Influenza A Viruses at the Swine-Human Interface – Exploring Genetic Markers of Zoonotic Potential

Influenza A virus (IAV) poses significant public health challenges globally, causing annual or endemic outbreaks in a wide range of hosts, including humans and swine. Interspecies transmissions can potentially lead to human pandemics, as demonstrated by the swine-origin H1N1 pandemic in 2009 and has resulted in a diverse genetic pool of IAVs circulating in swine populations worldwide. The genetic factors that facilitate this interplay between human and swine IAVs remain poorly understood. This underscores
the critical need for robust surveillance systems to monitor and understand genetic changes in IAVs that could potentially indicate increased risk of zoonotic transmission.
The importance of cross-species influenza surveillance was highlighted by the detection of the first zoonotic transmissions of IAVs from swine to human in Denmark in 2021, detailed in Manuscript I and Manuscript II. The two independent cases were detected ten months apart and were received as regular surveillance samples for human seasonal influenza. However, sequencing and genetic analysis revealed their closer resemblance to swine influenza viruses, prompting in-depth investigations into their clinical details, exposure history, and genetic backgrounds to evaluate their origin and risk as zoonotic strains.
These cases underscored the importance of genetic surveillance across human and animal hosts and naturally encourage the methodological optimizations presented in Manuscript III. This work focused on refining the extraction and amplification processes used before whole-genome sequencing of IAVs, ensuring accuracy and consistency across various host and sample types. Getting high-quality and complete genome sequences of influenza viruses is critical for thorough analysis of IAV genotypes and evolution. By testing different laboratory protocols, we aimed to optimize and unify the workflows for genomic analysis and surveillance of IAVs across host-origins in a One Health perspective.
Tracking the evolution of IAVs within and between species through genomic sequencing is an integral part of understanding their host-specificity and zoonotic potential. In Manuscript IV we investigated the evolutionary relationship between IAVs circulating in humans and swine with a specific interest in finding host-specific genetic patterns around interspecies transmissions. Through detailed phylogenetic and statistical analyses of extensive IAV sequence datasets from human and swine, we analyzed genetic and mutational patterns associated with different types of IAV transmissions to identify associated genetic signatures.
Identifying markers in the sequences of IAVs that indicate their adaptive status and zoonotic potential is a primary aim of the FluZooMark project. The research presented in this PhD thesis advances our knowledge of these mechanisms and proposes candidate protein markers for further investigation, potentially aiding in the prediction of zoonotic risks posed by IAVs from swine.