Is the rapid evolution of SARS-CoV-2 in white-tailed deer complicating our fight against the pandemic?

By Vijay Kumar MalesuAug 31 2023Reviewed by Benedette Cuffari, M.Sc.

In a recent study published in Nature Communications, researchers investigate the introduction, transmission, and accelerated evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer (WTD) populations in Ohio and assess its potential implications for human and livestock health.

Study: Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Image Credit: Tom Reichner / Shutterstock.com

Can SARS-CoV-2 infect animals?

By December 2022, 645 million people had been infected with SARS-CoV-2, which resulted in 6.6 million pandemic-related deaths. The rapid evolution of SARS-CoV-2 has produced variants with altered transmission and immunity dynamics, thus complicating global recovery efforts.

Although various animals, like mink and canines, have been infected with SARS-CoV-2, WTD presents unique challenges, as culling is not feasible. By July 2021, 40% of tested WTD in the United States had SARS-CoV-2 antibodies.

Subsequent studies detected multiple transmission events between humans and deer and vice versa. These observations emphasize the importance of gaining a better understanding of SARS-CoV-2 transmission and evolution in WTD.

About the study

Between October 2021 to March 2022, researchers collected 1,522 nasal samples from WTD across Ohio, predominantly during hunting season, and from culled deer for population control. Viral ribonucleic acid (RNA) was extracted from nasal samples for real-time reverse transcription polymerase chain reaction (rRT-PCR) analysis, whereas blood samples were examined for SARS-CoV-2 antibodies.

Genomic sequencing was performed on SARS-CoV-2-positive samples to study the genetic makeup of the virus. Using ArcMap for data representation and rigorous statistical analysis, phylogenetic analysis was used to compare the WTD virus with those in humans and other animals in an effort to identify potential transmission clusters.

Bayesian methodologies were used to study the evolutionary relationships between the SARS-CoV-2 Alpha and Delta variants in humans and WTD. To this end, distinct datasets were established for analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST49) software. BEAST49 also allowed for the assessment of viral gene flow patterns while also analyzing epidemiological data from Ohio alongside mutation patterns using specialized computational tools.

Gene selection in WTD was assessed using the Hypothesis Testing using Phylogenies (HyPhy) package; however, no positive gene-wise selection was identified. Ethical animal studies using Syrian hamsters for virus challenges were conducted. Neutralizing antibody activity against SARS-CoV-2 strains was assessed in tandem with viral growth kinetics in cell lines.

Study results 

Over 10% of samples obtained from WTD tested positive for SARS-CoV-2. The affected deer spanned across 59% of Ohio counties, including urban areas surrounding major cities and rural locales. While the rural northwest was the only region devoid of positive cases, potentially due to limited sample collection, male WTD slightly outnumbered females in infection rates.

Furthermore, the likelihood of infection spiked in December as compared to November and declined by January. February and March of 2022 yielded no positive samples.

In urban counties, only a small percentage of culled deer tested positive for active infection, whereas over 20% of their blood samples were seropositive for antibodies. This indicates prior exposure without current active infection.

About 25% of Ohio's WTD exhibited SARS-CoV-2 seroprevalence. In counties like Franklin, despite no active infections being detected in culled deer, previous exposure was still highly probable.

Out of the counties with positive cases, sequences were procured from 69.4% of WTD, with about 70% of these sequences associated with rural counties. Although the Delta variant was dominant when 95% of the sequenced WTD viruses were sampled, the Alpha variant also persisted within Ohio's WTD population. A vast majority of the sequences matched the dominant circulating strain of SARS-CoV-2 in humans at the time of sampling. 

There were also nine instances where the virus matched an earlier strain from humans, thus suggesting that these deer had been carriers for more extended periods. These findings also indicate multiple introductions of SARS-CoV-2 to the deer population and subsequent deer-to-deer transmission over extended periods.

Correlating the rise of the Delta variant in humans with deer infection, a high frequency of transmission from humans to WTD was observed. Genetically, the viral strains in deer mirrored those in humans during the same timeframe. Thus, although the virus spread across counties, not all transmissions led to widespread outbreaks.

When tracing the movement of SARS-CoV-2 within the WTD population, deer-to-deer transmission clusters were evident. The majority were in rural regions, and while Delta clusters typically spread to neighboring counties, Alpha clusters were associated with a wider reach.

SARS-CoV-2 was found to evolve faster in deer than in humans. An exploration into the rapid evolution of the virus within deer revealed a threefold increase in the rate of evolution for the Alpha variant as compared to humans, which is attributed to factors like mutation patterns that are distinct to deer. The current mutations were also noted in SARS-CoV-2 strains within deer, which suggests adaptive evolution or responses to different immune pressures in deer compared to humans.