Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene
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Date
2020
Authors
Opanda, Silvanos
Bulimo, Wallace
Gachara, George
Ekuttan, Christopher
Amukoye, Evans
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
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. Hemagglutinationinhibition
(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.
Description
https://doi.org/10.1371/journal.pone.0228029
Keywords
Citation
PLOS ONE, https://doi.org/10.1371/journal.pone.0228029; February 11, 2020