Genetic Characterization of Circulating 2015 A(H1N1)pdm09 Influenza Viruses from Eastern India

Abstract

In 2015, the swine derived A(H1N1)pdm09 pandemic strain outbreak became widespread throughout the different states of India. The reported cases and deaths in 2015 surpassed the previous years with more than 39000 laboratory confirmed cases and a death toll of more than 2500 people. There are relatively limited complete genetic sequences available for this virus from Asian countries. In this study, we describe the full genome analysis of influenza 2015 A(H1N1)pdm09 viruses isolated from West Bengal between January through December 2015. The phylogenetic analysis of the haemagglutinin sequence revealed clustering with globally circulating strains of genogroup 6B. This was further confirmed by the constructed concatenated tree using all eight complete gene segments of Kolkata A(H1N1)pdm09 isolates with the other strains from different timeline and lineages. A study from Massachusetts Institute of Technology (MIT) in 2015 reported novel mutations T200A and D225N in haemagglutinin gene of a 2014 Indian strain (A/India/6427/2014). However, in all the pandemic strains of 2014-2015 reported from India, so far including A(H1N1)pdm09 strains from Kolkata, D225N mutation was not observed, though the T200A mutation was found to be conserved. Neuraminidase gene of the analyzed strains did not show any oseltamivir resistant mutation H275Y suggesting continuation of Tamiflu® as drug of choice. The amino acid sequences of the all gene segments from 2015 A(H1N1)pdm09 isolates identified several new mutations compared to the 2009 A(H1N1)pdm09 strains, which may have contributed towards enhanced virulence, compared to 2009 A(H1N1)pdm09 strains.

Fig 1. Phylogenetic tree of concatenated whole genomes of 2015 A(H1N1)pdm09 isolates of Kolkata, India and representative global isolates from different clades.

The strains characterized in this study are designated with purple circle. The global influenza A A(H1N1)pdm09 virus clades are indicated in different colors.

Fig 2. Phylogenetic analysis of the Hemagglutinin (HA) gene of 2015 A(H1N1)pdm09 strains from Kolkata, India (designated with black triangle).

The tree was constructed with globally distributed A(H1N1)pdm09 HA amino acid sequences representing all genogroups from different timeline and lineages. Amino acid substitutions are depicted on the major branches at the nodes.

Fig 3

Mutations in the HA (A), NA (B) and M (C) gene segments of 2015 A(H1N1)pdm09 isolates from Kolkata, India with respect to A/California/04/2009 and other circulating viruses. Identical residues to A/California/04/2009 strain are indicated by dots.

Fig 4

Three-dimensional quaternary structure of HA (A) and NA (B) proteins of 2015 A(H1N1)pdm09 strains from this study identifying mutations compared to A/California/04/2009 strain. The three mutations at the antigenic epitopes within the receptor-binding pocket of HA protein were indicated. Probable binding position of oseltamivir in the NA protein of 2015 A(H1N1)pdm09 strain is shown in purple colour. The mutations are indicated in red and the amino acids responsible for oseltamivir binding are shown in black.