Abstract
Coronaviruses are known for their potential to cross species barriers, based on high mutation rates and interstrain recombinations. The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a bidirectional zoonotic pathogen in 2019 is only one of many examples. Given the detection of SARS-CoV-2 with a high prevalence in white-tailed deer (Odocoileus virginianus) in 2020 in North America, the importance of monitoring for SARS-CoV-2 infections in a broad spectrum of animal species, including additional cervids, grew considerably. Therefore, we analyzed samples from red deer (Cervus elaphus), collected in southern Bavaria between May 2021 and February 2023, for genomic evidence of SARS-CoV-2 and bovine coronavirus (BCoV). The latter has been previously shown to infect wild mammals, including deer species. In 727 colon tissue samples and 807 upper respiratory tract swabs respective genomes were detected rarely and in low genome copy numbers only. Bovine coronavirus sequences were detected in six upper respiratory tract swabs (0.74%) and 10 colon tissue samples (1.38%). Additionally, SARS-CoV-2 sequences were detected in one colon tissue sample from an adult female individual. It appears that red deer in Bavarian alpine regions rarely carry viruses such as SARS-CoV-2 and BCoV. Furthermore, none of the samples showed any indication of a coinfection with both viruses, which putatively could trigger recombination and in consequence the emergence of new viruses.