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Severe acute respiratory syndrome-associated coronavirus genotype and its characterization.

Abstract：

OBJECTIVE:To study the severe acute respiratory syndrome (SARS)-associated coronavirus genotype and its characteristics. METHODS:A SARS-associated coronavirus isolate named ZJ01 was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of ZJ01 consisted of 29,715 bp (GenBank accession: AY297028, version: gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done. RESULTS:By bioinformatics processing and analysis, the 5 loci nucleotides at ZJ01 genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C:G:C:C/T:T:T:T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C:G:A:C:C/T:T:G:T:T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the ZJ01 isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in mainland China. Phylogenetic analysis of the spike protein gene fragments of these SARS-associated coronavirus strains showed that the GZ01 isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of BJ01 and CUHK-W1 were more closely related to the GZ01 isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to Ile in the protein, respectively. CONCLUSION:Attention should be paid to whether these genotype and mutation patterns are related to the virus's biological activities,epidemic characteristics and host clinical symptoms.

journal_name

Chin Med J (Engl)

journal_title

Chinese medical journal

authors

Li L,Wang Z,Lu Y,Bao Q,Chen S,Wu N,Cheng S,Weng J,Zhang Y,Yan J,Mei L,Wang X,Zhu H,Yu Y,Zhang M,Li M,Yao J,Lu Q,Yao P,Bo X,Wo J,Wang S,Hu S

keywords:

subject

Has Abstract

pub_date

2003-09-01 00:00:00

pages

1288-92

issue

eissn

0366-6999

issn

2542-5641

journal_volume

116

pub_type

杂志文章

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Severe acute respiratory syndrome-associated coronavirus genotype and its characterization.