Searching for SARS-CoV-2 in animals

Sharon-Brookes-banner.jpg 1
© iStock/nopparit

Aligned with our mission to advance the understanding and impact of microbiology, the Society reached out to our community of microbiologists to share their experiences in responding to SARS-CoV-2. We aim to showcase the perspective of scientists during the COVID-19 pandemic and the variety of roles adopted to mitigate the global crisis.

This case study was submitted by Dr Sharon Brookes, who is currently the Lead Scientist for the Animal and Zoonotic Viral Diseases at Animal and Plant Health Agency (APHA), UK. She discusses the projects that APHA have been are involved with since the start of the pandemic, exploring SARS-CoV-2 in animals and its ability to transmit to, from and between people and animals, the development of new testing techniques and how these experiences aided the development of the APHA coronavirus team.

How did you respond to SARS-CoV-2 during the COVID-19 pandemic?

At APHA we were able to respond to the national and global needs facilitated by the Department for Environment, Food and Rural Affairs (DEFRA), UK and the Scottish and Welsh Governments. When SARS-CoV-2 entered the UK as human COVID, we immediately engaged in the national effort by providing expertise; hazard, threat and risk assessments; test development; and testing and science facilities. In addition, we increased our capability and capacity to work on the pandemic by deploying APHA staff to testing hubs. We also began projects to explore SARS-CoV-2 in animals and its ability to transmit to, from and between people and animals.

Through in-house and collaborative working, APHA surveillance, diagnostic and research laboratories rapidly established quality assured testing algorithms for veterinary diagnosis of animal SARS-CoV-2 infections as part of our leadership of the UK National Reference Laboratory, to fulfil the requirements for reporting to The Human Animal Infections and Risk Surveillance (HAIRS) group and the World Organisation for Animal Health (OIE). We provided robust evidence for new and emerging disease policy for the UK, Europe and globally.

APHA has had 15 animal submissions (dog, cat, camel, tiger, snow leopard, ferret and civet) for disease confirmation with six cases diagnosed as SARS-CoV-2 positive (cat, dogs, tigers and ferrets). These tests were validated and accredited, utilising research samples following successful adaptation of APHA’s animal (ferret) model for Influenza A viruses to SARS-CoV-2, via collaboration with Public Health England (now UK Health Security Agency) in 2020. Genome sequencing of the SARS-CoV-2 human and animal origin viruses allowed APHA to contribute to the National COVID-19 efforts via the New and Emerging Respiratory Virus Threats Advisory Group and the National Core Study PROTECT programme. Our science and analytical groups fed into SAGE and provided UK Chief Veterinary Officers with data to support policy decision making, animal regulation updates and public awareness. 

At APHA we also conducted an exciting pilot study in partnership with the University of Southampton, UK. We trialled a community-wide surveillance programme in the south of England, using an alternative testing approach to detect COVID-19 infections in people, using saliva rather than swabs. This loop-mediated isothermal amplification (LAMP) based detection technique is much simpler, faster and cheaper compared to the standard real time Polymerase Chain Reaction (RT-PCR) method.

You can read more about ongoing APHA projects and findings in our Science Blog.

Was this response related to your work prior to the outbreak?

Our work at APHA revolves around conducting research on veterinary zoonoses/zooanthroponoses (infectious diseases that can transmit from animal to human or vice versa).  This includes endemic and exotic disease outbreak responses, for example: TB, salmonella, vector borne disease, bird flu, rabies and ebola. Therefore, preparing for disease-X (known unknowns and unknown unknowns) has been an integral part of our strategic mission.

What were some of the challenges that you faced during this time?

COVID-19 posed a few challenges for our team, one of these being the impact on staff by the virus itself and associated restrictions. Our response to the outbreak was prioritised, and therefore we had to re-schedule some of our usual work. One additional challenge we faced was ensuring reliable reagents, personal protective equipment and other essential supplies were available.

How did your experience throughout the response aid in your development?

The APHA staff experiences throughout the COVID-19 pandemic have further developed our early career scientists as part of our Public Sector Research Establishment (PSRE) status and heightened their responsiveness, broadening our interactions between veterinary and public health. It has provided opportunities to reignite collaborations and set up new partnerships with other microbiologists and policy makers. It has allowed us to offer our expertise and facilities to UK health and global responses (WHO & OIE), and provided professional development opportunities. We have expanded our Coronavirus programme from pre-COVID to include further research and development investment until 2025. 

From a personal perspective, I became a member of the UK International Coronavirus Network (ICN) directors’ group, became a special editions editor for two SARS-CoV-2 publication collections, obtained funding as a principal and as a co-investigator for research projects and initiated a new research team with two post-docs focused on SARS-CoV-2 investigations. In addition, I have had the pleasure of working with a wider remit of scientists in PSRE, academia and industry.

What can we learn about the importance of microbiology from the COVID-19 pandemic?

This pandemic has taught us about knowns, known unknowns and unknown unknowns. APHA’s microbiological work on SARS-CoV-2 has enabled us to increase preparedness and responsiveness strategies that can assist on a national or global scale for this and future pandemics.

How did the Microbiology Society play a role in your response?

In response to the pandemic, the Microbiology Society set up the 'SARS-CoV-2 and COVID-19 Hub'. On this hub, digital events, press releases, journal collections, podcasts and blogs were uploaded. Regularly consulting this resource was something we at APHA found useful to help stay up-to-date and complement our research in this area. Being part of the Microbiology Society allowed us to tap into each other's skills, facilitating the establishment of the UCK-ICN partnership.

References
  1. Lean, F. Z. X., Núñez, A., Spiro, S., Priestnall, S. L., Vreman, S., Bailey, D., James, J., Wrigglesworth, E., Suarez-Bonnet, A., Conceicao, C., Thakur, N., Byrne, A. M. P., Ackroyd, S., Delahay, R. J., van der Poel, W. H. M., Brown, I. H., Fooks, A. R., Brookes, S. M. Differential susceptibility of SARS-CoV-2 in animals: Evidence of ACE2 host receptor distribution in companion animals, livestock and wildlife by immunohistochemical characterisation. Transbound Emerg Dis. 2021.
     
  2. James, J., Rhodes, S., Ross, C. S., Skinner, P., Smith, S. P., Shipley, R., Warren, C. J., Goharriz, H., McElhinney, L. M., Temperton, N., Wright, E., Fooks, A. R., Clark, T. W., Brookes, S. M., Brown, I. H., Banyard, A. C. Comparison of Serological Assays for the Detection of SARS-CoV-2 Antibodies. Viruses. 2021; 13(4), 713.
     

  3. Delahay, R. J., de la Fuente, J., Smith, G. C., Sharun, K., Snary, E. L., Flores Girón, L., Nziza, J., Fooks, A. R., Brookes, S. M., Lean, F. Z. X., Breed, A. C., Gortazar, C. Assessing the risks of SARS-CoV-2 in wildlife. One Health Outlook. 2021; 3:7.

  4. Everett, H. E., Lean, F. Z. X., Byrne, A. M. P., van Diemen, P. M., Rhodes, S., James, J., Mollett, B., Coward, V. J., Skinner, P., Warren, C. J., Bewley, K. R., Watson, S., Hurley, S., Ryan, K. A., Hall, Y., Simmons, H., Núñez, A., Carroll, M. W., Brown, I. H., Brookes, S. M. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viruses. 2021; 13(1), 113.

  5. Lean, F. Z. X., Lamers, M. M., Smith, S. P., Shipley, R., Schipper, D., Temperton, N., Haagmans, B. L., Banyard, A. C., Bewley, K. R., Carroll, M. W., Brookes, S. M., Brown, I., Nuñez, A. Development of immunohistochemistry and in situ hybridisation for the detection of SARS-CoV and SARS-CoV-2 in formalin-fixed paraffin-embedded specimens. Sci Rep. 2020; 10(1), 21894.

 

Sharon-Brookes-headshot.jpg
About the author

Dr Sharon Brookes is currently the Lead Scientist for Animal and Zoonotic Viral Diseases at Animal and Plant Health Agency (APHA), working closely with the Department for Environment, Food and Rural Affairs (Defra).