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Severe acute respiratory syndrome-associated coronavirus genotype and its characterization



Severe acute respiratory syndrome-associated coronavirus genotype and its characterization



Chinese Medical Journal 116(9): 1288-1292



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 muta tions. 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.

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Accession: 012550763

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PMID: 14527350


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