The current H5N1 (2.3.4.4b) avian influenza panzootic poses significant threats to poultry production, wildlife, and human health. South-East Asia (SEA) is a critical region for the movement of avian influenza viruses and could serve as a pathway for these viruses to enter Australia. However, the lack of extensive virus surveillance in SEA limits our understanding of the regional transmission and evolution of avian influenza lineages. This project aims to elucidate the evolution of H5 avian influenza lineages in SEA, focusing on lineage recombination, key hosts, and the correlation of lineage evolution with regional characteristics.
We model diffusion patterns of SEA H5 AI lineages using existing surveillance data, primarily from poultry outbreak monitoring. Our analysis includes a comprehensive H5 AI genome database of 2057 sequences from SEA, supplemented by 409 SEA H5 AI genomes from our role as a WOAH reference lab.
Our approach involves phylogenetic, phylodynamic, and phylogeographic analyses, starting with data from the Philippines. We have constructed HA maximum-likelihood (ML) trees using IQ-TREE, identifying 2.3.4.4e lineages (59 unpublished members) from 2017-2021 and 2.3.4.4b lineages (31 unpublished members) from 2022-2023. We are also conducting incongruence analysis of ML trees across all 8 influenza A segments to explore the distribution and evolution of genotypes in the region, assessing SEA's role as a reservoir and contributor of accessory gene segments to influenza lineages.
TempEST and BEAST2 are being used to reconstruct the evolutionary dynamics of Philippine H5 HA sequences, employing a relaxed molecular clock and Extended Bayesian Skyline model. This, combined with continuous phylogeographic analysis using BEAST2 and the GEO_SPHERE package, will help us associate virus phylodynamics with bird migration and distribution patterns over four years.