Molecular epidemiology and evolutionary dynamics of zoonotic influenza viruses

Abstract

Influenza A viruses (IAVs) are rapidly evolving RNA viruses with a broad host range, causing substantial disease in poultry, swine, and human populations. Zoonotic transmission of IAVs has led to severe pandemics, notably the 1918 ‘Spanish’ influenza and the 2009 H1N1 swine flu. Swine and poultry host diverse IAV lineages, enabling genetic reassortment and the emergence of novel strains with zoonotic potential, posing public health risks. With constant circulation in animal populations, several IAV subtypes have become endemic, allowing the viruses to persist and adapt, increasing genetic diversity. Robust genomic surveillance is essential for understanding viral epidemiology in poultry and swine, assessing the potential risk of spillover to humans, and enhancing pandemic preparedness and risk reduction. Despite ongoing surveillance, comprehensive longitudinal genomic analysis to track and understand these evolutionary processes remains limited. This thesis utilizes genomic surveillance data and applies various phylogenetic methods to investigate the long-term genetic diversity and evolution of IAVs in swine and poultry across different farming systems, providing insights into how these viruses persist and reassort, potentially leading to novel zoonotic threats. Chapter One provides a detailed introduction to IAVs, offering an overview of their genetic diversity. The application of genomic surveillance data using phylogenetic methods in the context of IAVs is discussed in Chapter Two. In Chapter Three, genomic surveillance data revealed vast genetic diversity among swine populations in Vietnam, with 28 genotypes in circulation. Phylogenetic analysis of the HA gene identified 17 reverse zoonosis introductions of H1N1pdm09. Notably, the North American H1-δ1a strain was identified, with a possible route of introduction via the importation of breeding hogs. Chapter Four investigated the role of U.S. exhibition swine as an active, dynamic breeding ground for new viral diversity with zoonotic potentials. Each year, the introduction of IAV lineages from commercial swine injected genetic lineages into exhibition swine, further facilitating virus spread. Since 2010, at least 26 distinct genotypes of swine IAVs, each with one of 12 different HA clades, have infected humans in the U.S., originating from exhibition swine. The analysis also revealed a recent surge in the detection and expansion of H1-δ2 lineages among exhibition swine. In Chapter Five, the virological surveillance of IAVs in Hong Kong poultry resulted in the detection of 147 whole genomes of H9N2 subtype viruses from 2017 to 2021. All HA genes belonged to the Y280 lineage and were distinct from previously circulating Hong Kong viruses, forming five monophyletic clusters. These clusters were traced back to mainland China and belonged to the G57 genotype, identified as a potential zoonotic threat. Most reported zoonotic infections were attributed to G57. Stringent control measures implemented to eliminate H5 at various time points substantially reduced the genetic diversity of H9-HA lineages. The final chapter summarizes key findings, discusses impacts and perspectives, and emphasizes the value of genomic surveillance in understanding the virus circulation and evolution in swine and poultry.