Developing Genomic Analysis and Modelling Tools for Highly Pathogenic Influenza A Viruses

H5N1, commonly known as avian influenza or bird flu, is a highly pathogenic strain of the influenza virus (HPAI) primarily affecting birds but capable of crossing species barriers to infect humans and other animals. First identified in domestic poultry in Southeast Asia in the late 20th century, H5N1 has since sparked global concern due to its severe symptoms, high mortality rate in humans, and the potential to cause pandemics. While human-to-human transmission remains rare and sustained human-to-human transmission has not been documented, the virus's ability to evolve and mutate poses significant challenges for public health systems worldwide. The prevention of widespread H5N1 outbreaks will require a robust sentinel surveillance system capable of rapidly detecting and responding to sustained transmission events. While many clinical microbiology laboratories can detect influenza in patient samples, most labs and assays currently used in diagnostic testing do not differentiate H5N1 from other circulating strains of influenza strains. Therefore, it is critical to develop and implement rapid genomics and modelling to identify potential cases and sources. Here we propose to use the existing sequencing infrastructure to develop an amplicon-based genomics assay standardizing sequencing protocols, bioinformatics pipelines, and reporting of new and emerging strains of influenza from clinical, environmental (wastewater samples), and animal sources. We will also develop and validate phylodynamic models, using specimens that have been linked as being part of an outbreak and unrelated specimens from past influenza seasons, to estimate influenza epidemic potential during an outbreak, and to estimate and identify factors (attack rates, reproduction numbers, viral mutations) that may play a role in viral dissemination