Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04)

Abstract

Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.

Fig. 1

Accumulated number of probable cases and deaths of SARS in Beijing, China, and the world. Data sources: http://www.moh.gov.cn/zhgl/yqfb/index.htm; http://www.who.int/csr/sars/country/en/.

Fig. 2

Distribution of the non-synonymous substitutions in the SARS-CoV genome from the known cases. The tall vertical bars represent the substitutions detected from the BJ Group and the low bars denote those from non-BJ Groups. The scale marks the nucleotide positions in reference to BJ01.

Fig. 3

Two-scale substitution rates of the SARS-CoV in the first and second round of the transmission of the BJ Group. The numbers above the lines that connect each isolate are nonsynonymous substitution counts believed as results of the first round and second round of the transmission. The numbers in the parentheses are synonymous substitution counts between the connected isolates.

Fig. 4

A rooted phylogenetic tree (GD01 as the postulated root) indicates the defined haplotypes and possible transmission path of the SARS-CoV based on the complete genome sequences of 17 SARS-CoV isolates. The neighbor-joining trees are generated by using the program Clustalw 1.81. The sources and abbreviations of the sequences are referred to Table 2.

Fig. 5A (all substitutions)

Fig. 5B (haplotypes)

Fig. 5C (non-synonymous)

Fig. 5D (synonymous)