Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data

The patterns of spread of influenza A viruses in local populations in tropical and sub-tropical regions are unclear due to sparsity of representative spatiotemporal sequence data. We sequenced and analyzed 58 influenza A(H3N2) virus genomes sampled between December 2015 and December 2016 from nine health facilities within the Kilifi Health and Demographic Surveillance System (KHDSS), a predominantly rural region, covering approximately 891 km² along the Kenyan coastline. The genomes were compared with 1571 contemporaneous global sequences from 75 countries. We observed at least five independent introductions of A(H3N2) viruses into the region during the one-year period, with the importations originating from Africa, Europe, and North America. We also inferred 23 virus location transition events between the nine facilities included in the study. International virus imports into the study area were captured at the facilities of Chasimba, Matsangoni, Mtondia, and Mavueni, while all four exports from the region were captured from the Chasimba facility, all occurring to Africa destinations. A strong spatial clustering of virus strains at all locations was observed associated with local evolution. Our study shows that influenza A(H3N2) virus epidemics in local populations appear to be characterized by limited introductions followed by significant local spread and evolution. Knowledge of the viral lineages that circulate within specific populations in understudied tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses and to inform vaccination strategies within these populations.