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One Health - Building an Early Warning System for SARS-CoV-2 and Other Animal Diseases


One Health SARS-CoV-2 in Animals Building an Early Warning System Keeping Animals and People Safe Animal Health Officials and Veterinarians Funding Opportunities

With funding from the American Rescue Plan Act, we are bringing together experts from across APHIS—whether they focus on wildlife diseaseslivestock, or companion and zoo animals—and partnering with other agencies that protect human and environmental health to take a One Health approach to the problems the global SARS-CoV-2 pandemic has highlighted. Our priority is to understand SARS-CoV-2 and how it moves between people and animals. This includes learning more about the virus, which animals it affects, and how it is spreading to new locations or species. Long term we expect to build national capacity to potentially prevent or limit the next zoonotic disease outbreak, or the next global pandemic.

Current Projects

SARS-CoV-2 virus detection in deer located in the Management Units for the Conservation of Wildlife (UMA's) of the State of Nuevo León 


Start Date: Fall 2022  

APHIS and the Nuevo León State of Mexico are partnering to assess SARS-CoV-2 virus in white-tailed deer populations. Nuevo León borders the United States. With a high rate of national and foreign hunters coming into the region having close physical contact with wildlife, it is increasingly important to implement actions that will aid in the prevention and control of zoonotic diseases. Partnering with Parks and Wildlife in Nuevo León State (PWNL), we will collect samples from white-tailed deer (WTD) in Nuevo León State and APHIS will test them for SARS-CoV-2 at the USDA APHIS Wildlife Disease Diagnostic Laboratory.  This project will establish baseline SARS-CoV-2 infection rates amongst the deer populations in that region. If the virus is present, APHIS will analyze available data to estimate the likely incidence of the disease within these animal populations and evaluate the potential implications for animal and public health.  

Gaining a greater understanding of susceptibility, prevalence, transmission, and disease processes of SARS-CoV-2 in WTD populations is important to protect human and animal health, and for development of risk mitigation strategies. 


Spillover of SARS-CoV-2 Into Wildlife from Wastewater Treatment Plants in Colorado 


Start Date: Fall 2022  

SARS-CoV-2 is shed in human feces; therefore, surveillance of Wastewater Treatment Plants (WWTPs) has become an important mechanism for identifying communities experiencing outbreaks of COVID-19. It is unknown if SARS-CoV-2 can survive the treatment process, and once introduced into bodies of water, whether it can be transmitted to wildlife.  

This project will examine whether WWTPs are a source of SARS-CoV-2 spillover into nearby wildlife that could then be a source of spillback into humans. In partnership with the Colorado Department of Public Health, APHIS will collect fecal samples from targeted wildlife at or near WWTPs across 10 municipalities on the Colorado Front Range. Wildlife species include deer mice, bushy-tailed woodrats, mink, white-tailed deer, mule deer, red fox, and the Arizona myotis bat. These samples will be tested for SARS-CoV-2 and those genetically sequenced will be compared to existing variants previously found in humans and animals. The goal of this study is to test the transmission mechanisms through a conceptual model that assumes WWTPs are a source of SARS-CoV-2 transmission to wildlife. Studying transmission pathways of SARS-CoV-2 among humans and wildlife is essential to understand sources of infection, risks of future outbreaks and where these might occur.    

For more information, please contact: APHISpress@usda.gov.


Investigation of Unusual Morbidity and Mortality Events 


Start Date: Fall 2022  

Partnering with the National Animal Health Laboratory Network (NAHLN), states, animal owners, and local communities, APHIS will develop and implement an enhanced process for investigating unusual deaths or illness in animals, also called unusual morbidity and mortality events (UME).  This effort will focus on diseases not routinely regulated or surveilled for under current testing methods. This new testing process will improve APHIS’ and our partners’ ability to identify new or emerging SARS-CoV-2 variants or other emerging diseases and increase the country’s ability to detect and respond to these threats earlier.

Aptamer-based pen-side diagnostics for rapid detection of SARS-CoV-2 variants  


Start Date: Fall 2022  

APHIS and USDA’s Agricultural Research Service (ARS) will work together develop a tool to rapidly detect SARS-CoV-2 variants in livestock herds and other wildlife species. 

Experts at APHIS and ARS will develop an aptamer-based lateral flow assay or aLFA, which is a pen-shaped, or pen-side diagnostic tool that can be easily used by veterinarians and farm workers throughout the nation. The pen-side tool is used as a pre-clinical SARS CoV-2 detection test capable of identifying multiple virus variants in animals. This rapid, non-invasive point-of-care test will facilitate the monitoring of animal health. It can also be used as a surveillance tool to help farmers, veterinarians, and regulatory agencies rapidly address and monitor SARS CoV-2 in animals. 

Development of a quick and easy SARS-CoV-2 detection tool will help protect farm workers, animals, and the public from exposure to the virus. 


Companion Animal Emerging and Zoonotic Disease Framework: Establishing a Network for SARS CoV-2 Surveillance and Assay Methods Comparison Study 


Start Date: Fall 2022  

There are over 135 million pet cats and dogs in almost 80 million households across the United States, and even though the risk of getting SARS-CoV-2 from your pets is low, we lack the full understanding of how SARS-CoV-2 impacts animal and human health. APHIS aims to enhance our surveillance for SARS-CoV-2 at the interface between animals and humans that share the same environment. Through this project, APHIS will work with veterinary partners to offer SARS-CoV-2 testing for dogs and cats with signs that could be SARS-CoV-2 infection; a few healthy animals will be tested as a control for the project. This effort will allow APHIS to establish a framework and build networks for information sharing and outreach with companion animal stakeholders for both the private and commercial veterinary industry. APHIS’ strategic framework outlines how the agency is focusing its efforts to prevent, detect, investigate, and respond to SARS-CoV-2 in animals, as well as other emerging diseases that could pose a threat to humans and animals. 

Investigation of SARS-CoV-2 in Wildlife Rehabilitation Facilities


Start Date: Summer 2022  

Some wildlife species have been confirmed positive with SARS-CoV-2, but the full range of species that are susceptible to the virus is unknown. Human-wildlife-environmental interactions occur in various settings, including wildlife rehabilitation facilities, where ill or injured wildlife are temporarily housed in human care. This project aims to help us learn more about how this virus behaves in various wildlife species. Working with wildlife rehab facilities across the U.S., we plan to test a wide range of terrestrial and aquatic mammalian species to determine which are susceptible or may carry the virus with no outward signs of infection.  We will also assess biosecurity practices to determine how we can better protect the animals and the people who work with them. This project is an exciting opportunity to build and strengthen One Health partnerships and will create a template for data collection and assessment, info sharing and communication to help limit or prevent future zoonotic outbreaks or pandemics. 


Animal reservoirs of SARS-CoV-2: Prioritization for monitoring and surveillance


Start Date: Summer 2022

Multiple studies have detected the SARS-CoV-2 virus in farmed, domestic, zoo, and wild animals. The animal reservoirs study will examine whether multiple animal species could become long-term hosts or reservoirs of the virus, and if so, could they contribute to the potential evolution of novel virus variants. APHIS-Wildlife Services and University of Missouri researchers will conduct experimental examinations of cells from different animal species, testing for susceptibility to SARS-CoV-2, supporting development of mitigation strategies and practices to help break potential virus transmission cycles. The resulting data from this study will assist in developing a rapid screening tool that enables determination of whether an animal species is susceptible to SARS-CoV-2 without a requirement to infect the animal. This research and development of a rapid screening tool will support more additional species surveillance beyond those examined in this study and the development of strategies and practices to break potential transmission cycles between animals and humans. 

For more information, please contact: APHISpress@usda.gov


Field Assessment of Wildlife-Human Interactions


Start Date: Summer 2022

APHIS, in partnership with George Mason University and the University of Maryland, is working to identify when and where interactions between deer and humans occur to better understand the risks of SARS-CoV-2 transmission. The project uses existing human and wildlife image data from motion-activated camera systems, aggregate mobile device data, and GPS-collared wildlife to better understand how often deer and humans are in the same area and what factors – such as land type – are associated with high levels of deer and human interactions. The project will also examine potential interventions for lowering human-deer interactions and the risk of SARS-CoV-2 transmission.

For more information, please contact: APHISpress@usda.gov


SARS-CoV-2 Experimental Infection in Priority Wildlife Species


Start Date: Spring 2022

This project will assess the ability of SARS-CoV-2 to replicate and be shed into the environment by wildlife species that are experimentally inoculated with the virus. It will also determine the virus’ biological and physical impacts and disease outcomes. Trials will focus on wildlife species that are often found close to humans in urban and suburban environments. Species studied will be canids, felids, mustelids, cervids, marsupials, and rodents. Other species may be studied as more information becomes available. This project will help USDA and other researchers understand potential spread by animals and will inform targeted animal surveillance. Results will help identify species that may potentially serve as SARS-CoV-2 wildlife reservoirs and gauge the possibility they may contribute to additional virus variants or infection in additional species.

For more information, please contact: APHISpress@usda.gov


Zoo and Aquarium Serology Study


Start Date: Spring 2022

The Zoo and Aquarium Serology Study will solicit and test serum samples from participating zoos and aquariums across the country to identify animals that may have been exposed to SARS-CoV-2. The study will also test free-ranging wildlife species on and around zoo premises for SARS-CoV-2 exposure and infection.  APHIS will assess biosecurity and epidemiological risks at each facility, using a standard protocol to be developed by One Health partners. Researchers will use the assessments to compare practices and risks against the percentage of animals with a history of exposure to SARS-CoV-2. This will help identify recommended practices that facilities may adopt to prevent future SARS-CoV-2 infections. APHIS will publish a final report that can be used to strengthen the Secure Zoo Strategy.


Serosurvey of SARS-CoV-2 in Wild Canids and other Susceptible Mesocarnivores


Start Date: Spring 2022

Research shows that SARS-CoV-2 infections are not limited to people, and that multiple wild and domestic animal species can also be infected by the virus. Currently, there is no evidence that animals play a significant role in spreading SARS-CoV-2, the virus that causes COVID-19, to people. More studies are needed to understand if and how different animals could be affected by SARS-CoV-2. This project helps us start to answer that question. This project provides baseline data on the wild animal species exposed to SAR-CoV-2 by screening blood samples for SARS-CoV-2 antibodies from a variety of wildlife species in the United States. APHIS will leverage its existing wildlife sample archive to identify species exposed to SARS-CoV-2 and establish baseline data on antibody prevalence in those species. Results will help APHIS and other researchers target animal surveillance (species and locations) and experimental infection research, as well as shed light on novel SARS-CoV-2 wildlife reservoirs that could potentially seed future outbreaks and contribute to the evolution of novel virus variants.


Evaluation of Municipal Wastewater-Associated Wildlife as Potential Sources of Mutations of SARS-CoV-2


Start Date: Fall 2021

APHIS wildlife disease specialists are collaborating with University of Missouri researchers to capture and sample wildlife in and around wastewater systems in New York. Researchers are testing blood and tissue samples from rodents (Rattus sp.), raccoons, and other wildlife to look for evidence of exposure and infection to SARS-CoV-2 virus.  If the virus can be isolated from any samples, researchers will sequence the genome to identify any potential viral mutations and better understand its spread and transmissibility. Researchers are particularly interested in assessing whether rats or other wildlife can serve as reservoirs for the virus and whether this may play a role in emergence of new virus variants that may impact human and animal health.


SARS-CoV-2 in White-tailed Deer


Start Date: Fall 2021

White-tailed deer can be infected with SARS-CoV-2 and transmit the virus to other deer. This project will help APHIS and its partners better understand the impacts of SARS-CoV-2 in white-tailed deer and how widespread it is in the United States. This project will also help us understand if deer can serve as a reservoir for the virus, which could lead to new virus variants that may impact the health of deer, other animals, and people. In the initial phase of this project, APHIS will partner with state agencies and tribes across the United States to opportunistically collect samples from hunter harvested white-tailed deer. APHIS will also opportunistically sample deer during their wildlife damage management and state harvest activities.
Later phases of this project will focus on more targeted sampling based on what we learn during this initial phase.


Mink SARS-CoV-2 Transmission Avoidance and Monitoring Plan (Mink STAMP)


Start Date: Fall 2021

APHIS is launching a voluntary cooperative federal-state-industry effort to actively monitor for SARS-CoV-2 infection on mink farms and minimize risk of transmission of the virus between mink and human caretakers on U.S. mink farms. Our goal is to detect virus introduction into mink herds, conduct One Health investigations when SARS-CoV-2 is identified or suspected, and monitor for emergence of any new variants. The effort offers education, incentives, and infrastructure support for active SARS-CoV-2 monitoring and response, including surveillance of susceptible wildlife populations on or near mink farms; multimedia, multi-lingual biosecurity training materials for mink farm workers; and recommendations for herd management to help keep producers in business while still fully protecting people and mink from SARS-CoV-2.

For more information, please contact: APHISpress@usda.gov.


Strategic Framework

Our Strategic Framework outlines how we are focusing our efforts to prevent, detect, investigate and respond to SARS-CoV-2 in animals, as well as other emerging diseases that could pose a threat to both people and animals.


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