Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015

Abstract

We characterized influenza A(H1N1)pdm09 isolates from large-scale outbreaks that occurred in Nepal and India in early 2015. Although no specific viral features, which may have caused the outbreaks, were identified, an S84N substitution in hemagglutinin was frequently observed. Chronological phylogenetic analysis revealed that these Nepalese and Indian viruses possessing the S84N substitution constitute potential ancestors of the novel genetic subclade 6B.1 virus that spread globally in the following (2015/16) influenza season. Thus, active surveillance of circulating influenza viruses in the Southern Asia region, including Nepal and India, would be beneficial for detecting novel variant viruses prior to their worldwide spread.

Keywords: India; Nepal; influenza A(H1N1)pdm09 virus; outbreak.

Figure 1

Phylogenetic analysis of the hemagglutinin gene of H1N1pdm strains. Nucleotide sequence data of the former representative H1N1pdm strains and recent 2014/15 season H1N1pdm isolates from around the world were randomly selected from the GISAID database and used as the references. The phylogenetic trees were constructed using the MEGA6 software with the neighbor‐joining method. Nepalese and Indian strains analyzed in this study are colored in blue and red, respectively. Open squares indicate that only genetic sequence data were available in this study because of virus isolation failure. Previously reported8 strain A/Fukuoka/SDC1/2015 is underlined. Amino acid substitutions relative to the A/California/07/2009 virus and high bootstrap values (>80) are shown to the left of the nodes. The scale bar indicates the nucleotide substitutions per site. The GISAID EpiFlu database accession numbers for the sequence data of each reference strain are shown

Figure 2

Phylogenetic relationships of the hemagglutinin (HA) genes of Nepalese and Indian isolates and H1N1pdm isolates since 2009. Nucleotide sequence data of H1N1pdm isolates from around the world were obtained from the GISAID database and aligned using MAFFT (available from http://www.ebi.ac.uk/mafft/). MODELTEST was run on the aligned sequences, and GTR+I+gamma4 was determined as the most appropriate evolutionary model for phylogenetic tree construction. The tree was constructed using RAxML v813 according to the GTR+I+gamma4 model. Global optimization of branch topology was performed on the tree with the best likelihood score from RAxML using Garli v0.951 with a run of 150 000 generations. Isolates possessing an S84N substitution in HA are colored in light blue. Isolates possessing S84, S84G, and a mixed population of amino acids are colored in orange, gray, and black, respectively