Evidence in Kenya of Reassortment Between Seasonal Influenza A(H3N2) and Influenza A(H1N1)pdm09 to yield A(H3N2) Variants With the Matrix Gene Segment of A(H1N1)pdm09

Abstract

Background: Influenza viruses evolve rapidly and undergo frequent reassortment of different gene segments leadingto emergence of novel strains with new traits possessing pandemic potential.Objectives: To determine evidence of reassortment amongst A(H1N1)pdm09 and H3N2 co-circulating influenza virussubtypes and relate these to adamantine antiviral resistance.Methodology: Nasopharyngeal swabs in virus transport medium were collected from patients with influenza-likeillness. The presence of influenza was determined using real-time PCR followed by culture in MDCK cells.Haemagglutination inhibition was carried out to confirm the identity of the virus. Complete haemagglutinin (HA),matrix (M) and neuraminidase (NA) genes were sequenced and analyzed using a suite of bioinformatics tools.Results: Influenza A(H3N2) was detected in 32 out of 708 samples collected between October and December 2010.Analysis of the HA gene confirmed it to be of the H3 subtype. However, analysis of the matrix gene showed that 28 ofthe isolates had the M gene of influenza A(H3N2) viruses while 4 had the M gene of the A(H1N1)pdm09 viruses.Discussion: Our results show that four of the 32 influenza A(H3N2) viruses isolated had acquired the M gene segmentof the A(H1N1)pdm09 virus by reassortment. This has implications in their transmissibility as the M gene isimplicated in the increased transmissibility of the A(H1N1)pdm09 viruses.