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Apaa T, Withers AJ, Mackenzie L, Staley C, Dessi N, Blanchard A, Bennett M, Bremner-Harrison S, Chadwick EA, Hailer F, Harrison SWR, Lambin X, Loose M, Mathews F, Tarlinton R. Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat ( Mustela erminea) Minacovirus. J Gen Virol 2023; 104:001917. [PMID: 38059490 PMCID: PMC10770931 DOI: 10.1099/jgv.0.001917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
Repeat spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into new hosts has highlighted the critical role of cross-species transmission of coronaviruses and establishment of new reservoirs of virus in pandemic and epizootic spread of coronaviruses. Species particularly susceptible to SARS-CoV-2 spillover include Mustelidae (mink, ferrets and related animals), cricetid rodents (hamsters and related animals), felids (domestic cats and related animals) and white-tailed deer. These predispositions led us to screen British wildlife with sarbecovirus-specific quantitative PCR and pan coronavirus PCR assays for SARS-CoV-2 using samples collected during the human pandemic to establish if widespread spillover was occurring. Fourteen wildlife species (n=402) were tested, including: two red foxes (Vulpes vulpes), 101 badgers (Meles meles), two wild American mink (Neogale vison), 41 pine marten (Martes martes), two weasels (Mustela nivalis), seven stoats (Mustela erminea), 108 water voles (Arvicola amphibius), 39 bank voles (Myodes glareolous), 10 field voles (Microtus agrestis), 15 wood mice (Apodemus sylvaticus), one common shrew (Sorex aranaeus), two pygmy shrews (Sorex minutus), two hedgehogs (Erinaceus europaeus) and 75 Eurasian otters (Lutra lutra). No cases of SARS-CoV-2 were detected in any animals, but a novel minacovirus related to mink and ferret alphacoronaviruses was detected in stoats recently introduced to the Orkney Islands. This group of viruses is of interest due to pathogenicity in ferrets. The impact of this virus on the health of stoat populations remains to be established.
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Affiliation(s)
- Ternenge Apaa
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Amy J. Withers
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Laura Mackenzie
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ceri Staley
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Nicola Dessi
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, York, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Malcolm Bennett
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Samantha Bremner-Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
- Vincent Wildlife Trust, Eastnor, Ledbury, UK
| | | | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, Cardiff, UK
| | - Stephen W. R. Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Fiona Mathews
- School of Life Sciences, University of Sussex, Sussex, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
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2
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Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States. J Virol 2023; 97:e0082923. [PMID: 37882520 PMCID: PMC10688340 DOI: 10.1128/jvi.00829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.
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Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, Durham, USA
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, Ithaca, New York, USA
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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3
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Liu B, Zhao P, Xu P, Han Y, Wang Y, Chen L, Wu Z, Yang J. A comprehensive dataset of animal-associated sarbecoviruses. Sci Data 2023; 10:681. [PMID: 37805633 PMCID: PMC10560225 DOI: 10.1038/s41597-023-02558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023] Open
Abstract
Zoonotic spillover of sarbecoviruses (SarbeCoVs) from non-human animals to humans under natural conditions has led to two large-scale pandemics, the severe acute respiratory syndrome (SARS) pandemic in 2003 and the ongoing COVID-19 pandemic. Knowledge of the genetic diversity, geographical distribution, and host specificity of SarbeCoVs is therefore of interest for pandemic surveillance and origin tracing of SARS-CoV and SARS-CoV-2. This study presents a comprehensive repository of publicly available animal-associated SarbeCoVs, covering 1,535 viruses identified from 63 animal species distributed in 43 countries worldwide (as of February 14,2023). Relevant meta-information, such as host species, sampling time and location, was manually curated and included in the dataset to facilitate further research on the potential patterns of viral diversity and ecological characteristics. In addition, the dataset also provides well-annotated sequence sets of receptor-binding domains (RBDs) and receptor-binding motifs (RBMs) for the scientific community to highlight the potential determinants of successful cross-species transmission that could be aid in risk estimation and strategic design for future emerging infectious disease control and prevention.
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Affiliation(s)
- Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
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4
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Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.541188. [PMID: 37745528 PMCID: PMC10515766 DOI: 10.1101/2023.05.31.541188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Small to mid-sized carnivores, or meso-carnivores, comprise a group of diverse mammals, many of which can adapt to anthropogenically disturbed environments. Wild meso-carnivores living in urban areas may get exposed to or spread pathogens to other species, including stray/feral domestic animals. Several coronaviruses (CoVs) have been detected in domesticated and farmed meso-carnivores, but knowledge of CoVs circulating in free-ranging wild meso-carnivores remains limited. In this study, we analyzed 321 samples collected between 2016 and 2022 from 9 species of free-ranging wild meso-carnivores and stray/feral domestic cats in the northeastern United States. Using a pan-CoV PCR, we screened tissues, feces, and saliva, nasal, and rectal swabs. We detected CoV RNA in fecal and saliva samples of animals in four species: fisher (Pekania pennanti), bobcat (Lynx rufus), red fox (Vulpes vulpes), and domestic cat (Felis catus). Next-generation sequencing revealed that all these viruses belonged to the Luchacovirus subgenus (Alphacoronavirus genus), previously reported only in rodents and lagomorphs (i.e., rabbits). Genetic comparison of the 3'-end of the genome (~12,000bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct from those from rodents and lagomorphs. Genetic characterization of the spike protein revealed that the meso-carnivore luchacoviruses do not have an S1/S2 cleavage motif but do have highly variable structural loops containing cleavage motifs similar to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the spike protein of CoVs in wild species for further targeted epidemiologic monitoring.
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Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, 240 Farrier Road, Ithaca, NY 14853
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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5
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Tan CCS, Trew J, Peacock TP, Mok KY, Hart C, Lau K, Ni D, Orme CDL, Ransome E, Pearse WD, Coleman CM, Bailey D, Thakur N, Quantrill JL, Sukhova K, Richard D, Kahane L, Woodward G, Bell T, Worledge L, Nunez-Mino J, Barclay W, van Dorp L, Balloux F, Savolainen V. Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential. Nat Commun 2023; 14:3322. [PMID: 37369644 PMCID: PMC10300128 DOI: 10.1038/s41467-023-38717-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023] Open
Abstract
There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine complete genomes, including two novel coronavirus species, 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 warrants closer surveillance.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, Gower St, London, WC1E 6BT, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Jahcub Trew
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London, W2 1PG, UK
| | - Kai Yi Mok
- Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London, W2 1PG, UK
| | - Charlie Hart
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Kelvin Lau
- Protein Production and Structure Core Facility (PTPSP), School of Life Sciences, École Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy (LBEM), School of Basic Science, École Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - C David L Orme
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Emma Ransome
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - William D Pearse
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Christopher M Coleman
- Queen's Medical Centre, University of Nottingham, Derby Rd, Lenton, Nottingham, NG7 2UH, UK
| | | | - Nazia Thakur
- The Pirbright Institute, Surrey, GU24 0NF, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Jessica L Quantrill
- Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London, W2 1PG, UK
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London, W2 1PG, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, Gower St, London, WC1E 6BT, UK
| | - Laura Kahane
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Thomas Bell
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Lisa Worledge
- The Bat Conservation Trust, Studio 15 Cloisters House, Cloisters Business Centre, 8 Battersea Park Road, London, SW8 4BG, UK
| | - Joe Nunez-Mino
- The Bat Conservation Trust, Studio 15 Cloisters House, Cloisters Business Centre, 8 Battersea Park Road, London, SW8 4BG, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, St Marys Medical School, Paddington, London, W2 1PG, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower St, London, WC1E 6BT, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower St, London, WC1E 6BT, UK
| | - Vincent Savolainen
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.
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6
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Apaa T, Withers AJ, Staley C, Blanchard A, Bennett M, Bremner-Harrison S, Chadwick EA, Hailer F, Harrison SWR, Loose M, Mathews F, Tarlinton R. Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology. J Gen Virol 2023; 104. [PMID: 37319000 DOI: 10.1099/jgv.0.001859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposideros and R. ferrumequinum) present in Great Britain, collected in 2021-22 during the peak of COVID-19 pandemic. One hundred and ninety seven R. hipposideros samples from 33 roost sites and 277 R. ferrumequinum samples from 20 roost sites were tested. No coronaviruses were detected in any samples from R. ferrumequinum whereas 44 and 56 % of individual and pooled (respectively) faecal samples from R. hipposideros across multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95 % similarity to previously-reported European isolates from R. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread in R. hipposideros. Despite frequently sharing roost sites with R. ferrumequinum, no evidence of cross-species transmission was found.
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Affiliation(s)
- Ternenge Apaa
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Amy J Withers
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Ceri Staley
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Malcolm Bennett
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Samantha Bremner-Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
- Vincent Wildlife Trust, Herefordshire, UK
| | - Elizabeth A Chadwick
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
- Organisms and Environment, School of Biosciences, Cardiff University, UK
| | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, UK
| | - Stephen W R Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Fiona Mathews
- School of Life sciences, University of Sussex, Brighton, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
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7
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Gulati I, Khan S, Gulati G, Verma SR, Khan M, Ahmad S, Bantun F, Mathkor DM, Haque S. SARS-CoV-2 origins: zoonotic Rhinolophus vs contemporary models. Biotechnol Genet Eng Rev 2022:1-34. [PMID: 36036250 DOI: 10.1080/02648725.2022.2115682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
Abstract
The question of the origin of coronavirus spread like wildfire ever since it wreaked havoc among humankind, and ever since the scientific community has worked tirelessly to trace the history of the virus. In this review, we have tried to compile relevant literature pertaining to the different theories of origin of SARS-CoV-2, hopefully without any bias, and we strongly support the zoonotic origin of the infamous SARS-CoV-2 in bats and its transfer to human beings through the most probable evolutionary hosts, pangolins and minks. We also support the contemporary 'Circulation Model' that simply mirrors the concept of evolution to explain the origin of the virus which, the authors believe, is the most rational school of thought. The most recent variant of SARS-CoV-2, Omicron, has been taken as an example to clarify the concept. We recommend the community to refer to this model for further understanding and delving deep into this mystery of the origin of SARS-CoV-2.
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Affiliation(s)
- Ishika Gulati
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Garima Gulati
- Department of Applied Mechanics, Motilal Nehru National Institute of Technology, Prayagraj, Allahabad, India
| | | | - Mahvish Khan
- Department of Biology, College of science, University of Ha'il, Ha'il, Saudi Arabia
| | - Saheem Ahmad
- Department of clinical laboratory science, College of Applied Medical Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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8
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Abstract
Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should also be considered. Results: Here we show that the genomes of SARS-CoV-2 and SARS-CoV-1 significantly diverge from other SARS-like coronaviruses through short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for host cell invasion, virus replication, and host immune response. For SARS-CoV-1, we identify two sites: one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain; for SARS-CoV-2, one at the start of the viral replicase domain, and the other toward the end of the spike gene past its domain junction. At this junction, we detect a highly specific stretch of yeast origin covering the critical furin cleavage site insert PRRA, which has not been seen in other lineage b betacoronaviruses. As yeast is not a natural host for this virus family, we propose an artificial synthesis model for viral constructs in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential yeast sequence patterns congruent with chromosomes harboring specific auxotrophic markers further support yeast artificial synthesis. Conclusions: These results provide evidence that the genomes of SARS-CoV-1 and SARS-CoV-2 contain sequence information that points to their artificial synthesis in genetically modified yeast cells. Our data specifically allow the identification of the yeast S. cerevisiae as a potential recombination donor for the critical furin cleavage site in SARS-CoV-2.
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