1
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Buigues J, Viñals A, Martínez-Recio R, Monrós JS, Sanjuán R, Cuevas JM. Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces. Microbiol Spectr 2024; 12:e0067524. [PMID: 38990026 PMCID: PMC11323972 DOI: 10.1128/spectrum.00675-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 52 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 30 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential. IMPORTANCE Metagenomics has become a fundamental tool to characterize the global virosphere, allowing us not only to understand the existing viral diversity and its ecological implications but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we analyzed the DNA fraction of fecal samples from 22 Spanish bat species, identifying 52 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyze. Our work, however, has characterized a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant since this phenomenon could play a major role in cross-species transmission.
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Affiliation(s)
- Jaime Buigues
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Adrià Viñals
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Raquel Martínez-Recio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
| | - Juan S. Monrós
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València and Consejo Superior de Investigaciones Científicas, València, Spain
- Department of Genetics, Universitat de València, València, Spain
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2
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Couto RDS, Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats. Microorganisms 2024; 12:206. [PMID: 38276191 PMCID: PMC10819564 DOI: 10.3390/microorganisms12010206] [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: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences and Technology (SoHST), UPES, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
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3
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Li F, Ghiabi P, Hajian T, Klima M, Li ASM, Khalili Yazdi A, Chau I, Loppnau P, Kutera M, Seitova A, Bolotokova A, Hutchinson A, Perveen S, Boura E, Vedadi M. SS148 and WZ16 inhibit the activities of nsp10-nsp16 complexes from all seven human pathogenic coronaviruses. Biochim Biophys Acta Gen Subj 2023; 1867:130319. [PMID: 36764586 PMCID: PMC9908617 DOI: 10.1016/j.bbagen.2023.130319] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Seven coronaviruses have infected humans (HCoVs) to-date. SARS-CoV-2 caused the current COVID-19 pandemic with the well-known high mortality and severe socioeconomic consequences. MERS-CoV and SARS-CoV caused epidemic of MERS and SARS, respectively, with severe respiratory symptoms and significant fatality. However, HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43 cause respiratory illnesses with less severe symptoms in most cases. All coronaviruses use RNA capping to evade the immune systems of humans. Two viral methyltransferases, nsp14 and nsp16, play key roles in RNA capping and are considered valuable targets for development of anti-coronavirus therapeutics. But little is known about the kinetics of nsp10-nsp16 methyltransferase activities of most HCoVs, and reliable assays for screening are not available. Here, we report the expression, purification, and kinetic characterization of nsp10-nsp16 complexes from six HCoVs in parallel with previously characterized SARS-CoV-2. Probing the active sites of all seven by SS148 and WZ16, the two recently reported dual nsp14 / nsp10-nsp16 inhibitors, revealed pan-inhibition. Overall, our study show feasibility of developing broad-spectrum dual nsp14 / nsp10-nsp16-inhibitor therapeutics.
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Affiliation(s)
- Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Alice Shi Ming Li
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Almagul Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
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4
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Wallau GL, Barbier E, Tomazatos A, Schmidt-Chanasit J, Bernard E. The Virome of Bats Inhabiting Brazilian Biomes: Knowledge Gaps and Biases towards Zoonotic Viruses. Microbiol Spectr 2023; 11:e0407722. [PMID: 36625641 PMCID: PMC9927472 DOI: 10.1128/spectrum.04077-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Bats host a large variety of viruses, including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatiotemporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future. IMPORTANCE Bat-borne viruses have attracted much attention due to zoonotic outbreaks with large consequences to humans. Because of that, virus characterization in bats has been prioritized in tropical regions of the globe. However, bat-virus research in Latin America and particularly in Brazil, which are among the most bat species-rich regions of the world, are highly biased toward zoonotic viruses and known bat reservoir species. These results have direct implication for virus studies in general but also for new zoonotic virus and spillover events characterization. The limited knowledge we currently have about the virome of Brazilian bats drastically limits any broad assessment of zoonotic viruses they carry and calls for coordinated and large-scale studies to fill this crucial knowledge gap.
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Affiliation(s)
- Gabriel Luz Wallau
- Departamento de Entomologia and Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM) - Fundação Oswaldo Cruz (Fiocruz), Cidade Universitária, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Eder Barbier
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
| | - Alexandru Tomazatos
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
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5
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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6
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SURVEILLANCE OF BATS IN THE UNITED STATES FOR SARS-COV-2 AND OTHER CORONAVIRUSES. J Zoo Wildl Med 2023; 53:811-816. [PMID: 36640084 DOI: 10.1638/2022-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Bat coronaviruses (CoVs) are extremely prevalent throughout the globe and exhibit a wide range of genetic diversity. Currently, little is known about the susceptibility of New World bats to severe acute respiratory syndrome-2 (SARS-CoV-2), the causative agent of COVID-19. Also, there is limited information about the genetic diversity of other CoVs in the New World bats. The determination of genetic diversity of bat CoVs through continuous surveillance is essential to predict and mitigate the emergence of new CoVs and their impacts on the health of both humans and animals. In this study, 491 guano specimens collected from New World bats and 37 specimens collected from Old World bats during July 2020 to July 2021 were tested for SARS-COV-2 and other CoVs using a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) panel and pan-coronavirus PCR that target a highly conserved region of CoVs. No evidence of SARS-CoV-2 was found in the tested specimens. An alpha CoV was detected in a single specimen from a big brown bat (Eptesicus fuscus). This information was used by wildlife agencies and rehabilitation facilities to permit the release of bats during the pandemic while mitigating the risk of spreading SARS-CoV-2 among North American bats and other wild animal populations.
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7
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Opportunities and Limitations of Molecular Methods for Studying Bat-Associated Pathogens. Microorganisms 2022; 10:microorganisms10091875. [PMID: 36144476 PMCID: PMC9502413 DOI: 10.3390/microorganisms10091875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 01/03/2023] Open
Abstract
Bats have been identified as reservoirs of zoonotic and potentially zoonotic pathogens. Significant progress was made in the field of molecular biology with regard to infectious diseases, especially those that infect more than one species. Molecular methods, sequencing and bioinformatics have recently become irreplaceable tools in emerging infectious diseases research and even outbreak prediction. Modern methods in the molecular biology field have shed more light on the unique relationship between bats and viruses. Here we provide readers with a concise summary of the potential and limitations of molecular methods for studying the ecology of bats and bat-related pathogens and microorganisms.
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8
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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Barrón-Rodríguez RJ, Parra-Laca R, Rojas-Anaya E, Romero-Espinoza JÁI, Ayala-Sumuano JT, Vázquez-Pérez JA, García-Espinosa G, Loza-Rubio E. Evidence of Viral Communities in Three Species of Bats from Rural Environment in Mexico. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rodrigo J. Barrón-Rodríguez
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Rocío Parra-Laca
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Edith Rojas-Anaya
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - José Á. I. Romero-Espinoza
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Jorge T. Ayala-Sumuano
- Idix S.A. de C.V., Sonterra 3035 Interior 26, Fraccionamiento Sonterra, Santiago de Querétaro, Querétaro México, C.P. 76230, México
| | - Joel A. Vázquez-Pérez
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Gary García-Espinosa
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
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10
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Lan J, Chen P, Liu W, Ren W, Zhang L, Ding Q, Zhang Q, Wang X, Ge J. Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2. Structure 2022; 30:1432-1442.e4. [PMID: 35917815 PMCID: PMC9341007 DOI: 10.1016/j.str.2022.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and human coronavirus (hCoV)-NL63 utilize ACE2 as the functional receptor for cell entry, which leads to zoonotic infection. Horses (Equus caballus) attracted our attention because the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 and SARS-CoV-2-related coronaviruses bind equine ACE2 (eACE2) with high affinity. Here we show that eACE2 binds the RBDs of these three coronaviruses and also SARS-CoV-2 variants but with lower affinities compared with human ACE2 (hACE2). Structural analysis and mutation assays indicated that eACE2-H41 accounts for the lower binding affinity of eACE2 to the RBDs of SARS-CoV-2 variants (Alpha, Beta, and Gamma), SARS-CoV, and hCoV-NL63. Pseudovirus infection assays showed that the SARS-CoV-2 Delta strain (B.1.617.2) displayed a significantly increased infection efficiency in eACE2-expressing HeLa cells. Our results reveal the molecular basis of eACE2 binding to the RBDs of SARS-CoV, SARS-CoV-2, and hCoV-NL63, which provides insights into the potential animal transmission of these ACE2-dependent coronaviruses.
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Affiliation(s)
- Jun Lan
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weiming Liu
- Department of Critical Care Medicine, Beijing Boai Hospital, China Rehabilitation Research Centre, No. 10 Jiaomen Beilu, Fengtai District, Beijing 100068, China
| | - Wenlin Ren
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Qiang Ding
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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11
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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12
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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13
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Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating pandemic. Although most people infected with SARS-CoV-2 develop a mild to moderate disease with virus replication restricted mainly to the upper airways, some progress to having a life-threatening pneumonia. In this Review, we explore recent clinical and experimental advances regarding SARS-CoV-2 pathophysiology and discuss potential mechanisms behind SARS-CoV-2-associated acute respiratory distress syndrome (ARDS), specifically focusing on new insights obtained using novel technologies such as single-cell omics, organoid infection models and CRISPR screens. We describe how SARS-CoV-2 may infect the lower respiratory tract and cause alveolar damage as a result of dysfunctional immune responses. We discuss how this may lead to the induction of a 'leaky state' of both the epithelium and the endothelium, promoting inflammation and coagulation, while an influx of immune cells leads to overexuberant inflammatory responses and immunopathology. Finally, we highlight how these findings may aid the development of new therapeutic interventions against COVID-19.
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14
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Chourasia R, Padhi S, Phukon LC, Abedin MM, Sirohi R, Singh SP, Rai AK. Peptide candidates for the development of therapeutics and vaccines against β-coronavirus infection. Bioengineered 2022; 13:9435-9454. [PMID: 35387556 PMCID: PMC9161909 DOI: 10.1080/21655979.2022.2060453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/18/2023] Open
Abstract
Betacoronaviruses (β-CoVs) have caused major viral outbreaks in the last two decades in the world. The mutation and recombination abilities in β-CoVs resulted in zoonotic diseases in humans. Proteins responsible for viral attachment and replication are highly conserved in β-CoVs. These conserved proteins have been extensively studied as targets for preventing infection and the spread of β-CoVs. Peptides are among the most promising candidates for developing vaccines and therapeutics against viral pathogens. The immunostimulatory and viral inhibitory potential of natural and synthetic peptides has been extensively studied since the SARS-CoV outbreak. Food-derived peptides demonstrating high antiviral activity can be used to develop effective therapeutics against β-CoVs. Specificity, tolerability, and customizability of peptides can be explored to develop potent drugs against β-CoVs. However, the proteolytic susceptibility and low bioavailability of peptides pose challenges for the development of therapeutics. This review illustrates the potential role of peptides in eliciting an adaptive immune response and inhibiting different stages of the β-CoV life cycle. Further, the challenges and future directions associated with developing peptide-based therapeutics and vaccines against existing and future β-CoV pathogens have been discussed.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Ranjana Sirohi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, 02841, Republic of Korea
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81, S.A.S. Nagar, Mohali- 140306, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Mizoram Node, Aizawl, India
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15
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Zhao T, Dang YQ, Wang AN, Gao HT, Zhang HD, Xing D, Li BQ, Li YJ, Liu Z, Li CX. Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China. Front Microbiol 2022; 12:701089. [PMID: 35265046 PMCID: PMC8899188 DOI: 10.3389/fmicb.2021.701089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Objective Wild animal pathogen surveillance will help to understand the next possible pandemic in advance. Rodents, which have close contact with humans, are generally regarded as a key factor for zoonotic disease control. Given the variation in rodent virus composition in diverse ecologies, we conducted a study on the viral infection of rodents of diverse species in different typical environments of Heilongjiang and Yunnan Provinces, located in northeastern and southwestern China, respectively. Methods Viral metagenomics sequencing and bioinformatic analysis were performed to determine the different distributions of rodent-borne viruses in typical environments of Heilongjiang and Yunnan Provinces, China. After viral culture and PCR confirmation, genomic and phylogenetic quantitative analysis was performed on the detected hantaviruses (HVs) and Beilong viruses (BeiVs). Results Nineteen rodents from three species and 35 rodents from five species of rodents were collected from Heilongjiang and Yunnan Provinces, respectively. Although the number and number of species of rodents trapped in the northeast were fewer than those in the southwest, viruses annotated from rodents in Heilongjiang were more diverse than those in Yunnan. Rodents carried 22 virus families in Heilongjiang and 13 families in Yunnan. Sequences assembled from Rattus norvegicus were annotated to the M, L, and S segments of HV, and all were clustered within the Seoul-type hantavirus (SEOV). There were 2 (R81Q, S698T) and 4 (K153R, M168I, I279S, and R1790K) amino acid site substitutions in M and L compared with the versions in the most homologous strains. Two BeiV isolates from Rattus norvegicus were closely related to BeiV from brown rats in Hong Kong, with high bootstrap values of >90% in the N segment and > 95% in the L segment. They were further clustered with Tailam virus, forming a distinct group in Paramyxoviridae. Conclusion The rodents from Heilongjiang and Yunnan located in northeast and southwest China, respectively, had different viral spectra, and only one-third (10/32) of virus families were detected in both areas. The predominant viruses were HV and BeiV in the Hantaviridae and Paramyxoviridae families, respectively. Rodent-borne viruses in the same species were similar in different geographic disparate areas owing to their similar close contact with human habitats and human activities. Additional attention should be given to the monitoring of neglected rodent-borne viruses, especially opportunistic viruses with currently low loads.
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Affiliation(s)
- Teng Zhao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Yun-Qi Dang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.,College of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, China
| | - Ao-Nan Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.,College of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, China
| | - He-Ting Gao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Heng-Duan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo-Qi Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.,College of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, China
| | | | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, China
| | - Chun-Xiao Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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16
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Common SM, Shadbolt T, Walsh K, Sainsbury AW. The risk from SARS-CoV-2 to bat species in england and mitigation options for conservation field workers. Transbound Emerg Dis 2022; 69:694-705. [PMID: 33570837 PMCID: PMC8014681 DOI: 10.1111/tbed.14035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
The newly evolved coronavirus, SARS-CoV-2, which has precipitated a global COVID-19 pandemic among the human population, has been shown to be associated with disease in captive wild animals. Bats (Chiroptera) have been shown to be susceptible to experimental infection and therefore may be at risk from disease when in contact with infected people. Numerous conservation fieldwork activities are undertaken across the United Kingdom bringing potentially infected people into close proximity with bats. In this study, we analysed the risks of disease from SARS-CoV-2 to free-living bat species in England through fieldworkers undertaking conservation activities and ecological survey work, using a qualitative, transparent method devised for assessing threats of disease to free-living wild animals. The probability of exposure of bats to SARS-CoV-2 through fieldwork activities was estimated to range from negligible to high, depending on the proximity between bats and people during the activity. The likelihood of infection after exposure was estimated to be high and the probability of dissemination of the virus through bat populations medium. The likelihood of clinical disease occurring in infected bats was low, and therefore, the ecological, economic and environmental consequences were predicted to be low. The overall risk estimation was low, and therefore, mitigation measures are advisable. There is uncertainty in the pathogenicity of SARS-CoV-2 in bats and therefore in the risk estimation. Disease risk management measures are suggested, including the use of personal protective equipment, good hand hygiene and following the existing government advice. The disease risk analysis should be updated as information on the epidemiology of SARS-CoV-2 and related viruses in bats improves. The re-analysis may be informed by health surveillance of free-living bats.
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Affiliation(s)
| | - Tammy Shadbolt
- Institute of ZoologyZoological Society of LondonLondonUK
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17
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Hussein M, Andrade dos Ramos Z, Berkhout B, Herrera-Carrillo E. In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack. Viruses 2022; 14:v14020385. [PMID: 35215977 PMCID: PMC8880226 DOI: 10.3390/v14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
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Affiliation(s)
| | | | - Ben Berkhout
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
| | - Elena Herrera-Carrillo
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
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18
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Shehata AA, Attia YA, Rahman MT, Basiouni S, El-Seedi HR, Azhar EI, Khafaga AF, Hafez HM. Diversity of Coronaviruses with Particular Attention to the Interspecies Transmission of SARS-CoV-2. Animals (Basel) 2022; 12:ani12030378. [PMID: 35158701 PMCID: PMC8833600 DOI: 10.3390/ani12030378] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Coronaviruses are a broad group of viruses that may infect a wide range of animals, including humans. Despite the fact that each coronavirus has a limited host range, frequent interspecies transmission of coronaviruses across diverse hosts has resulted in a complex ecology. The recently discovered SARS-CoV-2 virus is the clearest evidence of the danger of a global pandemic spreading. Natural infection with SARS-CoV-2 has been reported in a variety of domestic and wild animals, which may complicate the virus’s epidemiology and influence its development. In this review, we discussed the potential determinants of SARS-CoV-2 interspecies transmission. Additionally, despite the efforts that have been made to control this pandemic and to implement the One Health policy, several problems, such as the role of animals in SARS-CoV-2 evolution and the dynamics of interspecies transmission, are still unanswered. Abstract In December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China with serious impacts on global health and economy that is still ongoing. Although interspecies transmission of coronaviruses is common and well documented, each coronavirus has a narrowly restricted host range. Coronaviruses utilize different receptors to mediate membrane fusion and replication in the cell cytoplasm. The interplay between the receptor-binding domain (RBD) of coronaviruses and their coevolution are determinants for host susceptibility. The recently emerged SARS-CoV-2 caused the coronavirus disease 2019 (COVID-19) pandemic and has also been reported in domestic and wild animals, raising the question about the responsibility of animals in virus evolution. Additionally, the COVID-19 pandemic might also substantially have an impact on animal production for a long time. In the present review, we discussed the diversity of coronaviruses in animals and thus the diversity of their receptors. Moreover, the determinants of the susceptibility of SARS-CoV-2 in several animals, with special reference to the current evidence of SARS-CoV-2 in animals, were highlighted. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to mitigate the threat for both humans and animals.
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Affiliation(s)
- Awad A. Shehata
- Birds and Rabbit Medicine Department, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt;
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
| | - Youssef A. Attia
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah 21589, Saudi Arabia;
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha 13736, Egypt;
| | - Hesham R. El-Seedi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Esam I. Azhar
- Special Infectious Agents Unit—BSL3, King Fahd Medical Research Center and Department of Medical Laboratory Science, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia;
| | - Asmaa F. Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt;
| | - Hafez M. Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany
- Correspondence:
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19
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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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20
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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21
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Gupta P, Singh MP, Goyal K, Tripti P, Ansari MI, Obli Rajendran V, Dhama K, Malik YS. Bats and viruses: a death-defying friendship. Virusdisease 2021; 32:467-479. [PMID: 34518804 PMCID: PMC8426161 DOI: 10.1007/s13337-021-00716-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 01/10/2023] Open
Abstract
Bats have a primeval evolutionary origin and have adopted various survival methods. They have played a central role in the emergence of various viral diseases. The sustenance of a plethora of virus species inside them has been an earnest area of study. This review explains how the evolution of viruses in bats has been linked to their metabolic pathways, flight abilities, reproductive abilities and colonization behaviors. The utilization of host immune response by DNA and RNA viruses is a commencement of the understanding of differences in the impact of viral infection in bats from other mammals. Rabies virus and other lyssa viruses have had long documented history as bat viruses. While many others like Ebola virus, Nipah virus, Hantavirus, SARS-CoV, MERS-CoV and other new emerging viruses like Sosuga virus, Menangle and Tioman virus are now being studied extensively for their transmission in new hosts. The ongoing pandemic SARS-CoV-2 virus has also been implicated to be originated from bats. Certain factors have been linked to spillover events while the scope of entitlement of other conditions in the spread of diseases from bats still exists. However, certain physiological and ecological parameters have been linked to specific transmission patterns, and more definite proofs are awaited for establishing these connections.
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Affiliation(s)
- Parakriti Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mini P. Singh
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pande Tripti
- Biological Standardization Division, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Dasauli, Kursi Road, Lucknow, Uttar Pradesh 226026 India
| | - Vinodhkumar Obli Rajendran
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab 141 004 India
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22
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Kayode AJ, Banji-Onisile FO, Olaniran AO, Okoh AI. An Overview of the Pathogenesis, Transmission, Diagnosis, and Management of Endemic Human Coronaviruses: A Reflection on the Past and Present Episodes and Possible Future Outbreaks. Pathogens 2021; 10:1108. [PMID: 34578140 PMCID: PMC8470645 DOI: 10.3390/pathogens10091108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the 2019 coronavirus pandemic caught the world by surprise in late 2019 and has held it hostage for months with an increasing number of infections and deaths. Although coronavirus was first discovered in the 1960s and was known to cause respiratory infection in humans, no information was available about the epidemic pattern of the virus until the past two decades. This review addresses the pathogenesis, transmission dynamics, diagnosis, management strategies, the pattern of the past and present events, and the possibility of future outbreaks of the endemic human coronaviruses. Several studies have described bats as presumptive natural reservoirs of coronaviruses. In essence, the identification of a diverse group of similar SARS coronaviruses in bats suggests the possibility of a future epidemic due to severe acute respiratory syndrome (SARS-like) coronaviruses originating from different reservoir hosts. The study also identified a lack of vaccines to prevent human coronavirus infections in humans in the past, however, the recent breakthrough in vaccine discovery and approval for emergency use for the treatment of Severe Acute Respiratory Syndrome Coronavirus 2 is commendable. The high rates of genomic substitution and recombination due to errors in RNA replication and the potential for independent species crossing suggest the chances of an entirely new strain evolving. Therefore, rapid research efforts should be deployed for vaccination to combat the COVID-19 pandemic and prevent a possible future outbreak. More sensitization and enlightenment on the need to adopt good personal hygiene practices, social distancing, and scientific evaluation of existing medications with promising antiviral effects against SARS-CoV-2 is required. In addition, intensive investigations to unravel and validate the possible reservoirs, the intermediate host, as well as insight into the ability of the virus to break the species barrier are needed to prevent future viral spillover and possible outbreaks.
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Affiliation(s)
- Adeoye J. Kayode
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
| | - Folasade O. Banji-Onisile
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Ademola O. Olaniran
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Department of Environmental Health Sciences, College Health Sciences, University of Sharjah, Sharjah 555588, United Arab Emirates
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Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol 2021; 12:682603. [PMID: 34335504 PMCID: PMC8317507 DOI: 10.3389/fmicb.2021.682603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.
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Affiliation(s)
- Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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24
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Hernández-Aguilar I, Lorenzo C, Santos-Moreno A, Naranjo EJ, Navarrete-Gutiérrez D. Coronaviruses in Bats: A Review for the Americas. Viruses 2021; 13:1226. [PMID: 34201926 PMCID: PMC8310043 DOI: 10.3390/v13071226] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022] Open
Abstract
The SARS-CoV-2 coronavirus is the focus of attention as it has caused more than three million human deaths globally. This and other coronaviruses, such as MERS-CoV, have been suggested to be related to coronaviruses that are hosted in bats. This work shows, through a bibliographic review, the frequency of detection of coronavirus in bats species of the Americas. The presence of coronavirus in bats has been examined in 25 investigations in 11 countries of the Americas between 2007 and 2020. Coronaviruses have been explored in 9371 individuals from 160 species of bats, and 187 coronavirus sequences have been deposited in GenBank distributed in 43 species of bats. While 91% of the coronaviruses sequences identified infect a single species of bat, the remainder show a change of host, dominating the intragenera change. So far, only Mex-CoV-6 is related to MERS-CoV, a coronavirus pathogenic for humans, so further coronavirus research effort in yet unexplored bat species is warranted.
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Affiliation(s)
- Itandehui Hernández-Aguilar
- El Colegio de la Frontera Sur, Unidad San Cristóbal, San Cristóbal de Las Casas 29290, Chiapas, Mexico; (C.L.); (E.J.N.); (D.N.-G.)
| | - Consuelo Lorenzo
- El Colegio de la Frontera Sur, Unidad San Cristóbal, San Cristóbal de Las Casas 29290, Chiapas, Mexico; (C.L.); (E.J.N.); (D.N.-G.)
| | - Antonio Santos-Moreno
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Oaxaca, Instituto Politécnico Nacional, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico;
| | - Eduardo J. Naranjo
- El Colegio de la Frontera Sur, Unidad San Cristóbal, San Cristóbal de Las Casas 29290, Chiapas, Mexico; (C.L.); (E.J.N.); (D.N.-G.)
| | - Darío Navarrete-Gutiérrez
- El Colegio de la Frontera Sur, Unidad San Cristóbal, San Cristóbal de Las Casas 29290, Chiapas, Mexico; (C.L.); (E.J.N.); (D.N.-G.)
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25
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Hardmeier I, Aeberhard N, Qi W, Schoenbaechler K, Kraettli H, Hatt JM, Fraefel C, Kubacki J. Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses. PLoS One 2021; 16:e0252534. [PMID: 34133435 PMCID: PMC8208571 DOI: 10.1371/journal.pone.0252534] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.
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Affiliation(s)
| | - Nadja Aeberhard
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | | | | | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, University of Zurich, Zurich, Switzerland
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26
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Lazov CM, Belsham GJ, Bøtner A, Rasmussen TB. Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark. Viruses 2021; 13:1073. [PMID: 34199948 PMCID: PMC8229204 DOI: 10.3390/v13061073] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.
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Affiliation(s)
- Christina M. Lazov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark
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27
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Ramos-Nino ME, Fitzpatrick DM, Eckstrom KM, Tighe S, Dragon JA, Cheetham S. The Kidney-Associated Microbiome of Wild-Caught Artibeus spp. in Grenada, West Indies. Animals (Basel) 2021; 11:ani11061571. [PMID: 34072244 PMCID: PMC8227013 DOI: 10.3390/ani11061571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Bats are increasingly being recognized as important integrants of zoonotic disease cycles. Studying bat microbiomes could potentially contribute to the epidemiology of emerging infectious diseases in humans. Furthermore, studying the bat’s microbiome gives us the opportunity to look at the microbiome evolution in mammals. Bat microbiome studies have focused mainly on the gut microbiome, but little is known of the microbiome of the kidney, another potential source of disease transmission. Furthermore, many studies on microbiome found in the literature are based on captive animals, which usually alters the natural microbiome. Here, we analyzed kidney samples of wild-caught Artibeus spp., a fructivorous bat species from Grenada, West Indies, using metagenomics. Abstract Bats are capable of asymptomatically carrying a diverse number of microorganisms, including human pathogens, due to their unique immune system. Because of the close contact between bats and humans, there is a possibility for interspecies transmission and consequential disease outbreaks. Herein, high-throughput sequencing was used to determine the kidney-associated microbiome of a bat species abundant in Grenada, West Indies, Artibeus spp. Results indicate that the kidney of these bats can carry potential human pathogens. An endogenous retrovirus, Desmodus rotundus endogenous retrovirus isolate 824, phylogenetically related to betaretroviruses from rodents and New World primates, was also identified.
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Affiliation(s)
- Maria E. Ramos-Nino
- Department of Microbiology, Immunology, and Pharmacology, School of Medicine, St. George’s University, West Indies, Grenada
- Correspondence: ; Tel.: +1-802-8936358
| | - Daniel M. Fitzpatrick
- Department of Pathobiology, School of Veterinary Medicine, St. George’s University, West Indies, Grenada; (D.M.F.); (S.C.)
| | - Korin M. Eckstrom
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Scott Tighe
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Julie A. Dragon
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Sonia Cheetham
- Department of Pathobiology, School of Veterinary Medicine, St. George’s University, West Indies, Grenada; (D.M.F.); (S.C.)
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28
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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29
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Neely BA, Janech MG, Fenton MB, Simmons NB, Bland AM, Becker DJ. 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] [MESH Headings] [Grants] [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, NIST Charleston, Charleston, South Carolina 29412, 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, 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
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
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30
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The virome of German bats: comparing virus discovery approaches. Sci Rep 2021; 11:7430. [PMID: 33795699 PMCID: PMC8016945 DOI: 10.1038/s41598-021-86435-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.
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31
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Comparison of Selected Characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The global pandemic known as coronavirus disease 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review article presents the taxonomy of SARS-CoV-2 coronaviruses, which have been classified as the seventh known human pathogenic coronavirus. The etiology of COVID-19 is also briefly discussed. Selected characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63 are compared in the article. The angiotensin converting enzyme-2 (ACE-2) has been identified as the receptor for the SARS-CoV-2 viral entry. ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAAS) and plays a key role in the cardiovascular system. In the therapy of patients with COVID-19, there has been a concern about the use of RAAS inhibitors. As a result, it is hypothesized that ACE inhibitors do not directly affect ACE2 activity in clinical use. Coronaviruses are zoonotic RNA viruses. Identification of the primary causative agent of the SARS-CoV-2 is essential. Sequencing showed that the genome of the Bat CoVRaTG13 virus found in bats matches the genome of up to (96.2%) of SARS-CoV-2 virus. Sufficient knowledge of the molecular and biological mechanisms along with reliable information related to SARS-CoV-2 gives hope for a quick solution to epidemiological questions and therapeutic processes.
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32
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Virome of Bat Guano from Nine Northern California Roosts. J Virol 2021; 95:JVI.01713-20. [PMID: 33115864 DOI: 10.1128/jvi.01713-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
Bats are hosts to a large variety of viruses, including many capable of cross-species transmissions to other mammals, including humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and from a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Nearly complete or complete genomes of a novel parvovirus, astrovirus, nodavirus, circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, and densoviruses, and more partial genomes of a novel alphacoronavirus and a bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found, likely reflecting their wide distribution among different bats. Unexpectedly, a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR; these possibly originated from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent, indicating that numerous viruses still remain to be characterized, even from such a heavily investigated order as Chiroptera.IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.
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Corduneanu A, Mihalca AD, Sándor AD, Hornok S, Malmberg M, Viso NP, Bongcam-Rudloff E. The heart microbiome of insectivorous bats from Central and South Eastern Europe. Comp Immunol Microbiol Infect Dis 2021; 75:101605. [PMID: 33421678 DOI: 10.1016/j.cimid.2020.101605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 12/03/2020] [Indexed: 02/03/2023]
Abstract
Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats' outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats, Nyctalus noctula, Pipistrellus pipistrellus and Rhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogens Bartonella spp. and Rickettsia spp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteria Bartonella spp. in samples of N. noctula and indications of Rickettsia spp. in R. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
| | - Attila D Sándor
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania; Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary.
| | - Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden; SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Natalia Pin Viso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, Castelar, 1712, Buenos Aires, Argentina
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
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34
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Elaswad A, Fawzy M, Basiouni S, Shehata AA. Mutational spectra of SARS-CoV-2 isolated from animals. PeerJ 2020; 8:e10609. [PMID: 33384909 PMCID: PMC7751428 DOI: 10.7717/peerj.10609] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/29/2020] [Indexed: 12/03/2022] Open
Abstract
Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94-99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.
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Affiliation(s)
- Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Awad A. Shehata
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat City, Egypt
- Research and Development Section, PerNaturam GmbH, Gödenroth, Germany
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35
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Rajeev R, Prathiviraj R, Kiran GS, Selvin J. Zoonotic evolution and implications of microbiome in viral transmission and infection. Virus Res 2020; 290:198175. [PMID: 33007342 PMCID: PMC7524452 DOI: 10.1016/j.virusres.2020.198175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 01/07/2023]
Abstract
The outbreak and spread of new strains of coronavirus (SARS-CoV-2) remain a global threat with increasing cases in affected countries. The evolutionary tree of SARS-CoV-2 revealed that Porcine Reproductive and Respiratory Syndrome virus 2, which belongs to the Beta arterivirus genus from the Arteriviridae family is possibly the most ancient ancestral origin of SARS-CoV-2 and other Coronaviridae. This review focuses on phylogenomic distribution and evolutionary lineage of zoonotic viral cross-species transmission of the Coronaviridae family and the implications of bat microbiome in zoonotic viral transmission and infection. The review also casts light on the role of the human microbiome in predicting and controlling viral infections. The significance of microbiome-mediated interventions in the treatment of viral infections is also discussed. Finally, the importance of synthetic viruses in the study of viral evolution and transmission is highlighted.
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Affiliation(s)
- Riya Rajeev
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
| | - R Prathiviraj
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India.
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India.
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Lvov DK, Gulyukin MI, Zaberezhniy AD, Gulyukin AM. Formation of population gene pools of zoonotic viruses, potentially threatening biosafety. ACTA ACUST UNITED AC 2020; 65:243-258. [DOI: 10.36233/0507-4088-2020-65-5-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/14/2020] [Indexed: 12/14/2022]
Affiliation(s)
- D. K. Lvov
- D.I. Ivanovsky Institute of Virology. N.F Gamaleya National Research Center of Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Russian Federation
| | - M. I. Gulyukin
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
| | - A. D. Zaberezhniy
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
| | - A. M. Gulyukin
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
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Guruprasad L. Human coronavirus spike protein-host receptor recognition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 161:39-53. [PMID: 33137344 PMCID: PMC7604128 DOI: 10.1016/j.pbiomolbio.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]
Abstract
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.
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Sriwilaijaroen N, Suzuki Y. Host Receptors of Influenza Viruses and Coronaviruses-Molecular Mechanisms of Recognition. Vaccines (Basel) 2020; 8:E587. [PMID: 33036202 PMCID: PMC7712180 DOI: 10.3390/vaccines8040587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
Among the four genera of influenza viruses (IVs) and the four genera of coronaviruses (CoVs), zoonotic αIV and βCoV have occasionally caused airborne epidemic outbreaks in humans, who are immunologically naïve, and the outbreaks have resulted in high fatality rates as well as social and economic disruption and losses. The most devasting influenza A virus (IAV) in αIV, pandemic H1N1 in 1918, which caused at least 40 million deaths from about 500 million cases of infection, was the first recorded emergence of IAVs in humans. Usually, a novel human-adapted virus replaces the preexisting human-adapted virus. Interestingly, two IAV subtypes, A/H3N2/1968 and A/H1N1/2009 variants, and two lineages of influenza B viruses (IBV) in βIV, B/Yamagata and B/Victoria lineage-like viruses, remain seasonally detectable in humans. Both influenza C viruses (ICVs) in γIV and four human CoVs, HCoV-229E and HCoV-NL63 in αCoV and HCoV-OC43 and HCoV-HKU1 in βCoV, usually cause mild respiratory infections. Much attention has been given to CoVs since the global epidemic outbreaks of βSARS-CoV in 2002-2004 and βMERS-CoV from 2012 to present. βSARS-CoV-2, which is causing the ongoing COVID-19 pandemic that has resulted in 890,392 deaths from about 27 million cases of infection as of 8 September 2020, has provoked worldwide investigations of CoVs. With the aim of developing efficient strategies for controlling virus outbreaks and recurrences of seasonal virus variants, here we overview the structures, diversities, host ranges and host receptors of all IVs and CoVs and critically review current knowledge of receptor binding specificity of spike glycoproteins, which mediates infection, of IVs and of zoonotic, pandemic and seasonal CoVs.
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Affiliation(s)
- Nongluk Sriwilaijaroen
- Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Pathumthani 12120, Thailand
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Shizuoka 422-8526, Japan
| | - Yasuo Suzuki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Shizuoka 422-8526, Japan
- College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
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Rahman MT, Sobur MA, Islam MS, Ievy S, Hossain MJ, El Zowalaty ME, Rahman AMMT, Ashour HM. Zoonotic Diseases: Etiology, Impact, and Control. Microorganisms 2020; 8:microorganisms8091405. [PMID: 32932606 PMCID: PMC7563794 DOI: 10.3390/microorganisms8091405] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
Most humans are in contact with animals in a way or another. A zoonotic disease is a disease or infection that can be transmitted naturally from vertebrate animals to humans or from humans to vertebrate animals. More than 60% of human pathogens are zoonotic in origin. This includes a wide variety of bacteria, viruses, fungi, protozoa, parasites, and other pathogens. Factors such as climate change, urbanization, animal migration and trade, travel and tourism, vector biology, anthropogenic factors, and natural factors have greatly influenced the emergence, re-emergence, distribution, and patterns of zoonoses. As time goes on, there are more emerging and re-emerging zoonotic diseases. In this review, we reviewed the etiology of major zoonotic diseases, their impact on human health, and control measures for better management. We also highlighted COVID-19, a newly emerging zoonotic disease of likely bat origin that has affected millions of humans along with devastating global consequences. The implementation of One Health measures is highly recommended for the effective prevention and control of possible zoonosis.
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Affiliation(s)
- Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.); (M.S.I.); (S.I.); (M.J.H.)
- Correspondence: (M.T.R.); (H.M.A.)
| | - Md. Abdus Sobur
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.); (M.S.I.); (S.I.); (M.J.H.)
| | - Md. Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.); (M.S.I.); (S.I.); (M.J.H.)
| | - Samina Ievy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.); (M.S.I.); (S.I.); (M.J.H.)
| | - Md. Jannat Hossain
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.S.); (M.S.I.); (S.I.); (M.J.H.)
| | - Mohamed E. El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE;
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, SE 75123 Uppsala, Sweden
| | | | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL 33701, USA
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Correspondence: (M.T.R.); (H.M.A.)
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Olival KJ, Cryan PM, Amman BR, Baric RS, Blehert DS, Brook CE, Calisher CH, Castle KT, Coleman JTH, Daszak P, Epstein JH, Field H, Frick WF, Gilbert AT, Hayman DTS, Ip HS, Karesh WB, Johnson CK, Kading RC, Kingston T, Lorch JM, Mendenhall IH, Peel AJ, Phelps KL, Plowright RK, Reeder DM, Reichard JD, Sleeman JM, Streicker DG, Towner JS, Wang LF. Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats. PLoS Pathog 2020; 16:e1008758. [PMID: 32881980 PMCID: PMC7470399 DOI: 10.1371/journal.ppat.1008758] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. The establishment of new wildlife reservoirs for SARS-CoV-2 would further complicate public health control measures and could lead to wildlife health and conservation impacts. Given the likely bat origin of SARS-CoV-2 and related beta-coronaviruses (β-CoVs), free-ranging bats are a key group of concern for spillover from humans back to wildlife. Here, we review the diversity and natural host range of β-CoVs in bats and examine the risk of humans inadvertently infecting free-ranging bats with SARS-CoV-2. Our review of the global distribution and host range of β-CoV evolutionary lineages suggests that 40+ species of temperate-zone North American bats could be immunologically naïve and susceptible to infection by SARS-CoV-2. We highlight an urgent need to proactively connect the wellbeing of human and wildlife health during the current pandemic and to implement new tools to continue wildlife research while avoiding potentially severe health and conservation impacts of SARS-CoV-2 "spilling back" into free-ranging bat populations.
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Affiliation(s)
- Kevin J. Olival
- EcoHealth Alliance, New York, New York, United States of America
| | - Paul M. Cryan
- US Geological Survey, Fort Collins Science Center, Ft. Collins, Colorado, United States of America
| | - Brian R. Amman
- US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David S. Blehert
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Cara E. Brook
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Charles H. Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology & Pathology, College of Veterinary Medicine & Biomedical Sciences, Colorado State University, Ft. Collins, Colorado, United States of America
| | - Kevin T. Castle
- Wildlife Veterinary Consulting, Livermore, Colorado, United States of America
| | | | - Peter Daszak
- EcoHealth Alliance, New York, New York, United States of America
| | | | - Hume Field
- EcoHealth Alliance, New York, New York, United States of America
- Bat Conservation International, Austin, Texas, United States of America
| | - Winifred F. Frick
- School of Veterinary Science, University of Queensland, Gatton, Queensland, Australia
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Amy T. Gilbert
- US Department of Agriculture, National Wildlife Research Center, Ft. Collins, Colorado, United States of America
| | - David T. S. Hayman
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Hon S. Ip
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | | | - Christine K. Johnson
- One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Rebekah C. Kading
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology & Pathology, College of Veterinary Medicine & Biomedical Sciences, Colorado State University, Ft. Collins, Colorado, United States of America
| | - Tigga Kingston
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Jeffrey M. Lorch
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore
| | - Alison J. Peel
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Kendra L. Phelps
- EcoHealth Alliance, New York, New York, United States of America
| | - Raina K. Plowright
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, United States of America
| | - DeeAnn M. Reeder
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | | | - Jonathan M. Sleeman
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Scotland, United Kingdom
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Jonathan S. Towner
- US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore
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41
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Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity. Viruses 2020; 12:v12080891. [PMID: 32824037 PMCID: PMC7472731 DOI: 10.3390/v12080891] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.
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42
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Liu B, Shao N, Wang J, Zhou S, Su H, Dong J, Sun L, Li L, Zhang T, Yang F. An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection. Front Microbiol 2020; 11:1552. [PMID: 32754134 PMCID: PMC7366072 DOI: 10.3389/fmicb.2020.01552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/23/2022] Open
Abstract
Respiratory virus infections are one of the major causes of acute respiratory disease or exacerbation of chronic obstructive pulmonary disease (COPD). However, next-generation sequencing has not been used for routine viral detection in clinical respiratory samples owing to its sophisticated technology. Here, several pharyngeal samples with COPD were collected to enrich viral particles using an optimized method (M3), which involved M1 with centrifugation, filtration, and concentration, M2 (magnetic beads) combined with mixed nuclease digestion, and M4 with no pretreatment as a control. Metagenomic sequencing and bioinformatics analyses showed that the M3 method for viral enrichment was superior in both viral sequencing composition and viral taxa when compared to M1, M2, and M4. M3 acquired the most viral reads and more complete sequences within 15-h performance, indicating that it might be feasible for viral detection in multiple respiratory samples in clinical practice. Based on sequence similarity analysis, 12 human viruses, including nine Anelloviruses and three coronaviruses, were characterized. Coronavirus OC43 with the largest number of viral reads accounted for nearly complete (99.8%) genome sequences, indicating that it may be a major viral pathogen involved in exacerbation of COPD.
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Affiliation(s)
- Bo Liu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Shao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - SiYu Zhou
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - HaoXiang Su
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - LiLian Sun
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Li
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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43
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Lvov DK, Alkhovsky SV. [Source of the COVID-19 pandemic: ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus).]. Vopr Virusol 2020; 65:62-70. [PMID: 32515561 DOI: 10.36233/0507-4088-2020-65-2-62-70] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/29/2020] [Indexed: 01/12/2023]
Abstract
Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir - bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus - a global challenge to science» of the Scientific Council «Life Science» of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020).
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Affiliation(s)
- D K Lvov
- D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - S V Alkhovsky
- D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
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44
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Cameron K, Hayes B, Olson SH, Smith BR, Pante J, Laudisoit A, Goldstein T, Joly DO, Bagamboula MPassi R, Lange CE. Detection of first gammaherpesvirus sequences in Central African bats. New Microbes New Infect 2020; 36:100705. [PMID: 32612842 PMCID: PMC7322348 DOI: 10.1016/j.nmni.2020.100705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 11/29/2022] Open
Abstract
Herpesviruses have been identified in many species; however, relatively few bat herpesvirus are known, considering the enormous diversity of bats. We used consensus PCR to test bats from the Republic of the Congo and found DNA of two different novel bat herpesviruses. One was detected in a Pipistrellus nanulus, the other in a Triaenops persicus bat and both resemble gammaherpesviruses. On the amino acid level, the amplified sequences differ by 55% from each other, and by 27% and 25% from the next closest known viruses. The findings point towards the diversity of herpesviruses in Central African bats.
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Affiliation(s)
- K Cameron
- Wildlife Conversation Society, Bronx, NY, USA.,United States Fish and Wildlife Service, Bailey's Crossroads, VA, USA
| | - B Hayes
- Monadh, Inveruglas, Kingussie, UK
| | - S H Olson
- Wildlife Conversation Society, Bronx, NY, USA
| | - B R Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J Pante
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | - T Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - D O Joly
- Wildlife Conversation Society, Bronx, NY, USA.,British Columbia Ministry of Environment and Climate Change Strategy, Victoria, BC, Canada
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45
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James S, Donato D, de Thoisy B, Lavergne A, Lacoste V. Novel herpesviruses in neotropical bats and their relationship with other members of the Herpesviridae family. INFECTION GENETICS AND EVOLUTION 2020; 84:104367. [PMID: 32450245 PMCID: PMC7244429 DOI: 10.1016/j.meegid.2020.104367] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023]
Abstract
In the past decade, a large number of studies have detected herpesvirus sequences from many bat species around the world. Nevertheless, the discovery of bat herpesviruses is geographically uneven. Of the various bat species tested to date, only a few were from the New World. Seeking to investigate the distribution and diversity of herpesviruses circulating in neotropical bats, we carried out molecular screening of 195 blood DNA samples from 11 species of three bat families (Phyllostomidae, Mormoopidae, and Molossidae). Using polymerase chain reaction amplification, with degenerate consensus primers targeting highly conserved amino acid motifs of the herpesvirus DNA polymerase and Glycoprotein B genes, we characterized novel viral sequences from all tested species. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, as well as phylogenetic analyses confirmed that they all belonged to the Herpesviridae family, of the Beta- and Gammaherpesvirinae subfamilies. Fourteen partial DNA polymerase gene sequences, of which three beta- and 11 gamma-herpesviruses, were detected. A total of 12 partial Glycoprotein B gene sequences, all gamma-herpesviruses, were characterized. Every sequence was specific to a bat species and in some species (Desmodus rotundus, Carollia perspicillata, and Pteronotus rubiginosus) multiple viruses were found. Phylogenetic analyses of beta- and gammaherpesvirus sequences led to the identification of bat-specific clades. Those composed of sequences obtained from different bat species belonging to distinct subfamilies follow the taxonomy of bats. This study confirms the astonishing diversity of bat herpesviruses and broadens our knowledge of their host range. Nevertheless, it also emphasizes the fact that, to better appreciate the evolutionary history of these viruses, much remains to be done at various taxonomic levels. Molecular screening was carried out on 11 bat species from French Guiana and Martinique (French West Indies). Partial DNA polymerase gene sequences of 14 viruses were characterized as well as 12 Glycoprotein B sequences. Genetic characterization of these sequences reveals a high degree of genetic divergence. Phylogenetically, most of the newly discovered sequences fall within bat-specific clades well correlated with the taxonomy of their hosts. This study is the largest conducted to date in terms of species diversity from the New World.
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Affiliation(s)
- Samantha James
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana; Université de la Guyane, Ecole doctorale 587 "Diversités, Santé et Développement en Amazonie", Cayenne, French Guiana
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Benoît de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana; Université de la Guyane, Ecole doctorale 587 "Diversités, Santé et Développement en Amazonie", Cayenne, French Guiana
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana; Université de la Guyane, Ecole doctorale 587 "Diversités, Santé et Développement en Amazonie", Cayenne, French Guiana
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana; Université de la Guyane, Ecole doctorale 587 "Diversités, Santé et Développement en Amazonie", Cayenne, French Guiana; Département de Virologie, Institut Pasteur, Paris, France; Unité de Biologie des Infections Virales Emergentes, Centre International de Recherche en Infectiologie, Institut Pasteur, Lyon, France.
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46
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Maganga GD, Pinto A, Mombo IM, Madjitobaye M, Mbeang Beyeme AM, Boundenga L, Ar Gouilh M, N'Dilimabaka N, Drexler JF, Drosten C, Leroy EM. Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon. Sci Rep 2020; 10:7314. [PMID: 32355260 PMCID: PMC7192909 DOI: 10.1038/s41598-020-64159-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/06/2020] [Indexed: 01/06/2023] Open
Abstract
Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). We explored the diversity of CoVs and determined the factors driving the infection of CoVs in wild animals. Based on a nested reverse transcription-polymerase chain reaction, only bats, belonging to the Hipposideros gigas (4/156), Hipposideros cf. ruber (13/262) and Miniopterus inflatus (1/249) species, were found infected with CoVs. We identified alphacoronaviruses in H. gigas and H. cf. ruber and betacoronaviruses in H. gigas. All Alphacoronavirus sequences grouped with Human coronavirus 229E (HCoV-229E). Ecological analyses revealed that CoV infection was significantly found in July and October in H. gigas and in October and November in H. cf ruber. The prevalence in the Faucon cave was significantly higher. Our findings suggest that insectivorous bats harbor potentially zoonotic CoVs; highlight a probable seasonality of the infection in cave-dwelling bats from the North-East of Gabon and pointed to an association between the disturbance of the bats' habitat by human activities and CoV infection.
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Affiliation(s)
- Gael Darren Maganga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon.
- Université des Sciences et Techniques de Masuku (USTM), Institut National Supérieur d'Agronomie et de Biotechnologies (INSAB), BP, 913, Franceville, Gabon.
| | - Anaïs Pinto
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
| | - Illich Manfred Mombo
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
| | - Mankomra Madjitobaye
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
| | - Antoine Mitte Mbeang Beyeme
- Université des Sciences et Techniques de Masuku (USTM), Institut National Supérieur d'Agronomie et de Biotechnologies (INSAB), BP, 913, Franceville, Gabon
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
| | - Meriadeg Ar Gouilh
- Normandie Université, EA2656, Groupe de Recherche sur l'Adaptation Microbienne, 14000, Caen, France
| | - Nadine N'Dilimabaka
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu, Berlin, Germany
- German Centre for Infection Research (DZIF), Heidelberg, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu, Berlin, Germany
- German Centre for Infection Research (DZIF), Heidelberg, Germany
| | - Eric Maurice Leroy
- Centre International de Recherches Médicales de Franceville (CIRMF), BP, 769, Franceville, Gabon
- UMR (IRD 224/CNRS 5290/UM1-UM2), Institut de Recherche pour le Développement, Montpellier, France
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47
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Bolatti EM, Zorec TM, Montani ME, Hošnjak L, Chouhy D, Viarengo G, Casal PE, Barquez RM, Poljak M, Giri AA. A Preliminary Study of the Virome of the South American Free-Tailed Bats ( Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses. Viruses 2020; 12:v12040422. [PMID: 32283670 PMCID: PMC7232368 DOI: 10.3390/v12040422] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Bats provide important ecosystem services as pollinators, seed dispersers, and/or insect controllers, but they have also been found harboring different viruses with zoonotic potential. Virome studies in bats distributed in Asia, Africa, Europe, and North America have increased dramatically over the past decade, whereas information on viruses infecting South American species is scarce. We explored the virome of Tadarida brasiliensis, an insectivorous New World bat species inhabiting a maternity colony in Rosario (Argentina), by a metagenomic approach. The analysis of five pooled oral/anal swab samples indicated the presence of 43 different taxonomic viral families infecting a wide range of hosts. By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. TbraPV1 is the first papillomavirus type identified in this host and the prototype of a novel genus. TbGkyV1 is the first genomovirus reported in New World bats and constitutes a new species within the genus Gemykibivirus. Our findings extend the knowledge about oral/anal viromes of a South American bat species and contribute to understand the evolution and genetic diversity of the novel characterized viruses.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Tomaž M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina;
- Programa de Investigaciones de Biodiversidad Argentina, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina;
- Programa de Investigaciones de Biodiversidad Argentina, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (D.C.); (G.V.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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48
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Ye ZW, Yuan S, Yuen KS, Fung SY, Chan CP, Jin DY. Zoonotic origins of human coronaviruses. Int J Biol Sci 2020; 16:1686-1697. [PMID: 32226286 PMCID: PMC7098031 DOI: 10.7150/ijbs.45472] [Citation(s) in RCA: 508] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022] Open
Abstract
Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted.
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Affiliation(s)
- Zi-Wei Ye
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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49
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Valouzi H, Hashemi SS, Wylie SJ, Ahadiyat A, Golnaraghi A. Wisteria Vein Mosaic Virus Detected for the First Time in Iran from an Unknown Host by Analysis of Aphid Vectors. THE PLANT PATHOLOGY JOURNAL 2020; 36:87-97. [PMID: 32089664 PMCID: PMC7012578 DOI: 10.5423/ppj.oa.10.2019.0268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
The development of reverse transcription-polymerase chain reaction using degenerate primers against conserved regions of most potyviral genomes enabled sampling of the potyvirome. However, these assays usually involve sampling potential host plants, but identifying infected plants when they are asymptomatic is challenging, and many plants, especially wild ones, contain inhibitors to DNA amplification. We used an alternative approach which utilized aphid vectors and indicator plants to identify potyviruses capable of infecting common bean (Phaseolus vulgaris). Aphids were collected from a range of asymptomatic leguminous weeds and trees in Iran, and transferred to bean seedlings under controlled conditions. Bean plants were tested serologically for potyvirus infections four-weeks post-inoculation. The serological assay and symptomatology together indicated the presence of one potyvirus, and symptomology alone implied the presence of an unidentified virus. The partial genome of the potyvirus, encompassing the complete coat protein gene, was amplified using generic potyvirus primers. Sequence analysis of the amplicon confirmed the presence of an isolate of Wisteria vein mosaic virus (WVMV), a virus species not previously identified from Western Asia. Phylogenetic analyses of available WVMV sequences categorized them into five groups: East Asian-1 to 3, North American and World. The Iranian isolate clustered with those in the World group. Multiple sequence alignment indicated the presence of some genogroup-specific amino acid substitutions among the isolates studied. Chinese isolates were sister groups of other isolates and showed higher nucleotide distances as compared with the others, suggesting a possible Eastern-Asian origin of WVMV, the main region where Wisteria might have originated.
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Affiliation(s)
- Hajar Valouzi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Seyedeh-Shahrzad Hashemi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Stephen J. Wylie
- Plant Biotechnology Research Group – Virology, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150,
Australia
| | - Ali Ahadiyat
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Alireza Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
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50
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Sheahan TP, Frieman MB. The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health. Curr Opin Virol 2020; 40:37-40. [PMID: 32569751 PMCID: PMC7269927 DOI: 10.1016/j.coviro.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
A new coronavirus (CoV) called SARS-CoV-2 emerged in Wuhan, China in December 2019 as the etiological agent of a viral pneumonia called COVID-19. The global spread of SARS-CoV-2 has been so extensive that the WHO declared COVID-19 a pandemic on March 11, 2020. Below, we discuss the emergence of SARS-CoV-2 and provide the historical context, which strongly suggests emerging CoVs provide an immediate threat to global public health and will continue to do so in the future.
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Affiliation(s)
- Timothy P Sheahan
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Matthew B Frieman
- Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, United States.
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