1
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Earnest R, Hahn AM, Feriancek NM, Brandt M, Filler RB, Zhao Z, Breban MI, Vogels CBF, Chen NFG, Koch RT, Porzucek AJ, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber HR, Cantoni JL, Pitzer VE, Olarte Castillo XA, Goodman LB, Wilen CB, Linske MA, Williams SC, Grubaugh ND. Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559030. [PMID: 37808797 PMCID: PMC10557615 DOI: 10.1101/2023.09.22.559030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Diverse mammalian species display susceptibility to and infection with SARS-CoV-2. Potential SARS-CoV-2 spillback into rodents is understudied despite their host role for numerous zoonoses and human proximity. We assessed exposure and infection among white-footed mice (Peromyscus leucopus) in Connecticut, USA. We observed 1% (6/540) wild-type neutralizing antibody seroprevalence among 2020-2022 residential mice with no cross-neutralization of variants. We detected no SARS-CoV-2 infections via RT-qPCR, but identified non-SARS-CoV-2 betacoronavirus infections via pan-coronavirus PCR among 1% (5/468) of residential mice. Sequencing revealed two divergent betacoronaviruses, preliminarily named Peromyscus coronavirus-1 and -2. Both belong to the Betacoronavirus 1 species and are ~90% identical to the closest known relative, Porcine hemagglutinating encephalomyelitis virus. Low SARS-CoV-2 seroprevalence suggests white-footed mice may not be sufficiently susceptible or exposed to SARS-CoV-2 to present a long-term human health risk. However, the discovery of divergent, non-SARS-CoV-2 betacoronaviruses expands the diversity of known rodent coronaviruses and further investigation is required to understand their transmission extent.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nicole M Feriancek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Matthew Brandt
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhe Zhao
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nicholas F G Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Abbey J Porzucek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Alexa Garbiel
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Claire Keanna
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Hannah Litwak
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Heidi R Stuber
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Jamie L Cantoni
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Ximena A Olarte Castillo
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Laura B Goodman
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Megan A Linske
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Scott C Williams
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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2
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [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: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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3
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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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4
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Lange CE, Coulibaly JK, Ako ABA, N'dri Vakou S, Koffi EK, Mendelsohn E, Ball S, Martinez S, Francisco L, Saylors K, Manzan J, Bamba D, Kouakou V, Koui ST, Frantz JL, Joly D, Yapi C, Daszak P, Dosso M, Laudisoit A. Human interactions with bats and bat coronaviruses in rural Côte d'Ivoire. One Health 2023; 16:100569. [PMID: 37275302 PMCID: PMC10229207 DOI: 10.1016/j.onehlt.2023.100569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Bats are presumed reservoirs of diverse α- and β- coronaviruses (CoVs) and understanding the diversity of bat-CoVs and the role bats play in CoV transmission is highly relevant in the context of the current COVID pandemic. We sampled bats in Côte d'Ivoire (2016-2018) living at ecotones between anthropogenic and wild habitats in the Marahoué National Park, a recently encroached protected area, to detect and characterize the CoVs circulating in bats and humans. A total of 314 bats were captured, mostly during the rainy season (78%), and CoV RNA was detected in three of the bats (0.96%). A CoV RNA sequence similar to Chaerephon bat coronavirus/Kenya/KY22/2006 (BtKY22) was found in a Chaerephon cf. pumilus and a Mops sp. fecal swab, while a CoV RNA sequence similar to the two almost identical Kenya bat coronaviruses BtKY55 and BtKY56 (BtKY55/56) was detected in an Epomops buettikoferi oral swab. Phylogenetic analyses indicated differences in the degree of evolutionary host-virus co-speciation for BtKY22 and BtKY55/56. To assess potential for human exposure to these viruses, we conducted human syndromic and community-based surveillance in clinics and high-risk communities. We collected data on participant characteristics, livelihoods, animal contact, and high-risk behaviors that may be associated with exposure to zoonotic diseases. We then collected biological samples for viral testing from 401 people. PCR testing of these biological samples revealed no evidence of CoV infection among the enrolled individuals. We identified higher levels of exposure to bats in people working in crop production and in hunting, trapping and fishing. Finally, we used the 'Spillover' risk-ranking tool to assess the potential for viral spillover and concluded that, while there is no evidence to suggest imminent risk of spillover for these CoVs, their host range and other traits suggest caution and vigilance are warranted in people with high exposure risk.
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Affiliation(s)
- Christian E Lange
- Metabiota Inc., 425 California Street, San Francisco, CA 94104, USA
- Labyrinth Global Health Inc., 546 15TH Ave NE, St. Petersburg, FL 33704, USA
- Kwantlen Polytechnic University, 12666 72 Avenue, Surrey, BC V3W 2M8, Canada
| | | | | | - Sabine N'dri Vakou
- Institute Pasteur of Côte d'Ivoire (IPCI), 01 BP 490, Abidjan, Côte d'Ivoire
| | | | - Emma Mendelsohn
- EcoHealth Alliance, 520 Eighth Ave, Suite 1200, New York, NY 10018, USA
| | - Shannon Ball
- EcoHealth Alliance, 520 Eighth Ave, Suite 1200, New York, NY 10018, USA
| | | | - Leilani Francisco
- The Henry M. Jackson Foundation, 6720A Rockledge Dr, Bethesda, MD 20817, USA
| | - Karen Saylors
- Metabiota Inc., 425 California Street, San Francisco, CA 94104, USA
- Labyrinth Global Health Inc., 546 15TH Ave NE, St. Petersburg, FL 33704, USA
| | - Jean Manzan
- Institute Pasteur of Côte d'Ivoire (IPCI), 01 BP 490, Abidjan, Côte d'Ivoire
| | - Djeneba Bamba
- Institute Pasteur of Côte d'Ivoire (IPCI), 01 BP 490, Abidjan, Côte d'Ivoire
| | - Valère Kouakou
- National Agricultural Development Support Laboratory (Laboratoire National d'Appui au Développement Agricole [in French], LANADA), BP 206, Bingerville, Côte d'Ivoire
| | | | | | - Damien Joly
- Metabiota Inc., 425 California Street, San Francisco, CA 94104, USA
| | - Cyprien Yapi
- National Agricultural Development Support Laboratory (Laboratoire National d'Appui au Développement Agricole [in French], LANADA), BP 206, Bingerville, Côte d'Ivoire
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Ave, Suite 1200, New York, NY 10018, USA
| | - Mireille Dosso
- Institute Pasteur of Côte d'Ivoire (IPCI), 01 BP 490, Abidjan, Côte d'Ivoire
| | - Anne Laudisoit
- EcoHealth Alliance, 520 Eighth Ave, Suite 1200, New York, NY 10018, USA
- University of Antwerp, EVECO, Campus Drie Eiken Universiteitsplein 1, 2610 Wilrijk, Belgium
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5
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Meta Djomsi D, Lacroix A, Soumah AK, Kinganda Lusamaki E, Mesdour A, Raulino R, Esteban A, Ndong Bass I, Mba Djonzo FA, Goumou S, Ndimbo-Kimugu SP, Lempu G, Mbala Kingebeni P, Bamuleka DM, Likofata J, Muyembe Tamfum JJ, Toure A, Mpoudi Ngole E, Kouanfack C, Delaporte E, Keita AK, Ahuka-Mundeke S, Ayouba A, Peeters M. Coronaviruses Are Abundant and Genetically Diverse in West and Central African Bats, including Viruses Closely Related to Human Coronaviruses. Viruses 2023; 15:337. [PMID: 36851551 PMCID: PMC9967053 DOI: 10.3390/v15020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Bats are at the origin of human coronaviruses, either directly or via an intermediate host. We tested swabs from 4597 bats (897 from the Democratic Republic of Congo (DRC), 2191 from Cameroon and 1509 from Guinea) with a broadly reactive PCR in the RdRp region. Coronaviruses were detected in 903 (19.6%) bats and in all species, with more than 25 individuals tested. The highest prevalence was observed in Eidolon helvum (239/733; 39.9%) and Rhinolophus sp. (306/899; 34.1%), followed by Hipposideros sp. (61/291; 20.9%). Frugivorous bats were predominantly infected with beta coronaviruses from the Nobecovirus subgenus (93.8%), in which at least 6 species/genus-specific subclades were observed. In contrast, insectivorous bats were infected with beta-coronaviruses from different subgenera (Nobecovirus (8.5%), Hibecovirus (32.8%), Merbecovirus (0.5%) and Sarbecovirus (57.6%)) and with a high diversity of alpha-coronaviruses. Overall, our study shows a high prevalence and genetic diversity of coronaviruses in bats and illustrates that Rhinolophus bats in Africa are infected at high levels with the Sarbecovirus subgenus, to which SARS-CoV-2 belongs. It is important to characterize in more detail the different coronavirus lineages from bats for their potential to infect human cells, their evolution and to study frequency and modes of contact between humans and bats in Africa.
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Affiliation(s)
- Dowbiss Meta Djomsi
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Audrey Lacroix
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
| | - Eddy Kinganda Lusamaki
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Asma Mesdour
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Raisa Raulino
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Amandine Esteban
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Innocent Ndong Bass
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | | | - Souana Goumou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
| | | | - Guy Lempu
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Placide Mbala Kingebeni
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Daniel Mukadi Bamuleka
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Institut National de Recherche Biomédicale (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Jacques Likofata
- Laboratoire Provincial de Mbandaka, Mbandaka, Democratic Republic of Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Abdoulaye Toure
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
- Department of Public Health, Faculty of Health Sciences and Techniques, Gamal Abdel Nasser University (UGANC), Conakry P.O. Box 1147, Guinea
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Charles Kouanfack
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Eric Delaporte
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Alpha Kabinet Keita
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
- Department of Public Health, Faculty of Health Sciences and Techniques, Gamal Abdel Nasser University (UGANC), Conakry P.O. Box 1147, Guinea
| | - Steve Ahuka-Mundeke
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Ahidjo Ayouba
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Martine Peeters
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
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6
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Cameron KN, Mombouli JV, Niama FR, Hayes B, Olson SH, Smith BR, Pante J, Roy S, Laudisoit A, Goldstein T, Joly DO, Bagamboula MPassi R, Lange CE. Orbivirus RNA in a Banana Serotine (Afronycteris nanus) Bat in the Republic of the Congo. ECOHEALTH 2022; 19:443-449. [PMID: 36629956 PMCID: PMC9838363 DOI: 10.1007/s10393-022-01619-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Orbiviruses are arthropod borne viruses of vertebrates, with some of them being important pathogens of veterinary, conservation and economic importance, while others are occasionally associated with human disease. Some apparently bat specific orbiviruses have been detected, but little is known about their distribution and diversity. We thus sampled and screened 52 bats living in the Congo Basin, and detected RNA indicative of a novel orbivirus in a single banana serotine (Afronycteris nanus) by PCR. The detected RNA clusters with epizootic haemorrhagic disease virus, bluetongue virus, and others. The findings highlight the need for more studies into arbovirus presence and diversity in bat species.
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Affiliation(s)
- Kenneth N Cameron
- Wildlife Conservation Society, Bronx, NY, USA
- Unites States Fish and Wildlife Service, Bailey's Crossroads, VA, USA
| | | | - Fabien R Niama
- National Laboratory of Public Health, Brazzaville, Republic of the Congo
| | - Ben Hayes
- Monadh, Inveruglas, Kingussie, Inverness-Shire, UK
| | | | - Brett R Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jasmine Pante
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Sanjit Roy
- Labyrinth Global Health, St. Petersburg, FL, USA
- University of Victoria, Victoria, BC, Canada
| | | | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Damien O Joly
- Wildlife Conservation Society, Bronx, NY, USA
- British Columbia Ministry of Environment and Climate Change Strategy, Victoria, BC, Canada
| | | | - Christian E Lange
- Labyrinth Global Health, St. Petersburg, FL, USA.
- Metabiota Inc, Nanaimo, BC, Canada.
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7
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Kuchinski KS, Loos KD, Suchan DM, Russell JN, Sies AN, Kumakamba C, Muyembe F, Mbala Kingebeni P, Ngay Lukusa I, N’Kawa F, Atibu Losoma J, Makuwa M, Gillis A, LeBreton M, Ayukekbong JA, Lerminiaux NA, Monagin C, Joly DO, Saylors K, Wolfe ND, Rubin EM, Muyembe Tamfum JJ, Prystajecky NA, McIver DJ, Lange CE, Cameron ADS. Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats. eLife 2022; 11:79777. [DOI: 10.7554/elife.79777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.
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Affiliation(s)
- Kevin S Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia
- Public Health Laboratory, British Columbia Centre for Disease Control
| | - Kara D Loos
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Danae M Suchan
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Jennifer N Russell
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Ashton N Sies
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | | | | | | | | | | | | | | | | | | | | | - Nicole A Lerminiaux
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Corina Monagin
- Metabiota Inc
- One Health Institute, School of Veterinary Medicine, University of California, Davis
| | | | | | | | | | | | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia
- Public Health Laboratory, British Columbia Centre for Disease Control
| | - David J McIver
- Metabiota
- Institute for Global Health Sciences, University of California, San Francisco
| | | | - Andrew DS Cameron
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
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8
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Montecino-Latorre D, Goldstein T, Kelly TR, Wolking DJ, Kindunda A, Kongo G, Bel-Nono SO, Kazwala RR, Suu-Ire RD, Barker CM, Johnson CK, Mazet JAK. Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa. PLoS One 2022; 17:e0274490. [PMID: 36107832 PMCID: PMC9477308 DOI: 10.1371/journal.pone.0274490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
The straw-colored fruit bat (Eidolon helvum) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E. helvum, by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E. helvum roosts during the pup “weaning” period. This recommendation can be applied across the many highly-populated urban sites occupied by E. helvum across Africa.
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Affiliation(s)
- Diego Montecino-Latorre
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (JAKM); (DML)
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Terra R. Kelly
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - David J. Wolking
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Adam Kindunda
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Godphrey Kongo
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Rudovick R. Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Richard D. Suu-Ire
- School of Veterinary Medicine, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Christopher M. Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christine Kreuder Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Jonna A. K. Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (JAKM); (DML)
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9
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Lane JK, Negash Y, Randhawa N, Kebede N, Wells H, Ayalew G, Anthony SJ, Smith B, Goldstein T, Kassa T, Mazet JAK, Consortium P, Smith WA. Coronavirus and Paramyxovirus Shedding by Bats in a Cave and Buildings in Ethiopia. ECOHEALTH 2022; 19:216-232. [PMID: 35771308 PMCID: PMC9243955 DOI: 10.1007/s10393-022-01590-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Bats are important hosts of zoonotic viruses with pandemic potential, including filoviruses, MERS-Coronavirus (CoV), SARS-CoV -1, and likely SARS-CoV-2. Viral infection and transmission among wildlife are dependent on a combination of factors that include host ecology and immunology, life history traits, roosting habitats, biogeography, and external stressors. Between 2016 and 2018, four species of insectivorous bats from a readily accessed roadside cave and buildings in Ethiopia were sampled and tested for viruses using consensus PCR assays for five viral families/genera. Previously identified and novel coronaviruses and paramyxoviruses were identified in 99 of the 589 sampled bats. Bats sampled from the cave site were more likely to test positive for a CoV than bats sampled from buildings; viral shedding was more common in the wet season; and rectal swabs were the most common sample type to test positive. A previously undescribed alphacoronavirus was detected in two bat species from different taxonomic families, sampling interfaces, geographic locations, and years. These findings expand knowledge of the range and diversity of coronaviruses and paramyxoviruses in insectivorous bats in Ethiopia and reinforce that an improved understanding of viral diversity and species-specific shedding dynamics is important for designing informed zoonotic disease surveillance and spillover risk reduction efforts.
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Affiliation(s)
- Jennifer K Lane
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, VM3B, Davis, CA, 95616, USA.
| | - Yohannes Negash
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Nistara Randhawa
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, VM3B, Davis, CA, 95616, USA
| | - Nigatu Kebede
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Heather Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Girma Ayalew
- Ethiopian Wildlife Conservation Authority, Ministry of Environment, Forestry and Climate Change, Addis Ababa, Ethiopia
| | - Simon J Anthony
- School of Veterinary Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Brett Smith
- Genome Center & Biomedical Engineering, School of Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Tracey Goldstein
- Zoological Pathology Program, University of Illinois at Urbana-Champaign, Brookfield, IL, 60513, USA
| | - Tesfu Kassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Jonna A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, VM3B, Davis, CA, 95616, USA
| | | | - Woutrina A Smith
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, VM3B, Davis, CA, 95616, USA.
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10
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Suu-Ire R, Obodai E, Bel-Nono SO, Ampofo WK, Mazet JAK, Goldstein T, Johnson CK, Smith B, Boaatema L, Asigbee TW, Awuni J, Opoku E, Kelly TR. Surveillance for potentially zoonotic viruses in rodent and bat populations and behavioral risk in an agricultural settlement in Ghana. ONE HEALTH OUTLOOK 2022; 4:6. [PMID: 35256013 PMCID: PMC8901269 DOI: 10.1186/s42522-022-00061-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/19/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND In Ghana, the conversion of land to agriculture, especially across the vegetative belt has resulted in fragmented forest landscapes with increased interactions among humans, domestic animals, and wildlife. METHODS We investigated viruses in bats and rodents, key reservoir hosts for zoonotic viral pathogens, in a small agricultural community in the vegetation belt of Ghana. We also administered questionnaires among the local community members to learn more about people's awareness and perceptions of zoonotic disease risks and the environmental factors and types of activities in which they engage that might influence pathogen transmission from wildlife. RESULTS Our study detected the RNA from paramyxoviruses and coronaviruses in rodents and bats, including sequences from novel viruses with unknown zoonotic potential. Samples collected from Epomophorus gambianus bats were significantly more likely to be positive for coronavirus RNA during the rainy season, when higher numbers of young susceptible individuals are present in the population. Almost all community members who responded to the questionnaire reported contact with wildlife, especially bats, rodents, and non-human primates in and around their homes and in the agricultural fields. Over half of the respondents were not aware or did not perceive any zoonotic disease risks associated with close contact with animals, such as harvesting and processing animals for food. To address gaps in awareness and mitigation strategies for pathogen transmission risks, we organized community education campaigns using risk reduction and outreach tools focused around living safely with bats and rodents. CONCLUSIONS These findings expand our knowledge of the viruses circulating in bats and rodents in Ghana and of the beliefs, perceptions, and practices that put community members at risk of zoonotic virus spillover through direct and indirect contact with bats and rodents. This study also highlights the importance of community engagement in research and interventions focused on mitigating risk and living safely with wildlife.
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Affiliation(s)
- Richard Suu-Ire
- School of Veterinary Medicine, University of Ghana, Legon, Accra, Ghana.
| | - Evangeline Obodai
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.
| | - Samuel Otis Bel-Nono
- One Health Institute, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, USA
- Military Veterinarian (Rtd), P.O. Box CT2585, Accra, Ghana
| | - William Kwabena Ampofo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jonna A K Mazet
- One Health Institute, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, USA
| | - Tracey Goldstein
- Zoological Pathology Program, c/o Chicago Zoological Society, 3300 Golf Rd., Brookfield, IL, 60513, USA
| | - Christine Kreuder Johnson
- One Health Institute, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, USA
| | - Brett Smith
- One Health Institute, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, USA
| | - Linda Boaatema
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | | | - Joseph Awuni
- Accra Veterinary Laboratory, Veterinary Services Directorate, Ring Road East, Accra, Ghana
| | - Eric Opoku
- Ghana Health Service, 28th February Road, Accra, Ghana
| | - Terra R Kelly
- One Health Institute, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, USA.
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11
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Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Roy S, Ayukekbong JA, Saylors KE, Joly DO, Wolfe ND, Rubin EM, Lange CE. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110. [PMID: 35233291 PMCID: PMC8867583 DOI: 10.1093/ve/veab110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/05/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
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Affiliation(s)
- Nkom F Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Amethyst Gillis
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Centre Region Route de Kribi, Yaoundé, BP 1364, Cameroon
| | - Joseph Le Doux Diffo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Jean-Michel Takuo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Julius Nwobegahay
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
| | | | - Anne W Rimoin
- Department of Epidemiology, University of California, 71-254 Center for Health Sciences, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bradley S Schneider
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Mosaic, Yaoundé, Centre Region, BP 35353, Cameroon
| | | | - David J McIver
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
- One Health Institute, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Sanjit Roy
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- University of Victoria, 3800 Finnerty Road, Victoria BC V8P 5C2, Canada
| | | | - Karen E Saylors
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
| | - Damien O Joly
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | | | - Edward M Rubin
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | - Christian E Lange
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
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12
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Enterovirus Sequence Data Obtained from Primate Samples in Central Africa Suggest a High Prevalence of Enteroviruses. Microbiol Resour Announc 2021; 10:e0088221. [PMID: 34881972 PMCID: PMC8656378 DOI: 10.1128/mra.00882-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Enteroviruses infect humans and animals and can cause disease, and some may be transmitted across species barriers. We tested Central African wildlife and found Enterovirus RNA in primates (17) and rodents (2). Some sequences were very similar, while others were dissimilar to known species, highlighting the underexplored enterovirus diversity in wildlife.
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13
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Stout AE, Millet JK, Stanhope MJ, Whittaker GR. Furin cleavage sites in the spike proteins of bat and rodent coronaviruses: Implications for virus evolution and zoonotic transfer from rodent species. One Health 2021; 13:100282. [PMID: 34179330 PMCID: PMC8216856 DOI: 10.1016/j.onehlt.2021.100282] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/02/2022] Open
Abstract
Bats and rodents comprise two of the world's largest orders of mammals and the order Chiroptera (bats) has been implicated as a major reservoir of coronaviruses in nature and a source of zoonotic transfer to humans. However, the order Rodentia (rodents) also harbors coronaviruses, with two human coronaviruses (HCoV-OC43 and HCoV-HKU1) considered to have rodent origins. The coronavirus spike protein mediates viral entry and is a major determinant of viral tropism; importantly, the spike protein is activated by host cell proteases at two distinct sites, designated as S1/S2 and S2’. SARS-CoV-2, which is considered to be of bat origin, contains a cleavage site for the protease furin at S1/S2, absent from the rest of the currently known betacoronavirus lineage 2b coronaviruses (Sarbecoviruses). This cleavage site is thought to be critical to its replication and pathogenesis, with a notable link to virus transmission. Here, we examine the spike protein across coronaviruses identified in both bat and rodent species and address the role of furin as an activating protease. Utilizing two publicly available furin prediction algorithms (ProP and PiTou) and based on spike sequences reported in GenBank, we show that the S1/S2 furin cleavage site is typically not present in bat virus spike proteins but is common in rodent-associated sequences, and suggest this may have implications for zoonotic transfer. We provide a phylogenetic history of the Embecoviruses (betacoronavirus lineage 2a), including context for the use of furin as an activating protease for the viral spike protein. From a One Health perspective, continued rodent surveillance should be an important consideration in uncovering novel circulating coronaviruses.
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Affiliation(s)
- Alison E Stout
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352, Jouy-en-Josas, France
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.,Master of Public Health Program, Cornell University, Ithaca, NY, USA
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