Phylodynamics of emerging infectious disease threats

National Library Of Medicine

Investigators

Linked publications, trials & patents

Abstract

Over the last year, this research project has been focused on understanding the multi-host ecology and evolution of two emerging pathogens, SARS-CoV-2 virus and highly pathogenic H5N1 avian influenza viruses. For SARS-CoV-2, my research has demonstrated that virus spillover from humans to animals occurs frequently, in farmed mink and particularly in white-tailed deer. We have shown that SARS-CoV-2 is capable of establishing new reservoirs in an animal host and evolving in new trajectories under different selection pressures, which presents a risk of future spillback to humans in an antigenically different form. For example, alpha variants were detected in deer in Ohio and Pennsylvania more than a year after they had gone extinct in humans in those states. SARS-CoV-2 does not appear to be symptomatic in white-tailed deer, but this allows the virus to circulate undetected for extended lengths of time and at high prevalence (~10%). Overall, these findings show that there are major gaps in our knowledge of SARS-CoV-2 circulation in wildlife, which are sampled at very low levels compared to humans, and this evolving risk needs to be monitored with active surveillance, in deer and other wildlife species. This research project has identified new mammalian-adapted avian H5N1 influenza A viruses in South American marine mammals and US dairy cattle that present a growing pandemic risk for humans. Genomic data from H5N1 viruses shows how the H5N1 outbreaks in South American marine mammals (e.g., sea lions, elephant seals) and US dairy cattle are each traceable back to a single introduction of H5N1 from wild birds. The bird-to-marine mammal introduction occurred in early 2023 on South America's Pacific coast (Peru or Chile). The bird-to-cattle introduction occurred approximately one year later (late 2023/early 2024), most likely in Texas. In both cases, H5N1 viruses adapted to become fitter in mammals through specific mutations in the polymerase genes. The bovine-adapted H5N1 virus has infected 13 farm workers in Texas, Michigan, and Colorado. Overall, these findings point to an alarming trend in H5N1 evolving to spread mammal-to-mammal and the need for intensified monitoring of an evolving pandemic risk.