title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China.
authors.forename: Lanjuan
authors.initials: L
authors.lastname: Li
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Wang
authors.forename: Yiyu
authors.initials: Y
authors.lastname: Lu
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Bao
authors.forename: Suhong
authors.initials: S
authors.lastname: Chen
authors.forename: Nanping
authors.initials: N
authors.lastname: Wu
authors.forename: Suyun
authors.initials: S
authors.lastname: Cheng
authors.forename: Jingqing
authors.initials: J
authors.lastname: Weng
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Zhang
authors.forename: Juying
authors.initials: J
authors.lastname: Yan
authors.forename: Lingling
authors.initials: L
authors.lastname: Mei
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Wang
authors.forename: Hanping
authors.initials: H
authors.lastname: Zhu
authors.forename: Yingpu
authors.initials: Y
authors.lastname: Yu
authors.forename: Minli
authors.initials: M
authors.lastname: Zhang
authors.forename: Minhong
authors.initials: M
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Yao
authors.forename: Qunying
authors.initials: Q
authors.lastname: Lu
authors.forename: Pingping
authors.initials: P
authors.lastname: Yao
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.forename: Jianer
authors.initials: J
authors.lastname: Wo
authors.forename: Shengqi
authors.initials: S
authors.lastname: Wang
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
mesh_terms: D005838:Genotype; D006801:Humans; D008875:Middle Aged; D009154:Mutation; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*