Identification of genetic and antigenic variation and evolution pattern among influenza a and b viruses in Thailand

Abstract

Seasonal influenza viruses commonly cause respiratory disease and have a considerable impact on public health threats which annually estimates 3 to 5 million cases of severe illness worldwide. The triggering of the seasonal influenza epidemic results from a complex interplay between viral, host and external factors such as climate. Although vaccination is an effective tool for influenza prevention and its complications, the composition of vaccine strain has been changed every year due to influenza constantly evolving. Here, we aim to examine the association between influenza activity and local climate factors, host immunity, genetic and antigenic variation and evolution pattern among influenza A and B viruses in Thailand. During 2010-18, we found 21.6% were tested positive for the influenza virus which typing as influenza A(H1N1)pdm09 (34.2%), A(H3N2) (46.0%), and influenza B virus (19.8%). There were two seasonal waves of increased influenza activity. Peak influenza A(H1N1)pdm09 and influenza B activity occurred in February and again in August, while influenza A(H3N2) viruses were primarily detected in August and September. The SARIMA model of all influenza and climate factors including temperature, relative humidity, and rainfall are the best performed to predict influenza activity. To gain insight into host immunity to influenza, we then study the elderly who are at high risk of infection. These findings showed the proportion of seropositivity (HI titers ≥40) to influenza A(H1N1)pdm09 (50%), A(H3N2) (66%) were higher than influenza B viruses such as B/Yamagata 2 (14%), B/Yamagata 3 (21%) and B/Victoria (25%). Additionally, only 5% of this population presented the cross-reactive antibodies to both the influenza A and B viruses, this suggests that a low proportion of individuals provided broadly protective antibodies. For the viral factors, we study the evolution of polymerase genes included PB1, PB2, and PA proteins that are considered as a further antiviral drug target. Mutations in the polymerase gene significantly affect viral replication, transmission, and virulence. We found the pattern of evolutionary dynamics of A(H3N2) and B/Victoria have considerably changed over time, while A(H1N1)pdm09 slightly stable and B/Yamagata was increasing in 2017. Our data reveal adaptive acquired mutations relatively occur as high genetic diversity in the polymerase gene and all PA gene has shown a higher evolution rate than PB2 and PB1, except A(H3N2). Furthermore, we then quantified the genetic and antigenic variation in the nucleotide of HA1 sequences and estimated predicted VE using the Pepitope model. Our data indicated that influenza A(H3N2) diverged from vaccine strain and formed 5 genetic groups in the 2016-2017 seasons. Such emergence of multiple subclades contributed to the declining predicted VE from 74% (2016) down to 48% (early 2017). During late 2017-2020, phylogeny revealed multiple clades/subclades of influenza A(H1N1)pdm09 (subclade: 6B.1A1 and 6B.1A5) and A(H3N2) (subclade: 3C.2a1b, 3C.2a2 and 3C.3a) were circulating simultaneously and evolved away from their vaccine strain. 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 predicted VE was observed in A(H1N1)pdm09. The predicted VE 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. Besides HA, the NA is also targeted for immune response and showed broadly protective but current seasonal vaccines poorly induce anti-NA antibodies. Our data suggest that extending the stalk domain of the NA with the 30 amino acid can induce significantly higher anti-NA IgG responses characterized by increased in vitro ADCC activity, while anti-HA IgG levels were unaffected. Moreover, this recombinant virus can show a protective effect in the mouse model. In conclusion, the ability to predict a seasonal pattern of influenza may enable better public health planning and underscores the importance of annual influenza vaccination prior to the rainy season. The host immune profile cloud also helps for the guidance of influenza vaccine policy. Our findings offer insights into the viral population dynamic of polymerase genes and the genetic and antigenic divergence from vaccine strains, which could aid antiviral drug development and vaccine updating. The extended NA stalk approach may assist in the efforts towards more effective influenza virus vaccines.