title: Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus.
abstract: BACKGROUND
  Despite annual co-circulation of different subtypes of seasonal influenza, co-infections between different viruses are rarely detected. These co-infections can result in the emergence of reassortant progeny.
  
  
  METHODS
  We document the detection of an influenza co-infection, between influenza A/H3N2 with A/H1N1pdm09 viruses, which occurred in a 3 year old male in Cambodia during April 2014. Both viruses were detected in the patient at relatively high viral loads (as determined by real-time RT-PCR CT values), which is unusual for influenza co-infections. As reassortment can occur between co-infected influenza A strains we isolated plaque purified clonal viral populations from the clinical material of the patient infected with A/H3N2 and A/H1N1pdm09.
  
  
  RESULTS
  Complete genome sequences were completed for 7 clonal viruses to determine if any reassorted viruses were generated during the influenza virus co-infection. Although most of the viral sequences were consistent with wild-type A/H3N2 or A/H1N1pdm09, one reassortant A/H3N2 virus was isolated which contained an A/H1N1pdm09 NS1 gene fragment. The reassortant virus was viable and able to infect cells, as judged by successful passage in MDCK cells, achieving a TCID50 of 10(4)/ml at passage number two. There is no evidence that the reassortant virus was transmitted further. The co-infection occurred during a period when co-circulation of A/H3N2 and A/H1N1pdm09 was detected in Cambodia.
  
  
  CONCLUSIONS
  It is unclear how often influenza co-infections occur, but laboratories should consider influenza co-infections during routine surveillance activities.
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia.
authors.forename: Sareth
authors.initials: S
authors.lastname: Rith
authors.affiliation: National Institute of Public Health, Phnom Penh, Cambodia.
authors.forename: Savuth
authors.initials: S
authors.lastname: Chin
authors.affiliation: National Institute of Public Health, Phnom Penh, Cambodia; Centers for Disease Control and Prevention, Cambodia Office, Phnom Penh, Cambodia.
authors.forename: Borann
authors.initials: B
authors.lastname: Sar
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia.
authors.forename: Phalla
authors.initials: P
authors.lastname: Y
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia.
authors.forename: Srey Viseth
authors.initials: SV
authors.lastname: Horm
authors.affiliation: Communicable Disease Department, Ministry of Health, Phnom Penh, Cambodia.
authors.forename: Sovann
authors.initials: S
authors.lastname: Ly
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia.
authors.forename: Philippe
authors.initials: P
authors.lastname: Buchy
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia.
authors.forename: Philippe
authors.initials: P
authors.lastname: Dussart
authors.affiliation: Institut Pasteur in Cambodia, Institut Pasteur International Network, Phnom Penh, Cambodia. Electronic address: phorwood@pasteur-kh.org.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Horwood
mesh_terms: D002160:Cambodia; D002675:Child, Preschool; D060085:Coinfection / Q000821:virology*; D016679:Genome, Viral; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics; D007251:Influenza, Human / Q000821:virology*; D008297:Male; D010802:Phylogeny; D016865:Reassortant Viruses / Q000235:genetics / Q000302:isolation & purification*
keywords: A/H1N1pdm09; A/H3N2; Co-infection; Influenza; Reassortant; Reassortment; Seasonal