Characterizing genetic and antigenic divergence from vaccine strain of influenza A and B viruses circulating in Thailand, 2017\u20132020

Nungruthai Suntronwong,Sumeth Korkong,Sompong Vongpunsawad,Preeyaporn Vichaiwattana,Thanunrat Thongmee,Sirapa Klinfueng,Yong Poovorawan

doi:10.1038/s41598-020-80895-w

Abstract

We monitored the circulating strains and genetic variation among seasonal influenza A and B viruses in Thailand between July 2017 and March 2020. The hemagglutinin gene was amplified and sequenced. We identified amino acid (AA) changes and computed antigenic relatedness using the Pepitope model. Phylogenetic analyses revealed multiple clades/subclades of influenza A(H1N1)pdm09 and A(H3N2) were circulating simultaneously and evolved away from their vaccine strain, but not the influenza B virus. The predominant circulating strains of A(H1N1)pdm09 belonged to 6B.1A1 (2017–2018) and 6B.1A5 (2019–2020) with additional AA substitutions. Clade 3C.2a1b and 3C.2a2 viruses co-circulated in A(H3N2) and clade 3C.3a virus was found in 2020. The B/Victoria-like lineage predominated since 2019 with an additional three AA deletions. Antigenic drift was dominantly facilitated at epitopes Sa and Sb of A(H1N1)pdm09, epitopes A, B, D and E of A(H3N2), and the 120 loop and 190 helix of influenza B virus. Moderate computed antigenic relatedness was observed in A(H1N1)pdm09. The computed antigenic relatedness of A(H3N2) indicated a significant decline in 2019 (9.17%) and 2020 (− 18.94%) whereas the circulating influenza B virus was antigenically similar (94.81%) with its vaccine strain. Our findings offer insights into the genetic divergence from vaccine strains, which could aid vaccine updating.

Highlights

Influenza A and B virus infection remains a common cause of respiratory disease worldwide[1]
20.90% (3654/17,480) of the nasopharyngeal swabs from influenza-like illness (ILI) patients tested positive for influenza virus, of which 74.2% (2711/3654) were influenza A virus and 25.8% (943/3654) were influenza B virus
We found that T185I, D187A, and Q189E mapped to the Sb antigenic site and overlapped the receptor-binding sites (RBSs), while S74R is on epitope Cb

Summary

Introduction

Influenza A and B virus infection remains a common cause of respiratory disease worldwide[1]. Accumulation of mutations in the HA protein, on the antigenic sites, RBSs and the surrounding region, has enabled the continuous evolution and the emergence of new influenza virus s trains[12,14,15], which escape the existing neutralizing antibodies[16]. The influenza virus strains to be included in the annual vaccine composition are carefully evaluated each y ear[8,17]. The vaccine composition for the southern hemisphere is determined many months before the actual influenza season begins in order to allow time for production and distribution[21,22]. Periodic monitoring of the influenza virus strains circulating in the region is important for antigenic characterization and improved vaccine design. Deduced amino acid changes were mapped on the HA three-dimensional structures, and the computed antigenic relatedness was analyzed for each influenza (sub)types

Methods

Results

Conclusion