Abstract

Influenza A (H1N1) pdm09 virus emerged in North America in 2009 and has been established as a seasonal strain in humans. After an antigenic stasis of about six years, new antigenically distinct variants of the virus emerged globally in 2016 necessitating a change in the vaccine formulation for the first time in 2017. Herein, we analyzed thirty-eight HA sequences of influenza A (H1N1) pdm09 strains isolated in Kenya during 2015-2018 seasons, to evaluate their antigenic and molecular properties based on the HA1 sub-unit. Our analyses revealed that the A (H1N1) pdm09 strains that circulated in Kenya during this period belonged to genetic clade 6B, subclade 6B.1 and 6B.2. The Kenyan 2015 and 2016 isolates differed from the vaccine strain A/California/07/2009 at nine and fourteen antigenic sites in the HA1 respectively. Further, those isolated in 2017 and 2018 correspondingly varied from A/Michigan/45/2015 vaccine strain at three and fifteen antigenic sites. The predicted vaccine efficacy of A/California/07/2009 against Kenyan 2015/2016 was estimated to be 32.4% while A/Michigan/45/2015 showed estimated vaccine efficacies of 39.6% - 41.8% and 32.4% - 42.1% against Kenyan 2017 and 2018 strains, respectively. Hemagglutination-inhibition (HAI) assay using ferret post-infection reference antiserum showed that the titers for the Kenyan 2015/2016 isolates were 2-8-fold lower compared to the vaccine strain. Overall, our results suggest the A (H1N1) pdm09 viruses that circulated in Kenya during 2015/2016 influenza seasons were antigenic variants of the recommended vaccine strains, denoting sub-optimal vaccine efficacy. Additionally, data generated point to a swiftly evolving influenza A (H1N1) pdm09 virus in recent post pandemic era, underscoring the need for sustained surveillance coupled with molecular and antigenic analyses, to inform appropriate and timely influenza vaccine update.

Highlights

  • The influenza A (H1N1) pdm09 virus emerged in North America in March 2009 and rapidly spread worldwide causing the first influenza pandemic of the 21st Century [1,2,3,4]

  • Homology analysis based on HA1 showed that Kenyan 2015/2016 strains shared 97.6–98.4% and 93.3–97.2% sequence identities with the vaccine strain A/California/7/2009, whereas the 2017/2018 strains had 97.9–99.4% and 97.5–99% identities with A/Michigan/45/2015 vaccine virus (Table 1)

  • Phylogenetic analysis based on HA1 domain of hemagglutinin gene showed that all A (H1N1) pdm09 viruses circulating in Kenya during 2015/2018 belonged to genetic clade 6B; subclade 6B.2 (2015/2016 isolates) and 6B.1 (2017/2018 isolates) (Fig 1)

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Summary

Introduction

The influenza A (H1N1) pdm virus emerged in North America in March 2009 and rapidly spread worldwide causing the first influenza pandemic of the 21st Century [1,2,3,4]. Antigenic drift of Kenyan A (H1N1) pdm virus. ARK18942; MH316121, MG815810; MH356637 MH356647 and MK692755 - MK692776. Additional accession numbers in GISAID and GenBank databases of HA gene sequences of A/ H1N1 pdm reference strains included in the analysis are in the S1 Table

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