Epidemiological dynamics of Influenza B virus across multiple seasons in Kenya and Uganda inferred from sequence data, 2010-2021

Influenza B virus (IBV) genomic surveillance occurs unevenly across the globe, obscuring its epidemiology. We analysed 83 near complete IBV genomes collected between 2010 and 2022 in Kenya and Uganda. Alternating IBV lineage predominance and clade turnover was observed consistent with global patterns. No B/Yamagata strains were detected at the study sites after 2019. Multiple B/Victoria clade/subclades (V1A, V1A.3, V1A.3a, V1A.3a.2) and B/Yamagata clades (Y2 and Y3) were identified with no inter-lineage reassortants observed. Over time, the clades/subclades appeared to diversify through the accumulation of amino acid changes along the hemagglutinin (HA) segment backbone, especially within the known antigenic sites. Local outbreak strains appeared to be introduced from both within and outside Africa. The congruence of local and global strains in circulating lineages and amino acid changes suggests potentially similar effectiveness of vaccines recommended for the Northern and Southern Hemispheres in East Africa.