title: Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus.
abstract: BACKGROUND
  SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper.
  
  
  METHODS
  Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods.
  
  
  RESULTS
  There were 188 point mutations in the 33 virus full genomes with the counts of mutation mounting to 297. Further analysis was carried out among 36 of 188 loci with more than two times of mutation. All the 36 mutation loci occurred in coding sequences and 22 loci were non-synonymous. The gene mutation rates of replicase 1AB, S2 domain of spike glycoprotein and nucleocapsid protein were lower (0.079% - 0.103%). There were 4 mutation loci in S1 domain of spike glycoprotein. The gene mutation rate of ORF10 was the highest (3.333%) with 4 mutation loci in this small domain (120 bp) and 3 of 4 loci related to deletion mutation. By bioinformatics processing and analysis, the nucleotides at 7 loci of genome (T:T:A:G:T:C:T/C:G:G:A:C:T:C) can classify SARS-CoV into two types. Therefore a novel definition is put forward that according to these 7 loci of mutation, 40 strains of SARS-CoV in GenBank can be grouped into two genotypes, T:T:A:G:T:C:T and C:G:G:A:C:T:C, and named as SARS-CoV Yexin genotype and Xiaohong genotype. The two genotypes can be further divided into some sub-genotypes. These genotypes can also be approved by phylogenetic tree of three levels of 44 loci of mutation, spike glycoprotein gene and complete genome sequence. Compared to various strains among SARS-CoV Yexin genotype and Xiaohong genotype, GD01 strain of Yexin genotype is more closely related to SARS-CoV like-virus from animals.
  
  
  CONCLUSIONS
  The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.
authors.affiliation: Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China. wzg188@sina.com.cn
authors.forename: Zhi-gang
authors.initials: ZG
authors.lastname: Wang
authors.forename: Lan-juan
authors.initials: LJ
authors.lastname: Li
authors.forename: Yun
authors.initials: Y
authors.lastname: Luo
authors.forename: Jun-yan
authors.initials: JY
authors.lastname: Zhang
authors.forename: Min-ya
authors.initials: MY
authors.lastname: Wang
authors.forename: Su-yun
authors.initials: SY
authors.lastname: Cheng
authors.forename: Yan-jun
authors.initials: YJ
authors.lastname: Zhang
authors.forename: Xiao-meng
authors.initials: XM
authors.lastname: Wang
authors.forename: Yi-yu
authors.initials: YY
authors.lastname: Lu
authors.forename: Nan-ping
authors.initials: NP
authors.lastname: Wu
authors.forename: Ling-ling
authors.initials: LL
authors.lastname: Mei
authors.forename: Zan-xin
authors.initials: ZX
authors.lastname: Wang
mesh_terms: D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D010802:Phylogeny; D017354:Point Mutation; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*