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Weber MN, da Silva MS. Corona- and Paramyxoviruses in Bats from Brazil: A Matter of Concern? Animals (Basel) 2023; 14:88. [PMID: 38200819 PMCID: PMC10778288 DOI: 10.3390/ani14010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Chiroptera are one of the most diverse mammal orders. They are considered reservoirs of main human pathogens, where coronaviruses (CoVs) and paramyxoviruses (PMVs) may be highlighted. Moreover, the growing number of publications on CoVs and PMVs in wildlife reinforces the scientific community's interest in eco-vigilance, especially because of the emergence of important human pathogens such as the SARS-CoV-2 and Nipha viruses. Considering that Brazil presents continental dimensions, is biologically rich containing one of the most diverse continental biotas and presents a rich biodiversity of animals classified in the order Chiroptera, the mapping of CoV and PMV genetics related to human pathogens is important and the aim of the present work. CoVs can be classified into four genera: Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus. Delta- and gammacoronaviruses infect mainly birds, while alpha- and betacoronaviruses contain important animal and human pathogens. Almost 60% of alpha- and betacoronaviruses are related to bats, which are considered natural hosts of these viral genera members. The studies on CoV presence in bats from Brazil have mainly assayed phyllostomid, molossid and vespertilionid bats in the South, Southeast and North territories. Despite Brazil not hosting rhinophilid or pteropodid bats, which are natural reservoirs of SARS-related CoVs and henipaviruses, respectively, CoVs and PMVs reported in Brazilian bats are genetically closely related to some human pathogens. Most works performed with Brazilian bats reported alpha-CoVs that were closely related to other bat-CoVs, despite a few reports of beta-CoVs grouped in the Merbecovirus and Embecovirus subgenera. The family Paramyxoviridae includes four subfamilies (Avulavirinae, Metaparamyxovirinae, Orthoparamyxovirinae and Rubulavirinae), and bats are significant drivers of PMV cross-species viral transmission. Additionally, the studies that have evaluated PMV presence in Brazilian bats have mainly found sequences classified in the Jeilongvirus and Morbillivirus genera that belong to the Orthoparamyxovirinae subfamily. Despite the increasing amount of research on Brazilian bats, studies analyzing these samples are still scarce. When surveying the representativeness of the CoVs and PMVs found and the available genomic sequences, it can be perceived that there may be gaps in the knowledge. The continuous monitoring of viral sequences that are closely related to human pathogens may be helpful in mapping and predicting future hotspots in the emergence of zoonotic agents.
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Affiliation(s)
- Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93525-075, RS, Brazil;
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Mena J, Hidalgo C, Estay-Olea D, Sallaberry-Pincheira N, Bacigalupo A, Rubio AV, Peñaloza D, Sánchez C, Gómez-Adaros J, Olmos V, Cabello J, Ivelic K, Abarca MJ, Ramírez-Álvarez D, Torregrosa Rocabado M, Durán Castro N, Carreño M, Gómez G, Cattan PE, Ramírez-Toloza G, Robbiano S, Marchese C, Raffo E, Stowhas P, Medina-Vogel G, Landaeta-Aqueveque C, Ortega R, Waleckx E, Gónzalez-Acuña D, Rojo G. Molecular surveillance of potential SARS-CoV-2 reservoir hosts in wildlife rehabilitation centers. Vet Q 2023; 43:1-10. [PMID: 36594266 PMCID: PMC9858396 DOI: 10.1080/01652176.2023.2164909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by SARS-CoV-2 infection, has become the most devastating zoonotic event in recent times, with negative impacts on both human and animal welfare as well as on the global economy. Although SARS-CoV-2 is considered a human virus, it likely emerged from animals, and it can infect both domestic and wild animals. This constitutes a risk for human and animal health including wildlife with evidence of SARS-CoV-2 horizontal transmission back and forth between humans and wild animals. AIM Molecular surveillance in different wildlife rehabilitation centers and wildlife associated institutions in Chile, which are critical points of animal-human interaction and wildlife conservation, especially since the aim of wildlife rehabilitation centers is to reintroduce animals to their original habitat. MATERIALS AND METHODS The survey was conducted in six WRCs and three wildlife associated institutions. A total of 185 samples were obtained from 83 individuals belonging to 15 different species, including vulnerable and endangered species. Each specimen was sampled with two different swabs: one oropharyngeal or nasopharyngeal according to the nostril diameter, and/or a second rectal sample. RNA was extracted from the samples and two different molecular assays were performed: first, a conventional RT-PCR with pan-coronavirus primers and a second SARS-CoV-2 qPCR targeting the N and S genes. RESULTS All 185 samples were negative for SARS-CoV-2. CLINICAL RELEVANCE This study constitutes the first report on the surveillance of SARS-CoV-2 from wildlife treated in rehabilitation centers in Chile, and supports the biosafety procedures adopted in those centers.
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Affiliation(s)
- Juan Mena
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| | - Christian Hidalgo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas (NIAVA), Universidad de Las Américas, Chile
| | - Daniela Estay-Olea
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| | - Nicole Sallaberry-Pincheira
- Unidad de Rehabilitación de Fauna Silvestre (UFAS), Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | - Antonella Bacigalupo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - André V. Rubio
- Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Diego Peñaloza
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal (CONAF), Región del Libertador General Bernardo O’Higgins, Rancagua, Chile
| | - Carolina Sánchez
- Unidad de Rehabilitación de Fauna Silvestre (UFAS), Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | | | - Valeria Olmos
- Centro de Rehabilitación y Exhibición de Fauna Silvestre, Rancagua, Chile
| | - Javier Cabello
- Centro de Conservación de la Biodiversidad, Ancud, Chile
| | - Kendra Ivelic
- Refugio Animal Cascada, Centro de Rehabilitación y Exhibición de fauna nativa de la Fundación Acción Fauna, Santiago, Chile
| | - María José Abarca
- Comité Nacional Pro Defensa de la Fauna y Flora (CODEFF), Santiago, Chile
| | - Diego Ramírez-Álvarez
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Rancagua, Chile
| | - Marisol Torregrosa Rocabado
- Médico Veterinaria Encargada Sección Salud Animal, Zoológico Nacional del Parque Metropolitano, Santiago, Chile
| | - Natalia Durán Castro
- Médico Veterinaria Sección Salud Animal, Zoológico Nacional del Parque Metropolitano, Santiago, Chile
| | | | - Gabriela Gómez
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal (CONAF), Región de Aysén, Chile
| | - Pedro E. Cattan
- Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Galia Ramírez-Toloza
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sofía Robbiano
- Centro de Rehabilitación de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Carla Marchese
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Valdivia, Chile
| | - Eduardo Raffo
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Valdivia, Chile
| | - Paulina Stowhas
- Programa Nacional Integrado de Gestión de Especies Exóticas Invasoras, Ministerio del Medio Ambiente, Santiago, Chile
| | - Gonzalo Medina-Vogel
- Centro de Investigación para la Sustentabilidad (CIS), Universidad Andres Bello, Santiago, Chile
| | - Carlos Landaeta-Aqueveque
- Departamento Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - René Ortega
- Departamento Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Etienne Waleckx
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD, CIRAD, Université de Montpellier, Montpellier, France,Laboratorio de Parasitología, Centro de Investigaciones Regionales “Dr Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, México
| | - Daniel Gónzalez-Acuña
- Departamento Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Gemma Rojo
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile,CONTACT Gemma Rojo Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
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Cerri A, Bolatti EM, Zorec TM, Montani ME, Rimondi A, Hosnjak L, Casal PE, Di Domenica V, Barquez RM, Poljak M, Giri AA. Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission. Microbiol Spectr 2023; 11:e0204723. [PMID: 37695063 PMCID: PMC10581097 DOI: 10.1128/spectrum.02047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023] Open
Abstract
Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.
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Affiliation(s)
- Agustina Cerri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
| | - Elisa M. Bolatti
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maria E. Montani
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Dr. Ángel Gallardo Provincial Museum of Natural Sciences, Rosario, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Agustina Rimondi
- Institute of Virology and Technological Innovations (INTA/CONICET), Castelar, Argentina
- Robert Koch Institute, Berlin, Germany
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Pablo E. Casal
- DETx MOL S.A. La Segunda Núcleo Corporate Building, Alvear, Argentina
| | - Violeta Di Domenica
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Ruben M. Barquez
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Adriana A. Giri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
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Brown N, Escobar LE. A review of the diet of the common vampire bat ( Desmodus rotundus) in the context of anthropogenic change. Mamm Biol 2023; 103:1-21. [PMID: 37363038 PMCID: PMC10258787 DOI: 10.1007/s42991-023-00358-3] [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: 08/15/2022] [Accepted: 03/30/2023] [Indexed: 06/28/2023]
Abstract
The common vampire bat (Desmodus rotundus) maintains a diverse, sanguivorous diet, utilizing a broad range of prey taxa. As anthropogenic change alters the distribution of this species, shifts in predator-prey interactions are expected. Understanding prey richness and patterns of prey selection is, thus, increasingly informative from ecological, epidemiological, and economic perspectives. We reviewed D. rotundus diet and assessed the geographical, taxonomical, and behavioral features to find 63 vertebrate species within 21 orders and 45 families constitute prey, including suitable host species in regions of invasion outside D. rotundus' range. Rodentia contained the largest number of species utilized by D. rotundus, though cattle were the most commonly reported prey source, likely linked to the high availability of livestock and visibility of bite wounds compared to wildlife. Additionally, there was tendency to predate upon species with diurnal activity and social behavior, potentially facilitating convenient and nocturnal predation. Our review highlights the dietary heterogeneity of D. rotundus across its distribution. We define D. rotundus as a generalist predator, or parasite, depending on the ecological definition of its symbiont roles in an ecosystem (i.e., lethal vs. non-lethal blood consumption). In view of the eminent role of D. rotundus in rabies virus transmission and its range expansion, an understanding of its ecology would benefit public health, wildlife management, and agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s42991-023-00358-3.
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Affiliation(s)
- Natalie Brown
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA USA
| | - Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA USA
- Global Change Center, Virginia Tech, Blacksburg, VA USA
- Center for Emerging Zoonotic and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA USA
- Doctorado en Agrociencias, Facultad de Ciencias Agropecuarias, Universidad de La Salle, Carrera 7 No. 179-03, Bogotá, Colombia
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Intestinal Tropism of a Betacoronavirus ( Merbecovirus) in Nathusius's Pipistrelle Bat ( Pipistrellus nathusii), Its Natural Host. J Virol 2023; 97:e0009923. [PMID: 36856426 PMCID: PMC10062147 DOI: 10.1128/jvi.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The emergence of several bat coronavirus-related disease outbreaks in human and domestic animals has fueled surveillance of coronaviruses in bats worldwide. However, little is known about how these viruses interact with their natural hosts. We demonstrate a Betacoronavirus (subgenus Merbecovirus), PN-βCoV, in the intestine of its natural host, Nathusius's Pipistrelle Bat (Pipistrellus nathusii), by combining molecular and microscopy techniques. Eighty-eight P. nathusii bat carcasses were tested for PN-βCoV RNA by RT-qPCR, of which 25 bats (28%) tested positive. PN-βCoV RNA was more often detected in samples of the intestinal tract than in other sample types. In addition, viral RNA loads were higher in intestinal samples compared to other sample types, both on average and in each individual bat. In one bat, we demonstrated Merbecovirus antigen and PN-βCoV RNA expression in intestinal epithelium and the underlying connective tissue using immunohistochemistry and in situ hybridization, respectively. These results indicate that PN-βCoV has a tropism for the intestinal epithelium of its natural host, Nathusius's Pipistrelle Bat, and imply that the fecal-oral route is a possible route of transmission. IMPORTANCE Virtually all mammal species circulate coronaviruses. Most of these viruses will infect one host species; however, coronaviruses are known to include species that can infect multiple hosts, for example the well-known virus that caused a pandemic, SARS-CoV-2. Chiroptera (bats) include over 1,400 different species, which are expected to harbor a great variety of coronaviruses. However, we know very little about how any of these coronaviruses interact with their bat hosts; for example, we do not know their modes of transmissions, or which cells they infect. Thus, we have a limited understanding of coronavirus infections in this important host group. The significance of our study is that we learned that a bat coronavirus that occurs in a common bat species in Europe has a tropism for the intestines. This implies the fecal-oral route is a likely transmission route.
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Role of Brazilian bats in the epidemiological cycle of potentially zoonotic pathogens. Microb Pathog 2023; 177:106032. [PMID: 36804526 DOI: 10.1016/j.micpath.2023.106032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/19/2023]
Abstract
Bats (Chiroptera) are flying mammals of great biodiversity and habits. These characteristics contribute for them being natural reservoirs and part of the epidemiological cycle of several potentially zoonotic pathogens, such as viruses, protozoa, fungi and bacteria. Brazil hosts approximately 15% of the world's bat diversity, with 181 distinct species, 68 genera and 9 families. About 60% of infectious diseases in humans are of zoonotic origin and, in the last decades, the detection of zoonotic pathogens in bats and their environment has been reported, such as Rabies virus (RABV) and Histoplasma capsulatum. Thus, the aim of this work was to review the reports of zoonotic pathogens associated with bats in Brazil in the past ten years. We reviewed the main pathogenic microorganisms described and the species of bats most frequently involved in the epidemiological cycles of these zoonotic agents. The obtained data show an upward trend in the detection of zoonotic pathogens in Brazilian bats, such as RABV, Bartonella sp., Histoplasma capsulatum and Leishmania spp., with emphasis on the bat species Artibeus lituratus, Carollia perspicillata, Desmodus rotundus and Molossus molossus. These findings highlight the importance of monitoring bat-associated microrganisms to early identify pathogens that may threaten bat populations, including potentially zoonotic microrganisms, emphasizing the importance of the One Health approach to prevent and mitigate the risks of the emergence of zoonotic diseases.
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Oral Sampling of Little Brown Bat (Myotis lucifugus) Maternity Colonies for SARS-CoV-2 in the Northeast and Mid-Atlantic, USA. Animals (Basel) 2023; 13:ani13040550. [PMID: 36830336 PMCID: PMC9951713 DOI: 10.3390/ani13040550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
The potential introduction of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, into North American bat populations is of interest to wildlife managers due to recent disease-mediated declines of several species. Populations of little brown bats (Myotis lucifugus) have collapsed due to white-nose syndrome (WNS), a disease caused by the introduction and spread of the fungal pathogen Pseudogymnoascus destructans (Pd). Throughout much of the United States and southern Canada, large colonies of the species routinely established diurnal roosts in anthropogenic structures, thereby creating the potential for direct human contact and cross-species disease transmission. Given recent declines and the potential for further disease impacts, we collected oral swabs from eight little brown bat maternity colonies to assess the presence and prevalence of SARS-CoV-2 by RT-qPCR analysis. Little brown bat colonies in Maryland (n = 1), New Hampshire (n = 1), New Jersey (n = 2), New York (n = 1), Rhode Island (n = 2), and Virginia (n = 1) were taken during May-August, 2022. From 235 assayed individuals, no bat tested positive for SARS-CoV-2. Our results indicate that little brown bats may not contract SARS-CoV-2 or that the virus persists at undetectable levels in populations of the Mid-Atlantic and Northeast during summer months. Nonetheless, continued monitoring and future work addressing other seasons may still be warranted to conclusively determine infection status.
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Caraballo DA, Sabio MS, Colombo VC, Piccirilli MG, Vico L, Hirmas Riade SM, Campos J, Martínez G, Beltrán F, Baumeister E, Cisterna DM. The Role of Molossidae and Vespertilionidae in Shaping the Diversity of Alphacoronaviruses in the Americas. Microbiol Spectr 2022; 10:e0314322. [PMID: 36222689 PMCID: PMC9769993 DOI: 10.1128/spectrum.03143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/20/2022] [Indexed: 01/10/2023] Open
Abstract
Bats are reservoirs of diverse coronaviruses (CoVs), including progenitors of severe acute respiratory syndrome CoV (SARS-CoV) and SARS-CoV-2. In the Americas, there is a contrast between alphacoronaviruses (alphaCoVs) and betaCoVs: while cospeciation prevails in the latter, alphaCoV evolution is dominated by deep and recent host switches. AlphaCoV lineages are maintained by two different bat family groups, Phyllostomidae and Vespertilionidae plus Molossidae. In this study, we used a Bayesian framework to analyze the process of diversification of the lineages maintained by Molossidae and Vespertilionidae, adding novel CoV sequences from Argentina. We provide evidence that the observed CoV diversity in these two bat families is shaped by their geographic distribution and that CoVs exhibit clustering at the level of bat genera. We discuss the causes of the cocirculation of two independent clades in Molossus and Tadarida as well as the role of Myotis as the ancestral host and a major evolutionary reservoir of alphaCoVs across the continent. Although more CoV sampling efforts are needed, these findings contribute to a better knowledge of the diversity of alphaCoVs and the links between bat host species. IMPORTANCE Bats harbor the largest diversity of coronaviruses among mammals. In the Americas, seven alphacoronavirus lineages circulate among bats. Three of these lineages are shared by members of two bat families: Vespertilionidae and Molossidae. Uncovering the relationships between these coronaviruses can help us to understand patterns of cross-species transmission and, ultimately, which hosts are more likely to be involved in spillover events. We found that two different lineages cocirculate among the bat genera Molossus and Tadarida, which share roosts and have common viral variants. The bat genus Myotis functions as a reservoir of coronavirus diversity and, as such, is a key host. Although there were some spillovers recorded, there is a strong host association, showing that once a successful host jump takes place, it is transmitted onward to members of the same bat genus.
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Affiliation(s)
- Diego A. Caraballo
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Ciudad Universitaria-Pabellón II, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - María S. Sabio
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria C. Colombo
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - María Guadalupe Piccirilli
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lorena Vico
- Departamento de Zoonosis Urbanas, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Stella Maris Hirmas Riade
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad de Genómica y Bioinformática, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gustavo Martínez
- Departamento de Zoonosis Urbanas, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Fernando Beltrán
- Instituto de Zoonosis Dr. Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Elsa Baumeister
- Servicio de Virosis Respiratorias, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
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Sikkema RS, Begeman L, Janssen R, Wolters WJ, Geurtsvankessel C, de Bruin E, Hakze‐van der Honing RW, Eblé P, van der Poel WHM, van den Brand JMA, Slaterus R, La Haye M, Koopmans MP, Velkers F, Kuiken T. Risks of SARS-CoV-2 transmission between free-ranging animals and captive mink in the Netherlands. Transbound Emerg Dis 2022; 69:3339-3349. [PMID: 35988158 PMCID: PMC9538022 DOI: 10.1111/tbed.14686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
In the Netherlands, 69 of the 126 (55%) mink farms in total became infected with SARS-CoV-2 in 2020. Despite strict biosecurity measures and extensive epidemiological investigations, the main transmission route remained unclear. A better understanding of SARS-CoV-2 transmission between mink farms is of relevance for countries where mink farming is still common practice and can be used as a case study to improve future emerging disease preparedness. We assessed whether SARS-CoV-2 spilled over from mink to free-ranging animals, and whether free-ranging animals may have played a role in farm-to-farm transmission in the Netherlands. The study encompassed farm visits, farm questionnaires, expert workshops and SARS-CoV-2 RNA and antibody testing of samples from target animal species (bats, birds and free-ranging carnivores). In this study, we show that the open housing system of mink allowed access to birds, bats and most free-ranging carnivores, and that direct and indirect contact with mink was likely after entry, especially for free-ranging carnivores and birds. This allowed SARS-CoV-2 exposure to animals entering the mink farm, and subsequent infection or mechanical carriage by the target animal species. Moreover, mink can escape farms in some cases, and two SARS-CoV-2-positive mink were found outside farm premises. No other SARS-CoV-2-RNA-positive free-ranging animals were detected, suggesting there was no abundant circulation in the species tested during the study period. To investigate previous SARS-CoV-2 infections, SARS-CoV-2 antibody detection using lung extracts of carcasses was set up and validated. One tested beech marten did have SARS-CoV-2 antibodies, but the closest SARS-CoV-2-infected mink farm was outside of its home range, making infection at a mink farm unlikely. Knowing that virus exchange between different species and the formation of animal reservoirs affects SARS-CoV-2 evolution, continued vigilance and monitoring of mink farms and surrounding wildlife remains vital.
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Affiliation(s)
| | | | | | - Wendy J. Wolters
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | | | - Erwin de Bruin
- Viroscience, ErasmusMCRotterdamThe Netherlands,Division of Pathology, Department of Biomedical Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | | | - Phaedra Eblé
- Wageningen Bioveterinary ResearchLelystadThe Netherlands
| | | | - Judith M. A. van den Brand
- Division of Pathology, Department of Biomedical Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands,Dutch Wildlife Health CentreUtrecht UniversityThe Netherlands
| | - Roy Slaterus
- Sovon, Dutch Centre for Field OrnithologyNijmegenThe Netherlands
| | | | | | - Francisca Velkers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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10
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Caraballo DA. Cross-Species Transmission of Bat Coronaviruses in the Americas: Contrasting Patterns between Alphacoronavirus and Betacoronavirus. Microbiol Spectr 2022; 10:e0141122. [PMID: 35770987 PMCID: PMC9431099 DOI: 10.1128/spectrum.01411-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 01/09/2023] Open
Abstract
Bats harbor the largest number of coronavirus (CoV) species among mammals, serving as major reservoirs of alphaCoVs and betaCoVs, which can jump between bat species or to different mammalian hosts, including humans. Bat-CoV diversity is correlated with host taxonomic diversity, with the highest number of CoV species found in areas with the highest levels of bat species richness. Although the Americas harbor a unique and distinctive CoV diversity, no cross-species transmission (CST) or phylogeographic analysis has yet been performed. This study analyzes a large sequence data set from across the Americas through a Bayesian framework to understand how codivergence and cross-species transmission have shaped long-term bat-CoV evolution and ultimately identify bat hosts and regions where the risk of CST is the highest. Substantial levels of CST were found only among alphaCoVs. In contrast, cospeciation prevailed along the evolution of betaCoVs. Brazil is the center of diversification for both alpha and betaCoVs, with the highest levels of bat species richness. The bat family Phyllostomidae has played a key role in the evolution of American bat-CoVs, supported by the highest values of host transition rates. Although the conclusions drawn from this study are supported by biological/ecological evidence, it is likely that novel lineages will be discovered, which could also reveal undetected CSTs given that sequences are available from 11 of the 35 countries encompassing the Americas. The findings of this study can be useful for conducting targeted discovery of bat-CoVs in the region, especially in countries of the Americas with no reported sequences. IMPORTANCE Coronaviruses (CoVs) have a strong zoonotic potential due to their high rates of evolvability and their capacity for overcoming host-specific barriers. Bats harbor the largest number of CoV species among mammals, with the highest CoV diversity found in areas with the highest levels of bat species richness. Understanding their origin and patterns of cross-species transmission is crucial for pandemic preparedness. This study aims to understand how bat-CoVs diversify in the Americas, circulate among and transmit between bat families and genera, and ultimately identify bat hosts and regions where the risk of CoV spillover is the highest.
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Affiliation(s)
- Diego A. Caraballo
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Ciudad Universitaria-Pabellón II, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
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11
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Bueno LM, Rizotto LS, Viana ADO, Silva LMN, de Moraes MVDS, Benassi JC, Scagion GP, Dorlass EG, Lopes BLT, Cunha IN, Melinski R, de Alvarenga IF, Leitão GL, Rodrigues RC, Pereira IMDS, Santos LDND, Fisch F, Rocha AD, Port D, Pereira GS, Greatti A, Barnabé ACDS, Tsukamoto J, Hingst-Zaher E, Junior SMDA, Junior WRT, Branco JO, Ometto T, de Araujo J, Arns CW, Ferreira HL, Durigon EEL. High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil. Transbound Emerg Dis 2022; 69:e2863-e2875. [PMID: 35729863 DOI: 10.1111/tbed.14636] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022]
Abstract
Bat coronaviruses (Bat-CoV) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversities, with 181 species of bats described so far. However, few Bat-CoV surveillance programs were carried out in the country. Thus, our aim was to evaluate the Bat-CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analyzed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.64%) targeting the RdRp gene from seven different bat species, three of them that have never been described as Bat-CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat-CoV previously detected in identical or congeneric bat species, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped with the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat-CoV hosts and the co-circulation of four Alphacoronavirus subgenera in Brazil. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Larissa Mayumi Bueno
- Department of Veterinary Medicine, FZEA- USP, University of Sao Paulo, 225 Av Duque de Caxias Norte, Pirassununga, SP, Brazil
| | - Laís Santos Rizotto
- Graduate Program in Experimental Epidemiology Applied to Zoonoses, FMVZ-USP, University of São Paulo, 87 Prof. Orlando Marques de Paiva Avenue, São Paulo, SP, Brazil
| | - Amanda de Oliveira Viana
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
| | - Laura Morais Nascimento Silva
- Graduate Program in Experimental Epidemiology Applied to Zoonoses, FMVZ-USP, University of São Paulo, 87 Prof. Orlando Marques de Paiva Avenue, São Paulo, SP, Brazil
| | - Maria Vitória Dos Santos de Moraes
- Graduate Program in Experimental Epidemiology Applied to Zoonoses, FMVZ-USP, University of São Paulo, 87 Prof. Orlando Marques de Paiva Avenue, São Paulo, SP, Brazil
| | - Julia Cristina Benassi
- Department of Veterinary Medicine, FZEA- USP, University of Sao Paulo, 225 Av Duque de Caxias Norte, Pirassununga, SP, Brazil
| | - Guilherme Pereira Scagion
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
| | - Erick Gustavo Dorlass
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
| | | | - Irineu Noberto Cunha
- Biological Museum, Instituto Butantan, 1500 Vital Brasil Avenue, São Paulo, SP, Brazil
| | - Ramiro Melinski
- Biological Museum, Instituto Butantan, 1500 Vital Brasil Avenue, São Paulo, SP, Brazil
| | | | - Gabriel Lins Leitão
- Biological Museum, Instituto Butantan, 1500 Vital Brasil Avenue, São Paulo, SP, Brazil
| | - Roberta Costa Rodrigues
- Biology Departament, Federal Rural University of Pernambuco, Dom Manuel de Medeiros Street, Recife, PE, Brazil
| | | | | | - Fabiane Fisch
- School of Sea, Science and Technology, University of Vale do Itajaí, 458 Uruguai Street, Itajaí, SC, Brazil
| | - Alana Drielle Rocha
- School of Sea, Science and Technology, University of Vale do Itajaí, 458 Uruguai Street, Itajaí, SC, Brazil
| | - Dagoberto Port
- Brusque Educational Foundation, 123 Dorval Luz Street, Brusque, SC, Brazil
| | - Gabriela Stahelin Pereira
- School of Sea, Science and Technology, University of Vale do Itajaí, 458 Uruguai Street, Itajaí, SC, Brazil
| | - Alessandra Greatti
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Ana Caroline de Souza Barnabé
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Junko Tsukamoto
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Erika Hingst-Zaher
- Biological Museum, Instituto Butantan, 1500 Vital Brasil Avenue, São Paulo, SP, Brazil
| | | | | | - Joaquim Olinto Branco
- School of Sea, Science and Technology, University of Vale do Itajaí, 458 Uruguai Street, Itajaí, SC, Brazil
| | - Tatiana Ometto
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
| | - Jansen de Araujo
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
| | - Clarice Weis Arns
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Helena Lage Ferreira
- Department of Veterinary Medicine, FZEA- USP, University of Sao Paulo, 225 Av Duque de Caxias Norte, Pirassununga, SP, Brazil.,Graduate Program in Experimental Epidemiology Applied to Zoonoses, FMVZ-USP, University of São Paulo, 87 Prof. Orlando Marques de Paiva Avenue, São Paulo, SP, Brazil
| | - E Edison Luiz Durigon
- Institute of Biomedical Science, University of São Paulo, 1374 Prof. Lineu Prestes Avenue, São Paulo, SP, Brazil
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12
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Schaeffer R, Temeeyasen G, Hause BM. Alphacoronaviruses Are Common in Bats in the Upper Midwestern United States. Viruses 2022; 14:v14020184. [PMID: 35215778 PMCID: PMC8877427 DOI: 10.3390/v14020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Bats are a reservoir for coronaviruses (CoVs) that periodically spill over to humans, as evidenced by severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. A collection of 174 bat samples originating from South Dakota, Minnesota, Iowa, and Nebraska submitted for rabies virus testing due to human exposure were analyzed using a pan-coronavirus PCR. A previously partially characterized CoV, Eptesicus bat CoV, was identified in 12 (6.9%) samples by nested RT-PCR. Six near-complete genomes were determined. Genetic analysis found a high similarity between all CoV-positive samples, Rocky Mountain bat CoV 65 and alphacoronavirus HCQD-2020 recently identified in South Korea. Phylogenetic analysis of genome sequences showed EbCoV is closely related to bat CoV HKU2 and swine acute diarrhea syndrome CoV; however, topological incongruences were noted for the spike gene that was more closely related to porcine epidemic diarrhea virus. Similar to some alphaCoVs, a novel gene, ORF7, was discovered downstream of the nucleocapsid, whose protein lacked similarity to known proteins. The widespread circulation of EbCoV with similarities to bat viruses that have spilled over to swine warrants further surveillance.
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