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Mo Y, Lim LS, Ng SK. A systematic review on current approaches in bat virus discovered between 2018 and 2022. J Virol Methods 2024; 329:115005. [PMID: 39128772 DOI: 10.1016/j.jviromet.2024.115005] [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: 05/13/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.
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Affiliation(s)
- Yaxin Mo
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Lee-Sim Lim
- School of Distance Education, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Siew Kit Ng
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia.
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2
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The Prevalence of Viral Pathogens among Bats in Kazakhstan. Viruses 2022; 14:v14122743. [PMID: 36560747 PMCID: PMC9788601 DOI: 10.3390/v14122743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Bats carry thousands of viruses from 28 different families. To determine the presence of various pathogens in bat populations in Kazakhstan, 1149 samples (393 oropharyngeal swabs, 349 brain samples, 407 guano) were collected. The samples were collected from four species of bats (Vespertilio murinus, Nyctalus noctula, Myotis blythii, Eptesicus serotinus) in nine regions. The Coronavirus RNA was found in 38 (4.75%) samples, and the rabies virus in 27 (7.74%) samples from bats. Coronaviruses and the rabies virus were found in bats in six out of nine studied areas. The RNAs of SARS-CoV-2, MERS, TBE, CCHF, WNF, influenza A viruses were not detected in the bat samples. The phylogeny of the RdRp gene of 12 samples made it possible to classify them as alphacoronaviruses and divide them into two groups. The main group (n = 11) was closely related to bat coronaviruses from Ghana, Zimbabwe and Kenya. The second group (n = 1) was closely related to viruses previously isolated in the south of Kazakhstan. The phylogeny of the N gene sequence from a bat from west Kazakhstan revealed its close relationship with isolates from the Cosmopolitan group of rabies viruses (Central Asia). These results highlight the need for a continuous monitoring of volatile populations to improve the surveillance and detection of infectious diseases.
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3
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Clerbaux LA, Mayasich SA, Muñoz A, Soares H, Petrillo M, Albertini MC, Lanthier N, Grenga L, Amorim MJ. Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19. J Clin Med 2022; 11:5691. [PMID: 36233559 PMCID: PMC9573230 DOI: 10.3390/jcm11195691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022] Open
Abstract
The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.
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Affiliation(s)
| | - Sally A. Mayasich
- University of Wisconsin-Madison Aquatic Sciences Center at US EPA, Duluth, MN 55804, USA
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | - Helena Soares
- Laboratory of Human Immunobiology and Pathogenesis, iNOVA4Health, Faculdade de Ciências Médicas—Nova Medical School, Universidade Nova de Lisboa, 1099-085 Lisbon, Portugal
| | | | | | - Nicolas Lanthier
- Laboratory of Hepatogastroenterology, Service d’Hépato-Gastroentérologie, Cliniques Universitaires Saint-Luc, UCLouvain, 1200 Brussels, Belgium
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, 91190 Paris, France
| | - Maria-Joao Amorim
- Instituto Gulbenkian de Ciência, 2780-156 Lisbon, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
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4
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Aicher SM, Streicher F, Chazal M, Planas D, Luo D, Buchrieser J, Nemcova M, Seidlova V, Zukal J, Serra-Cobo J, Pontier D, Pain B, Zimmer G, Schwartz O, Roingeard P, Pikula J, Dacheux L, Jouvenet N. Species-Specific Molecular Barriers to SARS-CoV-2 Replication in Bat Cells. J Virol 2022; 96:e0060822. [PMID: 35862713 PMCID: PMC9327701 DOI: 10.1128/jvi.00608-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
Bats are natural reservoirs of numerous coronaviruses, including the potential ancestor of SARS-CoV-2. Knowledge concerning the interaction between coronaviruses and bat cells is sparse. We investigated the ability of primary cells from Rhinolophus and Myotis species, as well as of established and novel cell lines from Myotis myotis, Eptesicus serotinus, Tadarida brasiliensis, and Nyctalus noctula, to support SARS-CoV-2 replication. None of these cells were permissive to infection, not even the ones expressing detectable levels of angiotensin-converting enzyme 2 (ACE2), which serves as the viral receptor in many mammalian species. The resistance to infection was overcome by expression of human ACE2 (hACE2) in three cell lines, suggesting that the restriction to viral replication was due to a low expression of bat ACE2 (bACE2) or the absence of bACE2 binding in these cells. Infectious virions were produced but not released from hACE2-transduced M. myotis brain cells. E. serotinus brain cells and M. myotis nasal epithelial cells expressing hACE2 efficiently controlled viral replication, which correlated with a potent interferon response. Our data highlight the existence of species-specific and cell-specific molecular barriers to viral replication in bat cells. These novel chiropteran cellular models are valuable tools to investigate the evolutionary relationships between bats and coronaviruses. IMPORTANCE Bats are host ancestors of several viruses that cause serious disease in humans, as illustrated by the ongoing SARS-CoV-2 pandemic. Progress in investigating bat-virus interactions has been hampered by a limited number of available bat cellular models. We have generated primary cells and cell lines from several bat species that are relevant for coronavirus research. The various permissivities of the cells to SARS-CoV-2 infection offered the opportunity to uncover some species-specific molecular restrictions to viral replication. All bat cells exhibited a potent entry-dependent restriction. Once this block was overcome by overexpression of human ACE2, which serves at the viral receptor, two bat cell lines controlled well viral replication, which correlated with the inability of the virus to counteract antiviral responses. Other cells potently inhibited viral release. Our novel bat cellular models contribute to a better understanding of the molecular interplays between bat cells and viruses.
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Affiliation(s)
- Sophie-Marie Aicher
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Felix Streicher
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Delphine Planas
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Dongsheng Luo
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Julian Buchrieser
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
| | - Monika Nemcova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Veronika Seidlova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Zukal
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno, Brno, Czech Republic
| | - Jordi Serra-Cobo
- Institut de Recerca de la Biodiversitat (IRBio), Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Dominique Pontier
- Université de Lyon, LabEx Ecofect, Lyon, France
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Bertrand Pain
- University of Lyon, Université Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, Bron, France
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Philippe Roingeard
- INSERM U1259 MAVIVH and Plateforme IBiSA de Microscopie Electronique, Faculté de Médecine, Université de Tours, Tours, France
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Laurent Dacheux
- Institut Pasteur, Université de Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
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5
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Urushadze L, Babuadze G, Shi M, Escobar LE, Mauldin MR, Natradeze I, Machablishvili A, Kutateladze T, Imnadze P, Nakazawa Y, Velasco-Villa A. A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia. Viruses 2021; 14:v14010072. [PMID: 35062276 PMCID: PMC8778869 DOI: 10.3390/v14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022] Open
Abstract
Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.
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Affiliation(s)
- Lela Urushadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - George Babuadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Biological Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Main Campus, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Mang Shi
- Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| | - Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA;
| | - Matthew R. Mauldin
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Ioseb Natradeze
- Institute of Zoology, Campus S, Ilia State University, Tbilisi 0162, Georgia;
| | - Ann Machablishvili
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Tamar Kutateladze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Department of Public Health and Epidemiology, Faculty of Medicine, Main Campus, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Yoshinori Nakazawa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Andres Velasco-Villa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
- Correspondence:
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6
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Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J. Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol 2021; 12:755599. [PMID: 34691006 PMCID: PMC8529330 DOI: 10.3389/fmicb.2021.755599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Research Institute of Public Heath, Nankai University, Tianjin, China
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7
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Giles JR, Peel AJ, Wells K, Plowright RK, McCallum H, Restif O. Optimizing noninvasive sampling of a zoonotic bat virus. Ecol Evol 2021; 11:12307-12321. [PMID: 34594501 PMCID: PMC8462156 DOI: 10.1002/ece3.7830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Outbreaks of infectious viruses resulting from spillover events from bats have brought much attention to bat-borne zoonoses, which has motivated increased ecological and epidemiological studies on bat populations. Field sampling methods often collect pooled samples of bat excreta from plastic sheets placed under-roosts. However, positive bias is introduced because multiple individuals may contribute to pooled samples, making studies of viral dynamics difficult. Here, we explore the general issue of bias in spatial sample pooling using Hendra virus in Australian bats as a case study. We assessed the accuracy of different under-roost sampling designs using generalized additive models and field data from individually captured bats and pooled urine samples. We then used theoretical simulation models of bat density and under-roost sampling to understand the mechanistic drivers of bias. The most commonly used sampling design estimated viral prevalence 3.2 times higher than individual-level data, with positive bias 5-7 times higher than other designs due to spatial autocorrelation among sampling sheets and clustering of bats in roosts. Simulation results indicate using a stratified random design to collect 30-40 pooled urine samples from 80 to 100 sheets, each with an area of 0.75-1 m2, and would allow estimation of true prevalence with minimum sampling bias and false negatives. These results show that widely used under-roost sampling techniques are highly sensitive to viral presence, but lack specificity, providing limited information regarding viral dynamics. Improved estimation of true prevalence can be attained with minor changes to existing designs such as reducing sheet size, increasing sheet number, and spreading sheets out within the roost area. Our findings provide insight into how spatial sample pooling is vulnerable to bias for a wide range of systems in disease ecology, where optimal sampling design is influenced by pathogen prevalence, host population density, and patterns of aggregation.
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Affiliation(s)
- John R. Giles
- Department of EpidemiologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMDUSA
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Alison J. Peel
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Hamish McCallum
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Olivier Restif
- Disease Dynamics UnitDepartment of Veterinary MedicineUniversity of CambridgeCambridgeUK
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8
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Dimkić I, Fira D, Janakiev T, Kabić J, Stupar M, Nenadić M, Unković N, Grbić ML. The microbiome of bat guano: for what is this knowledge important? Appl Microbiol Biotechnol 2021; 105:1407-1419. [PMID: 33512572 PMCID: PMC7845282 DOI: 10.1007/s00253-021-11143-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 12/17/2022]
Abstract
Bats as flying mammals are potent vectors and natural reservoir hosts for many infectious viruses, bacteria, and fungi, also detected in their excreta such as guano. Accelerated deforestation, urbanization, and anthropization hastily lead to overpopulation of the bats in urban areas allowing easy interaction with other animals, expansion, and emergence of new zoonotic disease outbreaks potentially harmful to humans. Therefore, getting new insights in the microbiome of bat guano from different places represents an imperative for the future. Furthermore, the use of novel high-throughput sequencing technologies allows better insight in guano microbiome and potentially indicated that some species could be typical guano-dwelling members. Bats are well known as a natural reservoir of many zoonotic viruses such as Ebola, Nipah, Marburg, lyssaviruses, rabies, henipaviruses, and many coronaviruses which caused a high number of outbreaks including ongoing COVID-19 pandemic. Additionally, many bacterial and fungal pathogens were identified as common guano residents. Thus, the presence of multi-drug-resistant bacteria as environmental reservoirs of extended spectrum β-lactamases and carbapenemase-producing strains has been confirmed. Bat guano is the most suitable substrate for fungal reproduction and dissemination, including pathogenic yeasts and keratinophilic and dimorphic human pathogenic fungi known as notorious causative agents of severe endemic mycoses like histoplasmosis and fatal cryptococcosis, especially deadly in immunocompromised individuals. This review provides an overview of bat guano microbiota diversity and the significance of autochthonous and pathogenic taxa for humans and the environment, highlighting better understanding in preventing emerging diseases. KEY POINTS: Bat guano as reservoir and source for spreading of autochthonous and pathogenic microbiota Bat guano vs. novel zoonotic disease outbreaks Destruction of bat natural habitats urgently demands increased human awareness.
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Affiliation(s)
- Ivica Dimkić
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.
| | - Djordje Fira
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Tamara Janakiev
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Jovana Kabić
- Faculty of Medicine, University of Belgrade, dr Subotića starijeg 1, Belgrade, 11000, Serbia
| | - Miloš Stupar
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Marija Nenadić
- Institute for Biological Research "Siniša Stanković", Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Nikola Unković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
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9
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Chan WS, Au CH, Lam HY, Wang CLN, Ho DNY, Lam YM, Chu DKW, Poon LLM, Chan TL, Zee JST, Ma ESK, Tang BSF. Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Virol J 2020; 17:183. [PMID: 33225958 PMCID: PMC7681180 DOI: 10.1186/s12985-020-01454-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/11/2020] [Indexed: 01/12/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has been a catastrophic burden to global healthcare systems. The fast spread of the etiologic agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need to identify unknown coronaviruses rapidly for prompt clinical and public health decision making. Moreover, owing to the high mutation rate of RNA viruses, periodic surveillance on emerging variants of key virus components is essential for evaluating the efficacy of antiviral drugs, diagnostic assays and vaccines. These 2 knowledge gaps formed the basis of this study. In the first place, we evaluated the feasibility of characterizing coronaviruses directly from respiratory specimens. We amplified partial RdRP gene, a stable genetic marker of coronaviruses, from a collection of 57 clinical specimens positive for SARS-CoV-2 or other human coronaviruses, and sequenced the amplicons with Nanopore Flongle and MinION, the fastest and the most scalable massively-parallel sequencing platforms to-date. Partial RdRP sequences were successfully amplified and sequenced from 82.46% (47/57) of specimens, ranging from 75 to 100% by virus type, with consensus accuracy of 100% compared with Sanger sequences available (n = 40). In the second part, we further compared 19 SARS-CoV-2 RdRP sequences collected from the first to third waves of COVID-19 outbreak in Hong Kong with 22,173 genomes from GISAID EpiCoV™ database. No single nucleotide variants (SNVs) were found in our sequences, and 125 SNVs were observed from global data, with 56.8% being low-frequency (n = 1-47) missense mutations affecting the rear part of RNA polymerase. Among the 9 SNVs found on 4 conserved domains, the frequency of 15438G > T was highest (n = 34) and was predominantly found in Europe. Our data provided a glimpse into the sequence diversity of a primary antiviral drug and diagnostic target. Further studies are warranted to investigate the significance of these mutations.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Ho Yin Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Candy Ling Na Wang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Dona Ngar-Yin Ho
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Yuk Man Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Daniel Ka Wing Chu
- School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | | | - Edmond Shiu Kwan Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China.
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10
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Yadav PD, Shete-Aich A, Nyayanit DA, Pardeshi P, Majumdar T, Balasubramanian R, Ullas PT, Mohandas S, Dighe H, Sawant P, Patil S, Patil D, Gokhale MD, Mathapati B, Sudeep AB, Baradkar S, Kumar A, Kharde R, Salve M, Joshi Y, Gupta N, Mourya DT. Detection of coronaviruses in Pteropus & Rousettus species of bats from different States of India. Indian J Med Res 2020; 151:226-235. [PMID: 32317409 PMCID: PMC7366549 DOI: 10.4103/ijmr.ijmr_795_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background & objectives: Bats are considered to be the natural reservoir for many viruses, of which some are potential human pathogens. In India, an association of Pteropus medius bats with the Nipah virus was reported in the past. It is suspected that the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also has its association with bats. To assess the presence of CoVs in bats, we performed identification and characterization of bat CoV (BtCoV) in P. medius and Rousettus species from representative States in India, collected during 2018 and 2019. Methods: Representative rectal swab (RS) and throat swab specimens of Pteropus and Rousettus spp. bats were screened for CoVs using a pan-CoV reverse transcription-polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene. A single-step RT-PCR was performed on the RNA extracted from the bat specimens. Next-generation sequencing (NGS) was performed on a few representative bat specimens that were tested positive. Phylogenetic analysis was carried out on the partial sequences of RdRp gene sequences retrieved from both the bat species and complete viral genomes recovered from Rousettus spp. Results: Bat samples from the seven States were screened, and the RS specimens of eight Rousettus spp. and 21 Pteropus spp. were found positive for CoV RdRp gene. Among these, by Sanger sequencing, partial RdRp sequences could be retrieved from three Rousettus and eight Pteropus bat specimens. Phylogenetic analysis of the partial RdRp region demonstrated distinct subclustering of the BtCoV sequences retrieved from these Rousettus and Pteropus spp. bats. NGS led to the recovery of four sequences covering approximately 94.3 per cent of the whole genome of the BtCoVs from Rousettus bats. Three BtCoV sequences had 93.69 per cent identity to CoV BtRt-BetaCoV/GX2018. The fourth BtCoV sequence was 96.8 per cent identical to BtCoV HKU9-1. Interpretation & conclusions: This study was a step towards understanding the CoV circulation in Indian bats. Detection of potentially pathogenic CoVs in Indian bats stresses the need for enhanced screening for novel viruses in them. One Health approach with collaborative activities by the animal health and human health sectors in these surveillance activities shall be of use to public health. This would help in the development of diagnostic assays for novel viruses with outbreak potential and be useful in disease interventions. Proactive surveillance remains crucial for identifying the emerging novel viruses with epidemic potential and measures for risk mitigation.
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Affiliation(s)
- Pragya D Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Dimpal A Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prachi Pardeshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - R Balasubramanian
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra; ICMR-National Institute of Virology Kerala Unit, Alappuzha, Kerala, India
| | | | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Hitesh Dighe
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pradeep Sawant
- Enteric Virus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Dilip Patil
- Animal House, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - M D Gokhale
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Basavaraj Mathapati
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A B Sudeep
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sreekant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Abhimanyu Kumar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rutuja Kharde
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yash Joshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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11
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Affiliation(s)
- Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
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