Genetic evolution of influenza A H9N2 viruses isolated from domestic poultry in Uganda

Abstract

A(H9N2) avian influenza A viruses were first detected in Uganda in 2017 and have since established themselves in live bird markets. The aim of this study was to establish the subsequent genetic evolution of H9N2 viruses in Uganda by whole genome sequencing and subsequent analysis of phylogenetic trees, molecular clock rates and identification of sequence features. Results from eighty H9N2 viruses that were isolated and sequenced suggested that the virus was first introduced into Uganda in 2014 from ancestors in the Middle East. There has since been an increase in nucleotide substitutions and reassortments among the viruses within and between the live bird markets, leading to variations in phylogeny of the different segments although overall diversity remained low. The isolates had several mutations such as HA-Q226L, NS-I106M that enable mammalian host adaptation, NP-M105V, PB1-D3V & M1- T215A for increased virulence/pathogenicity and replication, and PA-E199D, NS-P42S, & M2-S31N that promote drug resistance. H9N2 viruses have established an endemic situation in live bird markets because of poor biosecurity practices and pose a zoonotic threat. It is necessary to have regular surveillance and promote biosecurity measures to eliminate these viruses in the live bird markets in the country.