Eliciting Characteristics of H5N1 in High-Risk Regions Using Phylogeography and Phylodynamic Simulations

Avian influenza viruses (AIVs) undergo continuous antigenic drifts, causing annual epidemics in poultry and livestock that result in significant mortality and conspicuous socioeconomic losses. To design vaccines and mitigate epidemics, evolutionary characteristics of AIVs are typically studied through longitudinal surveillance and serological assays. However, such in vivo analysis is often reactive and limited due to the complexities and costs of long-term, multinational surveillance. Consequently, in vivo analysis is enhanced using in silico phylodynamic modeling and simulation methods that simultaneously model evolutionary and epidemiological characteristics of AIVs. This study proposes a novel in silico approach that combines two different agent-based simulation methods: epidemiological simulation and phylogeographic annotations to identify high-risk countries, and phylodynamic simulations to elicit their AIVs evolutionary characteristics. The proposed method elicits detailed ecological characteristics of AIVs that can inform design of vaccines and prophylactic strategies.