Tracking the silent spread of COVID-19

Tracking the genetic code of the COVID 19 virus revealed that six of the 23 commonly studied wild species species in Virginia have shown signs of SARS-CoV-2 infections.

Research from Virginia Tech has revealed widespread presence of SARS-CoV-2 among diverse wildlife in Virginia, with evidence of human-to-wildlife transmission and novel viral mutations, highlighting the need for enhanced surveillance and research into the behavior of the virus in different hosts.

COVID-19 spread in wildlife

SARS-CoV-2, the virus that causes COVID-19, is widespread in wildlife, according to a Virginia Tech study published today (July 29, 2024) in Nature Communications. The virus was detected in six common backyard species, and antibodies indicating prior exposure to the virus were found in five species, with exposure rates ranging from 40 to 60 percent depending on the species.

Genetic tracking in wild animals confirmed both the presence of SARS-CoV-2 and the existence of unique viral mutations with lineages closely matching variants circulating in humans at the time, further supporting human-to-animal transmission, the study said.

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Transmission and mutation of viruses in nature

The highest exposure to SARS-CoV-2 was seen in animals near hiking trails and high-traffic public areas, suggesting the virus jumped from humans to wildlife, according to scientists from VTC’s Fralin Biomedical Research Institute, Virginia Tech’s College of Science Department of Biological Sciences and the Fralin Life Sciences Institute.

The results of this study highlight the identification of new mutations of SARS-CoV-2 in wild animals and the need for broader surveillance, the researchers say. These mutations could be more harmful and transmissible, complicating vaccine development.

Human influence and viral adaptation

Scientists stressed, however, that they had found no evidence of transmission of the virus from animals to humans, and that people should not fear typical interactions with wildlife.

The researchers tested animals from 23 common Virginia species for active infections and antibodies indicating past infections. They found evidence of the virus in deer mice, Virginia opossums, raccoons, marmots, cottontail rabbits and eastern red bats. The virus isolated from one opossum showed viral mutations that had not been previously reported and could potentially impact how the virus affects humans and their immune response.

“The virus can jump from humans to wildlife when we come into contact with them, like a hitchhiker switching vehicles to a new, more suitable host,” says Carla Finkielstein, a professor of biological sciences at VTC’s Fralin Biomedical Research Institute and one of the study’s co-authors. “The goal of the virus is to spread to survive. The virus aims to infect more humans, but vaccines protect many humans. So the virus turns to animals, adapts, and mutates to thrive in the new hosts.”

Expanding research and monitoring needs

SARS-CoV-2 infections have previously been identified in wild animals, primarily in wild white-tailed deer and mink. The Virginia Tech study significantly expands the number of species examined and the understanding of virus transmission to and between wild animals. The data suggest that exposure to the virus has been widespread among wild animals and that areas of high human activity may serve as points of contact for cross-species transmission.

“This study was motivated by the recognition of a significant gap in our knowledge about SARS-CoV-2 transmission in the broader wildlife community,” said Joseph Hoyt, assistant professor of biological sciences in the College of Science at Virginia Tech and corresponding author of the paper. “Many studies to date have focused on white-tailed deer, while what is happening in much of our common backyard wildlife remains unknown.”

The research team collected 798 nasal and oral samples in Virginia from animals that were live-caught in the field and released or treated at wildlife rehabilitation centers. The team also obtained 126 blood samples from six species. The sites were chosen to compare the presence of the virus in animals in sites with different levels of human activity, from urban areas to remote wilderness areas.

The study also identified two mice at the same site on the same day with the exact same variant, indicating that they had both contracted it from the same human or that one had infected the other.

Researchers aren’t sure how the virus spreads from humans to animals. Sewage is one possibility, but Virginia Tech scientists believe trash and discarded food are more likely sources.

“I think the takeaway is that the virus is pretty ubiquitous,” said Amanda Goldberg, a former postdoctoral fellow in Hoyt’s lab and first author of the study. “We found positive cases in a lot of backyard animals.”

Although this study focused on the state of Virginia, many of the species that tested positive are common wildlife across North America. They are likely exposed in other areas as well, and broader region-wide surveillance is urgently needed, Hoyt said.

“The virus doesn’t care whether its host walks on two legs or four. Its primary goal is survival. Mutations that don’t give the virus a survival or replication advantage won’t persist and will eventually die out,” said Finkielstein, who is also director of Virginia Tech’s Molecular Diagnostics Laboratory. The Roanoke lab was established in April 2020 to expand COVID-19 testing.

“We understood the critical importance of sequencing the genome of the virus infecting these species,” Finkielstein said. “It was a monumental task that could only be accomplished by a talented group of molecular biologists, bioinformaticians and modelers in a state-of-the-art facility. I am proud of my team and collaborators, their professionalism and all that they contributed to our success.”

Monitoring for these mutations must continue and should not be neglected, the scientists said. Further research is needed to understand how the virus is transmitted from humans to wildlife, how it can spread within species and perhaps from species to species.

“This study highlights the broad host range that SARS-CoV-2 can have in nature and its true magnitude,” Hoyt said. “Much work remains to be done to understand which wildlife species, if any, will be important for the long-term maintenance of SARS-CoV-2 in humans.”

“But what we have already learned,” Finkielstein said, “is that SARS-CoV-2 is not just a human problem, and that it takes a multidisciplinary team to effectively address its impact on diverse species and ecosystems.”

Reference: “Widespread exposure to SARS-CoV-2 in wild communities” July 29, 2024, Nature Communications.
DOI: 10.1038/s41467-024-49891-w