Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea

Abstract

Seasonal influenza is caused by two influenza A subtype (H1N1 and H3N2) and two influenza B lineage (Victoria and Yamagata) viruses. Of these antigenically distinct viruses, the H3N2 virus was consistently detected in substantial proportions in Korea during the 2010/11-2013/14 seasons when compared to the other viruses and appeared responsible for the influenza-like illness rate peak during the first half of the 2011/12 season. To further scrutinize possible causes for this, we investigated the evolutionary and serological relationships between the vaccine and Korean H3N2 strains during the 2011/12 season for the main antigenic determinants of influenza viruses, the hemagglutinin (HA) and neuraminidase (NA) genes. In the 2011/12 season, when the number of H3N2 cases peaked, the majority of the Korean strains did not belong to the HA clade of A/Perth/16/2009 vaccine, and no Korean strains were of this lineage in the NA segment. In a serological assay, post-vaccinated human sera exhibited much reduced hemagglutination inhibition antibody titers against the non-vaccine clade Korean H3N2 strains. Moreover, Korean strains harbored several amino acid differences in the HA antigenic sites and in the NA with respect to vaccine lineages during this season. Of these, the HA antigenic site C residues 45 and 261 and the NA residue 81 appeared to be the signatures of positive selection. In subsequent seasons, when H3N2 cases were lower, the HA and NA genes of vaccine and Korean strains were more phylogenetically related to each other. Combined, our results provide indirect support for using phylogenetic clustering patterns of the HA and possibly also the NA genes in the selection of vaccine viruses and the assessment of vaccine effectiveness.

Increased genetic variation of A(H3N2) virus from influenza surveillance at the end of the 2016/17 season for Shanghai port

“…The pepitope model was used to quantify antigenic distance between the circulating strains and the corresponding vaccine strains. In several previous studies, the results of the the pepitope model showed a vaccine mismatch of A(H3N2) in the 2014/15 and 2015/16 seasons, which was consistent with the particular situation at that time 40,41 . Since 2016, the component of seasonal in uenza vaccines for the southern hemisphere is A/Hong Kong/4801/2014 belonging to clade 3C.2a.…”

Co-circulation and persistence of multiple A/H3N2 influenza variants in China

“…Similarly, based on our phylogenetic analysis (Supplementary file 2) and two recent reports [21,22], we also determined the NA genotypes of these viruses (Table S1). In the 2014–2015 influenza season, the dominant genotype was 3C.3, which continued to circulate during our surveillance.…”

Genome-informed investigation of the molecular evolution and genetic reassortment of severe fever with thrombocytopenia syndrome virus

“…Our phylogenies of three gene segments uniformly depicted that endemic SFTSVs have mainly caused human infection within limited local areas. However, even with the genetic homogeneity of endemic SFTSVs by countries, we occasionally observed polyphyletic genealogy in the phylogenies likely depicting the long-distance spread of endemic SFTSVs among China, Japan, and South Korea [ 27 , 30 ], but not frequent as the phylogenies of influenza virus or SARS-CoV-2 with highly intensive international spread [ 45 , 46 ]. Chinese SFTSV genotype B was most prevalent on Zhoushan Island located in the East China Sea but also caused human infection in South Korea and Japan [ 27 ].…”