SURVEILLANCE OF BATS IN THE UNITED STATES FOR SARS-COV-2 AND OTHER CORONAVIRUSES.

Bat coronaviruses (CoVs) are extremely prevalent throughout the globe and exhibit a wide range of genetic diversity. Currently, little is known about the susceptibility of New World bats to severe acute respiratory syndrome-2 (SARS-CoV-2), the causative agent of COVID-19. Also, there is limited information about the genetic diversity of other CoVs in the New World bats. The determination of genetic diversity of bat CoVs through continuous surveillance is essential to predict and mitigate the emergence of new CoVs and their impacts on the health of both humans and animals. In this study, 491 guano specimens collected from New World bats and 37 specimens collected from Old World bats during July 2020 to July 2021 were tested for SARS-COV-2 and other CoVs using a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) panel and pan-coronavirus PCR that target a highly conserved region of CoVs. No evidence of SARS-CoV-2 was found in the tested specimens. An alpha CoV was detected in a single specimen from a big brown bat (Eptesicus fuscus). This information was used by wildlife agencies and rehabilitation facilities to permit the release of bats during the pandemic while mitigating the risk of spreading SARS-CoV-2 among North American bats and other wild animal populations.

Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania.

The SARS-CoV-2 pandemic began by viral spillover from animals to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus, are infected in North America at substantial levels, and genomic data suggests that a variant in deer may have spilled back to humans. Here, we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole genome sequences were obtained, together with six more partial spike gene sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer. IMPORTANCE Coronaviruses have been documented to replicate in numerous species of vertebrates, and multiple spillovers of coronaviruses from animals into humans have founded human epidemics. The COVID-19 epidemic likely derived from a spillover of SARS-CoV-2 from bats into humans, possibly via an intermediate host. There are now several examples of SARS-CoV-2 jumping from humans into other mammals, including mink and deer, creating the potential for new animal reservoirs from which spillback into humans could occur. For this reason, data on formation of new animal reservoirs is of great importance for understanding possible sources of future infection. Here, we identify extensive infection in white-tailed deer in Pennsylvania, including what appear to be multiple independent transmissions. Data further suggests possible transmission among deer. These data thus help identify a potential new animal reservoir and provide background information relevant to its management.