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Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Cedric C.S. Tan, Jahcub Trew, Thomas P. Peacock, Kai Yi Mok, Charlie Hart, View ORCID ProfileKelvin Lau, Dongchun Ni, David Orme, Emma Ransome, William D. Pearse, Christopher M. Coleman, Dalan Bailey, Nazia Thakur, Jessica L. Quantrill, Ksenia Sukhova, Damien Richard, Laura Kahane, Guy Woodward, Thomas Bell, Lisa Worledge, Joe Nunez-Mino, Wendy Barclay, Lucy van Dorp, Francois Balloux, View ORCID ProfileVincent Savolainen
doi: https://doi.org/10.1101/2023.01.17.524183
Cedric C.S. Tan
1UCL Genetics Institute, University College London, Gower St, London WC1E 6BT, UK
2The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
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Jahcub Trew
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Thomas P. Peacock
4Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London W2 1PG, UK
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Kai Yi Mok
4Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London W2 1PG, UK
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Charlie Hart
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Kelvin Lau
5Protein Production and Structure Core Facility (PTPSP), School of Life Sciences, École Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015 Lausanne, Switzerland
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  • ORCID record for Kelvin Lau
Dongchun Ni
6Laboratory of Biological Electron Microscopy (LBEM), School of Basic Science, École Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015 Lausanne, Switzerland
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David Orme
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Emma Ransome
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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William D. Pearse
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Christopher M. Coleman
7Queen’s Medical Centre, University of Nottingham, Derby Rd, Lenton, Nottingham NG7 2UH, UK
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Dalan Bailey
8The Pirbright Institute, Surrey GU24 0NF, UK
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Nazia Thakur
8The Pirbright Institute, Surrey GU24 0NF, UK
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Jessica L. Quantrill
4Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London W2 1PG, UK
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Ksenia Sukhova
4Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London W2 1PG, UK
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Damien Richard
1UCL Genetics Institute, University College London, Gower St, London WC1E 6BT, UK
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Laura Kahane
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Guy Woodward
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Thomas Bell
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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Lisa Worledge
9The Bat Conservation Trust, Studio 15 Cloisters House, Cloisters Business Centre, 8 Battersea Park Road, London SW8 4BG, UK
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Joe Nunez-Mino
9The Bat Conservation Trust, Studio 15 Cloisters House, Cloisters Business Centre, 8 Battersea Park Road, London SW8 4BG, UK
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Wendy Barclay
4Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London W2 1PG, UK
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Lucy van Dorp
1UCL Genetics Institute, University College London, Gower St, London WC1E 6BT, UK
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Francois Balloux
1UCL Genetics Institute, University College London, Gower St, London WC1E 6BT, UK
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Vincent Savolainen
3Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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  • ORCID record for Vincent Savolainen
  • For correspondence: v.savolainen@imperial.ac.uk
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Abstract

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses 48 faecal samples from 16 of the 17 bat species breeding in the UK and collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely-related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown but warrants closer surveillance.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Viral metagenomics and additional analyses are presented

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 21, 2023.
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Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Cedric C.S. Tan, Jahcub Trew, Thomas P. Peacock, Kai Yi Mok, Charlie Hart, Kelvin Lau, Dongchun Ni, David Orme, Emma Ransome, William D. Pearse, Christopher M. Coleman, Dalan Bailey, Nazia Thakur, Jessica L. Quantrill, Ksenia Sukhova, Damien Richard, Laura Kahane, Guy Woodward, Thomas Bell, Lisa Worledge, Joe Nunez-Mino, Wendy Barclay, Lucy van Dorp, Francois Balloux, Vincent Savolainen
bioRxiv 2023.01.17.524183; doi: https://doi.org/10.1101/2023.01.17.524183
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Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Cedric C.S. Tan, Jahcub Trew, Thomas P. Peacock, Kai Yi Mok, Charlie Hart, Kelvin Lau, Dongchun Ni, David Orme, Emma Ransome, William D. Pearse, Christopher M. Coleman, Dalan Bailey, Nazia Thakur, Jessica L. Quantrill, Ksenia Sukhova, Damien Richard, Laura Kahane, Guy Woodward, Thomas Bell, Lisa Worledge, Joe Nunez-Mino, Wendy Barclay, Lucy van Dorp, Francois Balloux, Vincent Savolainen
bioRxiv 2023.01.17.524183; doi: https://doi.org/10.1101/2023.01.17.524183

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