Molecular characterization and evolutionary dynamics of influenza A(H1N1) strains isolated from 2015 to 2017 in North India

Sonakshi Srivastava; Radha Kanta Ratho; Mini P Singh; Subhabrata Sarkar; Binod K Pati

doi:10.18502/ijm.v16i2.15358

Sonakshi Srivastava Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
Radha Kanta Ratho Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
Mini P Singh Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
Subhabrata Sarkar Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
Binod K Pati Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India

DOI: https://doi.org/10.18502/ijm.v16i2.15358

Keywords: Influenza A virus; H1N1 subtype; Phylogeny; Heamagglutinins; Mutation; Genotype; India

Abstract

Background and Objectives: The influenza A(H1N1) virus is known for large outbreaks, epidemics and pandemics world- wide owing to its genome plasticity which evolves constantly. In the year 2015 and then in 2017, India witnessed an upsurge in cases.

Materials and Methods: The study was carried out in this period (2015-2017) with samples from 5 states across north India. The hemagglutinin 1 (HA1) and non-structural 1 (NS1) gene segments of the viral genome were characterised by phylogenetic analysis, selection pressure analysis, prediction of potential glycosylation sites and phylodynamic analysis of the study strains.

Results: The study strains belonged to genogroup 6B. A total of 12 mutations were observed, half of which were located on the key receptor binding region of the HA1 protein. Established virulence markers D222G, S183P were observed in 2017 samples. Acquisition of an extra glycosylation site was observed in few strains from 2017 and 2016. Selection pressure analysis found the average dN/dS (v) ratio of 0.2106 and few codon sites in particular showed significant evidence of being under negative selection.

Conclusion: The genogroup 6B continues to be the dominant circulating strain in Indian subcontinent region however the presence of pathogenic mutations in the 2017 strains from north India underlines the importance of continued molecular surveillance.