SARS CoV-2 in Pennsylvania deer sampled in fall and winter 2021
In a recent study published on medRxiv* preprint server, researchers investigated whether white-tailed deer infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be the new animal reservoir likely to return new variants of SARS-CoV-2 to the man.
Coronavirus disease 2019 (COVID-19) first spread from bats to humans in late 2019. Since then, several animal species have become prone to SARS-CoV-2 infection, including deer from Virginia Odocoileus virginianus. Over one million white-tailed deer live in counties in Pennsylvania (PA), USA; several of them have become infected with SARS-CoV-2, raising concerns that a new animal reservoir for SARS-CoV-2 is being formed from which new variants could impact the man.
About the study
In the current study, researchers used quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2 in nasal swab samples from 93 white-tailed deer in Pennsylvania during fall-winter 2021.
Samples were taken within hours of the animal’s death, placed in phosphate-buffered saline (PBS), and stored in commercial refrigerators at field offices. These samples were transferred to the University of Pennsylvania within a week of collection and stored at -80°C until ribonucleic acid (RNA) extraction. The researchers used chi-square tests to test for differences in the proportions of deer samples positive for SARS-CoV-2 by sex, age, and deer source (collected by volunteers, collected by vet techs, harvested by hunters, roadkill, etc.).
The researchers collected human samples following the research protocol reviewed by the University of Pennsylvania Institutional Review Board. They collected samples from hospitalized COVID-19 subjects, asymptomatic subjects and symptomatic subjects.
Of 93 deer samples, 18 (19.3%) were positive for SARS-CoV-2 with a 95% confidence interval (CI), and these deer were present in 10 of the 31 Pennsylvania counties studied from October 2 2021 to December 27, 2021 Of 66 deer samples collected by volunteers and 27 by veterinary technicians, there were 11 and seven positive for SARS-CoV-2, indicating no difference in the proportion of positives between the two groups.
With a prevalence estimate of 35% in females versus 7.5% in males, the prevalence estimate was higher in females; however, there are no data indicating disease symptoms in the animals studied. However, the authors noted that deer sampled as roadkill were significantly more likely to be SARS-CoV-2 positive than the 11/66 hunters shot, 6/13 roadkill and other 1/14.
Eight of the 93 samples showed the lowest threshold cycle (Cyou) values in RT-qPCR, indicating the highest viral RNA levels, were therefore subjected to viral whole genome (WGS) sequencing. Subsequently, the authors recovered seven high-quality deer genomic sequences.
Non-viral genomic sequence reads from deer and human samples were analyzed in parallel. While all of the deer samples had genomic reads mapped to the deer genome, human sample reads mapped to the human genome, thus confirming that the deer acquired SARS-CoV-2 infection by spillover of human hosts.
The two Alpha sequences taken from deer in neighboring counties in northeastern PA differed by 45 substitutions, indicating that they were introduced independently into deer and then diversified during transmission within deer. Additionally, these deer-derived Alpha genomes emerged, particularly divergent from previously sequenced human Alpha genomes in the same region.
Regarding the Delta variants, two deer genomes were assigned to clade AY.103 and differed only by seven substitutions. Two other SARS-CoV-2 deer genomes belonged to the rare AY.88 Delta lineage, with only 0.14% of human-derived PA Delta genomes being AY.88; moreover, the last Delta sample belonged to the AY.5 line.
Taken together, these results support at least four independent spillovers of SARS-CoV-2 from humans to deer, two from alpha and two from delta, although the mechanism of transmission from humans to deer remains incomprehensible.
WGS data showed selective persistence of the SARS-CoV-2 Alpha variant in white-tailed deer, although this variant was replaced by the Delta variant in humans long ago. Moreover, Alpha isolates derived from deer differed significantly from those from humans, showing a distinct evolutionary trajectory in deer. However, there is no scientific evidence explaining how SARS-CoV-2 evolves in new directions in deer species.
medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be considered conclusive, guide clinical practice/health-related behaviors, or treated as established information.