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Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by United States Department of Agriculture, Animal and Plant Health Inspection Service and state natural resources agencies to quantify infection of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) using a hierarchical epidemiological model in the eastern half of the United States. Our model found that male deer had higher positivity than female deer, and positivity was higher in counties with higher human population density or deer habitat. Estimated SARS-CoV-2 local epidemiological reproduction numbers were between 1 and 2.5 in most well-sampled counties, with local epidemics in WTD peaking earlier in the northeast and mid-Atlantic relative to the Midwest and Southeast. Similar peak infection prevalence times across many counties provided indirect evidence for widespread transmission via human-to-deer spillover, while the widespread high estimates of local epidemiological reproduction number suggested that sustained deer-to-deer transmission is also probable. The model estimated 10% of infected WTD were infected due to human infection pressure.

While SARS-CoV-2 has sporadically infected a wide range of animal species worldwide1, the virus has been repeatedly and frequently detected in white-tailed deer in North America2â€"7. The zoonotic origins of this pandemic virus highlight the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. Here, we detected SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2-8 months, which disseminated across hundreds of kilometers. We discovered that alpha and delta variants evolved in white-tailed deer at three-times the rate observed in humans. Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only faster in white-tailed deer but driven by different mutational biases and selection pressures. White-tailed deer are not just short-term recipients of human viral diversity but serve as reservoirs for alpha and other variants to evolve in new directions after going extinct in humans. The long-term effect of this accelerated evolutionary rate remains to be seen as no critical phenotypic changes were observed in our animal model experiments using viruses isolated from white-tailed deer. Still, SARS-CoV-2 viruses have transmitted in white-tailed deer populations for a relatively short duration, and the risk of future changes may have serious consequences for humans and livestock. ispartof: Res Sq ispartof: location:United States status: Published online

Black-tailed prairie dogs are considered an important “keystone” species of the prairies, on one hand, and a nuisance rodent causing considerable damage on the other. To effectively manage prairie dog colonies, a better understanding is needed of the effects of management practices on prairie dogs, their burrow systems, and other species that may use those burrow systems. For example, when fumigants are used to control prairie dog populations, to what extent may other species be affected? We used a burrow-probe camera system to observe animal use of 777 burrow openings. These included colonies both in urban/suburban and natural prairie settings as well as active versus inactive colonies. Burrows were usually probed to a depth of about 2 m, requiring only a few minutes each. Relatively few animals were seen and most were invertebrates. More animals were observed in urban/suburban burrow systems versus prairie burrow systems. Somewhat more animals were observed in active versus abandoned burrow systems. The vertebrates observed were prairie dogs, rabbits, ground squirrels, snakes, a mouse, and a salamander. The implications and possible short-comings of this study are discussed.