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Agusi ER, Schön J, Allendorf V, Eze EA, Asala O, Shittu I, Balkema-Buschmann A, Wernike K, Tekki I, Ofua M, Adefegha O, Olubade O, Ogunmolawa O, Dietze K, Globig A, Hoffmann D, Meseko CA. SARS-CoV and SARS-CoV -2 cross-reactive antibodies in domestic animals and wildlife in Nigeria suggest circulation of sarbecoviruses. One Health 2024; 18:100709. [PMID: 38533194 PMCID: PMC10963646 DOI: 10.1016/j.onehlt.2024.100709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Anthropogenic exposure of domestic animals, as well as wildlife, can result in zoonotic transmission events with known and unknown pathogens including sarbecoviruses. During the COVID-19 pandemic, SARS-CoV-2 infections in animals, most likely resulting from spill-over from humans, have been documented worldwide. However, only limited information is available for Africa. The anthropozoonotic transmission from humans to animals, followed by further inter- and intraspecies propagation may contribute to viral evolution, and thereby subsequently alter the epidemiological patterns of transmission. To shed light on the possible role of domestic animals and wildlife in the ecology and epidemiology of sarbecoviruses in Nigeria, and to analyze the possible circulation of other, undiscovered, but potentially zoonotic sarbecoviruses in animals, we tested 504 serum samples from dogs, rabbits, bats, and pangolins collected between December 2020 and April 2022. The samples were analyzed using an indirect multi-species enzyme-linked immunosorbent assay (ELISA) based on the receptor binding domain (RBD) of SARS-CoV and SARS-CoV -2, respectively. ELISA reactive sera were further analyzed by highly specific virus neutralization test and indirect immunofluorescence assay for confirmation of the presence of antibodies. In this study, we found SARS-CoV reactive antibodies in 16 (11.5%) dogs, 7 (2.97%) rabbits, 2 (7.7%) pangolins and SARS-CoV-2 reactive antibodies in 20 (13.4%) dogs, 6 (2.5%) rabbits and 2 (7.7%) pangolins, respectively. Interestingly, 2 (2.3%) bat samples were positive only for SARS-CoV RBD reactive antibodies. These serological findings of SARS-CoV and/or SARS-CoV-2 infections in both domestic animals and wildlife indicates exposure to sarbecoviruses and requires further One Health-oriented research on the potential reservoir role that different species might play in the ecology and epidemiology of coronaviruses at the human-animal interface.
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Affiliation(s)
- Ebere R Agusi
- National Veterinary Research Institute, Vom, Nigeria
- University of Nigeria, Nsukka, Nigeria
| | - Jacob Schön
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Valerie Allendorf
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | | | | | | | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Kerstin Wernike
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Ishaya Tekki
- National Veterinary Research Institute, Vom, Nigeria
| | - Mark Ofua
- SaintMarks-Lagos Urban Forest Sanctuary Initiative (LUFASI), Lagos, Nigeria
| | | | | | | | - Klaas Dietze
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Anja Globig
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Donata Hoffmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
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2
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Cohen LE, Fagre AC, Chen B, Carlson CJ, Becker DJ. Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis. Nat Microbiol 2023; 8:1176-1186. [PMID: 37231088 PMCID: PMC10234814 DOI: 10.1038/s41564-023-01375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.
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Affiliation(s)
- Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
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3
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Abstract
Zoonoses are diseases and infections naturally transmitted between humans and vertebrate animals. Over the years, zoonoses have become increasingly significant threats to global health. They form the dominant group of diseases among the emerging infectious diseases (EID) and currently account for 73% of EID. Approximately 25% of zoonoses originate in domestic animals. The etiological agents of zoonoses include different pathogens, with viruses accounting for approximately 30% of all zoonotic infections. Zoonotic diseases can be transmitted directly or indirectly, by contact, via aerosols, through a vector, or vertically in utero. Zoonotic diseases are found in every continent except Antarctica. Numerous factors associated with the pathogen, human activities, and the environment play significant roles in the transmission and emergence of zoonotic diseases. Effective response and control of zoonotic diseases call for multiple-sector involvement and collaboration according to the One Health concept.
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Affiliation(s)
- Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria; ,
| | - Daniel O Oluwayelu
- Department of Veterinary Microbiology and Centre for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Oyo State, Nigeria; ,
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4
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Agusi ER, Allendorf V, Eze EA, Asala O, Shittu I, Dietze K, Busch F, Globig A, Meseko CA. SARS-CoV-2 at the Human-Animal Interface: Implication for Global Public Health from an African Perspective. Viruses 2022; 14:2473. [PMID: 36366571 PMCID: PMC9696393 DOI: 10.3390/v14112473] [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: 09/28/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has become the most far-reaching public health crisis of modern times. Several efforts are underway to unravel its root cause as well as to proffer adequate preventive or inhibitive measures. Zoonotic spillover of the causative virus from an animal reservoir to the human population is being studied as the most likely event leading to the pandemic. Consequently, it is important to consider viral evolution and the process of spread within zoonotic anthropogenic transmission cycles as a global public health impact. The diverse routes of interspecies transmission of SARS-CoV-2 offer great potential for a future reservoir of pandemic viruses evolving from the current SARS-CoV-2 pandemic circulation. To mitigate possible future infectious disease outbreaks in Africa and elsewhere, there is an urgent need for adequate global surveillance, prevention, and control measures that must include a focus on known and novel emerging zoonotic pathogens through a one health approach. Human immunization efforts should be approached equally through the transfer of cutting-edge technology for vaccine manufacturing throughout the world to ensure global public health and one health.
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Affiliation(s)
- Ebere Roseann Agusi
- National Veterinary Research Institute, Vom 930001, Nigeria
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- Department of Microbiology, University of Nigeria Nsukka, Enugu 410001, Nigeria
| | - Valerie Allendorf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | | | - Olayinka Asala
- National Veterinary Research Institute, Vom 930001, Nigeria
| | - Ismaila Shittu
- National Veterinary Research Institute, Vom 930001, Nigeria
| | - Klaas Dietze
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - Frank Busch
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - Clement Adebajo Meseko
- National Veterinary Research Institute, Vom 930001, Nigeria
- College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Kabantiyok D, Ninyio N, Shittu I, Meseko C, Emeto TI, Adegboye OA. Human Respiratory Infections in Nigeria: Influenza and the Emergence of SARS-CoV-2 Pandemic. Vaccines (Basel) 2022; 10:1551. [PMID: 36146628 PMCID: PMC9506385 DOI: 10.3390/vaccines10091551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing outbreak of zoonotic diseases presents challenging times for nations and calls for a renewed effort to disrupt the chain of events that precede it. Nigeria's response to the 2006 bird flu provided a platform for outbreak response, yet it was not its first experience with Influenza. This study describes the impact of SARS-CoV-2 on Influenza surveillance and, conversely, while the 1918 Influenza pandemic remains the most devastating (500,000 deaths in 18 million population) in Nigeria, the emergence of SARS CoV-2 presented renewed opportunities for the development of vaccines with novel technology, co-infection studies outcome, and challenges globally. Although the public health Intervention and strategies left some positive outcomes for other viruses, Nigeria and Africa's preparation against the next pandemic may involve prioritizing a combination of technology, socioeconomic growth, and active surveillance in the spirit of One Health.
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Affiliation(s)
- Dennis Kabantiyok
- Laboratory Diagnostic Services Division, National Veterinary Research Institute, PMB 01, Vom 930001, Nigeria
| | - Nathaniel Ninyio
- School of Medical Sciences, Örebro University, 70182 Örebro, Sweden
| | - Ismaila Shittu
- Department of Avian Influenza and Transboundary Animal Diseases, National Veterinary Research Institute, PMB 01, Vom 930010, Nigeria
| | - Clement Meseko
- Department of Avian Influenza and Transboundary Animal Diseases, National Veterinary Research Institute, PMB 01, Vom 930010, Nigeria
| | - Theophilus I. Emeto
- Public Health & Tropical Medicine, College of Public Health, Medical and Veterinary Sciences, Department, James Cook University, Townsville, QLD 4811, Australia
- World Health Organization Collaborating Center for Vector-Borne, Neglected Tropical Diseases Department, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
| | - Oyelola A. Adegboye
- Public Health & Tropical Medicine, College of Public Health, Medical and Veterinary Sciences, Department, James Cook University, Townsville, QLD 4811, Australia
- World Health Organization Collaborating Center for Vector-Borne, Neglected Tropical Diseases Department, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
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6
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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
| | - 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
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7
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George U, George O, Oragwa A, Motayo B, Kamani J, Adamu A, Sowemimo O, Adeleke R, Abalaka S, Sani N, Oguzie J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C. Detection of Alpha- and Betacoronaviruses in Frugivorous and Insectivorous Bats in Nigeria. Pathogens 2022; 11:pathogens11091017. [PMID: 36145450 PMCID: PMC9502725 DOI: 10.3390/pathogens11091017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The rise of bat-associated zoonotic viruses necessitates a close monitoring of their natural hosts. Since the detection of severe acute respiratory syndrome coronavirus (SARS-CoV), it is evident that bats are vital reservoirs of coronaviruses (CoVs). In this study, we investigated the presence of CoVs in multiple bat species in Nigeria to identify viruses in bats at high-risk human contact interfaces. Four hundred and nine bats comprising four bat species close to human habitats were individually sampled from five states in Nigeria between 2019 and 2021. Coronavirus detection was done using broadly reactive consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene of CoVs. Coronavirus RNA was detected in 39 samples (9.5%, CI 95%: [7.0, 12.8]), of which 29 were successfully sequenced. The identified CoVs in Nigerian bats were from the unclassified African alphacoronavirus lineage and betacoronavirus lineage D (Nobecovirus), with one sample from Hipposideros ruber coinfected with alphacoronavirus and betacoronavirus. Different bat species roosting in similar or other places had CoVs from the same genetic lineage. The phylogenetic and evolutionary dynamics data indicated a high CoV diversity in Nigeria, while host switching may have contributed to CoV evolution. Robust sentinel surveillance is recommended to enhance our knowledge of emerging and re-emerging coronaviruses.
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Affiliation(s)
- Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232102, Osun State, Nigeria
| | - Oluwadamilola George
- Ibadan Diagnostic and Epidemiology Laboratory, National Veterinary Research Institute, Mokola, Ibadan 200212, Oyo State, Nigeria
| | - Arthur Oragwa
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos,
Jos 930003, Plateau State, Nigeria
| | - Babatunde Motayo
- Department of Medical Microbiology, Federal Medical Centre, Abeokuta 110222, Ogun State, Nigeria
| | - Joshua Kamani
- Parasitology Division, National Veterinary Research Institute (NVRI), PMB 01,
Vom 930103, Plateau State, Nigeria
| | - Andrew Adamu
- Australian Institute of Tropical Health and Medicine, Division of Tropical Health and Medicine,
James Cook University, Townsville, QLD 4811, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Bebegu Yumba Campus, Douglas, QLD 4811, Australia
- Department of Veterinary Public Health and Preventive Medicine, University of Abuja,
Abuja 900105, Federal Capital Territory, Nigeria
| | - Oluyomi Sowemimo
- Department of Zoology, Faculty of Science, Obafemi Awolowo University, Ile Ife 220005, Osun State, Nigeria
| | - Richard Adeleke
- Immunology and Infectious Diseases, College of Veterinary Medicine, Cornell University, New York, NY 14853, USA
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ibadan,
Ibadan 200132, Oyo State, Nigeria
| | - Samson Abalaka
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Abuja,
Abuja 900105, Federal Capital Territory, Nigeria
| | - Nuhu Sani
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Abuja,
Abuja 900105, Federal Capital Territory, Nigeria
| | - Judith Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232102, Osun State, Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
| | - Onikepe Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232102, Osun State, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Correspondence: (I.K.); (C.H.)
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232102, Osun State, Nigeria
- Correspondence: (I.K.); (C.H.)
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8
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Shapiro JT, Mollerup S, Jensen RH, Olofsson JK, Nguyen NPD, Hansen TA, Vinner L, Monadjem A, McCleery RA, Hansen AJ. Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini. ECOHEALTH 2021; 18:421-428. [PMID: 34970712 PMCID: PMC8718178 DOI: 10.1007/s10393-021-01567-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 09/30/2021] [Accepted: 10/29/2021] [Indexed: 06/07/2023]
Abstract
We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.
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Affiliation(s)
- Julie Teresa Shapiro
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA.
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.
- University of Lyon, CIRI INSERM U1111 - CNRS UMR5308 - ENS Lyon, 46 Allée d'Italie, 69364, Lyon, France.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Nam-Phuong D Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ara Monadjem
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
- Department of Biological Sciences, University of Eswatini, Private Bag 4, Kwaluseni, Eswatini
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Robert A McCleery
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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9
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Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations. Viruses 2021; 13:v13050936. [PMID: 34070175 PMCID: PMC8158508 DOI: 10.3390/v13050936] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/13/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.
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10
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Motayo BO, Oluwasemowo OO, Akinduti PA. Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats. PeerJ 2020; 8:e10434. [PMID: 33304657 PMCID: PMC7700737 DOI: 10.7717/peerj.10434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022] Open
Abstract
Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10-3, HPD (1.064 × 10-3-1.434 × 10-3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.
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Affiliation(s)
- Babatunde O Motayo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Medical Microbiology and Parasitology, Federal Medical Center, Abeokuta, Nigeria, Abeokuta, Ogun, Nigeria
| | | | - Paul A Akinduti
- Department of Biological Science, Covenant University, Otta, Ogun, Nigeria
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Meseko C, Shittu I, Adedeji A. The bush meat trade thrives in Nigeria despite anxiety over coronavirus. Trans R Soc Trop Med Hyg 2020; 114:639-641. [PMID: 32730611 PMCID: PMC7454903 DOI: 10.1093/trstmh/traa060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 03/31/2020] [Accepted: 07/04/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Clement Meseko
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Ismaila Shittu
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Adeyinka Adedeji
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
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12
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Phelps KL, Hamel L, Alhmoud N, Ali S, Bilgin R, Sidamonidze K, Urushadze L, Karesh W, Olival KJ. Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia. Viruses 2019; 11:v11030240. [PMID: 30857374 PMCID: PMC6466127 DOI: 10.3390/v11030240] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 02/06/2023] Open
Abstract
Bat research networks and viral surveillance are assumed to be at odds due to seemingly conflicting research priorities. Yet human threats that contribute to declines in bat populations globally also lead to increased transmission and spread of bat-associated viruses, which may pose a threat to global health and food security. In this review, we discuss the importance of and opportunities for multidisciplinary collaborations between bat research networks and infectious disease experts to tackle shared threats that jeopardize bat conservation as well as human and animal health. Moreover, we assess research effort on bats and bat-associated viruses globally, and demonstrate that Western Asia has limited published research and represents a gap for coordinated bat research. The lack of bat research in Western Asia severely limits our capacity to identify and mitigate region-specific threats to bat populations and detect interactions between bats and incidental hosts that promote virus spillover. We detail a regional initiative to establish the first bat research network in Western Asia (i.e., the Western Asia Bat Research Network, WAB-Net), with the aim of integrating ecological research on bats with virus surveillance to find “win-win” solutions that promote bat conservation and safeguard public and animal health across the region.
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Affiliation(s)
| | - Luke Hamel
- EcoHealth Alliance, New York, NY 10001, USA.
| | - Nisreen Alhmoud
- Biosafety and Biosecurity Center, Royal Scientific Society, 11941 Amman, Jordan.
| | - Shahzad Ali
- Department of Wildlife & Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.
| | - Rasit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, 34342 Istanbul, Turkey.
| | | | - Lela Urushadze
- National Center for Disease Control & Public Health, 0198 Tbilisi, Georgia.
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13
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Sasaki M, Kajihara M, Changula K, Mori-Kajihara A, Ogawa H, Hang'ombe BM, Mweene AS, Simuunza M, Yoshida R, Carr M, Orba Y, Takada A, Sawa H. Identification of group A rotaviruses from Zambian fruit bats provides evidence for long-distance dispersal events in Africa. INFECTION GENETICS AND EVOLUTION 2018; 63:104-109. [PMID: 29792990 PMCID: PMC7173303 DOI: 10.1016/j.meegid.2018.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 11/28/2022]
Abstract
Group A rotavirus (RVA) is a major cause of diarrhea in children worldwide. Although RVA infects many animals, little is known about RVA in bats. The present study investigated the genetic diversity of RVA in Zambian bats. We identified RVA from two straw-colored fruit bats (Eidolon helvum) and an Egyptian fruit bat (Rousettus aegyptiacus), and analyzed the genome sequences of these strains. Genome segments of the RVA strains from Zambian E. helvum showed 97%–99% nucleotide sequence identity with those of other RVA strains from E. helvum in Cameroon, which is 2800 km from the sampling locations. These findings suggest that migratory straw-colored fruit bat species, distributed across sub-Saharan Africa, have the potential to disseminate RVA across long distances. By contrast, the RVA strain from Zambian R. aegyptiacus carried highly divergent NSP2 and NSP4 genes, leading us to propose novel genotypes N21 and E27, respectively. Notably, this RVA strain also shared the same genotype for VP6 and NSP3 with the RVA strains from Zambian E. helvum, suggesting interspecies transmission and genetic reassortment may have occurred between these two bat species in the past. Our study has important implications for RVA dispersal in bat populations, and expands our knowledge of the ecology, diversity and evolutionary relationships of RVA. Detection of group A rotavirus from Zambian fruit bats. Some viral genes were almost identical to those of rotavirus from Cameroonian bats. The findings provide evidence for long-distance dispersal events of rotavirus. First report of novel N21 and E27 genotypes.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan.
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Hirohito Ogawa
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia; Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia; Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, PO Box 32379, Lusaka, Zambia; Global Virus Network, Baltimore, MD 21201, USA
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Reiko Yoshida
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Michael Carr
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan; National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; Global Virus Network, Baltimore, MD 21201, USA; Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0020, Japan.
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14
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Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 58:279-289. [PMID: 29355607 PMCID: PMC7106311 DOI: 10.1016/j.meegid.2018.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 01/01/2023]
Abstract
Coronaviruses (CoVs) have been documented in almost every species of bat sampled. Bat CoVs exhibit both extensive genetic diversity and a broad geographic range, indicative of a long-standing host association. Despite this, the respective roles of long-term virus-host co-divergence and cross-species transmission (host-jumping) in the evolution of bat coronaviruses are unclear. Using a phylogenetic approach we provide evidence that CoV diversity in bats is shaped by both species richness and their geographical distribution, and that CoVs exhibit clustering at the level of bat genera, with these genus-specific clusters largely associated with distinct CoV species. Co-phylogenetic analyses revealed that cross-species transmission has been more common than co-divergence across coronavirus evolution as a whole, and that cross-species transmission events were more likely between sympatric bat hosts. Notably, however, an analysis of the CoV RNA polymerase phylogeny suggested that many such host-jumps likely resulted in short-term spill-over infections, with little evidence for sustained onward transmission in new co-roosting host species.
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Affiliation(s)
- Stefania Leopardi
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michele Gastaldelli
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Luca Tassoni
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | | | | | - Gianpiero Zamperin
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Paola De Benedictis
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
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Yinda CK, Ghogomu SM, Conceição-Neto N, Beller L, Deboutte W, Vanhulle E, Maes P, Van Ranst M, Matthijnssens J. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. Virus Evol 2018; 4:vey008. [PMID: 29644096 PMCID: PMC5888411 DOI: 10.1093/ve/vey008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Department of Biochemistry and Molecular Biology, University of Buea, Buea, 237, Cameroon
| | - Nádia Conceição-Neto
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | | | | | | | - Piet Maes
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
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