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Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, Eloit M. Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence. Viruses 2023; 15:1897. [PMID: 37766303 PMCID: PMC10536463 DOI: 10.3390/v15091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.
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Affiliation(s)
- Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Cong Tu
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR3528, Université Paris Cité, 75015 Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Léa Vendramini
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Vu Phong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Nguyen Thi Yen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Hoang Ngoc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Hai Son
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Pham Tuan Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Faustine Amara
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015 Paris, France
| | - Sandie Munier
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), Hanoi 70072, Vietnam
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, National Reference Center for Respiratory Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 77420 Maisons-Alfort, France
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George U, George O, Oguzie J, Osasona O, Motayo B, Kamani J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C. Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria. Virus Res 2023; 334:199174. [PMID: 37467933 PMCID: PMC10392604 DOI: 10.1016/j.virusres.2023.199174] [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: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.
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Affiliation(s)
- Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | | | - Judith Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwadamilola Osasona
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde Motayo
- Department of Medical Microbiology, Federal Medical Centre, Abeokuta, Nigeria
| | - Joshua Kamani
- Parasitology Division National Veterinary Research Institute NVRI PMB 01, Vom, Plateau state Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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Muzeniek T, Perera T, Siriwardana S, Bas D, Bayram F, Öruc M, Becker-Ziaja B, Perera I, Weerasena J, Handunnetti S, Schwarz F, Premawansa G, Premawansa S, Yapa W, Nitsche A, Kohl C. Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka. Sci Rep 2023; 13:12859. [PMID: 37553373 PMCID: PMC10409741 DOI: 10.1038/s41598-023-39534-3] [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: 11/13/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.
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Affiliation(s)
- Therese Muzeniek
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Thejanee Perera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, 00300, Sri Lanka
| | - Sahan Siriwardana
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo, 00300, Sri Lanka
| | - Dilara Bas
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Fatimanur Bayram
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Mizgin Öruc
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Beate Becker-Ziaja
- Centre for International Health Protection, Public Health Laboratory Support (ZIG 4), Robert Koch Institute, 13353, Berlin, Germany
| | - Inoka Perera
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo, 00300, Sri Lanka
| | - Jagathpriya Weerasena
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, 00300, Sri Lanka
| | - Shiroma Handunnetti
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, 00300, Sri Lanka
| | - Franziska Schwarz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | | | - Sunil Premawansa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo, 00300, Sri Lanka
| | - Wipula Yapa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo, 00300, Sri Lanka
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353, Berlin, Germany.
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Perera T, Schwarz F, Muzeniek T, Siriwardana S, Becker-Ziaja B, Perera IC, Handunnetti S, Weerasena J, Premawansa G, Premawansa S, Nitsche A, Yapa W, Kohl C. First Complete Cytochrome B Sequences and Molecular Taxonomy of Bat Species from Sri Lanka. Animals (Basel) 2022; 12:ani12131674. [PMID: 35804573 PMCID: PMC9264896 DOI: 10.3390/ani12131674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/16/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022] Open
Abstract
This is the first report on the molecular identification and phylogeny of the Rousettus leschenaultii Desmarest, 1810, Rhinolophus rouxii Temminck, 1835, Hipposideros speoris Schneider, 1800, Hipposideros lankadiva Kelaart, 1850, and Miniopterus fuliginosus Kuhl, 1817, bat species in Sri Lanka, inferred from analyses by mitochondrially encoded cytochrome b gene sequences. Recent research has indicated that bats show enormous cryptic genetic diversity. Moreover, even within the same species, the acoustic properties of echolocation calls and morphological features such as fur color could vary in different populations. Therefore, we have used molecular taxonomy for the accurate identification of five bat species recorded in one of the largest cave populations in Sri Lanka. The bats were caught using a hand net, and saliva samples were collected non-invasively from each bat by using a sterile oral swab. Nucleic acids were extracted from the oral swab samples, and mitochondrial DNA was amplified by using primers targeting the mitochondrially encoded cytochrome b gene. This study reports the first molecular evidence for the identification of five bat species in Sri Lanka. Our findings will contribute to future conservation and systematic studies of bats in Sri Lanka. This study will also provide the basis for a genetic database of Sri Lankan bats which will contribute significantly to the investigation of potentially zoonotic bat viruses.
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Affiliation(s)
- Thejanee Perera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 00300 Colombo, Sri Lanka; (S.H.); (J.W.)
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, 00300 Colombo, Sri Lanka; (S.S.); (I.C.P.); (S.P.); (W.Y.)
- Correspondence: ; Tel.: +94-7-433-83-46
| | - Franziska Schwarz
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (F.S.); (T.M.); (A.N.); (C.K.)
| | - Therese Muzeniek
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (F.S.); (T.M.); (A.N.); (C.K.)
| | - Sahan Siriwardana
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, 00300 Colombo, Sri Lanka; (S.S.); (I.C.P.); (S.P.); (W.Y.)
| | - Beate Becker-Ziaja
- Centre for International Health Protection, Public Health Laboratory Support (ZIG 4), Robert Koch Institute, 13353 Berlin, Germany;
| | - Inoka C. Perera
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, 00300 Colombo, Sri Lanka; (S.S.); (I.C.P.); (S.P.); (W.Y.)
| | - Shiroma Handunnetti
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 00300 Colombo, Sri Lanka; (S.H.); (J.W.)
| | - Jagathpriya Weerasena
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, 00300 Colombo, Sri Lanka; (S.H.); (J.W.)
| | | | - Sunil Premawansa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, 00300 Colombo, Sri Lanka; (S.S.); (I.C.P.); (S.P.); (W.Y.)
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (F.S.); (T.M.); (A.N.); (C.K.)
| | - Wipula Yapa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, 00300 Colombo, Sri Lanka; (S.S.); (I.C.P.); (S.P.); (W.Y.)
| | - Claudia Kohl
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (F.S.); (T.M.); (A.N.); (C.K.)
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Paramyxovirus Diversity within One Population of Miniopterus fuliginosus Bats in Sri Lanka. Pathogens 2022; 11:pathogens11040434. [PMID: 35456109 PMCID: PMC9030695 DOI: 10.3390/pathogens11040434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/06/2023] Open
Abstract
Bats are known as typical reservoirs for a number of viruses, including viruses of the family Paramyxoviridae. Representatives of the subfamily Orthoparamyxovirinae are distributed worldwide and can cause mild to fatal diseases when infecting humans. The research on Paramyxoviruses (PMVs) from different bat hosts all over the world aims to understand the diversity, evolution and distribution of these viruses and to assess their zoonotic potential. A high number of yet unclassified PMVs from bats are recorded. In our study, we investigated bat species from the families Rhinolophidae, Hipposiderae, Pteropodidae and Miniopteridae that are roosting sympatrically in the Wavul Galge cave (Koslanda, Sri Lanka). The sampling at three time points (March and July 2018; January 2019) and screening for PMVs with a generic PCR show the presence of different novel PMVs in 10 urine samples collected from Miniopterus fuliginosus. Sequence analysis revealed a high similarity of the novel strains among each other and to other unclassified PMVs collected from Miniopterus bats. In this study, we present the first detection of PMVs in Sri Lanka and the presence of PMVs in the bat species M. fuliginosus for the first time.
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