title: Mutation analysis of 20 SARS virus genome sequences: evidence for negative selection in replicase ORF1b and spike gene.
abstract: OBJECTIVE
  Recently, more SARS-CoV virus genome sequences are released to the GenBank database. The aim of this study is to reveal the evolution forces of SARS-CoV virus by analyzing the nucleotide mutations in these sequences.
  
  
  METHODS
  We obtained 20 SARS-CoV virus genome sequences from NCBI database, and calculated the ratio of non-synonymous nucleotide substitution per non-synonymous site (Ka) and synonymous nucleotide substitution per synonymous site (Ks) for SARS-CoV virus genes.
  
  
  RESULTS
  The Ka/Ks ratios for replicase polyprotein ORF1a, ORF1b, and spike protein gene are 1.09 (P=0.6501), 0.38 (P=0.0074), 0.65 (P=0.0685) respectively.
  
  
  CONCLUSIONS
  SARS-CoV virus replicase polyprotein ORF1b is undergoing negative selection; negative selection force is also probably operating on spike protein gene. These results provide basis for future developing a new drug and vaccine against SARS.
authors.affiliation: Health Science Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Second Medical University, Shanghai 200025, China.
authors.forename: Lan-Dian
authors.initials: LD
authors.lastname: Hu
authors.forename: Guang-Yong
authors.initials: GY
authors.lastname: Zheng
authors.forename: Hai-Song
authors.initials: HS
authors.lastname: Jiang
authors.forename: Yu
authors.initials: Y
authors.lastname: Xia
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xiang-Yin
authors.initials: XY
authors.lastname: Kong
mesh_terms: D001483:Base Sequence; D000086862:Coronavirus M Proteins; D004279:DNA, Viral / Q000032:analysis; D004259:DNA-Directed DNA Polymerase / Q000235:genetics*; D016679:Genome, Viral; D008562:Membrane Glycoproteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*; D016415:Sequence Alignment; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins / Q000235:genetics*; D014763:Viral Matrix Proteins / Q000235:genetics
chemical_list: D000086862:Coronavirus M Proteins; D004279:DNA, Viral; C000706237:M protein, SARS-CoV; D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; D014763:Viral Matrix Proteins; C023140:DNA replicase; D004259:DNA-Directed DNA Polymerase