1
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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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2
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Andrianiaina A, Andry S, Gentles A, Guth S, Héraud JM, Ranaivoson HC, Ravelomanantsoa NAF, Treuer T, Brook CE. Reproduction, seasonal morphology, and juvenile growth in three Malagasy fruit bats. J Mammal 2022; 103:1397-1408. [PMID: 36686611 PMCID: PMC9841406 DOI: 10.1093/jmammal/gyac072] [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: 10/30/2021] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
The island nation of Madagascar is home to three endemic species of Old World fruit bat in the family Pteropodidae: Pteropus rufus, Eidolon dupreanum, and Rousettus madagascariensis, all three of which are IUCN Red Listed under some category of threat. Delineation of seasonal limits in the reproductive calendar for threatened mammals can inform conservation efforts by clarifying parameters used in population viability models, as well as elucidate understanding of the mechanisms underpinning pathogen persistence in host populations. Here, we define the seasonal limits of a staggered annual birth pulse across the three species of endemic Madagascar fruit bat, known reservoirs for viruses of high zoonotic potential. Our field studies indicate that this annual birth pulse takes place in September/October for P. rufus, November for E. dupreanum, and December for R. madagascariensis in central-eastern Madagascar where the bulk of our research was concentrated. Juvenile development periods vary across the three Malagasy pteropodids, resulting in near-synchronous weaning of pups for all species in late January-February at the height of the fruiting season for this region. We here document the size range in morphological traits for the three Malagasy fruit bat species, with P. rufus and E. dupreanum among the larger of pteropodids globally and R. madagascariensis among the smaller. All three species demonstrate subtle sexual dimorphism with males being larger than females. We explore seasonal variation in adult body condition by comparing observed body mass with body mass predicted by forearm length, demonstrating that pregnant females add weight during staggered gestation periods and males lose weight during the nutritionally deficit Malagasy winter. Finally, we quantify forearm, tibia, and ear length growth rates in juvenile bats, demonstrating both faster growth and more protracted development times for P. rufus as compared with E. dupreanum and R. madagascariensis. The longer development period for the already-threatened P. rufus further undermines the conservation status of this species as human hunting is particularly detrimental to population viability during reproductive periods. Our work highlights the importance of longitudinal field studies in collecting critical data for mammalian conservation efforts and human public health alike.
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Affiliation(s)
- Angelo Andrianiaina
- Mention Zoologie et Biodiversité Animale, Université d’Antananarivo, Antananarivo 101, Madagascar
| | - Santino Andry
- Mention Entomologie, Université d’Antananarivo, Antananarivo 101, Madagascar
| | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens 30609, Georgia, USA
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley 94720, California, USA
| | - Jean-Michel Héraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar 10200, Senegal
- Ecole Doctorale Science de la Vie et de l’Environnement, Faculté des Sciences, Université d’Antananarivo, Antananarivo 101, Madagascar
| | - Hafaliana Christian Ranaivoson
- Mention Zoologie et Biodiversité Animale, Université d’Antananarivo, Antananarivo 101, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar
| | | | - Timothy Treuer
- Gund Institute for Environment, The University of Vermont, Burlington 05405, Vermont, USA
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley 94720, California, USA
- Department of Ecology and Evolution, University of Chicago, Chicago 60637, Illinois, USA
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3
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Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Central and West African Populations. Viruses 2022; 14:v14102259. [PMID: 36298814 PMCID: PMC9611584 DOI: 10.3390/v14102259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
For more than two years after the emergence of COVID-19 (Coronavirus Disease-2019), significant regional differences in morbidity persist. These differences clearly show lower incidence rates in several regions of the African and Asian continents. The work reported here aimed to test the hypothesis of a pre-pandemic natural immunity acquired by some human populations in central and western Africa, which would, therefore, pose the hypothesis of an original antigenic sin with a virus antigenically close to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To identify such pre-existing immunity, sera samples collected before the emergence of COVID-19 were tested to detect the presence of IgG reacting antibodies against SARS-CoV-2 proteins of major significance. Sera samples from French blood donors collected before the pandemic served as a control. The results showed a statistically significant difference of antibodies prevalence between the collected samples in Africa and the control samples collected in France. Given the novelty of our results, our next step consists in highlighting neutralizing antibodies to evaluate their potential for pre-pandemic protective acquired immunity against SARS-CoV-2. In conclusion, our results suggest that, in the investigated African sub-regions, the tested populations could have been potentially and partially pre-exposed, before the COVID-19 pandemic, to the antigens of a yet non-identified Coronaviruses.
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4
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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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5
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
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6
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Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Roy S, Ayukekbong JA, Saylors KE, Joly DO, Wolfe ND, Rubin EM, Lange CE. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110. [PMID: 35233291 PMCID: PMC8867583 DOI: 10.1093/ve/veab110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/05/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
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Affiliation(s)
- Nkom F Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Amethyst Gillis
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Centre Region Route de Kribi, Yaoundé, BP 1364, Cameroon
| | - Joseph Le Doux Diffo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Jean-Michel Takuo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Julius Nwobegahay
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
| | | | - Anne W Rimoin
- Department of Epidemiology, University of California, 71-254 Center for Health Sciences, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bradley S Schneider
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Mosaic, Yaoundé, Centre Region, BP 35353, Cameroon
| | | | - David J McIver
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
- One Health Institute, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Sanjit Roy
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- University of Victoria, 3800 Finnerty Road, Victoria BC V8P 5C2, Canada
| | | | - Karen E Saylors
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
| | - Damien O Joly
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | | | - Edward M Rubin
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | - Christian E Lange
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
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7
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Hoarau AOG, Goodman SM, Al Halabi D, Ramasindrazana B, Lagadec E, Le Minter G, Köster M, Dos Santos A, Schoeman MC, Gudo ES, Mavingui P, Lebarbenchon C. Investigation of astrovirus, coronavirus and paramyxovirus co-infections in bats in the western Indian Ocean. Virol J 2021; 18:205. [PMID: 34641936 PMCID: PMC8506490 DOI: 10.1186/s12985-021-01673-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/10/2022] Open
Abstract
Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.
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Affiliation(s)
- Axel O G Hoarau
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar.,Field Museum of Natural History, Chicago, USA
| | - Dana Al Halabi
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.,Association Vahatra, Antananarivo, Madagascar.,Institut Pasteur de Madagascar, Antananarivo 101, BP 1274, Ambatofotsikely, Madagascar
| | - Erwan Lagadec
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Marie Köster
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Patrick Mavingui
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
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8
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Kumakamba C, Niama FR, Muyembe F, Mombouli JV, Kingebeni PM, Nina RA, Lukusa IN, Bounga G, N'Kawa F, Nkoua CG, Atibu Losoma J, Mulembakani P, Makuwa M, Tamufe U, Gillis A, LeBreton M, Olson SH, Cameron K, Reed P, Ondzie A, Tremeau-Bravard A, Smith BR, Pante J, Schneider BS, McIver DJ, Ayukekbong JA, Hoff NA, Rimoin AW, Laudisoit A, Monagin C, Goldstein T, Joly DO, Saylors K, Wolfe ND, Rubin EM, Bagamboula MPassi R, Muyembe Tamfum JJ, Lange CE. Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents. PLoS One 2021; 16:e0236971. [PMID: 34106949 PMCID: PMC8189465 DOI: 10.1371/journal.pone.0236971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 05/19/2021] [Indexed: 12/21/2022] Open
Abstract
Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 alpha- and 6 betacoronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.
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Affiliation(s)
| | - Fabien R Niama
- National Laboratory of Public Health, Brazzaville, Republic of the Congo
| | | | | | | | - Rock Aime Nina
- Ministry of Agriculture and Livestock, Brazzaville, Republic of the Congo
| | - Ipos Ngay Lukusa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Gerard Bounga
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Frida N'Kawa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Cynthia Goma Nkoua
- National Laboratory of Public Health, Brazzaville, Republic of the Congo
| | | | | | - Maria Makuwa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo.,Labyringth Global Health St. Petersburg, Florida, United States of America
| | - Ubald Tamufe
- Metabiota Cameroon Ltd, Yaoundé, Centre, Cameroon
| | - Amethyst Gillis
- Metabiota Inc, San Francisco, California, United States of America
| | | | - Sarah H Olson
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Kenneth Cameron
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Patricia Reed
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Alain Ondzie
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Alex Tremeau-Bravard
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Brett R Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Jasmine Pante
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | | | | | | | - Nicole A Hoff
- Fielding School of Public Health, University of California, Los Angeles, California, United States of America
| | - Anne W Rimoin
- Fielding School of Public Health, University of California, Los Angeles, California, United States of America
| | - Anne Laudisoit
- EcoHealth Alliance, New York, New York, United States of America
| | - Corina Monagin
- Metabiota Inc, San Francisco, California, United States of America.,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
| | - Damien O Joly
- Wildlife Conversation Society, Bronx, New York, United States of America.,Metabiota Inc, Nanaimo, British Columbia, Canada
| | - Karen Saylors
- Labyringth Global Health St. Petersburg, Florida, United States of America.,Metabiota Inc, San Francisco, California, United States of America
| | - Nathan D Wolfe
- Metabiota Inc, San Francisco, California, United States of America
| | - Edward M Rubin
- Metabiota Inc, San Francisco, California, United States of America
| | | | - Jean J Muyembe Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Christian E Lange
- Labyringth Global Health St. Petersburg, Florida, United States of America.,Metabiota Inc, Nanaimo, British Columbia, Canada
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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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Wilkinson DA, Joffrin L, Lebarbenchon C, Mavingui P. Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses. J Gen Virol 2020; 101:1261-1269. [PMID: 32902374 PMCID: PMC7819353 DOI: 10.1099/jgv.0.001494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.
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Affiliation(s)
- David A. Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Present address: Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
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11
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Lacroix A, Vidal N, Keita AK, Thaurignac G, Esteban A, De Nys H, Diallo R, Toure A, Goumou S, Soumah AK, Povogui M, Koivogui J, Monemou JL, Raulino R, Nkuba A, Foulongne V, Delaporte E, Ayouba A, Peeters M. Wide Diversity of Coronaviruses in Frugivorous and Insectivorous Bat Species: A Pilot Study in Guinea, West Africa. Viruses 2020; 12:v12080855. [PMID: 32764506 PMCID: PMC7472279 DOI: 10.3390/v12080855] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/04/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022] Open
Abstract
Zoonoses can constitute a threat for public health that can have a global importance, as seen with the current COVID-19 pandemic of severe acute respiratory syndrome coronavirus (SARS-CoV2). Bats have been recognized as an important reservoir of zoonotic coronaviruses (CoVs). In West Africa, where there is a high diversity of bat species, little is known on the circulation of CoVs in these hosts, especially at the interface with human populations. In this study, in Guinea, we tested a total of 319 bats belonging to 14 genera and six families of insectivorous and frugivorous bats across the country, for the presence of coronaviruses. We found CoVs in 35 (11%) of the tested bats—in three insectivorous bat species and five fruit bat species that were mostly captured close to human habitat. Positivity rates varied from 5.7% to 100%, depending on bat species. A wide diversity of alpha and beta coronaviruses was found across the country, including three sequences belonging to SarbeCoVs and MerbeCoVs subgenera known to harbor highly pathogenic human coronaviruses. Our findings suggest that CoVs are widely spread in West Africa and their circulation should be assessed to evaluate the risk of exposure of potential zoonotic CoVs to humans.
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Affiliation(s)
- Audrey Lacroix
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Alpha K. Keita
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Guillaume Thaurignac
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Amandine Esteban
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Hélène De Nys
- ASTRE, CIRAD, INRA, University of Montpellier, 34398 Montpellier, France;
- CIRAD, UMR ASTRE, Harare, Zimbabwe
| | - Ramadan Diallo
- Laboratoire Central de Diagnostic Vétérinaire, Ministère de l’Elevage et des Productions Animales, Conakry BP3982, Guinea;
| | - Abdoulaye Toure
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
- Institut National de Sante Publique (INSP), Conakry BP6623, Guinea
| | - Souana Goumou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Moriba Povogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Joel Koivogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Jean-Louis Monemou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (M.P.); (J.K.); (J.-L.M.)
| | - Raisa Raulino
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Antoine Nkuba
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
- Institut National de Recherche Biomédicale and Service de Microbiologie, Cliniques Universitaires de Kinshasa, Gombe, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Vincent Foulongne
- Département de Bacteriologie-Virologie, CHU de Montpellier, 34295 Montpellier, France;
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
| | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
- Correspondence: (A.A.); (M.P.)
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34394 Montpellier, France; (A.L.); (N.V.); (A.K.K.); (G.T.); (A.E.); (A.T.); (R.R.); (A.N.); (E.D.)
- Correspondence: (A.A.); (M.P.)
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12
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Joffrin L, Goodman SM, Wilkinson DA, Ramasindrazana B, Lagadec E, Gomard Y, Le Minter G, Dos Santos A, Corrie Schoeman M, Sookhareea R, Tortosa P, Julienne S, Gudo ES, Mavingui P, Lebarbenchon C. Bat coronavirus phylogeography in the Western Indian Ocean. Sci Rep 2020; 10:6873. [PMID: 32327721 PMCID: PMC7181612 DOI: 10.1038/s41598-020-63799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.
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Affiliation(s)
- Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, USA
| | - David A Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Association Vahatra, Antananarivo, Madagascar
- Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar
| | - Erwan Lagadec
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Pablo Tortosa
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Simon Julienne
- Seychelles Ministry of Health, Victoria, Mahe, Seychelles
| | | | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
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13
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Ranaivoson HC, Héraud JM, Goethert HK, Telford SR, Rabetafika L, Brook CE. Babesial infection in the Madagascan flying fox, Pteropus rufus É. Geoffroy, 1803. Parasit Vectors 2019; 12:51. [PMID: 30674343 PMCID: PMC6343336 DOI: 10.1186/s13071-019-3300-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/07/2019] [Indexed: 01/01/2023] Open
Abstract
Background Babesiae are erythrocytic protozoans, which infect the red blood cells of vertebrate hosts to cause disease. Previous studies have described potentially pathogenic infections of Babesia vesperuginis in insectivorous bats in Europe, the Americas and Asia. To date, no babesial infections have been documented in the bats of Madagascar, or in any frugivorous bat species worldwide. Results We used standard microscopy and conventional PCR to identify babesiae in blood from the endemic Madagascan flying fox (Pteropus rufus). Out of 203 P. rufus individuals captured between November 2013 and January 2016 and screened for erythrocytic parasites, nine adult males (4.43%) were infected with babesiae. Phylogenetic analysis of sequences obtained from positive samples indicates that they cluster in the Babesia microti clade, which typically infect felids, rodents, primates, and canids, but are distinct from B. vesperuginis previously described in bats. Statistical analysis of ecological trends in the data suggests that infections were most commonly observed in the rainy season and in older-age individuals. No pathological effects of infection on the host were documented; age-prevalence patterns indicated susceptible-infectious (SI) transmission dynamics characteristic of a non-immunizing persistent infection. Conclusions To our knowledge, this study is the first report of any erythrocytic protozoan infecting Madagascan fruit bats and the first record of a babesial infection in a pteropodid fruit bat globally. Given the extent to which fruit bats have been implicated as reservoirs for emerging human pathogens, any new record of their parasite repertoire and transmission dynamics offers notable insights into our understanding of the ecology of emerging pathogens. Electronic supplementary material The online version of this article (10.1186/s13071-019-3300-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hafaliana C Ranaivoson
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | - Heidi K Goethert
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Sam R Telford
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Lydia Rabetafika
- Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | - Cara E Brook
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA. .,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
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14
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Wacharapluesadee S, Duengkae P, Chaiyes A, Kaewpom T, Rodpan A, Yingsakmongkon S, Petcharat S, Phengsakul P, Maneeorn P, Hemachudha T. Longitudinal study of age-specific pattern of coronavirus infection in Lyle's flying fox (Pteropus lylei) in Thailand. Virol J 2018; 15:38. [PMID: 29463282 PMCID: PMC5819653 DOI: 10.1186/s12985-018-0950-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/15/2018] [Indexed: 02/02/2023] Open
Abstract
Background Bats are natural reservoirs for several highly pathogenic and novel viruses including coronaviruses (CoVs) (mainly Alphacoronavirus and Betacoronavirus). Lyle’s flying fox (Pteropus lylei)‘s roosts and foraging sites are usually in the proximity to humans and animals. Knowledge about age-specific pattern of CoV infection in P. lylei, prevalence, and viral shedding at roosts and foraging sites may have an impact on infection-age-structure model to control CoV outbreak. Methods P. lylei bats were captured monthly during January–December 2012 for detection of CoV at three areas in Chonburi province; two human dwellings, S1 and S2, where few fruit trees were located with an open pig farm, 0.6 km and 5.5 km away from the bat roost, S3. Nested RT-PCR of RNA-dependent RNA polymerase (RdRp) gene from rectal swabs was used for CoV detection. The strain of CoV was confirmed by sequencing and phylogenetic analysis. Results CoV infection was found in both juveniles and adult bats between May and October (January, in adults only and April, in juveniles only). Of total rectal swab positives (68/367, 18.5%), ratio was higher in bats captured at S1 (11/44, 25.0%) and S2 (35/99, 35.4%) foraging sites than at roost (S3) (22/224, 9.8%). Juveniles (forearm length ≤ 136 mm) were found with more CoV infection than adults at all three sites; S1 (9/24, 37.5% vs 2/20, 10%), S2 (22/49, 44.9% vs 13/50, 26.0%), and S3 (10/30, 33.3% vs 12/194, 6.2%). The average BCI of CoV infected bats was significantly lower than uninfected bats. No gender difference related to infection was found at the sites. Phylogenetic analysis of conserved RdRp gene revealed that the detected CoVs belonged to group D betacoronavirus (n = 64) and alphacoronavirus (n = 4). Conclusions The fact that CoV infection and shedding was found in more juvenile than adult bats may suggest transmission from mother during peripartum period. Whether viral reactivation during parturition period or stress is responsible in maintaining transmission in the bat colony needs to be explored.
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Affiliation(s)
- Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases - Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, Chulalongkorn Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | | | - Aingorn Chaiyes
- Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thongchai Kaewpom
- Thai Red Cross Emerging Infectious Diseases - Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, Chulalongkorn Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apaporn Rodpan
- Thai Red Cross Emerging Infectious Diseases - Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, Chulalongkorn Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Sininat Petcharat
- Thai Red Cross Emerging Infectious Diseases - Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, Chulalongkorn Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Pattarapol Maneeorn
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, Thailand
| | - Thiravat Hemachudha
- Thai Red Cross Emerging Infectious Diseases - Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, Chulalongkorn Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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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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16
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17
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Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia. INFECTION GENETICS AND EVOLUTION 2016; 48:10-18. [PMID: 27932284 PMCID: PMC7106194 DOI: 10.1016/j.meegid.2016.11.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 01/01/2023]
Abstract
South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n = 55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii Coronaviruses detected in bats from Lao PDR and Cambodia. High diversity of αCoVs and βCoVs circulating in bats in Cambodia and Lao PDR. One strain of βCoV, a new member of the MERS-CoV sister-clade, detected from Pipistrellus coromandra. A αCoV strain genetically related to PEDV-CoV, detected from Myotis horsfieldii. CoVs detected for the first time in Megaerops niphanae, Myotis horsfieldii and Macroglossus sp.
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18
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Mendenhall IH, Borthwick S, Neves ES, Low D, Linster M, Liang B, Skiles M, Jayakumar J, Han H, Gunalan V, Lee BPYH, Okahara K, Wang LF, Maurer-Stroh S, Su YCF, Smith GJD. Identification of a Lineage D Betacoronavirus in Cave Nectar Bats (Eonycteris spelaea) in Singapore and an Overview of Lineage D Reservoir Ecology in SE Asian Bats. Transbound Emerg Dis 2016; 64:1790-1800. [PMID: 27637887 PMCID: PMC7159162 DOI: 10.1111/tbed.12568] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 12/11/2022]
Abstract
Coronaviruses are a diverse group of viruses that infect mammals and birds. Bats are reservoirs for several different coronaviruses in the Alphacoronavirus and Betacoronavirus genera. They also appear to be the natural reservoir for the ancestral viruses that generated the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus outbreaks. Here, we detected coronavirus sequences in next‐generation sequence data created from Eonycteris spelaea faeces and urine. We also screened by PCR urine samples, faecal samples and rectal swabs collected from six species of bats in Singapore between 2011 and 2014, all of which were negative. The phylogenetic analysis indicates this novel strain is most closely related to lineage D Betacoronaviruses detected in a diverse range of bat species. This is the second time that coronaviruses have been detected in cave nectar bats, but the first coronavirus sequence data generated from this species. Bat species from which this group of coronaviruses has been detected are widely distributed across SE Asia, South Asia and Southern China. They overlap geographically, often share roosting sites and have been witnessed to forage on the same plant. The addition of sequence data from this group of viruses will allow us to better understand coronavirus evolution and host specificity.
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Affiliation(s)
- I H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - S Borthwick
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - E S Neves
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - D Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - M Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - B Liang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - M Skiles
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - J Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - H Han
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - V Gunalan
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - B P Y-H Lee
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK.,National Parks Board, Singapore
| | - K Okahara
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - L-F Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Y C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - G J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Duke Global Health Institute, Duke University, Durham, NC, USA
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Bat-man disease transmission: zoonotic pathogens from wildlife reservoirs to human populations. Cell Death Discov 2016; 2:16048. [PMID: 27551536 PMCID: PMC4979447 DOI: 10.1038/cddiscovery.2016.48] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 12/11/2022] Open
Abstract
Bats are natural reservoir hosts and sources of infection of several microorganisms, many of which cause severe human diseases. Because of contact between bats and other animals, including humans, the possibility exists for additional interspecies transmissions and resulting disease outbreaks. The purpose of this article is to supply an overview on the main pathogens isolated from bats that have the potential to cause disease in humans.
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Cunhaalmeida F, Giannini NP, Simmons NB. The Evolutionary History of the African Fruit Bats (Chiroptera: Pteropodidae). ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.1.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Leopardi S, Oluwayelu D, Meseko C, Marciano S, Tassoni L, Bakarey S, Monne I, Cattoli G, De Benedictis P. The close genetic relationship of lineage D Betacoronavirus from Nigerian and Kenyan straw-colored fruit bats (Eidolon helvum) is consistent with the existence of a single epidemiological unit across sub-Saharan Africa. Virus Genes 2016; 52:573-7. [PMID: 27059240 PMCID: PMC7089189 DOI: 10.1007/s11262-016-1331-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/01/2016] [Indexed: 01/10/2023]
Abstract
Straw-colored fruit bats (Eidolon helvum), which have been identified as natural hosts for several zoonotic pathogens, such as lyssaviruses, henipaviruses, and ebolavirus, are associated with human settlements in Nigeria where they are commonly consumed as a delicacy. However, information on the viruses harbored by these bats is scarce. In this study, coronavirus sequences were detected using a nested RT-PCR targeting 440 bp of the RNA-dependent RNA polymerase (RdRp) in six of 79 fecal samples collected from an urban colony of E. helvum in Ibadan, Nigeria. Phylogenetic analysis revealed that all six sequences were monophyletic and clustered in lineage D of Betacoronavirus. The extension of two fragments allowed us to classify our sequences within the RdRp Group Unit defined for Kenyan Betacoronavirus from the same host species. These findings are consistent with the previous suggestion on the existence of a single epidemiological unit of E. helvum across sub-Saharan Africa. This theory, which is supported by the genetic structure of continental E. helvum, could facilitate viral mixing between different colonies across the continent.
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Affiliation(s)
- Stefania Leopardi
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy
| | - Daniel Oluwayelu
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
| | - Clement Meseko
- Virology Department, National Veterinary Research Institute, Vom, Nigeria
| | - Sabrina Marciano
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy
| | - Luca Tassoni
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy
| | - Solomon Bakarey
- Institute of Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Isabella Monne
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy
| | - Giovanni Cattoli
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy
| | - Paola De Benedictis
- National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita` 10, 35020, Legnaro, Padua, Italy.
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