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Sánchez CA, Phelps KL, Frank HK, Geldenhuys M, Griffiths ME, Jones DN, Kettenburg G, Lunn TJ, Moreno KR, Mortlock M, Vicente-Santos A, Víquez-R LR, Kading RC, Markotter W, Reeder DM, Olival KJ. Advances in understanding bat infection dynamics across biological scales. Proc Biol Sci 2024; 291:20232823. [PMID: 38444339 PMCID: PMC10915549 DOI: 10.1098/rspb.2023.2823] [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: 12/13/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.
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Affiliation(s)
| | | | - Hannah K. Frank
- Department of Ecology & Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Marike Geldenhuys
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Devin N. Jones
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | | | - Tamika J. Lunn
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Kelsey R. Moreno
- Department of Psychology, Saint Xavier University, Chicago, IL 60655, USA
| | - Marinda Mortlock
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Luis R. Víquez-R
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
| | - Rebekah C. Kading
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne and Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - DeeAnn M. Reeder
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
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2
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Zachariah A, Krishnankutty SP, Manazhi J, Omanakuttan V, Santosh S, Blanchard A, Tarlinton R. Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21. Access Microbiol 2024; 6:000686.v3. [PMID: 38361659 PMCID: PMC10866034 DOI: 10.1099/acmi.0.000686.v3] [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: 07/31/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).
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Affiliation(s)
| | | | | | | | | | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
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3
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Tambe LAM, Mathobo P, Munzhedzi M, Bessong PO, Mavhandu-Ramarumo LG. Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review. Viruses 2023; 15:2146. [PMID: 38005824 PMCID: PMC10675249 DOI: 10.3390/v15112146] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Centre for Global Health Equity, School of Medicine, 1400 University Ave, Charlottesville, VA 22903, USA
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
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4
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Geldenhuys M, Ross N, Dietrich M, de Vries JL, Mortlock M, Epstein JH, Weyer J, Pawęska JT, Markotter W. Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover. Sci Rep 2023; 13:15829. [PMID: 37739999 PMCID: PMC10517123 DOI: 10.1038/s41598-023-42938-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/16/2023] [Indexed: 09/24/2023] Open
Abstract
Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.
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Affiliation(s)
- Marike Geldenhuys
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa.
| | | | - Muriel Dietrich
- UMR Processus Infectieux en Milieu Insulaire Tropical, Sainte-Clotilde, Reunion Island, France
| | - John L de Vries
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Marinda Mortlock
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Jonathan H Epstein
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa
- EcoHealth Alliance, New York, USA
| | - Jacqueline Weyer
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, Gauteng, South Africa
- Department of Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Janusz T Pawęska
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, Gauteng, South Africa
- Department of Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa.
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Poonsin P, Wiwatvisawakorn V, Chansaenroj J, Poovorawan Y, Piewbang C, Techangamsuwan S. Canine respiratory coronavirus in Thailand undergoes mutation and evidences a potential putative parent for genetic recombination. Microbiol Spectr 2023; 11:e0226823. [PMID: 37707446 PMCID: PMC10581155 DOI: 10.1128/spectrum.02268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/27/2023] [Indexed: 09/15/2023] Open
Abstract
Canine respiratory coronavirus (CRCoV) is associated with canine infectious respiratory disease complex. Although its detection has been reported worldwide, the genomic characteristics and evolutionary patterns of this virus remain poorly defined. In this study, 21 CRCoV sequences obtained from dogs in Thailand during two episodes (2013-2015, group A; 2021-2022, group B) were characterized and analyzed. The genomic characteristics of Thai CRCoVs changed from 2013 to 2022 and showed a distinct phylogenetic cluster. Phylogenetic analysis of the spike (S) genes divided the analyzed CRCoV strains into five clades. The full-length genome characterization revealed that all Thai CRCoVs possessed a nonsense mutation within the nonstructural gene located between the S and envelope genes, leading to a truncated putative nonstructural protein. Group B Thai CRCoV strains represented the signature nonsynonymous mutations in the S gene that was not identified in group A Thai CRCoVs, suggesting the ongoing evolutionary process of Thai CRCoVs. Although no evidence of recombination of Thai CRCoV strains was found, our analysis identified one Thai CRCoV strain as a potential parent virus for a CRCoV strain found in the United States. Selective pressure analysis of the hypervariable S region indicated that the CRCoV had undergone purifying selection during evolution. Evolutionary analysis suggested that the CRCoV was emerged in 1992 and was first introduced in Thailand in 2004, sharing a common ancestor with Korean CRCoV strains. These findings regarding the genetic characterization and evolutionary analysis of CRCoVs add to the understanding of CRCoVs. IMPORTANCE Knowledge of genomic characterization of the CRCoV is still limited and its evolution remains poorly investigated. We, therefore, investigated the full-length genome of CRCoV in Thailand for the first time and analyzed the evolutionary dynamic of CRCoV. Genomic characterization of Thai CRCoV strains revealed that they possess unique genome structures and have undergone nonsynonymous mutations, which have not been reported in previously described CRCoV strains. Our work suggests that the Thai CRCoVs were not undergone mutation through genetic recombination for their evolution. However, one Thai CRCoV strain PP158_THA_2015 was found to be a potential parent virus for the CRCoV strains found in the United States. This study provides an understanding of the genomic characterization and highlights the signature mutations and ongoing evolutionary process of CRCoV that could be crucial for monitoring in the future.
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Affiliation(s)
- Panida Poonsin
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Jira Chansaenroj
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Flies AS, Flies EJ, Fountain-Jones NM, Musgrove RE, Hamede RK, Philips A, Perrott MRF, Dunowska M. Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles. mBio 2023; 14:e0071523. [PMID: 37439571 PMCID: PMC10470586 DOI: 10.1128/mbio.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.
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Affiliation(s)
- Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Emily J. Flies
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Healthy Landscapes Research Group, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Ruth E. Musgrove
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Annie Philips
- Natural Resources and Environment Tasmania, Hobart, Tasmania, Australia
| | | | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Italiya J, Vacek V, Matějů P, Dering C, Celina SS, Ndiaye A, Černý J. First Detection of SARS-CoV-2 in White Rhinoceros during a Small-Scale Coronavirus Surveillance in the Bandia Reserve, Senegal. Animals (Basel) 2023; 13:2593. [PMID: 37627384 PMCID: PMC10451883 DOI: 10.3390/ani13162593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The SARS-CoV-2 pandemic has heightened interest in the monitoring and surveillance of coronaviruses in wildlife. Testing for the virus in animals can provide valuable insights into viral reservoirs, transmission, and pathogenesis. In this study, we present the results of the molecular surveillance project focused on coronaviruses in Senegalese wildlife. During the project, we screened fecal samples of the wild animals living in the Bandia Reserve (ten non-human primates, one giraffe, and two white rhinoceros) and the free-living urban population of African four-toed hedgehogs in Ngaparou. The results showed the absence of coronaviruses in hedgehogs, non-human primates, and a giraffe. A single positive sample was obtained from a white rhinoceros. The sequencing results of amplified RdRp gene confirmed that the detected virus was SARS-CoV-2. This study represents the first documented instance of molecular detection of SARS-CoV-2 in white rhinoceros and, therefore, extends our knowledge of possible SARS-CoV-2 hosts.
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Affiliation(s)
- Jignesh Italiya
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
| | - Vojtěch Vacek
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Petr Matějů
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | | | - Seyma S. Celina
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
| | - Arame Ndiaye
- Centre d’Études pour la Génétique et la Conservation (CEGEC S.A.S.U.), Dakar 10455, Senegal;
| | - Jiří Černý
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
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8
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Detection and Characterization of an H9N2 Influenza A Virus in the Egyptian Rousette Bat in Limpopo, South Africa. Viruses 2023; 15:v15020498. [PMID: 36851712 PMCID: PMC9958621 DOI: 10.3390/v15020498] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
In recent years, bats have been shown to host various novel bat-specific influenza viruses, including H17N10 and H18N11 in the Americas and the H9N2 subtype from Africa. Rousettus aegyptiacus (Egyptian Rousette bat) is recognized as a host species for diverse viral agents. This study focused on the molecular surveillance of a maternal colony in Limpopo, South Africa, between 2017-2018. A pan-influenza hemi-nested RT-PCR assay targeting the PB1 gene was established, and influenza A virus RNA was identified from one fecal sample out of 860 samples. Genome segments were recovered using segment-specific amplification combined with standard Sanger sequencing and Illumina unbiased sequencing. The identified influenza A virus was closely related to the H9N2 bat-influenza virus, confirming the circulation of this subtype among Egyptian fruit bat populations in Southern Africa. This bat H9N2 subtype contained amino acid residues associated with transmission and virulence in either mammalian or avian hosts, though it will likely require additional adaptations before spillover.
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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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10
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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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11
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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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12
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Chidoti V, De Nys H, Pinarello V, Mashura G, Missé D, Guerrini L, Pfukenyi D, Cappelle J, Chiweshe N, Ayouba A, Matope G, Peeters M, Gori E, Bourgarel M, Liégeois F. Longitudinal Survey of Coronavirus Circulation and Diversity in Insectivorous Bat Colonies in Zimbabwe. Viruses 2022; 14:v14040781. [PMID: 35458511 PMCID: PMC9031365 DOI: 10.3390/v14040781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/24/2022] [Accepted: 04/03/2022] [Indexed: 12/22/2022] Open
Abstract
Background: Studies have linked bats to outbreaks of viral diseases in human populations such as SARS-CoV-1 and MERS-CoV and the ongoing SARS-CoV-2 pandemic. Methods: We carried out a longitudinal survey from August 2020 to July 2021 at two sites in Zimbabwe with bat–human interactions: Magweto cave and Chirundu farm. A total of 1732 and 1866 individual bat fecal samples were collected, respectively. Coronaviruses and bat species were amplified using PCR systems. Results: Analysis of the coronavirus sequences revealed a high genetic diversity, and we identified different sub-viral groups in the Alphacoronavirus and Betacoronavirus genus. The established sub-viral groups fell within the described Alphacoronavirus sub-genera: Decacovirus, Duvinacovirus, Rhinacovirus, Setracovirus and Minunacovirus and for Betacoronavirus sub-genera: Sarbecoviruses, Merbecovirus and Hibecovirus. Our results showed an overall proportion for CoV positive PCR tests of 23.7% at Chirundu site and 16.5% and 38.9% at Magweto site for insectivorous bats and Macronycteris gigas, respectively. Conclusions: The higher risk of bat coronavirus exposure for humans was found in December to March in relation to higher viral shedding peaks of coronaviruses in the parturition, lactation and weaning months of the bat populations at both sites. We also highlight the need to further document viral infectious risk in human/domestic animal populations surrounding bat habitats in Zimbabwe.
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Affiliation(s)
- Vimbiso Chidoti
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
| | - Hélène De Nys
- ASTRE, CIRAD, INRAE, University of Montpellier, 34980 Montpellier, France; (H.D.N.); (L.G.); (J.C.); (M.B.)
- CIRAD, UMR ASTRE, Harare, Zimbabwe;
| | - Valérie Pinarello
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
- ASTRE, CIRAD, INRAE, University of Montpellier, 34980 Montpellier, France; (H.D.N.); (L.G.); (J.C.); (M.B.)
- CIRAD, UMR ASTRE, Harare, Zimbabwe;
| | - Getrude Mashura
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
| | - Dorothée Missé
- MIVEGEC, University of Montpellier, IRD, CNRS, 34394 Montpellier, France;
| | - Laure Guerrini
- ASTRE, CIRAD, INRAE, University of Montpellier, 34980 Montpellier, France; (H.D.N.); (L.G.); (J.C.); (M.B.)
- CIRAD, UMR ASTRE, Harare, Zimbabwe;
| | - Davies Pfukenyi
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
| | - Julien Cappelle
- ASTRE, CIRAD, INRAE, University of Montpellier, 34980 Montpellier, France; (H.D.N.); (L.G.); (J.C.); (M.B.)
- CIRAD, UMR ASTRE, 34398 Montpellier, France
| | | | - Ahidjo Ayouba
- TransVIHMI, University of Montpellier, IRD, Inserm, 34394 Montpellier, France; (A.A.); (M.P.)
| | - Gift Matope
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
| | - Martine Peeters
- TransVIHMI, University of Montpellier, IRD, Inserm, 34394 Montpellier, France; (A.A.); (M.P.)
| | - Elizabeth Gori
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
| | - Mathieu Bourgarel
- ASTRE, CIRAD, INRAE, University of Montpellier, 34980 Montpellier, France; (H.D.N.); (L.G.); (J.C.); (M.B.)
- CIRAD, UMR ASTRE, Harare, Zimbabwe;
| | - Florian Liégeois
- Faculty of Veterinary Science, University of Zimbabwe, Harare P.O. Box MP 167, Zimbabwe; (V.C.); (V.P.); (G.M.); (D.P.); (G.M.); (E.G.)
- MIVEGEC, University of Montpellier, IRD, CNRS, 34394 Montpellier, France;
- Correspondence:
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13
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Urushadze L, Babuadze G, Shi M, Escobar LE, Mauldin MR, Natradeze I, Machablishvili A, Kutateladze T, Imnadze P, Nakazawa Y, Velasco-Villa A. A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia. Viruses 2021; 14:v14010072. [PMID: 35062276 PMCID: PMC8778869 DOI: 10.3390/v14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022] Open
Abstract
Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.
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Affiliation(s)
- Lela Urushadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - George Babuadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Biological Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Main Campus, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Mang Shi
- Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| | - Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA;
| | - Matthew R. Mauldin
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Ioseb Natradeze
- Institute of Zoology, Campus S, Ilia State University, Tbilisi 0162, Georgia;
| | - Ann Machablishvili
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Tamar Kutateladze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Department of Public Health and Epidemiology, Faculty of Medicine, Main Campus, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Yoshinori Nakazawa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Andres Velasco-Villa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
- Correspondence:
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14
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Islam A, Ferdous J, Sayeed MA, Islam S, Kaisar Rahman M, Abedin J, Saha O, Hassan MM, Shirin T. Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. PLoS One 2021; 16:e0260635. [PMID: 34910734 PMCID: PMC8673647 DOI: 10.1371/journal.pone.0260635] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, New York, United States of America
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Victoria, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Shariful Islam
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Md. Kaisar Rahman
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Josefina Abedin
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Otun Saha
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
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15
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Assessing the extent of land-use change around important bat-inhabited caves. BMC ZOOL 2021; 6:31. [PMID: 34840806 PMCID: PMC8605785 DOI: 10.1186/s40850-021-00095-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Background Modification and destruction of natural habitats are bringing previously unencountered animal populations into contact with humans, with bats considered important zoonotic transmission vectors. Caves and cave-dwelling bats are under-represented in conservation plans. In South Africa, at least two cavernicolous species are of interest as potential zoonotic hosts: the Natal long-fingered bat Miniopterus natalensis and the Egyptian fruit bat Rousettus aegyptiacus. Little information is available about the anthropogenic pressures these species face around important roost sites. Both bats are numerous and widespread throughout the country; land-use changes and urban expansions are a rising concern for both conservation and increased bat-human contact. Results Our study addressed this shortfall by determining the extent of land-cover change around 47 roosts between 2014 and 2018 using existing land cover datasets. We determined the land-cover composition around important roost sites (including maternity, hibernacula and co-roosts), distances to urban settlements and assessed the current protection levels of roost localities. We detected an overall 4% decrease in natural woody vegetation (trees) within 5 km buffer zones of all roost sites, with a 10% decrease detected at co-roost sites alone. Agricultural land cover increased the most near roost sites, followed by plantations and urban land-cover. Overall, roosts were located 4.15 ± 0.91 km from urban settlements in 2018, the distances decreasing as urban areas expand. According to the South African National Biodiversity Institute Ecosystem Threat Status assessment, 72% of roosts fall outside of well-protected ecosystems. Conclusions The current lack of regulatory protection of cavernicolous bats and their roosts, increasing anthropogenic expansions and proximity to human settlements raises concerns about increased human-bat contact. Furthermore, uncontrolled roost visitation and vandalism are increasing, contributing to bat health risks and population declines, though the extent of roosts affected is yet to be quantified. In an era where pandemics are predicted to become more frequent and severe due to land-use change, our research is an urgent call for the formal protection of bat-inhabited caves to safeguard both bats and humans. Supplementary Information The online version contains supplementary material available at 10.1186/s40850-021-00095-5.
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Pawęska JT, Jansen van Vuren P, Storm N, Markotter W, Kemp A. Vector Competence of Eucampsipoda africana (Diptera: Nycteribiidae) for Marburg Virus Transmission in Rousettus aegyptiacus (Chiroptera: Pteropodidae). Viruses 2021; 13:2226. [PMID: 34835032 PMCID: PMC8624361 DOI: 10.3390/v13112226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/04/2022] Open
Abstract
This study aimed to determine the vector competence of bat-associated nycteribiid flies (Eucamsipoda africana) for Marburg virus (MARV) in the Egyptian Rousette Bat (ERB), Rousettus aegyptiacus. In flies fed on subcutaneously infected ERBs and tested from 3 to 43 days post infection (dpi), MARV was detected only in those that took blood during the peak of viremia, 5-7 dpi. Seroconversion did not occur in control bats in contact with MARV-infected bats infested with bat flies up to 43 days post exposure. In flies inoculated intra-coelomically with MARV and tested on days 0-29 post inoculation, only those assayed on day 0 and day 7 after inoculation were positive by q-RT-PCR, but the virus concentration was consistent with that of the inoculum. Bats remained MARV-seronegative up to 38 days after infestation and exposure to inoculated flies. The first filial generation pupae and flies collected at different times during the experiments were all negative by q-RT-PCR. Of 1693 nycteribiid flies collected from a wild ERB colony in Mahune Cave, South Africa where the enzootic transmission of MARV occurs, only one (0.06%) tested positive for the presence of MARV RNA. Our findings seem to demonstrate that bat flies do not play a significant role in the transmission and enzootic maintenance of MARV. However, ERBs eat nycteribiid flies; thus, the mechanical transmission of the virus through the exposure of damaged mucous membranes and/or skin to flies engorged with contaminated blood cannot be ruled out.
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Affiliation(s)
- Janusz T. Pawęska
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (P.J.v.V.); (N.S.); (A.K.)
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg 2050, South Africa
| | - Petrus Jansen van Vuren
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (P.J.v.V.); (N.S.); (A.K.)
- Australian Centre for Disease Preparedness, CSIRO Health & Biosecurity, Geelong, VIC 3220, Australia
| | - Nadia Storm
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (P.J.v.V.); (N.S.); (A.K.)
- Department of Microbiology, School of Medicine, Boston University, Boston, MA 02118, USA
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
| | - Alan Kemp
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa; (P.J.v.V.); (N.S.); (A.K.)
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17
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Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison. Viruses 2021; 13:v13101975. [PMID: 34696405 PMCID: PMC8538982 DOI: 10.3390/v13101975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/28/2022] Open
Abstract
Coronaviruses (CoVs) are widespread and highly diversified in wildlife and domestic mammals and can emerge as zoonotic or epizootic pathogens and consequently host shift from these reservoirs, highlighting the importance of veterinary surveillance. All genera can be found in mammals, with α and β showing the highest frequency and diversification. The aims of this study were to review the literature for features of CoV surveillance in animals, to test widely used molecular protocols, and to identify the most effective one in terms of spectrum and sensitivity. We combined a literature review with analyses in silico and in vitro using viral strains and archive field samples. We found that most protocols defined as pan-coronavirus are strongly biased towards α- and β-CoVs and show medium-low sensitivity. The best results were observed using our new protocol, showing LoD 100 PFU/mL for SARS-CoV-2, 50 TCID50/mL for CaCoV, 0.39 TCID50/mL for BoCoV, and 9 ± 1 log2 ×10−5 HA for IBV. The protocol successfully confirmed the positivity for a broad range of CoVs in 30/30 field samples. Our study points out that pan-CoV surveillance in mammals could be strongly improved in sensitivity and spectrum and propose the application of a new RT-PCR assay, which is able to detect CoVs from all four genera, with an optimal sensitivity for α-, β-, and γ-.
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Bonilla-Aldana DK, García-Barco A, Jimenez-Diaz SD, Bonilla-Aldana JL, Cardona-Trujillo MC, Muñoz-Lara F, Zambrano LI, Salas-Matta LA, Rodriguez-Morales AJ. SARS-CoV-2 natural infection in animals: a systematic review of studies and case reports and series. Vet Q 2021; 41:250-267. [PMID: 34406913 PMCID: PMC8428274 DOI: 10.1080/01652176.2021.1970280] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
COVID-19 pandemic is essentially a zoonotic disease. In this context, early in 2020, transmission from humans to certain animals began reporting; the number of studies has grown since. To estimate the pooled prevalence of SARS-CoV-2 natural infection in animals and to determine differences in prevalence between countries, years, animal types and diagnostic methods (RT-PCR or serological tests). A systematic literature review with meta-analysis using eight databases. Observational studies were included but analyzed separately. We performed a random-effects model meta-analysis to calculate the pooled prevalence and 95% confidence interval (95% CI) for prevalence studies and case series. After the screening, 65 reports were selected for full-text assessment and included for qualitative and quantitative analyses. A total of 24 reports assessed SARS-CoV-2 infection by RT-PCR, combining a total of 321,785 animals, yielding a pooled prevalence of 12.3% (95% CI 11.6%–13.0%). Also, a total of 17 studies additionally assessed serological response against SARS-CoV-2, including nine by ELISA, four by PRTN, one by MIA, one by immunochromatography (rest, two studies, the method was not specified), combining a total of 5319 animals, yielding a pooled prevalence of 29.4% (95% CI 22.9%–35.9%). A considerable proportion of animals resulted infected by SARS-CoV-2, ranking minks among the highest value, followed by dogs and cats. Further studies in other animals are required to define the extent and importance of natural infection due to SARS-CoV-2. These findings have multiple implications for public human and animal health. One Health approach in this context is critical for prevention and control.
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Affiliation(s)
- D Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación GISCA, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia
| | - Alejandra García-Barco
- Grupo Colaborativo de Investigación en Enfermedades Transmitidas por vectores, Zoonóticas y tropicales de Risaralda, Pereira, Risaralda, Colombia
| | - S Daniela Jimenez-Diaz
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación GISCA, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia
| | - Jorge Luis Bonilla-Aldana
- School of Veterinary Medicine and Zootechnics, Universidad de la Amazonia, Florencia, Caquetá, Colombia
| | - Maria C Cardona-Trujillo
- Grupo Colaborativo de Investigación en Enfermedades Transmitidas por vectores, Zoonóticas y tropicales de Risaralda, Pereira, Risaralda, Colombia
| | - Fausto Muñoz-Lara
- Department of Internal Medicine, Faculty of Medical Sciences, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras.,Department of Internal Medicine, Hospital Escuela, Tegucigalpa, Honduras
| | - Lysien I Zambrano
- Unit of Scientific Research, School of Medicine, Faculty of Medical Sciences, Universidad Nacional Autónoma de Honduras (UNAH), Tegucigalpa, Honduras
| | | | - Alfonso J Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima, Perú.,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia.,School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia
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