title: Evolutionary dynamics of 2009 pandemic influenza A virus subtype H1N1 in South Africa during 2009-2010.
abstract: BACKGROUND
  The 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) was first detected in June 2009 in South Africa and later resulted in extensive transmission throughout Africa. Established routine surveillance programs and collaboration between private and public sector laboratories allowed for comprehensive molecular epidemiological and antigenic investigation of the first and second waves of 2009-2010 pandemic influenza in South Africa.
  
  
  METHODS
  We used reverse-transcription polymerase chain reaction to screen for influenza virus in 9792 specimens recovered during 2009 and 6915 specimens recovered during 2010 from inpatients and outpatients with influenza-like illness or severe acute respiratory illness symptoms identified by surveillance programs. Influenza-positive specimens were subjected to genetic and antigenic characterization. Bayesian and maximum likelihood analyses of the hemagglutinin genes of 96 A(H1N1)pdm09 strains were used for molecular epidemiological investigations. Hemagglutination inhibition assays and sequencing of the PB2 and neuraminidase genes were used to investigate pathogenicity and resistance mutations.
  
  
  RESULTS
  The A(H1N1)pdm09 epidemic occurred as a second epidemic peak following seasonal influenza A virus subtype H3N2 cases in 2009 and in 2010. Progressive drift away from the A/California/7/2009 vaccine strain was observed at both the nucleotide and amino acid level, with 2010 strains clustering separate to 2009 strains. A few unique clusters of amino acid changes in severe cases were identified, but most strains were antigenically similar to the vaccine strain, and no resistance or known pathogenicity mutations were detected.
  
  
  CONCLUSIONS
  Despite limited drift observed over the 2 seasons in South Africa, circulating A(H1N1)pdm09 strains remained antigenically similar to strains identified in other northern and southern hemisphere countries from 2010 and 2011.
authors.affiliation: National Institute for Communicable Diseases Division, National Health Laboratory Service, Department of Medical Virology, University of Pretoria, Johannesburg, South Africa. marietjiev@nicd.ac.za
authors.forename: Marietjie
authors.initials: M
authors.lastname: Venter
authors.forename: Dhamari
authors.initials: D
authors.lastname: Naidoo
authors.forename: Marthi
authors.initials: M
authors.lastname: Pretorius
authors.forename: Amelia
authors.initials: A
authors.lastname: Buys
authors.forename: Johanna
authors.initials: J
authors.lastname: McAnerney
authors.forename: Lucille
authors.initials: L
authors.lastname: Blumberg
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
authors.forename: Cheryl
authors.initials: C
authors.lastname: Cohen
authors.forename: Barry
authors.initials: B
authors.lastname: Schoub
mesh_terms: D000956:Antigens, Viral / Q000032:analysis / Q000235:genetics / Q000276:immunology; D019143:Evolution, Molecular; D006385:Hemagglutination Inhibition Tests; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013019:South Africa / Q000453:epidemiology
chemical_list: D000956:Antigens, Viral; C543345:H1N1 virus hemagglutinin; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D012367:RNA, Viral