Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Gachara, George; Samuel, Shani; Otieno, Michael F.; Magana, Japheth; Opot, Benjamin; Bulimo, Wallace

doi:10.1016/j.meegid.2016.02.029

Cited by 17 publications

(34 citation statements)

References 25 publications

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“… Substitution rates are given as substitutions per nucleotide site per year (s/s/y). For the major groups ( dsDNA : double-stranded DNA viruses—BKV [ 5 , 7 , 28 ] (time span of sequences (TSS) of 29 years (y), 25 y, and 32 y, respectively), JC polyomavirus [ 27 , 31 ] (TSS 33 y and 13 y, respectively), herpes simplex virus 1 [ 32 , 33 ] (TSS not available and 21 y, respectively), human papillomavirus 18 [ 34 ] (TSS not available), monkeypox virus [ 35 ] (TSS 7 y), variola virus [ 5 ] (TSS 31 y), varicella zoster virus [ 5 ] (TSS 37 y); ssDNA : single-stranded DNA viruses—African cassava mosaic virus [ 25 ] (TSS 5 y), banana bunchy top virus [ 36 ] (TSS 2 months), human bocavirus [ 37 ] (TSS 1 y), human parvovirus B19 [ 38 , 39 ] (TSS 14 y and 28 y, respectively), porcine circovirus 2 [ 40 ] (TSS 27 y), tomato yellow leaf curl virus [ 41 ] (TSS 29 y); RT : retroviruses—avian hepatitis B virus [ 42 ] (TSS 22 y), human hepatitis B virus [ 42 – 44 ] (TSS 22 y, 25 y and 35 y, respectively); human immunodeficiency virus 1 [ 45 ] (TSS 2 y), primate T-cell lymphotropic virus [ 45 ] (TSS 2 y); dsRNA : double-stranded RNA viruses—bluetongue virus [ 46 ] (TSS 48 y), human rotavirus [ 47 ] (TSS 16 y), homalodisca vitripennis virus [ 48 ] (TSS 2 y); ss(-)RNA : single-stranded RNA viruses with negative polarity–Ebola virus [ 49 ] (TSS 4 months), fever, thrombocytopenia and leukocytopenia syndrome virus [ 50 ] (TSS 4 y), influenza A virus [ 51 , 52 ] (TSS 28 y and 1 y, respectively), hepatitis delta virus [ 53 ] (TSS 3 y), human respiratory syncytial virus [ 54 ] (TSS 10 y), rabies virus [ 55 ] (TSS 30 y...…”

Section: Resultsmentioning

confidence: 99%

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

et al. 2018

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Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus.

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Section: Resultsmentioning

confidence: 99%

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

et al. 2018

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“…The virus PLOS ONE | https://doi.org/10.1371/journal.pone.0228029 February 11, 2020 1 / 14 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 genome comprised a rare mixture of gene segments from swine, avian and human influenza viruses [5][6][7][8]. The A (H1N1) pdm09 virus was first detected in Kenya on June 2009 [9,10]. Presently, A (H1N1) pdm09 has become endemic in humans, co-circulating with A/H3N2 and B as seasonal influenza viruses [1,2,5,11].…”

Section: Introductionmentioning

confidence: 99%

Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene

et al. 2020

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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.

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“…Genomic analysis of virus sequence data from Kenya during the pandemic in 2009 reported the introduction of clade 2 and clade 7 viruses in Kenya, although clade 2 viruses did not circulate beyond the introductory foci while clade 7 viruses disseminated countrywide [51]. Here, through our detailed genomic analysis, we extend these earlier observations to show that clade 7 and clade 6 viruses were introduced into Kenya during the pandemic, disseminated countrywide, and persisted across multiple epidemics in multiple locations as local transmission clusters.…”

Section: Discussionmentioning

confidence: 99%

Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018

Owuor

Laurent

Kikwai

et al. 2021

Preprint

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Background: The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data is lacking. Methods: We isolated, sequenced, and analyzed 383 influenza A(H1N1)pdm09 viral genomes isolated from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. Results: The transmission dynamics of influenza A(H1N1)pdm09 virus in Kenya was characterized by: (i) multiple virus introductions into Kenya over the study period, although these were remarkably few, with only a few of those introductions instigating seasonal epidemics that then established local transmission clusters; (ii) persistence of transmission clusters over several epidemic seasons across the country; (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres; (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-11 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-17; and (v) virus migration from multiple geographical regions to multiple geographical destinations in Kenya. Conclusion: Considerable influenza virus diversity circulates within Africa, as demonstrated in this report, including virus lineages that are unique to the region, which may be capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.

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Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Cited by 17 publications

References 25 publications

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene

Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018

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