What's the Risk from and to European wildlife from SARS-like Coronaviruses?
Lead Research Organisation:
University of Nottingham
Department Name: School of Veterinary Medicine and Sci
Abstract
The current COVID-19 human pandemic had its origins in SE Asian wildlife, and although the natural, endemic host remains unknown (most likely bats), onward transmission from humans to other species including large outbreaks in farmed mink and cases in domestic cats keep occuring . The outbreak in mink in Europe and the USA with transmission back to humans has raised the spectre of the virus establishing itself in other animal hosts, creating a new reservoir for the virus, with potentially serious consequences for both humans and affected animals.
Europe is home to a large number of wild mustelid species, including feral mink, along with bats known to carry SARS-like viruses and cricetid rodents thought to be susceptible to SARs-CoV2. However, we currently have no idea whether any virus spill-over or circulation is occurring in these animals. This project will perform PCR based screening of faecal and lung samples from the highest risk wildlife species for SARS-CoV-2 like viruses in the UK (bats, mustelids and cricetid rodents), including retrieval of full virus sequences from any positive animals using NGS sequencing techniques (Illumina and Nanopore).
The project will determine:
a) If SARS-COV-2 spill-over from humans into wildlife is currently occurring
b) What other coronaviruses these animals are carrying
This will enable decisions to be made as to whether SARS-CoV-2 circulation in European wildlife represents a real risk to the human population and/or to wildlife, and if monitoring or mitigation programmes are necessary
Europe is home to a large number of wild mustelid species, including feral mink, along with bats known to carry SARS-like viruses and cricetid rodents thought to be susceptible to SARs-CoV2. However, we currently have no idea whether any virus spill-over or circulation is occurring in these animals. This project will perform PCR based screening of faecal and lung samples from the highest risk wildlife species for SARS-CoV-2 like viruses in the UK (bats, mustelids and cricetid rodents), including retrieval of full virus sequences from any positive animals using NGS sequencing techniques (Illumina and Nanopore).
The project will determine:
a) If SARS-COV-2 spill-over from humans into wildlife is currently occurring
b) What other coronaviruses these animals are carrying
This will enable decisions to be made as to whether SARS-CoV-2 circulation in European wildlife represents a real risk to the human population and/or to wildlife, and if monitoring or mitigation programmes are necessary
Publications
Apaa T
(2023)
Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus.
in The Journal of general virology
Apaa T
(2023)
Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology.
in The Journal of general virology
Cruz AVS
(2024)
Genomic characterization and cross-species transmission potential of hedgehog coronavirus.
in One health (Amsterdam, Netherlands)
Hinds J
(2024)
Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.
in Access microbiology
Tarlinton R
(2022)
Mustelid samples needed for coronavirus testing.
in The Veterinary record
| Description | Screening of UK wildlife for SARS-CoV-2 was negative (indicating that the virus was not transmitted into UK wildlife species). We did however find a number of other novel coronaviruses |
| Exploitation Route | A current PhD studentship is following up the work to further characterise the viruses found in this project |
| Sectors | Agriculture Food and Drink Environment Healthcare |
| Description | Further work from this project and the methods developed in it has been used in a follow on PhD studentship (BBSRC DTP) and European College of Veterinary Microbiology Resident externships contributing to critical clinical veterinary skills training in Europe |
| First Year Of Impact | 2023 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Societal Policy & public services |
| Description | European Microbiology training workshop |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Clinical microbiology specialists now trained in critical skills for pathogen ID |
| Description | Pump Priming Collaboration between UK and EU Partners |
| Amount | £7,115 (GBP) |
| Funding ID | PPHE210278 |
| Organisation | The British Academy |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 07/2022 |
| Title | Lack of detection of SARS-CoV-2 in British wildlife in 2020-21 and first description of a stoat (Mustela erminea) Minacovirus |
| Description | Supplementary material for 'Lack of detection of SARS-CoV-2 in British wildlife in 2020-21 and first description of a stoat (Mustela erminea) Minacovirus'. Demographic data for samples and Supplementary Figures:Figure 1: locations of sample collectionsFigure 2: Full spike gene minacoviruses and tegacoviruses phylogenetic treeFigure 3: Partial fragment (98 bp) spike gene minacoviruses and tegacoviruses phylogenetic treeFigure 4: Full N gene minacoviruses and tegacovirusesFigure 5: Partial fragment (315 bp) RDRP gene minacoviruses and tegacovirusesTable 1: List of reference genome sequences for full virus trees |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/Lack_of_detection_of_SARS-CoV-2_in_British_wildli... |
| Title | Lack of detection of SARS-CoV-2 in British wildlife in 2020-21 and first description of a stoat (Mustela erminea) Minacovirus |
| Description | Supplementary material for 'Lack of detection of SARS-CoV-2 in British wildlife in 2020-21 and first description of a stoat (Mustela erminea) Minacovirus'. Demographic data for samples and Supplementary Figures:Figure 1: locations of sample collectionsFigure 2: Full spike gene minacoviruses and tegacoviruses phylogenetic treeFigure 3: Partial fragment (98 bp) spike gene minacoviruses and tegacoviruses phylogenetic treeFigure 4: Full N gene minacoviruses and tegacovirusesFigure 5: Partial fragment (315 bp) RDRP gene minacoviruses and tegacovirusesTable 1: List of reference genome sequences for full virus trees |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://microbiology.figshare.com/articles/dataset/Lack_of_detection_of_SARS-CoV-2_in_British_wildli... |
| Title | Sequence data UK bats and stoats |
| Description | Illumina mRNA sequence of stoat and bat samples with derivative coronaviruses |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Provision of further wildlife coronavirus sequences to the sequencing databases |
| URL | https://www.ncbi.nlm.nih.gov/sra/PRJNA780532 |
| Title | hedgehog sequence |
| Description | Genebank Number PP724614 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | insight into cross species transmission risk of merbecoviruses |
| Description | European Microbiology College |
| Organisation | University of Porto |
| Country | Portugal |
| Sector | Academic/University |
| PI Contribution | Expertise on illumina sequencing of wildlife clinical diagnostic samples and bio-informatic retrieval of novel coronavirus sequences |
| Collaborator Contribution | Provision of labour and samples (these were externships by European Veterinary Microbiology Residents needing help to sequence novel coronaviruses in European Hedgehogs) |
| Impact | Several publications (one in press, one in preparation). Residents completed compulsory externship placements as part of their clinical specialist training requirements with the European College |
| Start Year | 2022 |
| Description | European Microbiology College |
| Organisation | University of Turin |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Expertise on illumina sequencing of wildlife clinical diagnostic samples and bio-informatic retrieval of novel coronavirus sequences |
| Collaborator Contribution | Provision of labour and samples (these were externships by European Veterinary Microbiology Residents needing help to sequence novel coronaviruses in European Hedgehogs) |
| Impact | Several publications (one in press, one in preparation). Residents completed compulsory externship placements as part of their clinical specialist training requirements with the European College |
| Start Year | 2022 |
| Description | International Conference on Livestock, Companion Animals and Wildlife Coronaviruses 2023 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Scientific meeting focused on coronaviruses in animals |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://uk-icn.co.uk/events/international-conference-on-livestock-companion-animals-and-wildlife-cor... |
| Description | SARS-CoV-2 in Wildlife Workshop (for UK researchers) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop for UK research groups involved in animal monitoring or testing in the UK. Presentation of data from monitoring and research projects in this area from UKRI/EU/DEFRA/PHE funded research projects. Representation from DEFRA scientists, PHE, University academic groups and UKRI research insitutes. The primary purpose of the day is to facilitate information sharing on the current situation with which animal species we are seeing SARS-CoV-2 spill over into in the UK, share best practice (or lessons learnt) on testing and monitoring, decrease duplicated research efforts, ensure more co-ordinated messaging to wildlife care groups and to begin to build larger consortia for follow up work to the current (very scattered) projects. Co-hosted by myself and Dan Horton at Surrey (UK co-ordinator of the EU funded COVRIN project). It has already acheived some of its aims in getting different government groups to share data with each other on deer monitoring (instead of attempting separate monitoring efforts) . |
| Year(s) Of Engagement Activity | 2022 |
| Description | Somerset badger group |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | talk to wildlife carer groups (some of whom had submitted samples) about the research outcomes |
| Year(s) Of Engagement Activity | 2022 |
| Description | Talk to kent mammal and bat carer groups about SARS-CoV-2 in wildlife |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Talk to regional bat and mammal carer groups about the risks and mitigations for SARS-CoV-2 in wildlife. Dissemination of current research knowledge to people at the coal face of risk for spill over. Some of these people have also submitted samples to our research project and we will be delivering the preliminary results to them |
| Year(s) Of Engagement Activity | 2022 |