Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons

Abstract

In 2009, Influenza A(H1N1)pdm09 caused the first influenza pandemic of the 21st century with high mortality rates of about 284 500 deaths. This virus, however, continues to circulate as a seasonal influenza virus and to cause illness and deaths worldwide. In this study, we describe the genetic diversity of A(H1N1)pdm09 viruses collected between 2014 and 2016 in Cameroon. Three gene segments (HA, NA and M) of Cameroon strains were studied. The phylogenetic tree of the coding nucleotide sequences was generated by MEGA version 6.0 using a Maximum Likelihood method. The NA and M protein coding sequences were analyzed for the reported genetic markers of resistance against neuraminidase inhibitors and adamantanes, while predicted vaccine efficacy was estimated using the Pepitope method. Overall 39 strains were obtained. Phylogenetic analysis of the HA gene of influenza A(H1N1)pdm09 showed that Cameroon strains belonged to two major clades. The 2014 Cameroon sequences belonged to clade 6C while all sequences collected between 2015 and 2016 belonged to clade 6B. Majority of the samples had some mutations in the NA gene notably: I117M, N248D, and N369K while the amantadine-resistant M mutant, S31N, was found to be absent only in the two sequences collected in 2014. Overall, A/California/07/2009 vaccine strain showed a predicted vaccine efficacy of 24.55% to 35.77% against Cameroon A(H1N1)pdm09 strains circulating between 2014 and 2016. Our findings confirms the fast evolution of A(H1N1)pdm09 since its first introduction and highlights on the importance of influenza vaccine in reducing the burden caused by influenza in the community.

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

“…The influenza A (H1N1) pdm09 virus emerged in North America in March 2009 and rapidly spread worldwide causing the first influenza pandemic of the 21 st Century [1][2][3][4]. 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]. Influenza virus hemagglutinin (HA) protein is the prime target of host's neutralizing antibodies [12][13][14][15].…”

“…Since 2010 the World Health Organization (WHO) recommended using A/California/7/2009 as the vaccine component for A (H1N1) pdm09 virus in Northern and Southern hemispheres [2,21]. This was later replaced in 2017 with A/Michigan/45/2015-like virus due to emergence of antigenic drift variants [2,15,24].…”

“…Since 2010 the World Health Organization (WHO) recommended using A/California/7/2009 as the vaccine component for A (H1N1) pdm09 virus in Northern and Southern hemispheres [2,21]. This was later replaced in 2017 with A/Michigan/45/2015-like virus due to emergence of antigenic drift variants [2,15,24]. The annually formulated influenza vaccine comprises HA antigens from A (H3N2), A (H1N1) pdm09 and one lineage of B (trivalent vaccine) or both lineages (quadrivalent vaccine) as predicted from circulating strains in the preceding seasons [16,25].…”

“…The annually formulated influenza vaccine comprises HA antigens from A (H3N2), A (H1N1) pdm09 and one lineage of B (trivalent vaccine) or both lineages (quadrivalent vaccine) as predicted from circulating strains in the preceding seasons [16,25]. The effectiveness of influenza vaccines fluctuate yearly in part due to genetic evolution of the virus leading to antigenic distance between the vaccine strain and circulating viruses [2,16,20,21]. Different methods including hemagglutination inhibition (HAI) assay and P epitope model may be used to estimate antigenic distance amongst influenza viruses and thus evaluate vaccine efficacy [26,27].…”