In a recent study posted to the medRxiv* preprint server, researchers examined whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected white-tailed deer could be the new animal reservoir with the potential to spillback new SARS-CoV-2 variants into humans.
Study: Evolutionary Trajectories of SARS-CoV-2 Alpha and Delta Variants in White-Tailed Deer in Pennsylvania. Image Credit: Amy Lutz/Shutterstock
This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources
Coronavirus disease 2019 (COVID-19) started by spillover from bats to humans in late 2019. Since then, several animal species have become prone to SARS-CoV-2 infection, including white-tailed deer Odocoileus virginianus. Over a million white-tailed deer live across counties of Pennsylvania (PA), United States; several of them became SARS-CoV-2-infected, raising concern that a new animal reservoir for SARS-CoV-2 is under formation from which new variants may spillback into humans.
About the study
In the present study, researchers used quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2 in nasal swab samples of 93 white-tailed deer in Pennsylvania during fall-winter 2021.
The samples were collected within hours of the animal’s death, placed in phosphate-buffered saline (PBS), and stored in commercial refrigerators in field offices. These samples were transferred to the University of Pennsylvania within one week of collection and kept at -80°C until ribonucleic acid (RNA) extraction. The researchers used Chi-squared tests to test for differences in proportions of SARS-CoV-2-positive deer samples by gender, age, and source of deer (volunteer-collected, veterinary technician-collected, hunter-harvested, road-killed, etc.).
The researchers collected human samples following the research protocol reviewed by the University of Pennsylvania Institutional Review Board. They collected samples from COVID-19-hospitalized subjects, asymptomatic subjects, and symptomatic subjects.
Study findings
Of 93 deer samples, 18 (19.3%) were positive for SARS-CoV-2 with a confidence interval (CI) of 95%, and these deer were present in 10 out of 31 Pennsylvania counties surveyed from 2 October 2021 to 27 December 2021. Of 66 volunteer-collected and 27 veterinary technicians-collected deer samples, there were 11 and seven SARS-CoV-2-positives, indicating no difference in the proportion of positives between the two groups.
With a prevalence estimate of 35% in females vs. 7.5% in male deer, the prevalence estimate was higher in female deer; however, there is no data indicating disease symptoms in the study animals. Although, authors noted that deer sampled as road-killed were significantly more likely to be SARS-CoV-2-positive than hunter-harvested 11/66, road-killed 6/13, and other 1/14.
Eight out of 93 samples showed the lowest cycle of threshold (Ct) values in the RT-qPCR, indicating the highest viral RNA levels, thus were subjected to viral whole-genome sequencing (WGS). Subsequently, the authors retrieved seven high-quality genome sequences from deer.
The non-viral genomic sequence reads of deer and human samples were analyzed in parallel. While all deer samples had genomic reads mapped to the deer genome, reads from human samples mapped to the human genome, thus confirming that deer contracted SARS-CoV-2 infection via spillover from human hosts.
The two Alpha sequences sampled from deer in adjoining counties in northeastern PA differed by 45 substitutions, indicating that they were introduced independently into deer and then diversified during transmission within deer. In addition, these deer-derived Alpha genomes appeared, particularly divergent in contrast to the human Alpha genomes sequenced previously in the same region.
Regarding the Delta variants, two deer genomes were assigned to the AY.103 clade and differed only by seven substitutions. Two other deer SARS-CoV-2 genomes fell under the uncommon AY.88 Delta lineage, with only 0.14% of human-derived PA Delta genomes being AY.88; additionally, the last Delta sample belonged to the AY.5 lineage.
Taken together, these findings support at least four independent spillovers of SARS-CoV-2 from humans into deer, two of alpha, and two of the delta, although the mechanism of transmission from humans to deer remains incomprehensible.
Conclusions
The WGS data showed selective persistence of the SARS-CoV-2 Alpha variant in white-tailed deer, although this variant had been replaced by the Delta variant in humans long back. Moreover, deer-derived Alpha isolates were significantly divergent from those in humans showing a distinct evolutionary trajectory in deer. However, there is no scientific evidence explaining how SARS-CoV-2 is evolving in new directions in the deer species.
This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources
Article Revisions
- May 12 2023 - The preprint preliminary research paper that this article was based upon was accepted for publication in a peer-reviewed Scientific Journal. This article was edited accordingly to include a link to the final peer-reviewed paper, now shown in the sources section.
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