ARS Scientists Developing New Ways to Track COVID in Wild, Domestic Animals

Scientists with the USDA Agricultural Research Service are developing new tests to identify the COVID virus and its variants and tools for tracking the virus in wild and domestic animals, thanks to five projects funded by the American Rescue Plan.

The USDA Animal and Plant Health Inspection Service (APHIS) is currently implementing a $300 million provision in the American Rescue Plan Act to conduct monitoring and surveillance of susceptible animals for the COVID virus. Through this initiative, ARS, in partnership with APHIS, is conducting five research projects to improve its understanding of the virus and to help APHIS accomplish its goal of building an early warning system to potentially prevent or limit the next zoonotic disease outbreak or global pandemic.

Two of the projects call for developing easy-to-use field tests to provide quick identification of COVID infection in wildlife and domestic animals—each based on a different basic technology. Both technologies are being worked on by scientists in the Produce Safety and Microbiology Research Unit (PS&MRU) at the ARS Western Regional Research Center in Albany, Calif.

Currently, all official testing of animals for COVID requires sending samples to certified laboratories and can take a week or more to provide answers. This may be too long to prevent early spread of infection.

ARS microbiologist and PS&MRU research leader Vivian Wu's goal is a hand-held, rapid test providing answers in 10-15 minutes, based on an aptamer lateral flow assay (aLFA) for animal and environmental COVID virus testing.

Aptamers are very small synthetic strands of DNA or RNA that can be tailored to tightly bind to very precise targets. These molecules also are very environmentally stable, especially to heat, making them ideal for use in the wild and on farms. As important, aptamers can be easily manufactured in a relatively short time and cost.

Since aptamers recognize very specific viral proteins, multiple, individual COVID variants could be detected with each test and kits be rapidly modified as new strains emerge. The rapidity of this point-of-care, noninvasive test would facilitate monitoring of animals. It could be used as a surveillance tool and help the decision-making process of farmers, veterinarians and regulatory agencies.

"Farmed and wildlife species that have already been reported to be susceptible to COVID are our first priority for species-specific tests," Wu said. "Besides farmed and wild mink, we are targeting white-tailed deer and hamsters. Tests for companion animals such as cats and dogs and animals in zoos such big cats and great apes also will be considered. Our list will be updated as new information becomes available on the susceptibility of animals with new variants. We also are looking at tests for on-farm environmental and wastewater sampling as a form of surveillance."

ARS molecular biologist Robert Hnasko with the PS&MRU is heading the second ARP project developing portable COVID tests for domestic and wild animals, this one based on antibody immunoassay technology, a more established technology.

'We are trying to build a better "mouse trap" that expands the utility of antibody-based tests with better sensitivity and viral variant identification,' Hnasko said. "And by using monoclonal antibody technology that has a good history of commercial acceptance, we expect easier licensing to industry and speedy production. Getting low cost, disposable tests available to facilitate detection at remote locations and to increase testing frequency is part of the solution to COVID in animals."

At the ARS National Animal Disease Center (NADC) in Ames, Iowa, medical veterinary officers Mitchell Palmer, Paola Boggiato, Alexandra Buckley and Eric Cassmann are using ARP funding, and working with APHIS Wildlife Services, to expand their studies of COVID and white-tailed deer. The ARS team, along with Cornell University collaborators, built on prior research showing that white-tailed deer carry a molecular receptor similar to one in humans in their cells that allows COVID virus to gain entry and replicate. Deer that the researchers exposed to the virus showed no clinical signs of illness but remained infectious to other deer for 5-6 days, primarily through nasal secretions and saliva. Both the virus and antibodies produced in response to it were detectable in the deer for at least 21 days—the length of the initial laboratory study.

"But we don't know what happens beyond that 21-day period," noted Palmer.

This latest round of studies supports field work being done by APHIS Wildlife Services to survey white-tailed deer populations for evidence of infection in the wild. The scientists have three key objectives 1) compare the different COVID variants in deer, 2) learn how long antibodies persist in their bodies and whether these antibodies protect deer from re-infection and 3) determine how long the virus is detectable in deer.

Ultimately, researchers want to know whether white-tailed deer can serve as a "reservoir species," meaning an intermediate animal host in which COVID virus could survive in the wild and potentially mutate into new variants capable of prolonging or exacerbating the disease pandemic in humans.

"It is possible that a new variant may be more easily transmitted from deer to humans. Transmission from humans to animals, and then transmission back from animals to humans, has already been documented in mink and hamsters," Palmer said. "There is a concern that this could happen in white-tailed deer, a more widespread species with a population of over 30 million in the United States."

In another ARP-funded project that began in October 2022, the NADC group began collaborating with APHIS Wildlife Services to study the susceptibility of elk to learn whether these larger relatives of white-tailed deer could also serve as COVID reservoirs in the wild.

Researchers at the ARS Exotic & Emerging Avian Viral Diseases Research Unit in Athens, Georgia, also are expanding the investigation into which species may serve as reservoirs or hosts for the COVID virus. The scientists have already developed a cell culture model to better predict host susceptibility to the virus in the laboratory. In their model, a receptor from a different animal species can be put onto cells that the virus normally cannot infect. After adding a new receptor, if the virus can infect those cells, then the virus may be able to infect the species the receptor came from.

"The impact of the cell line is that we are able to screen diverse animal species without doing actual animal studies to see if any given species can serve as a host for the COVID virus," said David Suarez, research leader of the unit in Athens. "Understanding the COVID virus' host range is essential to understanding the ecology of the virus and the role different species may play as reservoirs or bridge-species to humans.

Suarez's research team will be collaborating with APHIS Wildlife Services to apply their cell line technique to a larger number of wildlife species to screen for susceptibility to the COVID virus.

ARS is the U.S. Department of Agriculture's chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in U.S. agricultural research results in $20 of economic impact.