Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic
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Date
2016
Authors
Gachara, George
Symekher, S.
Otieno, M.
Magana, J.
Opot, B.
Bulimo, W.
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier
Abstract
An influenza pandemic caused by a novel influenza virus A(H1N1)pdm09 spread worldwide in 2009 and is estimated
to have caused between 151,700 and 575,400 deaths globally.Whilewhole genome data on newvirus enables
a deeper insight in the pathogenesis, epidemiology, and drug sensitivities of the circulating viruses, there
are relatively limited complete genetic sequences available for this virus from African countries. We describe
herein the full genome analysis of influenza A(H1N1)pdm09 viruses isolated in Kenya between June 2009 and
August 2010. A total of 40 influenza A(H1N1)pdm09 viruses isolated during the pandemic were selected. The
segments from each isolate were amplified and directly sequenced. The resulting sequences of individual gene
segments were concatenated and used for subsequent analysis. These were used to infer phylogenetic relationships
and also to reconstruct the time of most recent ancestor, time of introduction into the country, rates of substitution
and to estimate a time-resolved phylogeny. The Kenyan complete genome sequences clustered with
globally distributed clade 2 and clade 7 sequences but local clade 2 viruses did not circulate beyond the introductory
foci while clade 7 viruses disseminated country wide. The time of the most recent common ancestor was estimated
between April and June 2009, and distinct clusters circulated during the pandemic. The complete
genome had an estimated rate of nucleotide substitution of 4.9 × 10−3 substitutions/site/year and greater diversity
in surface expressed proteins was observed. We show that two clades of influenza A(H1N1)pdm09 virus
were introduced into Kenya from the UK and the pandemic was sustained as a result of importations. Several
closely related but distinct clusters co-circulated locally during the peak pandemic phase but only one cluster
dominated in the late phase of the pandemic suggesting that it possessed greater adaptability
Description
Research Article
Keywords
Influenza A(H1N1)pdm09, Whole genome, Sequencing, Kenya
Citation
Infection, Genetics and Evolution 40 (2016) 98–103