Characterization of mutations of Haemagglutinin (HA) and Neuraminidase (NA) genes of Influenza A H1N1pdm09 isolated during the 2018 outbreak in India

Abstract

Background: The influenza virus is a segmented RNA virus, has higher propensity to undergo mutations, which carry major implications, both clinically and epidemiologically. Mutations in HA and NA are of particular importance. Changes in the HA region are associated with increased virulence, antigenicity and host specificity as it is involved in receptor binding and membrane fusion. Hence is a major target for vaccine development. The NA gene is involved in virus release as well as drug susceptibility. These changes can trigger the emergence of new strains, which could lead to epidemics and pandemics. Therefore, it is important to monitor and characterize the mutations closely. Thus, this study was undertaken to understand the genetic variation in Influenza H1N1 pdm09 for the outbreak in 2018. Methods and materials: This study conducted in Regional Influenza Laboratory, Puducherry on the isolates positive for Influenza A pdm09 by real time RT PCR. Conventional PCR was done using the WHO primers. The PCR positive products were then subjected to Sanger sequencing in ABI3500. The sequences were then analysed on the MEGA X software and Flusurver software for detection of the mutations in HA and NA. Results: Phylogenetic analysis was performed for both HA and NA gene along with the clade-specific reference strains. All our isolates clustered along with the clade 6B.1. In HA region, of the 28 mutations documented, the most common mutation was R240Q (100%) followed by S181T, S200P and S91R. The mutation of N173K was detected for the 1st time globally in the antigenic site. Of the 12 mutations in the HA stem region, 4 new mutations documented – K71Q, V466L, R467T and Q529R. The most common mutations in NA observed were G77R, I188T, S200G/V, F74S/L and V81A. We documented 4 new mutations that could be associated with drug resistance – W179G, R225K, V267L and R293K. Conclusion: Continuous surveillance of Influenza virus is important to monitor the changes in the HA genes for providing recommendations for vaccine strain. Further, as the treatment options for influenza is limited, it makes it all the more important to have continuous surveillance to track the antiviral resistance.