Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.
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 seventy-four 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 sub-genotypes 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.
Wang
Zhi-Gang
ZG
Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China. wzg188@sina.com.cn
Zheng
Zhi-Hua
ZH
Shang
Lei
L
Li
Lan-Juan
LJ
Cong
Li-Ming
LM
Feng
Ming-Guang
MG
Luo
Yun
Y
Cheng
Su-Yun
SY
Zhang
Yan-Jun
YJ
Ru
Miao-Gui
MG
Wang
Zan-Xin
ZX
Bao
Qi-Yu
QY
D001483:Base Sequence; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA