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Amman BR, Schuh AJ, Sealy TK, Conteh I, Akurut GG, Koroma AH, Kamugisha K, Graziano JC, Saidu E, Bangura DF, Kamanda ES, Bakarr IA, Johnny J, Enyel EM, Musa JA, Osborne A, Foday IK, Bangura C, Sumaila C, Williams SMT, Fefegula GM, Atimnedi P, Lebbie A, Towner JS. Co-Infections with Orthomarburgviruses, Paramyxoviruses, and Orthonairoviruses in Egyptian Rousette Bats, Uganda and Sierra Leone. Emerg Infect Dis 2025; 31:1015-1018. [PMID: 40305387 PMCID: PMC12044226 DOI: 10.3201/eid3105.241669] [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] [Indexed: 05/02/2025] Open
Abstract
We report 1.3% (19/1,511) of Egyptian rousette bats (ERBs) in Uganda and Sierra Leone were co-infected with different combinations of Marburg, Sosuga, Kasokero, or Yogue viruses. To prevent infection by those viruses, we recommend avoiding ERB-populated areas, avoiding ERBs and ERB-contaminated objects, and thoroughly washing harvested fruits before consumption.
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Ma Y, Qin LY, Ding X, Wu AP. Diversity, Complexity, and Challenges of Viral Infectious Disease Data in the Big Data Era: A Comprehensive Review. CHINESE MEDICAL SCIENCES JOURNAL = CHUNG-KUO I HSUEH K'O HSUEH TSA CHIH 2025; 40:29-44. [PMID: 40165755 DOI: 10.24920/004461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Viral infectious diseases, characterized by their intricate nature and wide-ranging diversity, pose substantial challenges in the domain of data management. The vast volume of data generated by these diseases, spanning from the molecular mechanisms within cells to large-scale epidemiological patterns, has surpassed the capabilities of traditional analytical methods. In the era of artificial intelligence (AI) and big data, there is an urgent necessity for the optimization of these analytical methods to more effectively handle and utilize the information. Despite the rapid accumulation of data associated with viral infections, the lack of a comprehensive framework for integrating, selecting, and analyzing these datasets has left numerous researchers uncertain about which data to select, how to access it, and how to utilize it most effectively in their research.This review endeavors to fill these gaps by exploring the multifaceted nature of viral infectious diseases and summarizing relevant data across multiple levels, from the molecular details of pathogens to broad epidemiological trends. The scope extends from the micro-scale to the macro-scale, encompassing pathogens, hosts, and vectors. In addition to data summarization, this review thoroughly investigates various dataset sources. It also traces the historical evolution of data collection in the field of viral infectious diseases, highlighting the progress achieved over time. Simultaneously, it evaluates the current limitations that impede data utilization.Furthermore, we propose strategies to surmount these challenges, focusing on the development and application of advanced computational techniques, AI-driven models, and enhanced data integration practices. By providing a comprehensive synthesis of existing knowledge, this review is designed to guide future research and contribute to more informed approaches in the surveillance, prevention, and control of viral infectious diseases, particularly within the context of the expanding big-data landscape.
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Affiliation(s)
- Yun Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing 107302, China
| | - Lu-Yao Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing 107302, China
| | - Xiao Ding
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing 107302, China.
| | - Ai-Ping Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing 107302, China.
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Bakre A, Sweeney R, Espinoza E, Suarez DL, Kapczynski DR. The ACE2 Receptor from Common Vampire Bat ( Desmodus rotundus) and Pallid Bat ( Antrozous pallidus) Support Attachment and Limited Infection of SARS-CoV-2 Viruses in Cell Culture. Viruses 2025; 17:507. [PMID: 40284950 PMCID: PMC12031370 DOI: 10.3390/v17040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 03/26/2025] [Accepted: 03/28/2025] [Indexed: 04/29/2025] Open
Abstract
During the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SC2) infection was confirmed in various animal species demonstrating a wide host range of the virus. Prior studies have shown that the ACE2 protein is the primary receptor used by the virus to gain cellular entry and begin the replication cycle. In previous studies, we demonstrated that human and various bat ACE2 proteins can be utilized by SC2 viruses for entry. Bats are a suspected natural host of SC2 because of genetic homology with other bat coronaviruses. In this work, we demonstrate that expression of ACE2 genes from the common vampire bat (CVB) (Desmodus rotundus) and the pallid bat (PB) (Antrozous pallidus), supports infection and replication of some SC2 viruses in cell culture. Two cell lines were produced, CVB-ACE2 and PB-ACE2, expressing ACE2 from these bat species along with human TMPRSS2, in a model previously established using a non-permissive chicken DF-1 cell line. Results demonstrate that the original Wuhan lineage (WA1) virus and the Delta variant were able to infect and replicate in either of the bat ACE2 cell lines. In contrast, the Lambda and Omicron variant viruses infected both cell lines, but viral titers did not increase following infection. Viral detection using immunofluorescence demonstrated abundant spike (S) protein staining for the WA1 and Delta variants but little signal for the Lambda and Omicron variants. These studies demonstrate that while ACE2 from CVB and PB can be utilized by SC2 viruses to gain entry for infection, later variants (Lambda and Omicron) replicate poorly in these cell lines. These observations suggest more efficient human adaption in later SC2 variants that become less fit for replication in other animal species.
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Affiliation(s)
- Abhijeet Bakre
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA; (R.S.); (E.E.); (D.L.S.); (D.R.K.)
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4
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Owolabi IJ, Karim SU, Khanal S, Valdivia S, Frenzel C, Bai F, Flynt AS. Processing of genomic RNAs by Dicer in bat cells limits SARS-CoV-2 replication. Virol J 2025; 22:86. [PMID: 40133950 PMCID: PMC11934715 DOI: 10.1186/s12985-025-02693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 03/04/2025] [Indexed: 03/27/2025] Open
Abstract
Bats are reservoirs for numerous viruses that cause serious diseases in other animals and humans. Several mechanisms are proposed to contribute to the tolerance of bats to these pathogens. This study investigates the response of bat cells to double-stranded RNA generated by SARS-CoV-2 replication. Here, we found the involvement of Dicer in the processing of viral genomic RNAs during SARS-CoV-2 infection. Examining RNA sequencing of infected cells, small-interfering RNA (siRNA)-like fragments were found derived from viral RNAs. Depletion of Dicer showed a reduction in these RNAs and an increase in viral loads suggesting unlike other mammals, bats may use Dicer to limit viral replication. This prompted the exploration of key dsRNA sensors in bat cells. Our analysis showed significant upregulation of OAS1 and MX1 in response to dsRNA, while PKR levels remained low, suggesting alternative dsRNA-response mechanisms are present that eschew the common PKR-based system. These results further show how bats employ distinct strategies for antiviral defense that may contribute to tolerating viral infections. They suggest the involvement of Dicer in antiviral mechanisms in bats, a function not observed in other mammals. This highlights a mechanism for bat originating viruses to evolve features that in other animals could cause extreme antiviral responses such as is seen with SARS-CoV-2.
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Affiliation(s)
- Iyanuoluwani J Owolabi
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Shazeed-Ul Karim
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Sweta Khanal
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Sergio Valdivia
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Christopher Frenzel
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Fengwei Bai
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Alex S Flynt
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
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5
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Koul M, Kaushik S, Singh K, Sharma D. VITALdb: to select the best viroinformatics tools for a desired virus or application. Brief Bioinform 2025; 26:bbaf084. [PMID: 40063348 PMCID: PMC11892104 DOI: 10.1093/bib/bbaf084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 01/14/2025] [Accepted: 02/17/2025] [Indexed: 05/13/2025] Open
Abstract
The recent pandemics of viral diseases, COVID-19/mpox (humans) and lumpy skin disease (cattle), have kept us glued to viral research. These pandemics along with the recent human metapneumovirus outbreak have exposed the urgency for early diagnosis of viral infections, vaccine development, and discovery of novel antiviral drugs and therapeutics. To support this, there is an armamentarium of virus-specific computational tools that are currently available. VITALdb (VIroinformatics Tools and ALgorithms database) is a resource of ~360 viroinformatics tools encompassing all major viruses (SARS-CoV-2, influenza virus, human immunodeficiency virus, papillomavirus, herpes simplex virus, hepatitis virus, dengue virus, Ebola virus, Zika virus, etc.) and several diverse applications [structural and functional annotation, antiviral peptides development, subspecies characterization, recognition of viral recombination, inhibitors identification, phylogenetic analysis, virus-host prediction, viral metagenomics, detection of mutation(s), primer designing, etc.]. Resources, tools, and other utilities mentioned in this article will not only facilitate further developments in the realm of viroinformatics but also provide tremendous fillip to translate fundamental knowledge into applied research. Most importantly, VITALdb is an inevitable tool for selecting the best tool(s) to carry out a desired task and hence will prove to be a vital database (VITALdb) for the scientific community. Database URL: https://compbio.iitr.ac.in/vitaldb.
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Affiliation(s)
- Mira Koul
- Computational Biology and Translational Bioinformatics (CBTB) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Shalini Kaushik
- Computational Biology and Translational Bioinformatics (CBTB) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Kavya Singh
- Computational Biology and Translational Bioinformatics (CBTB) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Deepak Sharma
- Computational Biology and Translational Bioinformatics (CBTB) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Yan X, Liu Y, Hu T, Huang Z, Li C, Guo L, Liu Y, Li N, Zhang H, Sun Y, Yi L, Wu J, Feng J, Zhang F, Jiang T, Tu C, He B. A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics. Nat Microbiol 2025; 10:554-568. [PMID: 39833544 DOI: 10.1038/s41564-024-01884-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 11/13/2024] [Indexed: 01/22/2025]
Abstract
Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.
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Affiliation(s)
- Xiaomin Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Yang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Tingsong Hu
- Southern Center for Diseases Control and Prevention, Guangzhou, Guangdong Province, China
| | - Zhenglanyi Huang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin Province, China
| | - Chenxi Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Lei Guo
- Division of Wildlife and Plant Conservation, State Forestry and Grassland Administration, Changchun, Jilin Province, China
| | - Yuhang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Nan Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan Province, China
| | - Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Jianmin Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin Province, China
| | - Fuqiang Zhang
- Southern Center for Diseases Control and Prevention, Guangzhou, Guangdong Province, China.
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin Province, China.
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China.
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China.
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7
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Figueiroa T, Galvão Bueno M, Bento Moura PE, de Oliveira MB, Passos Cordeiro JL, Santos-Cavalcante N, Camacho Antevere Mazzarotto GA, Wallau GL, Corrêa da Silva Junior L, Resende PC, Siqueira MMM, Ogrzewalska M. Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations. Animals (Basel) 2025; 15:332. [PMID: 39943102 PMCID: PMC11816360 DOI: 10.3390/ani15030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 02/16/2025] Open
Abstract
The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.
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Affiliation(s)
- Thays Figueiroa
- Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil; (T.F.); (L.C.d.S.J.); (P.C.R.); (M.M.M.S.)
| | - Marina Galvão Bueno
- Fundação Oswaldo Cruz, IOC, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Patricia Emilia Bento Moura
- Fundação Oswaldo Cruz, IOC, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Marcione Brito de Oliveira
- Museu Nacional, Departamento de Vertebrados, Setor de Mastozoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, RJ, Brazil;
| | - José Luís Passos Cordeiro
- Fundação Oswaldo Cruz, Unidade do Ceará, Área de Saúde e Ambiente, Eusébio, Ceará 61773-270, CE, Brazil;
- Plataforma Internacional para Ciência, Tecnologia e Inovação em Saúde (PICTIS), Via do Conhecimento, Edifício Central, 3830-352 Ílhavo, Portugal
| | - Nádia Santos-Cavalcante
- Museu de História Natural do Ceará Prof. Dias da Rocha, Universidade Estadual do Ceará, Pacoti, Ceará 62770-000, CE, Brazil;
- Fundação Oswaldo Cruz, Instituto Lêonidas and Maria Deane (ILDM), Unidade da Amazônia, Manaus 69057-070, AM, Brazil
| | - Giovanny A. Camacho Antevere Mazzarotto
- Fundação Oswaldo Cruz, Unidade do Ceará, Laboratório Analítico de Competências Moleculares e Epidemiológicas, Plataforma de Camelídeos e Produção de Nanocorpos, Eusébio, Ceará 61773-270, CE, Brazil;
| | - Gabriel Luz Wallau
- Fundação Oswaldo Cruz, Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM), Cidade Universitária, Recife 50740-465, PE, Brazil;
- Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, 20359 Hamburg, Germany
| | - Leonardo Corrêa da Silva Junior
- Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil; (T.F.); (L.C.d.S.J.); (P.C.R.); (M.M.M.S.)
| | - Paola Cristina Resende
- Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil; (T.F.); (L.C.d.S.J.); (P.C.R.); (M.M.M.S.)
| | - Marilda M. Mendonça Siqueira
- Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil; (T.F.); (L.C.d.S.J.); (P.C.R.); (M.M.M.S.)
| | - Maria Ogrzewalska
- Fundação Oswaldo Cruz, IOC, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro 21040-900, RJ, Brazil; (T.F.); (L.C.d.S.J.); (P.C.R.); (M.M.M.S.)
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8
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Gonzalez V, Hurtado-Monzón AM, O'Krafka S, Mühlberger E, Letko M, Frank HK, Laing ED, Phelps KL, Becker DJ, Munster VJ, Falzarano D, Schountz T, Seifert SN, Banerjee A. Studying bats using a One Health lens: bridging the gap between bat virology and disease ecology. J Virol 2024; 98:e0145324. [PMID: 39499009 DOI: 10.1128/jvi.01453-24] [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] [Indexed: 11/07/2024] Open
Abstract
Accumulating data suggest that some bat species host emerging viruses that are highly pathogenic in humans and agricultural animals. Laboratory-based studies have highlighted important adaptations in bat immune systems that allow them to better tolerate viral infections compared to humans. Simultaneously, ecological studies have discovered critical extrinsic factors, such as nutritional stress, that correlate with virus shedding in wild-caught bats. Despite some progress in independently understanding the role of bats as reservoirs of emerging viruses, there remains a significant gap in the molecular understanding of factors that drive virus spillover from bats. Driven by a collective goal of bridging the gap between the fields of bat virology, immunology, and disease ecology, we hosted a satellite symposium at the 2024 American Society for Virology meeting. Bringing together virologists, immunologists, and disease ecologists, we discussed the intrinsic and extrinsic factors such as virus receptor engagement, adaptive immunity, and virus ecology that influence spillover from bat hosts. This article summarizes the topics discussed during the symposium and emphasizes the need for interdisciplinary collaborations and resource sharing.
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Affiliation(s)
- Victoria Gonzalez
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arianna M Hurtado-Monzón
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sabrina O'Krafka
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Elke Mühlberger
- Department of Virology, Immunology, and Microbiology, Boston University, Boston, Massachusetts, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Hannah K Frank
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | | | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Vincent J Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases (NIAID), Hamilton, Montana, USA
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Center for Vector-Borne Infectious Diseases, Colorado State University, Fort Collins, Colorado, USA
| | - Stephanie N Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Liu Q, Wang DS, Lian ZH, Fang J, Han PY, Qiu Y, Zhao JY, Zong LD, Zhang YZ, Ge XY. Identification and Characterization of an Alphacoronavirus in Rhinolophus sinicus and a Betacoronavirus in Apodemus ilex in Yunnan, China. Microorganisms 2024; 12:1490. [PMID: 39065258 PMCID: PMC11278907 DOI: 10.3390/microorganisms12071490] [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: 07/02/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. It is important to monitor the CoVs carried by bats and rodents. In this study, we collected 410 fecal samples from bats and 74 intestinal samples from rats in Yunnan Province, China. Using RT-PCR, we identified one positive sample for alphacoronavirus (TC-14) from Rhinolophus sinicus (Chinese rufous horseshoe bat) and two positive samples for betacoronavirus (GS-53, GS-56) from Apodemus ilex (Rodentia: Muridae). We successfully characterized the complete genomes of TC-14 and GS-56. Phylogenetic analysis revealed that TC-14 clustered with bat CoV HKU2 and SADS-CoV, while GS-56 was closely related to rat CoV HKU24. The identification of positive selection sites and estimation of divergence dates further helped characterize the genetic evolution of TC-14 and GS-56. In summary, this research reveals the genetic evolution characteristics of TC-14 and GS-56, providing valuable references for the study of CoVs carried by bats and rodents in Yunnan Province.
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Affiliation(s)
- Qian Liu
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
| | - Dan-Shu Wang
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
| | - Zhong-Hao Lian
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
| | - Jie Fang
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
| | - Pei-Yu Han
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (J.-Y.Z.); (L.-D.Z.)
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
| | - Jun-Ying Zhao
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (J.-Y.Z.); (L.-D.Z.)
| | - Li-Dong Zong
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (J.-Y.Z.); (L.-D.Z.)
| | - Yun-Zhi Zhang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (J.-Y.Z.); (L.-D.Z.)
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China; (Q.L.); (D.-S.W.); (Z.-H.L.); (J.F.); (Y.Q.)
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10
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Liu Z, Liu Q, Wang H, Yao X. Severe zoonotic viruses carried by different species of bats and their regional distribution. Clin Microbiol Infect 2024; 30:206-210. [PMID: 37805032 DOI: 10.1016/j.cmi.2023.09.025] [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: 07/20/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Bats have garnered increased attention in the field of life sciences for their typical biological characteristics of carrying a variety of zoonotic viruses without disease, long lifespans, low tumorigenesis rates, and high metabolism. When it was found that bats can carry the rabies virus, over 60 years of research revealed that bats host over 4100 distinct viruses, including Ebola virus and SARS-CoV. OBJECTIVES This paper primarily reviews the profiles of zoonotic viruses carried by bats across various regions globally. The review aims to provide a foundation and reference for future research on monitoring zoonotic viruses in diverse global regions and bat species, exploring the coevolutionary relationship between bats and viruses, understanding the tolerance mechanisms of bat B cells, prevention, and treatment of zoonotic diseases caused by bats. SOURCES The search used 'bat', 'bats', 'rabies virus', 'Dengue virus', 'West Nile virus', 'Zika virus', 'St. Louis encephalitis virus', 'Japanese encephalitis virus', 'Hantavirus', 'Novel hantavirus', 'Rift Valley fever virus', 'Crimean Congo hemorrhagic fever virus', 'Paramyxovirus', 'Nipah virus', 'Hendra virus', 'Menangle virus', 'Tioman virus', 'Marburg Virus', 'Bombali virus', 'Ebola virus', 'Influenza A virus', 'coronavirus', 'Hepatitis B virus', and 'Hepatitis E virus' as text in PubMed. CONTENT A total of 147 references were obtained. Surveys on severe zoonotic virus carriage have been limited to only 83 bat species belonging to nine families, which are distributed all over the world. We also briefly describe the antibody responses and B-cell molecules in bats. IMPLICATIONS Several viruses have been found in different species of bats. This suggests that bats may be important hosts for future viral infectious diseases. Particularly in recent years, the close correlation between human infection pandemics caused by coronaviruses and bats highlights the pressing need to comprehend the species, tolerance, and coevolutionary mechanisms of zoonotic viruses carried by different bat species.
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Affiliation(s)
- Zegang Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, China
| | - Qinlu Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, China
| | - Huifang Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi City, China.
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11
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Albuquerque NK, Silva SP, Aragão CF, Cunha TCAS, Paiva FAS, Coelho TFSB, Cruz ACR. Virome analysis of Desmodus rotundus tissue samples from the Amazon region. BMC Genomics 2024; 25:34. [PMID: 38177994 PMCID: PMC10768307 DOI: 10.1186/s12864-023-09950-w] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses. RESULTS Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages. CONCLUSION This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.
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Affiliation(s)
- Nádia K Albuquerque
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
| | - Sandro P Silva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Carine F Aragão
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Tânia Cristina A S Cunha
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Francisco A S Paiva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Taciana F S B Coelho
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Ana Cecília R Cruz
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil.
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12
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Paietta EN, Kraberger S, Regney M, Custer JM, Ehmke E, Yoder AD, Varsani A. Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs ( Varecia rubra). Viruses 2023; 16:37. [PMID: 38257737 PMCID: PMC10818365 DOI: 10.3390/v16010037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PVs) in speciose non-human primate lineages, particularly the lemuriform primates. Varecia variegata (black-and-white ruffed lemurs) and Varecia rubra (red ruffed lemurs), two closely related species comprising the Varecia genus, are critically endangered with large global captive populations. Varecia variegata papillomavirus (VavPV) types -1 and -2, the first PVs in lemurs with a fully identified genome, were previously characterized from captive V. variegata saliva. To build upon this discovery, saliva samples were collected from captive V. rubra with the following aims: (1) to identify PVs shared between V. variegata and V. rubra and (2) to characterize novel PVs in V. rubra to better understand PV diversity in the lemuriform primates. Three complete PV genomes were determined from V. rubra samples. Two of these PV genomes share 98% L1 nucleotide identity with VavPV2, denoting interspecies infection of V. rubra by VavPV2. This work represents the first reported case of interspecies PV infection amongst the strepsirrhine primates. The third PV genome shares <68% L1 nucleotide identity with that of all PVs. Thus, it represents a new PV species and has been named Varecia rubra papillomavirus 1 (VarPV1). VavPV1, VavPV2, and VarPV1 form a new clade within the Papillomaviridae family, likely representing a novel genus. Future work diversifying sample collection (i.e., lemur host species from multiple genera, sample type, geographic location, and wild populations) is likely to uncover a world of diverse lemur PVs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Melanie Regney
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
| | - Erin Ehmke
- Duke Lemur Center, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (S.K.); (M.R.); (J.M.C.)
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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13
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Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
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Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
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14
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Cantoni D, Mayora-Neto M, Derveni M, da Costa K, Del Rosario J, Ameh VO, Sabeta CT, Auld B, Hamlet A, Jones IM, Wright E, Scott SD, Giotis ES, Banyard AC, Temperton N. Serological evidence of virus infection in Eidolon helvum fruit bats: implications for bushmeat consumption in Nigeria. Front Public Health 2023; 11:1283113. [PMID: 38106901 PMCID: PMC10723585 DOI: 10.3389/fpubh.2023.1283113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction The Eidolon helvum fruit bat is one of the most widely distributed fruit bats in Africa and known to be a reservoir for several pathogenic viruses that can cause disease in animals and humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples from E. helvum bats that were captured for human consumption in Makurdi, Nigeria. Methods Using pseudotyped viruses, we screened 304 serum samples for neutralizing antibodies against viruses from the Coronaviridae, Filoviridae, Orthomyxoviridae and Paramyxoviridae families. Results We report the presence of neutralizing antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p < 0.001), Nipah virus (odds ratio 4.04; p = 0.00031), bat influenza H17N10 virus (odds ratio 7.25; p < 0.001) and no significant association with Ebola virus (odds ratio 0.56; p = 0.375) in this bat cohort. Conclusion The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses in E. helvum populations. These findings highlight the importance of maintaining sero-surveillance of E. helvum, and the necessity for further, more comprehensive investigations to monitor changes in virus prevalence, distribution over time, and across different geographic locations.
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Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Mariliza Derveni
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kelly da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Joanne Del Rosario
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Veronica O. Ameh
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Claude T. Sabeta
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- World Organisation for Animal Health Rabies Reference Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Bethany Auld
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Arran Hamlet
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Simon D. Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Efstathios S. Giotis
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
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Colombino E, Lelli D, Canziani S, Quaranta G, Guidetti C, Leopardi S, Robetto S, De Benedictis P, Orusa R, Mauthe von Degerfeld M, Capucchio MT. Main causes of death of free-ranging bats in Turin province (North-Western Italy): gross and histological findings and emergent virus surveillance. BMC Vet Res 2023; 19:200. [PMID: 37821925 PMCID: PMC10566203 DOI: 10.1186/s12917-023-03776-0] [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: 10/07/2022] [Accepted: 10/05/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Bats are recognized as reservoir species for multiple viruses. However, little is known on bats' health and mortality. Thus, this study aimed to investigate the main causes of death of bats from Turin province (North-western Italy) and to describe gross and histopathological lesions potentially associated with the presence of selected bat viruses. RESULTS A total of 71 bats belonging to 9 different species of the families Vespertilionidae and Molossidae were necropsied and samples of the main organs were submitted to histopathological examination. Also, aliquots of the small intestine, liver, spleen, lung, and brain were collected and submitted to biomolecular investigation for the identification of Coronaviridae, Poxviridae, Reoviridae (Mammalian orthoreovirus species), Rhabdoviridae (Vaprio ledantevirus and Lyssavirus species) and Kobuvirus. The majority of bats died from traumatic lesions due to unknown trauma or predation (n = 40/71, 56.3%), followed by emaciation (n = 13/71,18.3%). The main observed gross lesions were patagium and skin lesions (n = 23/71, 32.4%), forelimbs fractures (n = 15/71, 21.1%) and gastric distension (n = 10/71,14.1%). Histologically, the main lesions consisted of lymphoplasmacytic pneumonia (n = 24/71, 33.8%), skin/patagium dermatitis (n = 23/71, 32.4%), liver steatosis and hepatitis (n = 12, 16.9%), and white pulp depletion in the spleen (n = 7/71, 9.8%). Regarding emergent bat viruses, only poxvirus (n = 2, 2.8%) and orthoreovirus (n = 12/71, 16.9%) were detected in a low percentage of bats. CONCLUSIONS Trauma is the main lesion observed in bats collected in Turin province (North-western Italy) associated with forelimb fractures and the detected viral positivity rate seems to suggest that they did not represent a threat for human health.
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Affiliation(s)
- Elena Colombino
- Department of Veterinary Sciences, Centro Animali Non Convenzionali (C.A.N.C), University of Turin, Turin, Italy
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e Dell'Emilia Romagna, Brescia, Italy
- Molecular Medicine PhD Program, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Sabrina Canziani
- Istituto Zooprofilattico Sperimentale della Lombardia e Dell'Emilia Romagna, Brescia, Italy
| | - Giuseppe Quaranta
- Department of Veterinary Sciences, Centro Animali Non Convenzionali (C.A.N.C), University of Turin, Turin, Italy
| | - Cristina Guidetti
- Liguria e Valle d'Aosta, Istituto Zooprofilattico Sperimentale del Piemonte, National Reference Centre for Wild Animal Diseases (CeRMAS), Aosta, Italy
| | - Stefania Leopardi
- Istituto Zooprofilattico Sperimentale delle Venezie, FAO and National Reference Centre for Rabies, Legnaro, PD, Italy
| | - Serena Robetto
- Liguria e Valle d'Aosta, Istituto Zooprofilattico Sperimentale del Piemonte, National Reference Centre for Wild Animal Diseases (CeRMAS), Aosta, Italy
| | - Paola De Benedictis
- Istituto Zooprofilattico Sperimentale delle Venezie, FAO and National Reference Centre for Rabies, Legnaro, PD, Italy
| | - Riccardo Orusa
- Liguria e Valle d'Aosta, Istituto Zooprofilattico Sperimentale del Piemonte, National Reference Centre for Wild Animal Diseases (CeRMAS), Aosta, Italy
| | - Mitzy Mauthe von Degerfeld
- Department of Veterinary Sciences, Centro Animali Non Convenzionali (C.A.N.C), University of Turin, Turin, Italy
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, Centro Animali Non Convenzionali (C.A.N.C), University of Turin, Turin, Italy.
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16
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Cerri A, Bolatti EM, Zorec TM, Montani ME, Rimondi A, Hosnjak L, Casal PE, Di Domenica V, Barquez RM, Poljak M, Giri AA. Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission. Microbiol Spectr 2023; 11:e0204723. [PMID: 37695063 PMCID: PMC10581097 DOI: 10.1128/spectrum.02047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023] Open
Abstract
Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.
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Affiliation(s)
- Agustina Cerri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
| | - Elisa M. Bolatti
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maria E. Montani
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Dr. Ángel Gallardo Provincial Museum of Natural Sciences, Rosario, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Agustina Rimondi
- Institute of Virology and Technological Innovations (INTA/CONICET), Castelar, Argentina
- Robert Koch Institute, Berlin, Germany
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Pablo E. Casal
- DETx MOL S.A. La Segunda Núcleo Corporate Building, Alvear, Argentina
| | - Violeta Di Domenica
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Ruben M. Barquez
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Adriana A. Giri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
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17
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Ritsch M, Cassman NA, Saghaei S, Marz M. Navigating the Landscape: A Comprehensive Review of Current Virus Databases. Viruses 2023; 15:1834. [PMID: 37766241 PMCID: PMC10537806 DOI: 10.3390/v15091834] [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: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.
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Affiliation(s)
- Muriel Ritsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Noriko A. Cassman
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Shahram Saghaei
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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18
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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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19
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Kane Y, Chen J, Li L, Descorps-Declère S, Wong G, Berthet N. Diverse single-stranded DNA viruses from viral metagenomics on a cynopterus bat in China. Heliyon 2023; 9:e18270. [PMID: 37520955 PMCID: PMC10374907 DOI: 10.1016/j.heliyon.2023.e18270] [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: 05/29/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Bats serve as reservoirs for many emerging viruses. Cressdnaviruses can infect a wide range of animals, including agricultural species, such as pigs, in which porcine circoviruses cause severe gastroenteritis. New cressdnaviruses have also attracted considerable attention recently, due to their involvement with infectious diseases. However, little is known about their host range and many cressdnaviruses remain poorly characterized. We identified and characterized 11 contigs consisting of previously unknown cressdnaviruses from a rectal swab sample of a Cynopterus bat collected in Yunnan Province, China, in 2011. Full genomes of two cressdnaviruses (OQ267680, 2069 nt; OQ351951, 2382 nt), and a nearly complete genome for a third (OQ267683, 2361 nt) were obtained. Phylogenetic analyses and the characteristics of these viral genomes suggest a high degree of ssDNA virus diversity. These results shed light on cressdnavirus diversity and the probable role of Cynopterus bats as their hosts.
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Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicolas Berthet
- Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens Unit, Shanghai 200031, China
- Institut Pasteur, Unité Environnement et Risque Infectieux, Cellule D’Intervention Biologique D’Urgence, 75015 Paris, France
- Institut Pasteur, Université Paris-Cité, Unité Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris, France
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20
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Bártová E, Marková J, Sedláčková J, Banďouchová H, Račka K. Molecular Detection of Toxoplasma gondii, Neospora caninum and Encephalitozoon spp. in Vespertilionid Bats from Central Europe. Int J Mol Sci 2023; 24:9887. [PMID: 37373032 DOI: 10.3390/ijms24129887] [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: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Bats may carry various viruses and bacteria which can be harmful to humans, but little is known about their role as a parasitic source with zoonotic potential. The aim of this study was to test wild bats for the presence of selected parasites: Toxoplasma gondii, Neospora caninum and microsporidia Encephalitozoon spp. In total, brain and small intestine tissues of 100 bats (52 Myotis myotis, 43 Nyctalus noctula and 5 Vespertilio murinus) were used for the DNA isolation and PCR detection of the abovementioned agents. Toxoplasma gondii DNA was detected by real-time PCR in 1% of bats (in one male of M. myotis), while all bats were negative for N. caninum DNA. Encephalitozoon spp. DNA was detected by nested PCR in 25% of bats, including three species (twenty-two M. myotis, two N. noctula and one V. murinus). Positive samples were sequenced and showed homology with the genotypes Encephalitozoon cuniculi II and Encephalitozoon hellem 2C. This is the first study on wild vespertilionid bats from Central Europe and worldwide, with a relatively high positivity of Encephalitozoon spp. detected in bats.
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Affiliation(s)
- Eva Bártová
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 61242 Brno, Czech Republic
| | - Jiřina Marková
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 61242 Brno, Czech Republic
| | - Jana Sedláčková
- Department of Ecology and Diseases of Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 61242 Brno, Czech Republic
| | - Hana Banďouchová
- Department of Ecology and Diseases of Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 61242 Brno, Czech Republic
| | - Karol Račka
- Department of Epizootology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 04181 Košice, Slovakia
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21
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Černe D, Hostnik P, Toplak I, Presetnik P, Maurer-Wernig J, Kuhar U. Discovery of a novel bat lyssavirus in a Long-fingered bat (Myotis capaccinii) from Slovenia. PLoS Negl Trop Dis 2023; 17:e0011420. [PMID: 37384601 DOI: 10.1371/journal.pntd.0011420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023] Open
Abstract
Lyssaviruses are the causative agents of rabies, a zoonotic, fatal disease that is thought to be ancestral to bats. In the last decade, the detection of bat associated lyssaviruses is increasing also in Europe. Within a retrospective bat associated lyssavirus surveillance study a total of 225 dead bats of 21 bat species were collected in Slovenia between 2012 and 2019 and tested by specific real-time RT-PCR method. The first lyssavirus positive sample in bats in Slovenia was detected using the real-time RT-PCR, the fluorescent antibody test, and next generation sequencing, while the rabies tissue culture inoculation test was unsuccessful due to sample degradation and storage conditions. The nearly complete genome of Divača bat lyssavirus from Slovenia consists of 11,871 nucleotides and reflects the characteristic gene organization known for lyssaviruses, encoding the five viral proteins. Phylogenetic analysis of Divača bat lyssavirus revealed that it belongs to phylogroup I lyssaviruses and is most closely related to Kotalahti bat lyssavirus (KBLV) with 87.20% nucleotide and 99.22% amino acid identity. Together with KBLV, Khujand virus, European bat lyssavirus 2, Bakeloh bat lyssavirus, and Aravan virus, Divača bat lyssavirus was detected in the genus Myotis suggesting its key role in the transmission and maintenance of certain lyssaviruses.
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Affiliation(s)
- Danijela Černe
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Hostnik
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivan Toplak
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana office, Ljubljana, Slovenia
| | - Jedrt Maurer-Wernig
- Administration of the Republic of Slovenia for food safety, veterinary sector, and plant protection, Ljubljana, Slovenia
| | - Urška Kuhar
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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22
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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23
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Froidevaux JSP, Toshkova N, Barbaro L, Benítez-López A, Kerbiriou C, Le Viol I, Pacifici M, Santini L, Stawski C, Russo D, Dekker J, Alberdi A, Amorim F, Ancillotto L, Barré K, Bas Y, Cantú-Salazar L, Dechmann DKN, Devaux T, Eldegard K, Fereidouni S, Furmankiewicz J, Hamidovic D, Hill DL, Ibáñez C, Julien JF, Juste J, Kaňuch P, Korine C, Laforge A, Legras G, Leroux C, Lesiński G, Mariton L, Marmet J, Mata VA, Mifsud CM, Nistreanu V, Novella-Fernandez R, Rebelo H, Roche N, Roemer C, Ruczyński I, Sørås R, Uhrin M, Vella A, Voigt CC, Razgour O. A species-level trait dataset of bats in Europe and beyond. Sci Data 2023; 10:253. [PMID: 37137926 PMCID: PMC10156679 DOI: 10.1038/s41597-023-02157-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.
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Affiliation(s)
- Jérémy S P Froidevaux
- University of Stirling, Biological and Environmental Sciences, Faculty of Natural Sciences, FK9 4LJ, Stirling, UK.
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France.
- School of Biological Sciences, University of Bristol, Life Sciences Building, BS8 1TQ, Bristol, UK.
| | - Nia Toshkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000, Sofia, Bulgaria
- National Museum of Natural History at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luc Barbaro
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- DYNAFOR, INRAE-INPT, University of Toulouse, Castanet-Tolosan, France
| | - Ana Benítez-López
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- Department of Zoology, University of Granada, Granada, Spain
| | - Christian Kerbiriou
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Isabelle Le Viol
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Michela Pacifici
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Luca Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Clare Stawski
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy.
| | - Jasja Dekker
- Jasja Dekker Dierecologie BV, Arnhem, the Netherlands
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francisco Amorim
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy
| | - Kévin Barré
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Yves Bas
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lisette Cantú-Salazar
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422, Belvaux, Luxemburg
| | - Dina K N Dechmann
- Max Planck Institute of Animal Behavior, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany
- University of Konstanz, Department of Biology, Universitätsstr. 10, 78464, Konstanz, Germany
| | - Tiphaine Devaux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Katrine Eldegard
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Sasan Fereidouni
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Joanna Furmankiewicz
- Department of Behavioural Ecology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Daniela Hamidovic
- Ministry of Economy and Sustainable Development, Institute for Environment and Nature, Radnička cesta 80, HR-10000, Zagreb, Croatia
- Croatian Biospeleological Society, Rooseveltov trg 6, HR-10000, Zagreb, Croatia
| | - Davina L Hill
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Carlos Ibáñez
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jean-François Julien
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Javier Juste
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP, 28220, Madrid, Spain
| | - Peter Kaňuch
- Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia
| | - Carmi Korine
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Midreshet Ben-Gurion, Israel
| | - Alexis Laforge
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Gaëlle Legras
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Camille Leroux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Auddicé Biodiversité- ZAC du Chevalement, 5 rue des Molettes, 59286, Roost-Warendin, France
| | - Grzegorz Lesiński
- Institute of Animal Science, Warsaw University of Life Sciences (SGGW), Ciszewskiego 8, 02-787, Warsaw, Poland
| | - Léa Mariton
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, CNRS, MNHN, IRD, 61 Rue Buffon, 75005, Paris, France
| | - Julie Marmet
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Clare M Mifsud
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | | | - Roberto Novella-Fernandez
- Technical University of Munich, Terrestrial Ecology Research Group, Department for Life Science Systems, School of Life Sciences, Freising, Germany
| | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- ESS, Polytechnic Institute of Setúbal, Campus do IPS - Estefanilha, 2910-761, Setúbal, Portugal
| | - Niamh Roche
- Bat Conservation Ireland, Carmichael House, 4-7, North Brunswick Street, Dublin, D07 RHA8, Ireland
| | - Charlotte Roemer
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Ireneusz Ruczyński
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Rune Sørås
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, P. J, Šafárik University in Košice, Košice, Slovakia
| | - Adriana Vella
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | - Christian C Voigt
- Department Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK.
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Zhu W, Huang Y, Gong J, Dong L, Yu X, Chen H, Li D, Zhou L, Yang J, Lu S. A Novel Bat Coronavirus with a Polybasic Furin-like Cleavage Site. Virol Sin 2023:S1995-820X(23)00047-0. [PMID: 37141989 PMCID: PMC10151251 DOI: 10.1016/j.virs.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
The current pandemic of COVID-19 caused by a novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), threatens human health around the world. Of particular concern is that bats are recognized as one of the most potential natural hosts of SARS-CoV-2; however, coronavirus ecology in bats is still nascent. Here, we performed a degenerate primer screening and next-generation sequencing analysis of 112 bats, collected from Hainan Province, China. Three coronaviruses, namely bat betacoronavirus (Bat CoV) CD35, Bat CoV CD36 and bat alphacoronavirus CD30 were identified. Bat CoV CD35 genome had 99.5% identity with Bat CoV CD36, both sharing the highest nucleotide identity with Bat Hp-betacoronavirus Zhejiang2013 (71.4%), followed by SARS-CoV-2 (54.0%). Phylogenetic analysis indicated that Bat CoV CD35 formed a distinct clade, and together with Bat Hp-betacoronavirus Zhejiang2013, was basal to the lineage of SARS-CoV-1 and SARS-CoV-2. Notably, Bat CoV CD35 harbored a canonical furin-like S1/S2 cleavage site that resembles the corresponding sites of SARS-CoV-2. The furin cleavage sites between CD35 and CD36 are identical. In addition, the receptor-binding domain of Bat CoV CD35 showed a highly similar structure to that of SARS-CoV-1 and SARS-CoV-2, especially in one binding loop. In conclusion, this study deepens our understanding of the diversity of coronaviruses and provides clues about the natural origin of the furin cleavage site of SARS-CoV-2.
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Affiliation(s)
- Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yuyuan Huang
- 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 102206, China
| | - Jian Gong
- 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 102206, China
| | - Lingzhi Dong
- 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 102206, China
| | - Xiaojie Yu
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Haiyun Chen
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Dandan Li
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Libo Zhou
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, 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 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, 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 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China.
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25
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Ortiz-Baez AS, Jaenson TGT, Holmes EC, Pettersson JHO, Wilhelmsson P. Substantial viral and bacterial diversity at the bat-tick interface. Microb Genom 2023; 9. [PMID: 36862584 PMCID: PMC10132063 DOI: 10.1099/mgen.0.000942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Ticks harbour a high diversity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle (Pipistrellus pygmaeus, Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae, while other invertebrate-associated viruses included members of the Dicistroviridae, Iflaviridae, Nodaviridae, Partitiviridae, Permutotetraviridae, Polycipiviridae and Solemoviridae. Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable diversity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas G T Jaenson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, SE-751 23 Uppsala, Sweden.,Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, 75237 Uppsala, Sweden
| | - Peter Wilhelmsson
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, SE-581 83 Linköping, Sweden.,Department of Clinical Microbiology, Region Jönköping County, SE-553 05 Jönköping, Sweden
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26
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Paskey AC, Lim XF, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo R, Cer RZ, Long KA, Lueder MR, Glang L, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Anderson DE, Wang LF, Bishop-Lilly KA. Genomic Characterization of a Relative of Mumps Virus in Lesser Dawn Bats of Southeast Asia. Viruses 2023; 15:v15030659. [PMID: 36992368 PMCID: PMC10053730 DOI: 10.3390/v15030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The importance of genomic surveillance on emerging diseases continues to be highlighted with the ongoing SARS-CoV-2 pandemic. Here, we present an analysis of a new bat-borne mumps virus (MuV) in a captive colony of lesser dawn bats (Eonycteris spelaea). This report describes an investigation of MuV-specific data originally collected as part of a longitudinal virome study of apparently healthy, captive lesser dawn bats in Southeast Asia (BioProject ID PRJNA561193) which was the first report of a MuV-like virus, named dawn bat paramyxovirus (DbPV), in bats outside of Africa. More in-depth analysis of these original RNA sequences in the current report reveals that the new DbPV genome shares only 86% amino acid identity with the RNA-dependent RNA polymerase of its closest relative, the African bat-borne mumps virus (AbMuV). While there is no obvious immediate cause for concern, it is important to continue investigating and monitoring bat-borne MuVs to determine the risk of human infection.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Justin H. J. Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Casandra W. Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Kyle A. Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Matthew R. Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gavin J. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Correspondence:
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27
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Wang Z, Huang G, Huang M, Dai Q, Hu Y, Zhou J, Wei F. Global patterns of phylogenetic diversity and transmission of bat coronavirus. SCIENCE CHINA LIFE SCIENCES 2022; 66:861-874. [PMID: 36378474 PMCID: PMC9664035 DOI: 10.1007/s11427-022-2221-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Bats are reservoirs for multiple coronaviruses (CoVs). However, the phylogenetic diversity and transmission of global bat-borne CoVs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat CoV RdRp gene sequences to study the phylogenetic diversity and transmission of bat-borne CoVs and the underlying driving factors. We found that host-switching events occurred more frequently for α-CoVs than for β-CoVs, and the latter was highly constrained by bat phylogeny. Bat species in the families Molossidae, Rhinolophidae, Miniopteridae, and Vespertilionidae had larger contributions to the cross-species transmission of bat CoVs. Regions of eastern and southern Africa, southern South America, Western Europe, and Southeast Asia were more frequently involved in cross-region transmission events of bat CoVs than other regions. Phylogenetic and geographic distances were the most important factors limiting CoV transmission. Bat taxa and global geographic hotspots associated with bat CoV phylogenetic diversity were identified, and bat species richness, mean annual temperature, global agricultural cropland, and human population density were strongly correlated with the phylogenetic diversity of bat CoVs. These findings provide insight into bat CoV evolution and ecological transmission among bat taxa. The identified hotspots of bat CoV evolution and transmission will guide early warnings of bat-borne CoV zoonotic diseases.
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Affiliation(s)
- Zhilin Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingpan Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhou
- School of Karst Science, Guizhou Normal University, Guiyang, 550000, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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28
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Cultivable Bacteria Associated with the Microbiota of Troglophile Bats. Animals (Basel) 2022; 12:ani12192684. [PMID: 36230424 PMCID: PMC9559301 DOI: 10.3390/ani12192684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
Simple Summary Troglophile bats live in colonies, often in sites exploited for agro-pastoral purposes. Determining the composition of the microbiome of bats is an important step in understanding their ecology and biology and can also provide information on the spread of pathogenic bacteria in their populations. This study aimed to determine how epidemiological factors shape the microbiome of troglophile bats and evaluate the occurrence of potentially pathogenic bacterial species. A total of 413 Gram-negative and 183 Gram-positive strains were isolated from 189 individuals of four species of troglophile bats living in Sicilian and Calabrian territory (Italy). Besides few potentially pathogenic bacteria, several strains with a hypothesized symbiotic role were found. Abstract Background: The study of bats is of significant interest from a systematic, zoogeographic, ecological, and physiological point of view. The aim of this study is to investigate the culturable aerobic enteric, conjunctival, and oral bacterial flora of bats to determine their physiological microbiome and to investigate the possible occurrence of pathogenic bacteria. Methods: Five hundred and sixty-seven samples were collected from 189 individuals of four species of troglophile bats (Myotis myotis, Myotis capaccinii, Miniopterus schreibersii, and Rhinolophus hipposideros) living in Sicilian and Calabrian territory (Italy). All samples were tested for Gram-negative bacteria; conjunctival and oral swabs were also submitted to bacteriological examination for Gram-positive bacteria. Results: Four hundred thirteen Gram-negative strains were isolated. Of these, 377 belonged to 17 different genera of the family Enterobacteriaceae and 30 to five other families. One hundred eighty-three Gram-positive strains were isolated. Of these, 73 belonged to the Staphylococcaceae family, 72 to the Bacillaceae family and 36 to four other families. Besides some potentially pathogenic strains, several bacterial species have been found that are common to all the bat species studied. These could perhaps play a physiological or nutritional role. Conclusion: A great variety of bacterial species were identified in the cultivable microbiota of southern-Italian troglophile bats, including several potentially pathogenic strains and numerous putatively symbiotic species.
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29
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Moore KA, Osterholm MT, Lackritz EM, Poland GA. A research and development (R&D) roadmap for broadly protective coronavirus vaccines: Setting a path to address coronavirus threats. Vaccine 2022; 40:6001-6003. [PMID: 36109277 PMCID: PMC9452409 DOI: 10.1016/j.vaccine.2022.08.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022]
Affiliation(s)
- Kristine A Moore
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN, USA; Center for Infectious Disease Research and Policy, C315 Mayo Memorial Building, MMC 263, 420 Delaware Street, SE, Minneapolis, MN 55455, USA.
| | - Michael T Osterholm
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN, USA
| | - Eve M Lackritz
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN, USA
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30
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Islam A, Ferdous J, Islam S, Sayeed MA, Rahman MK, Saha O, Hassan MM, Shirin T. Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics. Transbound Emerg Dis 2022; 69:2523-2543. [PMID: 34694705 PMCID: PMC8662162 DOI: 10.1111/tbed.14356] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/14/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022]
Abstract
The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.
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Affiliation(s)
- Ariful Islam
- EcoHealth AllianceNew YorkUnited States
- Centre for Integrative Ecology, School of Life and Environmental ScienceDeakin UniversityVictoriaAustralia
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Jinnat Ferdous
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Shariful Islam
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Abu Sayeed
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Kaisar Rahman
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Otun Saha
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary MedicineChattogram Veterinary and Animal Sciences UniversityChattogramBangladesh
| | - Tahmina Shirin
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
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31
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Robles-Fernández ÁL, Santiago-Alarcon D, Lira-Noriega A. Wildlife susceptibility to infectious diseases at global scales. Proc Natl Acad Sci U S A 2022; 119:e2122851119. [PMID: 35994656 PMCID: PMC9436312 DOI: 10.1073/pnas.2122851119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
Disease transmission prediction across wildlife is crucial for risk assessment of emerging infectious diseases. Susceptibility of host species to pathogens is influenced by the geographic, environmental, and phylogenetic context of the specific system under study. We used machine learning to analyze how such variables influence pathogen incidence for multihost pathogen assemblages, including one of direct transmission (coronaviruses and bats) and two vector-borne systems (West Nile Virus [WNV] and birds, and malaria and birds). Here we show that this methodology is able to provide reliable global spatial susceptibility predictions for the studied host-pathogen systems, even when using a small amount of incidence information (i.e., [Formula: see text] of information in a database). We found that avian malaria was mostly affected by environmental factors and by an interaction between phylogeny and geography, and WNV susceptibility was mostly influenced by phylogeny and by the interaction between geographic and environmental distances, whereas coronavirus susceptibility was mostly affected by geography. This approach will help to direct surveillance and field efforts providing cost-effective decisions on where to invest limited resources.
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Affiliation(s)
- Ángel L. Robles-Fernández
- Facultad de Física, Universidad Veracruzana, 91000 Xalapa, México
- School of Life Sciences, Arizona State University, Tempe, AZ 85281
| | | | - Andrés Lira-Noriega
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., 91073 Xalapa, México
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32
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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33
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Abstract
Bats perform important ecological roles in our ecosystem. However, recent studies have demonstrated that bats are reservoirs of emerging viruses that have spilled over into humans and agricultural animals to cause severe diseases. These viruses include Hendra and Nipah paramyxoviruses, Ebola and Marburg filoviruses, and coronaviruses that are closely related to severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently emerged SARS-CoV-2. Intriguingly, bats that are naturally or experimentally infected with these viruses do not show clinical signs of disease. Here we have reviewed ecological, behavioral, and molecular factors that may influence the ability of bats to harbor viruses. We have summarized known zoonotic potential of bat-borne viruses and stress on the need for further studies to better understand the evolutionary relationship between bats and their viruses, along with discovering the intrinsic and external factors that facilitate the successful spillover of viruses from bats.
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Affiliation(s)
- Victoria Gonzalez
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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34
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Barrón-Rodríguez RJ, Parra-Laca R, Rojas-Anaya E, Romero-Espinoza JÁI, Ayala-Sumuano JT, Vázquez-Pérez JA, García-Espinosa G, Loza-Rubio E. Evidence of Viral Communities in Three Species of Bats from Rural Environment in Mexico. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rodrigo J. Barrón-Rodríguez
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Rocío Parra-Laca
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Edith Rojas-Anaya
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - José Á. I. Romero-Espinoza
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Jorge T. Ayala-Sumuano
- Idix S.A. de C.V., Sonterra 3035 Interior 26, Fraccionamiento Sonterra, Santiago de Querétaro, Querétaro México, C.P. 76230, México
| | - Joel A. Vázquez-Pérez
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Gary García-Espinosa
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
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35
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Weinberg M, Yovel Y. Revising the paradigm: Are bats really pathogen reservoirs or do they possess an efficient immune system? iScience 2022; 25:104782. [PMID: 35982789 PMCID: PMC9379578 DOI: 10.1016/j.isci.2022.104782] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While bats are often referred to as reservoirs of viral pathogens, a meta-analysis of the literature reveals many cases in which there is not enough evidence to claim so. In many cases, bats are able to confront viruses, recover, and remain immune by developing a potent titer of antibodies, often without becoming a reservoir. In other cases, bats might have carried an ancestral virus that at some time point might have mutated into a human pathogen. Moreover, bats exhibit a balanced immune response against viruses that have evolved over millions of years. Using genomic tools, it is now possible to obtain a deeper understanding of that unique immune system and its variability across the order Chiroptera. We conclude, that with the exception of a few viruses, bats pose little zoonotic danger to humans and that they operate a highly efficient anti-inflammatory response that we should strive to understand.
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Affiliation(s)
- Maya Weinberg
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Corresponding author
| | - Yossi Yovel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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36
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Lv T, Wang X, Yu C, Wang Z, Xiang R, Li L, Yuan Y, Wang Y, Wei X, Yu Y, He X, Zhang L, Deng Q, Wu P, Hou Y, Chen J, Liu C, Wong G, Liu L. A map of bat virus receptors derived from single-cell multiomics. Sci Data 2022; 9:336. [PMID: 35701476 PMCID: PMC9195401 DOI: 10.1038/s41597-022-01447-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2022] [Indexed: 11/08/2022] Open
Abstract
Bats are considered reservoirs of many lethal zoonotic viruses and have been implicated in several outbreaks of emerging infectious diseases, such as SARS-CoV, MERS-CoV, and SARS-CoV-2. It is necessary to systematically derive the expression patterns of bat virus receptors and their regulatory features for future research into bat-borne viruses and the prediction and prevention of pandemics. Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) of major organ samples collected from Chinese horseshoe bats (Rhinolophus affinis) and systematically checked the expression pattern of bat-related virus receptors and chromatin accessibility across organs and cell types, providing a valuable dataset for studying the nature of infection among bat-borne viruses.
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Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Chao Yu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Rong Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Yue Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuhang Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoyu Wei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yeya Yu
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI College, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Bay Laboratory, Shenzhen, 518083, China.
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Bay Laboratory, Shenzhen, 518083, China.
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37
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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Affiliation(s)
- Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 Haping Road, Harbin 150069, China.
| | - Jiumeng Sun
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Dongyan Li
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Ningning Wang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Lifang Wang
- College of Veterinary Medicine, China Agricultural University, No. 17 Qinghua Donglu, Beijing 100083, China
| | - Chang Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Xiaorong Meng
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St., Charles Avenue, New Orleans, LA 70118, USA
| | - Marc A Suchard
- Departments of Biomathematics, Human Genetics and Biostatistics, David Geffen School of Medicine and Fielding School of Public Health, University of California, Los Angeles, Geffen Hall 885 Tiverton Drive, Los Angeles, CA 90095, USA
| | - Xu Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, 400 East Main St., Frankfort, KY 40601, USA
| | - Shuo Su
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany.
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38
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Uribe M, Rodríguez-Posada ME, Ramirez-Nieto GC. Molecular Evidence of Orthomyxovirus Presence in Colombian Neotropical Bats. Front Microbiol 2022; 13:845546. [PMID: 35558106 PMCID: PMC9087557 DOI: 10.3389/fmicb.2022.845546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/25/2022] [Indexed: 11/17/2022] Open
Abstract
The Orthomyxoviridae family includes the genera Influenzavirus, Isavirus, Quaranjavirus, and Thogotovirus. In turn, Influenzavirus can be classified into four types: α, β, γ, and δ (Formerly A, B, C, and D), from which Alphainfluenzavirus (AIV) has the broadest host range, including birds, mammals, reptiles, and amphibians. Additionally, AIV has shown global epidemiological relevance owing to its pandemic potential. The epidemiological relevance of Chiropteran due to its multiple functional characteristics makes them ideal reservoirs for many viral agents. Recently, new influenza-like subtypes have been reported in Neotropical bats, but little is known about the relevance of bats as natural reservoirs of influenza viruses. Therefore, the current study aimed to determine the presence of AIV and new influenza-like subtypes in South American bats. For a better understanding of the drivers and interactions between AIV and bats, we used molecular assays with different gene targets (i.e., M, NP, and PB1) to identify AIV in New World bats. A housekeeping gene (CytB) PCR was used to check for nucleic acid preservation and to demonstrate the bat-origin of the samples. A total of 87 free-living bats belonging to 25 different species of the families Phyllostomidae and Vespertilionidae were collected in Casanare, Colombia. As a result, this study found seven AIV-positive bat species, three of them reported for the first time as AIV prone hosts. Neither of the AIV-like analyzed samples were positive for H17N10/H18/N11 subtypes. Although additional information is needed, the presence of a completely new or divergent AIV subtype in neotropical bats cannot be discarded. Collectively, the results presented here expand the epidemiological knowledge and distribution of AIV in neotropical free-ranging bats and emphasize the need to continue studying these viruses to establish the role they could play as a threat to animal and public health.
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Affiliation(s)
- Manuel Uribe
- Microbiología y Epidemiologia Research Group, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá, Colombia.,CIBAV Research Group, Veterinary Medicine School, Universidad de Antioquia, Medellín, Colombia
| | - Miguel E Rodríguez-Posada
- Research Center Fundación Reserva Natural La Palmita, Grupo de Investigaciones Territoriales Parael uso y Conservación de la Biodiversidad, Trinidad, Colombia
| | - Gloria C Ramirez-Nieto
- Microbiología y Epidemiologia Research Group, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá, Colombia
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39
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Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol 2022; 20:299-314. [PMID: 34799704 PMCID: PMC8603903 DOI: 10.1038/s41579-021-00652-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002-2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat-coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic.
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Affiliation(s)
- Manuel Ruiz-Aravena
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Clifton McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tamika Lunn
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Aaron Morris
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Celine E Snedden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Claude Kwe Yinda
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Julia R Port
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - David W Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Christina Faust
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Elinor Jax
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lauren Dee
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Devin N Jones
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Maureen K Kessler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - Caylee Falvo
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Daniel Crowley
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Nita Bharti
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alison J Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Hudson
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Vincent J Munster
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Raina K Plowright
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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40
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Common SM, Shadbolt T, Walsh K, Sainsbury AW. The risk from SARS-CoV-2 to bat species in england and mitigation options for conservation field workers. Transbound Emerg Dis 2022; 69:694-705. [PMID: 33570837 PMCID: PMC8014681 DOI: 10.1111/tbed.14035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
The newly evolved coronavirus, SARS-CoV-2, which has precipitated a global COVID-19 pandemic among the human population, has been shown to be associated with disease in captive wild animals. Bats (Chiroptera) have been shown to be susceptible to experimental infection and therefore may be at risk from disease when in contact with infected people. Numerous conservation fieldwork activities are undertaken across the United Kingdom bringing potentially infected people into close proximity with bats. In this study, we analysed the risks of disease from SARS-CoV-2 to free-living bat species in England through fieldworkers undertaking conservation activities and ecological survey work, using a qualitative, transparent method devised for assessing threats of disease to free-living wild animals. The probability of exposure of bats to SARS-CoV-2 through fieldwork activities was estimated to range from negligible to high, depending on the proximity between bats and people during the activity. The likelihood of infection after exposure was estimated to be high and the probability of dissemination of the virus through bat populations medium. The likelihood of clinical disease occurring in infected bats was low, and therefore, the ecological, economic and environmental consequences were predicted to be low. The overall risk estimation was low, and therefore, mitigation measures are advisable. There is uncertainty in the pathogenicity of SARS-CoV-2 in bats and therefore in the risk estimation. Disease risk management measures are suggested, including the use of personal protective equipment, good hand hygiene and following the existing government advice. The disease risk analysis should be updated as information on the epidemiology of SARS-CoV-2 and related viruses in bats improves. The re-analysis may be informed by health surveillance of free-living bats.
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Affiliation(s)
| | - Tammy Shadbolt
- Institute of ZoologyZoological Society of LondonLondonUK
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41
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Bolatti EM, Viarengo G, Zorec TM, Cerri A, Montani ME, Hosnjak L, Casal PE, Bortolotto E, Di Domenica V, Chouhy D, Allasia MB, Barquez RM, Poljak M, Giri AA. Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses. Microorganisms 2022; 10:microorganisms10020266. [PMID: 35208721 PMCID: PMC8880087 DOI: 10.3390/microorganisms10020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Agustina Cerri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Eugenia Bortolotto
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Violeta Di Domenica
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - María Belén Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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Islam A, Ferdous J, Sayeed MA, Islam S, Kaisar Rahman M, Abedin J, Saha O, Hassan MM, Shirin T. Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. PLoS One 2021; 16:e0260635. [PMID: 34910734 PMCID: PMC8673647 DOI: 10.1371/journal.pone.0260635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, New York, United States of America
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Victoria, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Shariful Islam
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Md. Kaisar Rahman
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Josefina Abedin
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Otun Saha
- EcoHealth Alliance, New York, New York, United States of America
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
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43
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Faisal HMN, Katti KS, Katti DR. Binding of SARS-COV-2 (COVID-19) and SARS-COV to human ACE2: Identifying binding sites and consequences on ACE2 stiffness. Chem Phys 2021; 551:111353. [PMID: 34511698 PMCID: PMC8420131 DOI: 10.1016/j.chemphys.2021.111353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/20/2021] [Accepted: 09/02/2021] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 coronavirus (COVID-19) that is causing the massive global pandemic exhibits similar human cell invasion mechanism as the coronavirus SARS-CoV, which had significantly lower fatalities. The cell membrane protein Angiotensin-converting enzyme 2 (ACE2) is the initiation point for both the coronavirus infections in humans. Here, we model the molecular interactions and mechanical properties of ACE2 with both SARS-CoV and COVID-19 spike protein receptor-binding domains (RBD). We report that the COVID-19 spike RBD interacts with ACE2 more strongly and at only two protein residues, as compared to multi-residue interaction of the SARS-CoV. Although both coronaviruses stiffen the ACE2, the impact of COVID-19 is six times larger, which points towards differences in the severity of the reported respiratory distress. The recognition of specific residues of ACE2 attachments to coronaviruses is important as the residues suggest potential sites of intervention to inhibit attachment and subsequent entry of the COVID-19 into human host cells
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Affiliation(s)
- H M Nasrullah Faisal
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States
| | - Kalpana S Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States.,Center for Engineered Cancer Testbeds, North Dakota State University, Fargo, ND 58108, United States
| | - Dinesh R Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States.,Center for Engineered Cancer Testbeds, North Dakota State University, Fargo, ND 58108, United States
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44
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Wu Q, Li Q, Lu J. A One Health strategy for emerging infectious diseases based on the COVID-19 outbreak. JOURNAL OF BIOSAFETY AND BIOSECURITY 2021; 4:5-11. [PMID: 34729464 PMCID: PMC8552662 DOI: 10.1016/j.jobb.2021.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is as an emerging infectious disease (EID) that has caused the worst public health catastrophe of the 21st century thus far. In terms of impact, the COVID-19 pandemic is second only to the Spanish Flu pandemic of 1918 in modern world history. As of 7 September 2021, there have been 220 million confirmed cases of COVID-19 and more than 4.5 million deaths. EIDs pose serious public health and socio-economic risks, and 70% of EIDs originate from wildlife. Preventing development of EIDs such as COVID-19 is a pressing concern. Here, taking the COVID-19 pandemic as an example, we illustrate the disastrous effects of EIDs and assess their emergence and evolution from a One Health perspective. We propose a One Health strategy, centered on ‘moving the gates forward’, for EID prevention and control at the human–animal–environment interface. This strategy may be instructive and provide early warnings of EIDs in the future.
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Affiliation(s)
- Qin Wu
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Qianlin Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Jiahai Lu
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
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45
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Han HJ, Li ZM, Li X, Liu JX, Peng QM, Wang R, Gu XL, Jiang Y, Zhou CM, Li D, Xiao X, Yu XJ. Bats and their ectoparasites (Nycteribiidae and Spinturnicidae) carry diverse novel Bartonella genotypes, China. Transbound Emerg Dis 2021; 69:e845-e858. [PMID: 34695291 PMCID: PMC9543326 DOI: 10.1111/tbed.14357] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/28/2022]
Abstract
Bartonella species are facultative intracellular bacteria and recognized worldwide as emerging zoonotic pathogens. Bartonella were isolated or identified by polymerase chain reaction (PCR) in bats and their ectoparasites worldwide, whereas the association between them was scarce, especially in Asia. In this study, a retrospective analysis with frozen samples was carried out to identify the genetic diversity of Bartonella in bats and their ectoparasites and to investigate the relationships of Bartonella carried by bats and their ectoparasites. Bats and their ectoparasites (bat flies and bat mites) were collected from caves in Hubei Province, Central China, from May 2018 to July 2020. Bartonella were screened by PCR amplification and sequencing of three genes (gltA, rpoB, and ftsZ). Bats, bat flies, and bat mites carried diverse novel Bartonella genotypes with a high prevalence. The sharing of some Bartonella genotypes between bats and bat flies or bat mites indicated a potential role of bat flies and bat mites as vectors of bartonellae, while the higher genetic diversity of Bartonella in bat flies than that in bats might be due to the vertical transmission of this bacterium in bat flies. Therefore, bat flies might also act as reservoirs of Bartonella. In addition, human‐pathogenic B. mayotimonesis was identified in both bats and their ectoparasites, which expanded our knowledge on the geographic distribution of this bacterium and suggested a potential bat origin with bat flies and bat mites playing important roles in the maintenance and transmission of Bartonella.
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Affiliation(s)
- Hui-Ju Han
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Ze-Min Li
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Xia Li
- Microbiological Laboratory, Yantai Center for Disease Control and Prevention, Yantai, China
| | - Jian-Xiao Liu
- Clinical Laboratory, Xingtai Third Hospital, Xingtai, China
| | - Qiu-Ming Peng
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Rui Wang
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Xiao-Lan Gu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Yuan Jiang
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Chuan-Min Zhou
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Dan Li
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
| | - Xiao Xiao
- Institute of Epidemiology Research, Hubei University of Chinese Medicine, Wuhan, China
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, China
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46
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Zhou S, Liu B, Han Y, Wang Y, Chen L, Wu Z, Yang J. ZOVER: the database of zoonotic and vector-borne viruses. Nucleic Acids Res 2021; 50:D943-D949. [PMID: 34634795 PMCID: PMC8728136 DOI: 10.1093/nar/gkab862] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/08/2021] [Accepted: 09/16/2021] [Indexed: 12/03/2022] Open
Abstract
Emerging infectious diseases significantly threaten global public health and socioeconomic security. The majority of emerging infectious disease outbreaks are caused by zoonotic/vector-borne viruses. Bats and rodents are the two most important reservoir hosts of many zoonotic viruses that can cross species barriers to infect humans, whereas mosquitos and ticks are well-established major vectors of many arboviral diseases. Moreover, some emerging zoonotic diseases require a vector to spread or are intrinsically vector-borne and zoonotically transmitted. In this study, we present a newly upgraded database of zoonotic and vector-borne viruses designated ZOVER (http://www.mgc.ac.cn/ZOVER). It incorporates two previously released databases, DBatVir and DRodVir, for bat- and rodent-associated viruses, respectively, and further collects up-to-date knowledge on mosquito- and tick-associated viruses to establish a comprehensive online resource for zoonotic and vector-borne viruses. Additionally, it integrates a set of online visualization tools for convenient comparative analyses to facilitate the discovery of potential patterns of virome diversity and ecological characteristics between/within different viral hosts/vectors. The ZOVER database will be a valuable resource for virologists, zoologists and epidemiologists to better understand the diversity and dynamics of zoonotic and vector-borne viruses and conduct effective surveillance to monitor potential interspecies spillover for efficient prevention and control of future emerging zoonotic diseases.
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Affiliation(s)
- Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
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47
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Islam A, Ferdous J, Islam S, Sayeed MA, Dutta Choudhury S, Saha O, Hassan MM, Shirin T. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses 2021; 13:1908. [PMID: 34696338 PMCID: PMC8537103 DOI: 10.3390/v13101908] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
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48
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Gupta P, Singh MP, Goyal K, Tripti P, Ansari MI, Obli Rajendran V, Dhama K, Malik YS. Bats and viruses: a death-defying friendship. Virusdisease 2021; 32:467-479. [PMID: 34518804 PMCID: PMC8426161 DOI: 10.1007/s13337-021-00716-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 01/10/2023] Open
Abstract
Bats have a primeval evolutionary origin and have adopted various survival methods. They have played a central role in the emergence of various viral diseases. The sustenance of a plethora of virus species inside them has been an earnest area of study. This review explains how the evolution of viruses in bats has been linked to their metabolic pathways, flight abilities, reproductive abilities and colonization behaviors. The utilization of host immune response by DNA and RNA viruses is a commencement of the understanding of differences in the impact of viral infection in bats from other mammals. Rabies virus and other lyssa viruses have had long documented history as bat viruses. While many others like Ebola virus, Nipah virus, Hantavirus, SARS-CoV, MERS-CoV and other new emerging viruses like Sosuga virus, Menangle and Tioman virus are now being studied extensively for their transmission in new hosts. The ongoing pandemic SARS-CoV-2 virus has also been implicated to be originated from bats. Certain factors have been linked to spillover events while the scope of entitlement of other conditions in the spread of diseases from bats still exists. However, certain physiological and ecological parameters have been linked to specific transmission patterns, and more definite proofs are awaited for establishing these connections.
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Affiliation(s)
- Parakriti Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mini P. Singh
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pande Tripti
- Biological Standardization Division, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Dasauli, Kursi Road, Lucknow, Uttar Pradesh 226026 India
| | - Vinodhkumar Obli Rajendran
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab 141 004 India
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49
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Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
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50
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Liang J, Zhu C, Zhang L. Cospeciation of coronavirus and paramyxovirus with their bat hosts in the same geographical areas. BMC Ecol Evol 2021; 21:148. [PMID: 34325659 PMCID: PMC8319908 DOI: 10.1186/s12862-021-01878-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Bat-borne viruses are relatively host specific. We hypothesize that this host specificity is due to coevolution of the viruses with their hosts. To test this hypothesis, we investigated the coevolution of coronavirus and paramyxovirus with their bat hosts. Published nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) gene of 60 coronavirus strains identified from 37 bat species, the RNA polymerase large (L) gene of 36 paramyxovirus strains from 29 bat species, and the cytochrome B (cytB) gene of 35 bat species were analyzed for coevolution signals. Each coevolution signal detected was tested and verified by global-fit cophylogenic analysis using software ParaFit, PACo, and eMPRess. Results Significant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry closely related viruses. Conclusions Our results suggest that paramyxovirus and coronavirus coevolve with their hosts.
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Affiliation(s)
- Jie Liang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Chunchao Zhu
- Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
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