1
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Sjodin AR, Willig MR, Rodríguez‐Durán A, Anthony SJ. Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses. Ecol Evol 2024; 14:e11501. [PMID: 38895563 PMCID: PMC11183940 DOI: 10.1002/ece3.11501] [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: 10/03/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.
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Affiliation(s)
- Anna R. Sjodin
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Michael R. Willig
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Center for Environmental Sciences & Engineering and Institute of the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Simon J. Anthony
- Center for Infection and ImmunityColumbia UniversityNew YorkNew YorkUSA
- Department of Pathology, Microbiology, and ImmunologyUC Davis School of Veterinary MedicineDavisCaliforniaUSA
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2
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Wang D, Yang X, Ren Z, Hu B, Zhao H, Yang K, Shi P, Zhang Z, Feng Q, Nawenja CV, Obanda V, Robert K, Nalikka B, Waruhiu CN, Ochola GO, Onyuok SO, Ochieng H, Li B, Zhu Y, Si H, Yin J, Kristiansen K, Jin X, Xu X, Xiao M, Agwanda B, Ommeh S, Li J, Shi ZL. Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation. MICROBIOME 2024; 12:72. [PMID: 38600530 PMCID: PMC11005217 DOI: 10.1186/s40168-024-01782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown. RESULTS Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes. CONCLUSIONS The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. Video Abstract.
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Affiliation(s)
- Daxi Wang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Xinglou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Hubei Jiangxia Lab, Wuhan, 430071, China
| | - Zirui Ren
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Hailong Zhao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Kaixin Yang
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Peibo Shi
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Zhipeng Zhang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Qikai Feng
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Carol Vannesa Nawenja
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Kityo Robert
- Department of Zoology, Entomology and Fisheries Sciences, School of BioSciences, Makerere University, Kampala, Uganda
| | - Betty Nalikka
- Department of Zoology, Entomology and Fisheries Sciences, School of BioSciences, Makerere University, Kampala, Uganda
| | - Cecilia Njeri Waruhiu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Harold Ochieng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | | | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Minfeng Xiao
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China.
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya.
| | - Sheila Ommeh
- Center for Animal Science, Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Junhua Li
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China.
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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3
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Arnaout Y, Picard-Meyer E, Robardet E, Cappelle J, Cliquet F, Touzalin F, Jimenez G, Djelouadji Z. Assessment of virus and Leptospira carriage in bats in France. PLoS One 2023; 18:e0292840. [PMID: 37862301 PMCID: PMC10588846 DOI: 10.1371/journal.pone.0292840] [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: 03/21/2022] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
With over 1,400 species worldwide, bats represent the second largest order of mammals after rodents, and are known to host major zoonotic pathogens. Here, we estimate the presence of pathogens in autochthonous bat populations. First, we set out to check our samples for PCR amplification efficiency by assessing the occurrence of inhibited PCR reactions from different types of bat samples with amplifying the housekeeping gene β-actin. Second, we investigated the presence of five targeted pathogens in a French bat population using PCR. We targeted viral RNA of Canine distemper virus, Alphacoronavirus, Lyssavirus, Rotavirus and bacterial Leptospira DNA. To do so, we screened for these viruses in bat faecal samples as well as in oropharyngeal swab samples. The presence of Leptospira was assessed in urine, kidney, lung and faecal samples. Results showed a frequency of inhibited reactions ranging from 5 to 60% of samples, varying according to the sample itself and also suspected to vary according to sampling method and the storage buffer solution used, demonstrating the importance of the sampling and storage on the probability of obtaining negative PCR results. For pathogen assessment, rotavirus and alphacoronavirus RNA were detected in Myotis myotis, Myotis daubentonii, Myotis emarginatus and Rhinolophus ferrumequinum bats. Rotaviruses were also detected in Barbastella barbastellus. The presence of alphacoronavirus also varied seasonally, with higher frequencies in late summer and October, suggesting that juveniles potentially play an important role in the dynamics of these viruses. Leptospira DNA was detected in M. myotis and M. daubentonii colonies. The 16S rRNA sequences obtained from Leptospira positive samples showed 100% genetic identity with L. borgpetersenii. Neither canine distemper virus nor lyssavirus RNA were detected in any of the tested samples. This study is the first to show the presence of Leptospira in autochthonous French bats in addition to coronavirus and rotavirus RNA previously reported in European autochthonous bats.
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Affiliation(s)
- Youssef Arnaout
- Lyssavirus Unit, Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France
- USC 1233-INRAE Rongeurs Sauvages, Risque Sanitaire et Gestion des Populations, VetAgro Sup, Marcy l’Etoile, France
| | - Evelyne Picard-Meyer
- Lyssavirus Unit, Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France
| | - Emmanuelle Robardet
- Lyssavirus Unit, Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France
| | - Julien Cappelle
- UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Montpellier, France
- UMR EPIA, INRAE, VetAgro Sup, Theix, France
| | - Florence Cliquet
- Lyssavirus Unit, Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville, France
| | - Frédéric Touzalin
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | | | - Zouheira Djelouadji
- USC 1233-INRAE Rongeurs Sauvages, Risque Sanitaire et Gestion des Populations, VetAgro Sup, Marcy l’Etoile, France
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4
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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5
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Coertse J, Mortlock M, Grobbelaar A, Moolla N, Markotter W, Weyer J. Development of a Pan- Filoviridae SYBR Green qPCR Assay for Biosurveillance Studies in Bats. Viruses 2023; 15:v15040987. [PMID: 37112966 PMCID: PMC10145118 DOI: 10.3390/v15040987] [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: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no pan-filovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3-31.7 copies/reaction and was evaluated against the field collected samples. The assay's performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples.
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Affiliation(s)
- Jessica Coertse
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Marinda Mortlock
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Antoinette Grobbelaar
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Naazneen Moolla
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Jacqueline Weyer
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
- Department of Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg 2131, South Africa
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6
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Warmuth VM, Metzler D, Zamora-Gutierrez V. Human disturbance increases coronavirus prevalence in bats. SCIENCE ADVANCES 2023; 9:eadd0688. [PMID: 37000877 PMCID: PMC10065436 DOI: 10.1126/sciadv.add0688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Human land modification is a known driver of animal-to-human transmission of infectious agents (zoonotic spillover). Infection prevalence in the reservoir is a key predictor of spillover, but landscape-level associations between the intensity of land modification and infection rates in wildlife remain largely untested. Bat-borne coronaviruses have caused three major disease outbreaks in humans: severe acute respiratory syndrome (SARS), Middle East respiratory syndrome, and coronavirus disease 2019 (COVID-19). We statistically link high-resolution land modification data with bat coronavirus surveillance records and show that coronavirus prevalence significantly increases with the intensity of human impact across all climates and levels of background biodiversity. The most significant contributors to the overall human impact are agriculture, deforestation, and mining. Regions of high predicted bat coronavirus prevalence coincide with global disease hotspots, suggesting that infection prevalence in wildlife may be an important factor underlying links between human land modification and zoonotic disease emergence.
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Affiliation(s)
- Vera M. Warmuth
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Veronica Zamora-Gutierrez
- CONACYT - Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Durango (CIIDIR), Instituto Politécnico Nacional, Durango, México
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7
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Boeger WA, Brooks DR, Trivellone V, Agosta SJ, Hoberg EP. Ecological super-spreaders drive host-range oscillations: Omicron and risk-space for emerging infectious disease. Transbound Emerg Dis 2022; 69:e1280-e1288. [PMID: 35411706 PMCID: PMC9115439 DOI: 10.1111/tbed.14557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
Abstract
The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modelling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro‐colonized humans from an unidentified nonhuman mammal, likely originally infected by humans. The relationship between Omicron and all other SARS‐CoV‐2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre‐existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol, DAMA, to accomplish this goal. DAMA comprises: DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks and ACT to prevent outbreaks when possible and minimize their impact when they occur.
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Affiliation(s)
- Walter A Boeger
- Biological Interactions, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Daniel R Brooks
- Eötvös Loránd Research Network, Centre for Ecological Research, Institute of Evolution, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Budapest, Hungary.,Stellenbosch Institute for Advanced Study, Stellenbosch, South Africa.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61821, USA
| | - Salvatore J Agosta
- Stellenbosch Institute for Advanced Study, Stellenbosch, South Africa.,Center for Environmental Studies, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Eric P Hoberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53716, USA.,Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, 87138, USA
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8
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Reprogrammed Pteropus Bat Stem Cells as A Model to Study Host-Pathogen Interaction during Henipavirus Infection. Microorganisms 2021; 9:microorganisms9122567. [PMID: 34946167 PMCID: PMC8706405 DOI: 10.3390/microorganisms9122567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 01/13/2023] Open
Abstract
Bats are natural hosts for numerous zoonotic viruses, including henipaviruses, which are highly pathogenic for humans, livestock, and other mammals but do not induce clinical disease in bats. Pteropus bats are identified as a reservoir of henipaviruses and the source of transmission of the infection to humans over the past 20 years. A better understanding of the molecular and cellular mechanisms allowing bats to control viral infections requires the development of relevant, stable, and permissive cellular experimental models. By applying a somatic reprogramming protocol to Pteropus bat primary cells, using a combination of ESRRB (Estrogen Related Receptor Beta), CDX2 (Caudal type Homeobox 2), and c-MYC (MYC proto-oncogene) transcription factors, we generated bat reprogrammed cells. These cells exhibit stem cell-like characteristics and neural stem cell molecular signature. In contrast to primary fibroblastic cells, these reprogrammed stem cells are highly permissive to henipaviruses and exhibit specific transcriptomic profiles with the particular expression of certain susceptibility factors such as interferon-stimulated genes (ISG), which may be related to viral infection. These Pteropus bat reprogrammed stem cells should represent an important experimental tool to decipher interactions during henipaviruses infection in Pteropus bats, facilitate isolation and production of bat-borne viruses, and to better understand the bat biology.
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9
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Albery GF, Becker DJ, Brierley L, Brook CE, Christofferson RC, Cohen LE, Dallas TA, Eskew EA, Fagre A, Farrell MJ, Glennon E, Guth S, Joseph MB, Mollentze N, Neely BA, Poisot T, Rasmussen AL, Ryan SJ, Seifert S, Sjodin AR, Sorrell EM, Carlson CJ. The science of the host-virus network. Nat Microbiol 2021; 6:1483-1492. [PMID: 34819645 DOI: 10.1038/s41564-021-00999-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/18/2021] [Indexed: 01/21/2023]
Abstract
Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington DC, USA.
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Liam Brierley
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad A Dallas
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maxwell J Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emma Glennon
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maxwell B Joseph
- Earth Lab, Cooperative Institute for Research in Environmental Science, University of Colorado Boulder, Boulder, CO, USA
| | - Nardus Mollentze
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, SC, USA
| | - Timothée Poisot
- Québec Centre for Biodiversity Sciences, Montréal, Québec, Canada.,Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sadie J Ryan
- Department of Geography, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Stephanie Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Anna R Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Erin M Sorrell
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA.,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA. .,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA.
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10
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McEvoy JF, Kishbaugh JC, Valitutto MT, Aung O, Tun KYN, Win YT, Maw MT, Thein WZ, Win HH, Chit AM, Vodzak ME, Murray S. Movements of Indian Flying Fox in Myanmar as a Guide to Human-Bat Interface Sites. ECOHEALTH 2021; 18:204-216. [PMID: 34448977 PMCID: PMC8390844 DOI: 10.1007/s10393-021-01544-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Frugivorous bats play a vital role in tropical ecosystems as pollinators and seed dispersers but are also important vectors of zoonotic diseases. Myanmar sits at the intersection of numerous bioregions and contains habitats that are important for many endangered and endemic species. This rapidly developing country also forms a connection between hotspots of emerging human diseases. We deployed Global Positioning System collars to track the movements of 10 Indian flying fox (Pteropus giganteus) in the agricultural landscapes of central Myanmar. We used clustering analysis to identify foraging sites and high-utilization areas. As part of a larger viral surveillance study in bats of Myanmar, we also collected oral and rectal swab samples from 29 bats to test for key emerging viral diseases in this colony. There were no positive results detected for our chosen viruses. We analyzed their foraging movement behavior and evaluated selected foraging sites for their potential as human-wildlife interface sites.
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Affiliation(s)
- John F McEvoy
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA.
| | - Jennifer C Kishbaugh
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Marc T Valitutto
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Ohnmar Aung
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Kyaw Yan Naing Tun
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock, and Irrigation, Yangon, Myanmar
| | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock, and Irrigation, Yangon, Myanmar
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock, and Irrigation, Yangon, Myanmar
| | - Wai Zin Thein
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock, and Irrigation, Yangon, Myanmar
| | - Htay Htay Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock, and Irrigation, Yangon, Myanmar
| | - Aung Myo Chit
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Megan E Vodzak
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Suzan Murray
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
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11
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Neely BA, Becker DJ, Janech MG, Fenton MB, Simmons NB, Bland AM. Surveying the Vampire Bat ( Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res 2021; 20:2547-2559. [PMID: 33840197 PMCID: PMC9812275 DOI: 10.1021/acs.jproteome.0c00995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.
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Affiliation(s)
- Benjamin A. Neely
- Chemical Sciences Division, National, Institute of Standards and Technology, Charleston, South, Carolina 29412, United States
| | - Daniel J. Becker
- Department of Biology, University of, Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
| | - M. Brock Fenton
- Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of, Vertebrate Zoology, American Museum of Natural History, New York 10024, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
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12
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Brierley L, Fowler A. Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. PLoS Pathog 2021; 17:e1009149. [PMID: 33878118 PMCID: PMC8087038 DOI: 10.1371/journal.ppat.1009149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/30/2021] [Accepted: 04/09/2021] [Indexed: 12/21/2022] Open
Abstract
The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging task for emerging disease investigations. Coevolution with hosts leads to specific evolutionary signatures within viral genomes that can inform likely animal origins. We obtained a set of 650 spike protein and 511 whole genome nucleotide sequences from 222 and 185 viruses belonging to the family Coronaviridae, respectively. We then trained random forest models independently on genome composition biases of spike protein and whole genome sequences, including dinucleotide and codon usage biases in order to predict animal host (of nine possible categories, including human). In hold-one-out cross-validation, predictive accuracy on unseen coronaviruses consistently reached ~73%, indicating evolutionary signal in spike proteins to be just as informative as whole genome sequences. However, different composition biases were informative in each case. Applying optimised random forest models to classify human sequences of MERS-CoV and SARS-CoV revealed evolutionary signatures consistent with their recognised intermediate hosts (camelids, carnivores), while human sequences of SARS-CoV-2 were predicted as having bat hosts (suborder Yinpterochiroptera), supporting bats as the suspected origins of the current pandemic. In addition to phylogeny, variation in genome composition can act as an informative approach to predict emerging virus traits as soon as sequences are available. More widely, this work demonstrates the potential in combining genetic resources with machine learning algorithms to address long-standing challenges in emerging infectious diseases.
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Affiliation(s)
- Liam Brierley
- Department of Health Data Science, University of Liverpool, Brownlow Street, Liverpool, United Kingdom
| | - Anna Fowler
- Department of Health Data Science, University of Liverpool, Brownlow Street, Liverpool, United Kingdom
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13
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Letko M, Seifert SN, Olival KJ, Plowright RK, Munster VJ. Bat-borne virus diversity, spillover and emergence. Nat Rev Microbiol 2020; 18:461-471. [PMID: 32528128 PMCID: PMC7289071 DOI: 10.1038/s41579-020-0394-z] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2020] [Indexed: 12/15/2022]
Abstract
Most viral pathogens in humans have animal origins and arose through cross-species transmission. Over the past 50 years, several viruses, including Ebola virus, Marburg virus, Nipah virus, Hendra virus, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory coronavirus (MERS-CoV) and SARS-CoV-2, have been linked back to various bat species. Despite decades of research into bats and the pathogens they carry, the fields of bat virus ecology and molecular biology are still nascent, with many questions largely unexplored, thus hindering our ability to anticipate and prepare for the next viral outbreak. In this Review, we discuss the latest advancements and understanding of bat-borne viruses, reflecting on current knowledge gaps and outlining the potential routes for future research as well as for outbreak response and prevention efforts.
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Affiliation(s)
- Michael Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, USA. .,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.
| | - Stephanie N Seifert
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, USA
| | | | - Raina K Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT, USA.
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15
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Valitutto MT, Aung O, Tun KYN, Vodzak ME, Zimmerman D, Yu JH, Win YT, Maw MT, Thein WZ, Win HH, Dhanota J, Ontiveros V, Smith B, Tremeau-Brevard A, Goldstein T, Johnson CK, Murray S, Mazet J. Detection of novel coronaviruses in bats in Myanmar. PLoS One 2020; 15:e0230802. [PMID: 32271768 PMCID: PMC7144984 DOI: 10.1371/journal.pone.0230802] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/09/2020] [Indexed: 12/25/2022] Open
Abstract
The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.
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Affiliation(s)
- Marc T. Valitutto
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Ohnmar Aung
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Kyaw Yan Naing Tun
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Megan E. Vodzak
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Dawn Zimmerman
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Jennifer H. Yu
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Wai Zin Thein
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Htay Htay Win
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Naypyitaw, Myanmar
| | - Jasjeet Dhanota
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Victoria Ontiveros
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Brett Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Alexandre Tremeau-Brevard
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Christine K. Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Suzan Murray
- Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, District of Columbia, United States of America
| | - Jonna Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
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16
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Affiliation(s)
- Colin J Carlson
- Department of Biology and Center for Global Health Science and Security, Georgetown University, Washington, DC 20007, USA
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17
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJH, Cer RZ, Long KA, Lueder MR, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. The temporal RNA virome patterns of a lesser dawn bat ( Eonycteris spelaea) colony revealed by deep sequencing. Virus Evol 2020; 6:veaa017. [PMID: 33747541 PMCID: PMC7079719 DOI: 10.1093/ve/veaa017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat-human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.
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Affiliation(s)
- Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Justin H J Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gregory K Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Casandra W Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Defense Threat Reduction Agency, 8725 John J. Kingman Rd., Fort Belvoir, VA 22060, USA
| | - Randy J H Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Matthew R Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gavin J Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
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18
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Lee DN, Angiel M. Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma. Virus Genes 2019; 56:99-103. [PMID: 31797220 PMCID: PMC7089485 DOI: 10.1007/s11262-019-01719-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/25/2019] [Indexed: 11/28/2022]
Abstract
Bats are carriers of potentially zoonotic viruses, therefore it is crucial to identify viruses currently found in bats to better understand how they are maintained in bat populations and evaluate risks for transmission to other species. Adenoviruses have been previously detected in bats throughout the world, but sampling is still limited. In this study, 30 pooled-guano samples were collected from a cave roost of Myotis velifer in Oklahoma. A portion of the DNA polymerase gene from Adenoviridae was amplified successfully in 18 M. velifer samples; however, DNA sequence was obtained from only 6 of these M. velifer samples. One was collected in October 2016, one in March 2017, and 4 in July 2017. The October and March samples contained viral DNA that was 3.1% different from each other but 33% different than the novel viral sequence found in the July 2017 samples. Phylogenetic analysis of these fragments confirmed our isolates were from the genus Mastadenovirus and had genetic diversity ranging from 20 to 50% when compared to other bat adenoviruses.
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Affiliation(s)
- Dana N Lee
- Department of Agriculture, Biology & Health Sciences, Cameron University, 2800 W. Gore Blvd, Lawton, OK, 73505, USA.
| | - Meagan Angiel
- Department of Agriculture, Biology & Health Sciences, Cameron University, 2800 W. Gore Blvd, Lawton, OK, 73505, USA
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19
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Bergner LM, Orton RJ, Benavides JA, Becker DJ, Tello C, Biek R, Streicker DG. Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Mol Ecol 2019; 29:26-39. [PMID: 31561274 PMCID: PMC7004108 DOI: 10.1111/mec.15250] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023]
Abstract
Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.
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Affiliation(s)
- Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Julio A Benavides
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Departamento de Ecología, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Daniel J Becker
- Odum School of Ecology, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Department of Biology, Indiana University, Bloomington, IN, USA
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, Lima, Peru.,Yunkawasi, Lima, Peru
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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20
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Withdrawn as duplicate: Guild-level responses of bats to habitat conversion in a lowland Amazonian rainforest: species composition and biodiversity. J Mammal 2019; 100:e1. [DOI: 10.1093/jmammal/gyz008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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Carlson CJ, Zipfel CM, Garnier R, Bansal S. Global estimates of mammalian viral diversity accounting for host sharing. Nat Ecol Evol 2019; 3:1070-1075. [PMID: 31182813 DOI: 10.1038/s41559-019-0910-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/23/2019] [Indexed: 11/09/2022]
Abstract
Present estimates suggest there are over 1 million virus species found in mammals alone, with about half a million posing a possible threat to human health. Although previous estimates assume linear scaling between host and virus diversity, we show that ecological network theory predicts a non-linear relationship, produced by patterns of host sharing among virus species. To account for host sharing, we fit a power law scaling relationship for host-virus species interaction networks. We estimate that there are about 40,000 virus species in mammals (including ~10,000 viruses with zoonotic potential), a reduction of two orders of magnitude from present projections of viral diversity. We expect that the increasing availability of host-virus association data will improve the precision of these estimates and their use in the sampling and surveillance of pathogens with pandemic potential. We suggest host sharing should be more widely included in macroecological approaches to estimating biodiversity.
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Affiliation(s)
- Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA.
| | - Casey M Zipfel
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Romain Garnier
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA
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22
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Mishra N, Fagbo SF, Alagaili AN, Nitido A, Williams SH, Ng J, Lee B, Durosinlorun A, Garcia JA, Jain K, Kapoor V, Epstein JH, Briese T, Memish ZA, Olival KJ, Lipkin WI. A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia. PLoS One 2019; 14:e0214227. [PMID: 30969980 PMCID: PMC6457491 DOI: 10.1371/journal.pone.0214227] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/09/2019] [Indexed: 12/31/2022] Open
Abstract
Bats are implicated as natural reservoirs for a wide range of zoonotic viruses including SARS and MERS coronaviruses, Ebola, Marburg, Nipah, Hendra, Rabies and other lyssaviruses. Accordingly, many One Health surveillance and viral discovery programs have focused on bats. In this report we present viral metagenomic data from bats collected in the Kingdom of Saudi Arabia [KSA]. Unbiased high throughput sequencing of fecal samples from 72 bat individuals comprising four species; lesser mouse-tailed bat (Rhinopoma hardwickii), Egyptian tomb bat (Taphozous perforatus), straw-colored fruit bat (Eidolon helvum), and Egyptian fruit bat (Rousettus aegyptiacus) revealed molecular evidence of a diverse set of viral families: Picornaviridae (hepatovirus, teschovirus, parechovirus), Reoviridae (rotavirus), Polyomaviridae (polyomavirus), Papillomaviridae (papillomavirus), Astroviridae (astrovirus), Caliciviridae (sapovirus), Coronaviridae (coronavirus), Adenoviridae (adenovirus), Paramyxoviridae (paramyxovirus), and unassigned mononegavirales (chuvirus). Additionally, we discovered a bastro-like virus (Middle East Hepe-Astrovirus), with a genomic organization similar to Hepeviridae. However, since it shared homology with Hepeviridae and Astroviridae at ORF1 and in ORF2, respectively, the newly discovered Hepe-Astrovirus may represent a phylogenetic bridge between Hepeviridae and Astroviridae.
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Affiliation(s)
- Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
- * E-mail: (NM); (ZAM)
| | - Shamsudeen F. Fagbo
- One Health Unit, Executive Directorate for Surveillance and Response, National Center for Disease Prevention and Control, Riyadh, Saudi Arabia
| | - Abdulaziz N. Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Adam Nitido
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Simon H. Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Bohyun Lee
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | - Joel A. Garcia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Ziad A. Memish
- The College of Medicine, Al faisal University & Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
- * E-mail: (NM); (ZAM)
| | - Kevin J. Olival
- EcoHealth Alliance, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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23
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Frick WF, Kingston T, Flanders J. A review of the major threats and challenges to global bat conservation. Ann N Y Acad Sci 2019; 1469:5-25. [PMID: 30937915 DOI: 10.1111/nyas.14045] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 01/03/2023]
Abstract
Bats are an ecologically and taxonomically diverse group accounting for roughly a fifth of mammalian diversity worldwide. Many of the threats bats face (e.g., habitat loss, bushmeat hunting, and climate change) reflect the conservation challenges of our era. However, compared to other mammals and birds, we know significantly less about the population status of most bat species, which makes prioritizing and planning conservation actions challenging. Over a third of bat species assessed by the International Union for Conservation of Nature (IUCN) are considered threatened or data deficient, and well over half of the species have unknown or decreasing population trends. That equals 988 species, or 80% of bats assessed by IUCN, needing conservation or research attention. Delivering conservation to bat species will require sustained efforts to assess population status and trends and address data deficiencies. Successful bat conservation must integrate research and conservation to identify stressors and their solutions and to test the efficacy of actions to stabilize or increase populations. Global and regional networks that connect researchers, conservation practitioners, and local stakeholders to share knowledge, build capacity, and prioritize and coordinate research and conservation efforts, are vital to ensuring sustainable bat populations worldwide.
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Affiliation(s)
- Winifred F Frick
- Bat Conservation International, Austin, Texas.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Tigga Kingston
- Department of Biological Science, Texas Tech University, Lubbock, Texas
| | - Jon Flanders
- Bat Conservation International, Austin, Texas.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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24
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Fagre AC, Kading RC. Can Bats Serve as Reservoirs for Arboviruses? Viruses 2019; 11:E215. [PMID: 30832426 PMCID: PMC6466281 DOI: 10.3390/v11030215] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/22/2022] Open
Abstract
Bats are known to harbor and transmit many emerging and re-emerging viruses, many of which are extremely pathogenic in humans but do not cause overt pathology in their bat reservoir hosts: henipaviruses (Nipah and Hendra), filoviruses (Ebola and Marburg), and coronaviruses (SARS-CoV and MERS-CoV). Direct transmission cycles are often implicated in these outbreaks, with virus shed in bat feces, urine, and saliva. An additional mode of virus transmission between bats and humans requiring further exploration is the spread of disease via arthropod vectors. Despite the shared ecological niches that bats fill with many hematophagous arthropods (e.g. mosquitoes, ticks, biting midges, etc.) known to play a role in the transmission of medically important arboviruses, knowledge surrounding the potential for bats to act as reservoirs for arboviruses is limited. To this end, a comprehensive literature review was undertaken examining the current understanding and potential for bats to act as reservoirs for viruses transmitted by blood-feeding arthropods. Serosurveillance and viral isolation from either free-ranging or captive bats are described in relation to four arboviral groups (Bunyavirales, Flaviviridae, Reoviridae, Togaviridae). Further, ecological associations between bats and hematophagous viral vectors are characterized (e.g. bat bloodmeals in mosquitoes, ingestion of mosquitoes by bats, etc). Lastly, knowledge gaps related to hematophagous ectoparasites (bat bugs and bed bugs (Cimicidae) and bat flies (Nycteribiidae and Streblidae)), in addition to future directions for characterization of bat-vector-virus relationships are described.
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Affiliation(s)
- Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rebekah C Kading
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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25
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Willig MR, Presley SJ, Plante JL, Bloch CP, Solari S, Pacheco V, Weaver SC. Guild-level responses of bats to habitat conversion in a lowland Amazonian rainforest: species composition and biodiversity. J Mammal 2019; 100:223-238. [PMID: 30846887 PMCID: PMC6394116 DOI: 10.1093/jmammal/gyz023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/18/2022] Open
Abstract
Landscape modification represents one of the most severe threats to biodiversity from local to global scales. Conversion of forest to agricultural production generally results in patches of habitat that subdivide or isolate populations, alter the behavior of species, modify interspecific interactions, reduce biodiversity, and compromise ecosystem processes. Moreover, conversion may increase exposure of humans to zoonoses to which they would otherwise rarely be exposed. We evaluated the effects of forest conversion to agriculture, and its subsequent successional dynamics, on bat communities in a region of the Amazon that was predominantly closed-canopy rainforest. Based on a nonmanipulative experiment, we quantified differences in species composition, community structure, and taxonomic biodiversity among closed-canopy forest (bosque), agricultural lands (chacra), and secondary forest (purma) for two phyllostomid guilds (frugivores and gleaning animalivores) during the wet and dry seasons. Responses were complex and guild-specific. For frugivores, species composition (species abundance distributions) differed between all possible pairs of habitats in both wet and dry seasons. For gleaning animalivores, species composition differed between all possible pairs of habitats in the dry season, but no differences characterized the wet season. Ecological structure (rank abundance distributions) differed among habitats in guild-specific and season-specific manners. For frugivores, mean diversity, evenness, and dominance were greater in bosque than in purma; mean dominance was greater in bosque than in chacra, but local rarity was greater in chacra than in bosque, and no differences were manifest between purma and chacra. For gleaning animalivores, mean diversity and evenness were greater in bosque than in purma, but no differences were manifest between chacra and bosque, or between purma and chacra. Such results have important implications for management, conservation, and the epidemiology of zoonotic diseases. La actual modificación del paisaje, a escalas que van de lo local a lo global, es una de las amenazas más severas a la biodiversidad. De manera general, la conversión de bosques a áreas agrícolas produce parches de hábitat que subdividen o aíslan poblaciones, alteran la conducta de las especies, modifican las interacciones interespecíficas, reducen la biodiversidad y comprometen las funciones de los ecosistemas. Más aún, la transformación de estos ambientes puede incrementar la probabilidad de que las poblaciones humanas interactúen con zoonosis con las que de otra manera raramente entrarían en contacto. Evaluamos los efectos de la conversión de hábitat en comunidades de murciélagos en una región de Amazonia en la que la vegetación dominante es un bosque lluvioso de copas cerradas, y en la cual los efectos de la conversión a usos agrícolas sobre la biodiversidad, y la subsecuente dinámica sucesional, son aún poco comprendidos. Por medio de un experimento no-manipulativo, cuantificamos las diferencias en composición de especies, estructura de la comunidad y diversidad taxonómica entre bosque cerrado (bosque), áreas agrícolas (chacra) y bosque secundario (purma) para dos gremios tróficos de murciélagos filostómidos (frugívoros y forrajeadores de sustrato) durante dos temporadas (secas y lluvias). Las respuestas fueron complejas y diferentes para cada gremio. Para los frugívoros, la composición de especies (distribución de las abundancias) fue diferente para todos los posibles pares de hábitats tanto para secas como para lluvias. Para los forrajeadores de sustrato, la composición de especies difirió entre todos los posibles pares de hábitats en la temporada seca, pero no en la de lluvias. La estructura ecológica (distribuciones rango-abundancia) fue también específica para gremios y temporadas. Para los frugívoros, la diversidad promedio, equidad y dominancia fueron mayores en bosque que en purma; la dominancia promedio fue mayor en bosque que en chacra, pero la rareza local fue mayor en chacra que en bosque, y no se encontraron diferencias entre purma y chacra. Para los forrajeadores de sustrato, la diversidad promedio y la dominancia fueron mayores en bosque que en purma, pero no se detectaron diferencias entre chacra y bosque, o entre purma y chacra. Estos resultados tienen importantes implicaciones para el manejo, conservación y epidemiología de zoonosis.
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Affiliation(s)
- Michael R Willig
- Center for Environmental Sciences & Engineering and Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Steven J Presley
- Center for Environmental Sciences & Engineering and Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jean-Luc Plante
- Center for Environmental Sciences & Engineering and Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christopher P Bloch
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA, USA
| | - Sergio Solari
- Grupo Mastozoología, Instituto de Biología, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Victor Pacheco
- Departamento de Mastozooloía, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima-14, Perú
| | - Scott C Weaver
- Institute for Human Infections and Immunity, Center for Tropical Diseases, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
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26
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Alston Virus, a Novel Paramyxovirus Isolated from Bats Causes Upper Respiratory Tract Infection in Experimentally Challenged Ferrets. Viruses 2018; 10:v10120675. [PMID: 30487438 PMCID: PMC6315912 DOI: 10.3390/v10120675] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022] Open
Abstract
Multiple viruses with zoonotic potential have been isolated from bats globally. Here we describe the isolation and characterization of a novel paramyxovirus, Alston virus (AlsPV), isolated from urine collected from an Australian pteropid bat colony in Alstonville, New South Wales. Characterization of AlsPV by whole-genome sequencing and analyzing antigenic relatedness revealed it is a rubulavirus that is closely related to parainfluenza virus 5 (PIV5). Intranasal exposure of mice to AlsPV resulted in no clinical signs of disease, although viral RNA was detected in the olfactory bulbs of two mice at 21 days post exposure. Oronasal challenge of ferrets resulted in subclinical upper respiratory tract infection, viral shedding in respiratory secretions, and detection of viral antigen in the olfactory bulb of the brain. These results imply that AlsPV may be similar to PIV5 in its ability to infect multiple mammalian host species. This isolation of a novel paramyxovirus with the potential to transmit from bats to other mammalian species reinforces the importance of continued surveillance of bats as a source of emerging viruses.
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27
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Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 58:279-289. [PMID: 29355607 PMCID: PMC7106311 DOI: 10.1016/j.meegid.2018.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 01/01/2023]
Abstract
Coronaviruses (CoVs) have been documented in almost every species of bat sampled. Bat CoVs exhibit both extensive genetic diversity and a broad geographic range, indicative of a long-standing host association. Despite this, the respective roles of long-term virus-host co-divergence and cross-species transmission (host-jumping) in the evolution of bat coronaviruses are unclear. Using a phylogenetic approach we provide evidence that CoV diversity in bats is shaped by both species richness and their geographical distribution, and that CoVs exhibit clustering at the level of bat genera, with these genus-specific clusters largely associated with distinct CoV species. Co-phylogenetic analyses revealed that cross-species transmission has been more common than co-divergence across coronavirus evolution as a whole, and that cross-species transmission events were more likely between sympatric bat hosts. Notably, however, an analysis of the CoV RNA polymerase phylogeny suggested that many such host-jumps likely resulted in short-term spill-over infections, with little evidence for sustained onward transmission in new co-roosting host species.
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Affiliation(s)
- Stefania Leopardi
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michele Gastaldelli
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Luca Tassoni
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | | | | | - Gianpiero Zamperin
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
| | - Paola De Benedictis
- National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy
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28
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Seltmann A, Corman VM, Rasche A, Drosten C, Czirják GÁ, Bernard H, Struebig MJ, Voigt CC. Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests. ECOHEALTH 2017; 14:272-284. [PMID: 28500421 PMCID: PMC7087689 DOI: 10.1007/s10393-017-1245-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 04/06/2017] [Accepted: 04/06/2017] [Indexed: 05/21/2023]
Abstract
Emerging infectious diseases (EIDs) are considered a major threat to global health. Most EIDs appear to result from increased contact between wildlife and humans, especially when humans encroach into formerly pristine habitats. Habitat deterioration may also negatively affect the physiology and health of wildlife species, which may eventually lead to a higher susceptibility to infectious agents and/or increased shedding of the pathogens causing EIDs. Bats are known to host viruses closely related to important EIDs. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the occurrence of astro- and coronaviruses in eight bat species. In contrast to our hypothesis, anthropogenic habitat disturbance was not associated with corona- and astrovirus detection rates in fecal samples. However, we found that bats infected with either astro- or coronaviruses were likely to be coinfected with the respective other virus. Additionally, we identified two more risk factors influencing astrovirus shedding. First, the detection rate of astroviruses was higher at the beginning of the rainy compared to the dry season. Second, there was a trend that individuals with a poor body condition had a higher probability of shedding astroviruses in their feces. The identification of risk factors for increased viral shedding that may potentially result in increased interspecies transmission is important to prevent viral spillovers from bats to other animals, including humans.
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Affiliation(s)
- Anne Seltmann
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.
- Institute of Biology, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany.
| | - Victor M Corman
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Bonn, Germany
| | - Andrea Rasche
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Bonn, Germany
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Christian C Voigt
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
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29
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Johnson RI, Smith IL. Virus discovery in bats. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Comprising approximately 20% of known mammalian species, bats are abundant throughout the world1. In recent years, bats have been shown to be the reservoir host for many highly pathogenic viruses, leading to increased attempts to identify other zoonotic bat-borne viruses. These efforts have led to the discovery of over 200 viruses in bats and many more viral nucleic acid sequences from 27 different viral families2,3 (Table 1). Over half of the world’s recently emerged infectious diseases originated in wildlife15, with the genetic diversity of viruses greater in bats than in any other animal16. As humans continue to encroach on the habitat of bats, the risk of spillover of potentially zoonotic viruses is also continuing to increase. Therefore, the surveillance of bats and discovery of novel pathogens is necessary to prepare for these spillover events17.
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30
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Han BA, Kramer AM, Drake JM. Global Patterns of Zoonotic Disease in Mammals. Trends Parasitol 2016; 32:565-577. [PMID: 27316904 PMCID: PMC4921293 DOI: 10.1016/j.pt.2016.04.007] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/04/2016] [Accepted: 04/11/2016] [Indexed: 12/16/2022]
Abstract
As the frequency and prevalence of zoonotic diseases increase worldwide, investigating how mammal host distributions determine patterns of human disease and predicting which regions are at greatest risk for future zoonotic disease emergence are two goals which both require better understanding of the current distributions of zoonotic hosts and pathogens. We review here the existing data about mammalian host species, comparing and contrasting these patterns against global maps of zoonotic hosts from all 27 orders of terrestrial mammals. We discuss the zoonotic potential of host species from the top six most species-rich mammal groups, and review the literature to identify analytical and conceptual gaps that must be addressed to improve our ability to generate testable predictions about zoonotic diseases originating from wild mammals. Predicting zoonotic disease events remains a prominent scientific challenge. In response to increasing frequency of emerging infectious disease events caused by animal-borne (zoonotic) pathogens, recent advances assess the biogeographic patterns of human infectious diseases. A disproportionate representation of mammal-borne zoonoses among emerging human disease has sparked research emphasis on mammal reservoirs because improved understanding of mammal host distributions may lead to improved predictions of future hotspots for zoonotic disease emergence. In addition to spatial distributions of animal hosts and human disease, the concept of ‘disease risk’ is a topic of intense analysis, and has been quantified on the basis of hindsight where regions undergoing frequent or intense human disease events are categorized as possessing numerous factors that interact to increase disease risk.
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Affiliation(s)
- Barbara A Han
- Cary Institute of Ecosystem Studies, Box AB Millbrook, NY 12545, USA.
| | - Andrew M Kramer
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
| | - John M Drake
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
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