Severe acute respiratory syndrome-associated coronavirus genotype and its characterization

• Published in: Chinese medical journal Vol. 116; no. 9; pp. 1288 - 1292
• Main Author: 李兰娟 王志刚 卢亦愚 包其郁 陈苏红 吴南屏 程苏云 翁景清 张严峻 严菊英 梅玲玲 王晓萌 朱函坪 余迎朴 张敏丽 李敏红 姚军 陆群英 姚苹苹 伯晓晨 沃健尔 王升启 胡松年
• Format: Journal Article
• Language: English
• Published: China Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China%Hangzhou Genomics Institute/James D. Watson Genomics Science Institute, Zhejiang University, Hangzhou 310000, China%Infectious Disease Key Laboratory of Health Ministry, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China%Beijing Institute of Radiation Medicine, Academy of Military Medical Science, Beijing 100850, China 01-09-2003
• Subjects: Genotype; Humans; Middle Aged; Mutation; SARS Virus - genetics; 严重急性呼吸综合征; 冠状病毒; 基因型; 病原学; coronavirus,genotype; phylogeny; polymorphism; severe acute respiratory syndrome
• ISSN: 0366-6999; 2542-5641

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 Z J01 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 F1and F2 of the T genotype, the isolates of BJ01and CUHK-Wl 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 lie 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 svmotoms.