ORF8 region was correlated with the different phases of the epidemic. These findings were subsequently verified by researchers who studied the SARS-CoV isolated in different countries (Chiu et al, 2005;Lan et al, 2005;Qin et al, 2003;Wang et al, 2004Wang et al, , 2005.…”

Evolution of genomes, host shifts and the geographic spread of SARS‐CoV and related coronaviruses

“…GD03T0013 is closely related to SARS‐CoV isolated from civets served in a restaurant in Guangzhou, China in late 2003 and early 2004. No epidemiological data link the GD03T0013 human case to exposure to laboratory isolates of SARS‐CoV (Wang et al., 2005).…”

Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong

“…Several studies have documented various SNVs in the SARS-CoV genome, with some even proposing them as the basis for a genotypic classification (Poon et al, 2005a,b;Ruan et al, 2003;Tsui et al, 2003;Wang et al, 2005;Yeh et al, 2004). In this study, the SNV G23220T that was found in all of the patients (56/56, 100%) has been reported elsewhere (Yeh et al, 2004), though the functional significance of this is presently uncertain.…”

“…The second, less frequently found SNV (C25114T) present in 17/56 (30.4%) of these S-gene sequences has also been found in four sequences from Guangdong (GUAN LC2, AY394999; GUAN LC3, AY395000; GUAN LC4, AY395001; GUAN LC5, AY395002, but not in GUAN LC1, AY394998), of which GUAN LC3 and GUAN LC5 have been previously reported by Wang et al (2005). The 17 CUHK S-gene sequences containing this polymorphism all occur in samples collected towards the end of the SARS outbreaks in Hong Kong (from 4 April to 31 May 2003).…”

“…Only bootstrap values > 70 are shown. Three distinct clusters can be seen, the sequences of which have been characterized and discussed elsewhere (CSMEC, 2004;Kan et al, 2005;Lan et al, 2005;Song et al, 2005;Wang et al, 2005;Yeh et al, 2004). All the CUHK S-gene sequence lie within cluster 3 'worldwide', together with other S-gene sequences from Hong Kong (CUHK-W1, AY278554; CUHK-AG01, AY345986; CUHK-AG02, AY345987; CUHK-AG03, AY345988; CUHK-Su10, AY282752; HKU-39849, AY278491).…”