Objective To explore the complete genome evolution and molecular characteristics of influenza B virus Victoria lineage in Fujian province from 2019 to 2022.

Methods A total of 48 strains of influenza B Victoria lineage isolated in Fujian province from 2019 to 2022 were selected, and software CLC Genomics Workbench 11.0 was used for segment joining after whole genome amplification sequencing. The phylogenetic and molecular characteristics of each segment were analyzed by using MEGA 5.0.

Results The hemagglutinin (HA) gene of influenza B virus Victoria lineage isolated in Fujian during 2019−2022 had multiple antigen determinant (120 loop, 150 loop, 160 loop, 190 helix) and receptor binding site variants compared with vaccine strain B/Austria/1359417/2021. The number of HA glycosylation sites decreased over time. Neuraminidase gene resistance sites and enzyme active sites were conserved. The phylogenetic tree branches and evolutionary distances of polymerase acidic protein, polymerase basic protein 1, polymerase basic protein 2, nucleoprotein, nonstructural protein, matrix protein genes were more conservative than those of HA genes, but each had different characteristics.

Conclusion There was genetic diversity in different gene segments of influenza B virus Victoria lineage circulating in Fujian from 2019 to 2022, which could provide reference for vaccine or drug development.