title: Replacement and positive evolution of subtype A and B respiratory syncytial virus G-protein genotypes from 1997-2012 in South Africa.
abstract: BACKGROUND
  Of the respiratory syncytial virus (RSV) genotypes previously described in South Africa during 1997-2002, only GA2 and GA5 persisted until 2006, with BA having replaced all previous RSV-B genotypes. This poses the question whether RSV-A is more stable than RSV-B and whether positive selection drives evolution of genotypes.
  
  
  METHODS
  RSV-positive specimens were randomly selected during 2009-2012, subtyped, sequenced, and compared to RSV recovered from specimens obtained during 1997-2001 and 2006-2009. Bayesian phylogenetic analysis was performed on the G-protein.
  
  
  RESULTS
  Phylogenetic analysis indicated that RSV-A genotype GA2 dissolved to form SAA2 (unique to South Africa), NA1 and NA2 (identified in Japan), and ON1 (identified in Canada and having a 72-bp insertion) and that GA5 drifted from 1999-2012 to form 3 subgenotypes (GA5 I-III). RSV-B genotypes all had the 60-bp insertion typical of BA genotypes but clustered into subgenotypes BA8-10. Positive selection was identified in the G-protein of both subtypes, but RSV-A's rate of evolution was slower than that of RSV-B, with the most recent common ancestors dating from 1945 and 1951, respectively. Seven new positively selected sites were identified in South African strains, 2 for RSV-A and 5 for RSV-B.
  
  
  CONCLUSIONS
  Positive selection drove both RSV-A and -B genotypes to evolve, resulting in replacement of all genotypes over the 15-year study period in South Africa.
authors.affiliation: Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS).
authors.forename: Marthi A
authors.initials: MA
authors.lastname: Pretorius
authors.forename: Stephanie
authors.initials: S
authors.lastname: van Niekerk
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Moyes
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002648:Child; D002675:Child, Preschool; D019143:Evolution, Molecular; D005260:Female; D005838:Genotype; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology* / Q000821:virology*; D018113:Respiratory Syncytial Virus, Human / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013019:South Africa / Q000453:epidemiology; D014760:Viral Fusion Proteins / Q000235:genetics*; D055815:Young Adult
chemical_list: C502275:G glycoprotein, Respiratory syncytial virus; D014760:Viral Fusion Proteins
keywords: evolutionary rate; genotypes; positive selection; respiratory syncytial virus