1
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Tse AL, Acreman CM, Ricardo-Lax I, Berrigan J, Lasso G, Balogun T, Kearns FL, Casalino L, McClain GL, Chandran AM, Lemeunier C, Amaro RE, Rice CM, Jangra RK, McLellan JS, Chandran K, Miller EH. Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600393. [PMID: 38979151 PMCID: PMC11230278 DOI: 10.1101/2024.06.24.600393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the spike N-terminal domain, uncovered through forward-genetic selection, interacted epistatically with the FPPR substitution to synergistically enhance spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures.
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2
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Meyer M, Melville DW, Baldwin HJ, Wilhelm K, Nkrumah EE, Badu EK, Oppong SK, Schwensow N, Stow A, Vallo P, Corman VM, Tschapka M, Drosten C, Sommer S. Bat species assemblage predicts coronavirus prevalence. Nat Commun 2024; 15:2887. [PMID: 38575573 PMCID: PMC10994947 DOI: 10.1038/s41467-024-46979-1] [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: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
Anthropogenic disturbances and the subsequent loss of biodiversity are altering species abundances and communities. Since species vary in their pathogen competence, spatio-temporal changes in host assemblages may lead to changes in disease dynamics. We explore how longitudinal changes in bat species assemblages affect the disease dynamics of coronaviruses (CoVs) in more than 2300 cave-dwelling bats captured over two years from five caves in Ghana. This reveals uneven CoV infection patterns between closely related species, with the alpha-CoV 229E-like and SARS-related beta-CoV 2b emerging as multi-host pathogens. Prevalence and infection likelihood for both phylogenetically distinct CoVs is influenced by the abundance of competent species and naïve subadults. Broadly, bat species vary in CoV competence, and highly competent species are more common in less diverse communities, leading to increased CoV prevalence in less diverse bat assemblages. In line with the One Health framework, our work supports the notion that biodiversity conservation may be the most proactive measure to prevent the spread of pathogens with zoonotic potential.
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Affiliation(s)
- Magdalena Meyer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany.
| | - Dominik W Melville
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Heather J Baldwin
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Evans Ewald Nkrumah
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ebenezer K Badu
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel Kingsley Oppong
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Nina Schwensow
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Adam Stow
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peter Vallo
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany.
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3
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Hu B, Guo H, Si H, Shi Z. Emergence of SARS and COVID-19 and preparedness for the next emerging disease X. Front Med 2024; 18:1-18. [PMID: 38561562 DOI: 10.1007/s11684-024-1066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/04/2024]
Abstract
Severe acute respiratory syndrome (SARS) and Coronavirus disease 2019 (COVID-19) are two human Coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.
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Affiliation(s)
- Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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4
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Cell Host Microbe 2023; 31:1961-1973.e11. [PMID: 37989312 PMCID: PMC10913562 DOI: 10.1016/j.chom.2023.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rhinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. We determine a cryo-EM structure of the PRD-0038 RBD bound to Rhinolophus alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryo-EM and monoclonal antibody reactivity reveals its distinct antigenicity relative to SARS-CoV-2 and identifies PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared with SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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5
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Wang Q, Noettger S, Xie Q, Pastorio C, Seidel A, Müller JA, Jung C, Jacob T, Sparrer KMJ, Zech F, Kirchhoff F. Determinants of species-specific utilization of ACE2 by human and animal coronaviruses. Commun Biol 2023; 6:1051. [PMID: 37848611 PMCID: PMC10582019 DOI: 10.1038/s42003-023-05436-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
Utilization of human ACE2 allowed several bat coronaviruses (CoVs), including the causative agent of COVID-19, to infect humans directly or via intermediate hosts. However, the determinants of species-specific differences in ACE2 usage and the frequency of the ability of animal CoVs to use human ACE2 are poorly understood. Here we applied VSV pseudoviruses to analyze the ability of Spike proteins from 26 human or animal CoVs to use ACE2 receptors across nine reservoir, potential intermediate and human hosts. We show that SARS-CoV-2 Omicron variants evolved towards more efficient ACE2 usage but mutation of R493Q in BA.4/5 and XBB Spike proteins disrupts utilization of ACE2 from Greater horseshoe bats. Variations in ACE2 residues 31, 41 and 354 govern species-specific differences in usage by coronaviral Spike proteins. Mutation of T403R allows the RaTG13 bat CoV Spike to efficiently use all ACE2 orthologs for viral entry. Sera from COVID-19 vaccinated individuals neutralize the Spike proteins of various bat Sarbecoviruses. Our results define determinants of ACE2 receptor usage of diverse CoVs and suggest that COVID-19 vaccination may protect against future zoonoses of bat coronaviruses.
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Affiliation(s)
- Qingxing Wang
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Qinya Xie
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Institute of Virology, Philipps University Marburg, 35043, Marburg, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081, Ulm, Germany
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081, Ulm, Germany
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081, Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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6
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Liu B, Zhao P, Xu P, Han Y, Wang Y, Chen L, Wu Z, Yang J. A comprehensive dataset of animal-associated sarbecoviruses. Sci Data 2023; 10:681. [PMID: 37805633 PMCID: PMC10560225 DOI: 10.1038/s41597-023-02558-5] [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: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023] Open
Abstract
Zoonotic spillover of sarbecoviruses (SarbeCoVs) from non-human animals to humans under natural conditions has led to two large-scale pandemics, the severe acute respiratory syndrome (SARS) pandemic in 2003 and the ongoing COVID-19 pandemic. Knowledge of the genetic diversity, geographical distribution, and host specificity of SarbeCoVs is therefore of interest for pandemic surveillance and origin tracing of SARS-CoV and SARS-CoV-2. This study presents a comprehensive repository of publicly available animal-associated SarbeCoVs, covering 1,535 viruses identified from 63 animal species distributed in 43 countries worldwide (as of February 14,2023). Relevant meta-information, such as host species, sampling time and location, was manually curated and included in the dataset to facilitate further research on the potential patterns of viral diversity and ecological characteristics. In addition, the dataset also provides well-annotated sequence sets of receptor-binding domains (RBDs) and receptor-binding motifs (RBMs) for the scientific community to highlight the potential determinants of successful cross-species transmission that could be aid in risk estimation and strategic design for future emerging infectious disease control and prevention.
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Affiliation(s)
- Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
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7
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557371. [PMID: 37745523 PMCID: PMC10515872 DOI: 10.1101/2023.09.12.557371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad ACE2 usage and that RBD mutations further expand receptor promiscuity and enable human ACE2 utilization. We determined a cryoEM structure of the PRD-0038 RBD bound to R. alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryoEM and monoclonal antibody reactivity revealed its distinct antigenicity relative to SARS-CoV-2 and identified PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicited greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared to SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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8
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Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, Eloit M. Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence. Viruses 2023; 15:1897. [PMID: 37766303 PMCID: PMC10536463 DOI: 10.3390/v15091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.
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Affiliation(s)
- Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Cong Tu
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR3528, Université Paris Cité, 75015 Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Léa Vendramini
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Vu Phong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Nguyen Thi Yen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Hoang Ngoc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Hai Son
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Pham Tuan Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Faustine Amara
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015 Paris, France
| | - Sandie Munier
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), Hanoi 70072, Vietnam
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, National Reference Center for Respiratory Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 77420 Maisons-Alfort, France
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9
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Evans TS, Tan CW, Aung O, Phyu S, Lin H, Coffey LL, Toe AT, Aung P, Aung TH, Aung NT, Weiss CM, Thant KZ, Htun ZT, Murray S, Wang L, Johnson CK, Thu HM. Exposure to diverse sarbecoviruses indicates frequent zoonotic spillover in human communities interacting with wildlife. Int J Infect Dis 2023; 131:57-64. [PMID: 36870470 PMCID: PMC9981523 DOI: 10.1016/j.ijid.2023.02.015] [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: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/19/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Sarbecoviruses are a subgenus of Coronaviridae that mostly infect bats with known potential to infect humans (SARS-CoV and SARS-CoV-2). Populations in Southeast Asia, where these viruses are most likely to emerge, have been undersurveyed to date. METHODS We surveyed communities engaged in extractive industries and bat guano harvesting from rural areas in Myanmar. Participants were screened for exposure to sarbecoviruses, and their interactions with wildlife were evaluated to determine the factors associated with exposure to sarbecoviruses. RESULTS Of 693 people screened between July 2017 and February 2020, 12.1% were seropositive for sarbecoviruses. Individuals were significantly more likely to have been exposed to sarbecoviruses if their main livelihood involved working in extractive industries (logging, hunting, or harvesting of forest products; odds ratio [OR] = 2.71, P = 0.019) or had been hunting/slaughtering bats (OR = 6.09, P = 0.020). Exposure to a range of bat and pangolin sarbecoviruses was identified. CONCLUSION Exposure to diverse sarbecoviruses among high-risk human communities provides epidemiologic and immunologic evidence that zoonotic spillover is occurring. These findings inform risk mitigation efforts needed to decrease disease transmission at the bat-human interface, as well as future surveillance efforts warranted to monitor isolated populations for viruses with pandemic potential.
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Affiliation(s)
- Tierra Smiley Evans
- Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, USA.
| | - Chee Wah Tan
- Duke-National University of Singapore, Singapore
| | - Ohnmar Aung
- Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, USA
| | - Sabai Phyu
- Tropical and Infectious Diseases Department, Specialist Hospital Waibargi, University of Medicine (2), Yangon, Myanmar
| | - Htin Lin
- Department of Medical Research, Yangon, Myanmar
| | - Lark L Coffey
- Department of Pathology, Microbiology and Immunology Department, University of California, Davis, USA
| | - Aung Than Toe
- Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, USA
| | - Pyaephyo Aung
- Nature Conservation Society Myanmar, Yangon, Myanmar
| | - Tin Htun Aung
- Nature Conservation Society Myanmar, Yangon, Myanmar
| | - Nyein Thu Aung
- Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, USA
| | - Christopher M Weiss
- Department of Pathology, Microbiology and Immunology Department, University of California, Davis, USA
| | | | | | - Suzan Murray
- Global Health Program, Smithsonian Institution, Washington, USA
| | - Linfa Wang
- Duke-National University of Singapore, Singapore
| | - Christine Kreuder Johnson
- Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, USA
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10
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Allen JD, Ivory DP, Song SG, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses related to SARS-CoV-2. Cell Rep 2023; 42:112307. [PMID: 36972173 PMCID: PMC10015101 DOI: 10.1016/j.celrep.2023.112307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Vaccines remain successful at limiting severe disease and death, but the potential for further coronavirus zoonosis motivates the search for pan-coronavirus vaccines. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of 12 sarbecovirus glycan shields. Of the 22 N-linked glycan attachment sites present on SARS-CoV-2, 15 are shared by all 12 sarbecoviruses. However, there are significant differences in the processing state at glycan sites in the N-terminal domain, such as N165. Conversely, glycosylation sites in the S2 domain are highly conserved and contain a low abundance of oligomannose-type glycans, suggesting a low glycan shield density. The S2 domain may therefore provide a more attractive target for immunogen design efforts aiming to generate a pan-coronavirus antibody response.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Dylan P Ivory
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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11
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Gao B, Zhu S. Mutation-driven parallel evolution in emergence of ACE2-utilizing sarbecoviruses. Front Microbiol 2023; 14:1118025. [PMID: 36910184 PMCID: PMC9996049 DOI: 10.3389/fmicb.2023.1118025] [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: 12/07/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
Mutation and recombination are two major genetic mechanisms that drive the evolution of viruses. They both exert an interplay during virus evolution, in which mutations provide a first ancestral source of genetic diversity for subsequent recombination. Sarbecoviruses are a group of evolutionarily related β-coronaviruses including human severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 and a trove of related animal viruses called SARS-like CoVs (SL-CoVs). This group of members either use or not use angiotensin-converting enzyme 2 (ACE2) as their entry receptor, which has been linked to the properties of their spike protein receptor binding domains (RBDs). This raises an outstanding question regarding how ACE2 binding originated within sarbecoviruses. Using a combination of analyses of phylogenies, ancestral sequences, structures, functions and molecular dynamics, we provide evidence in favor of an evolutionary scenario, in which three distinct ancestral RBDs independently developed the ACE2 binding trait via parallel amino acid mutations. In this process, evolutionary intermediate RBDs might be firstly formed through loop extensions to offer key functional residues accompanying point mutations to remove energetically unfavorable interactions and to change the dynamics of the functional loops, all required for ACE2 binding. Subsequent optimization in the context of evolutionary intermediates led to the independent emergence of ACE2-binding RBDs in the SARS-CoV and SARS-CoV-2 clades of Asian origin and the clade comprising SL-CoVs of European and African descent. These findings will help enhance our understanding of mutation-driven evolution of sarbecoviruses in their early history.
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Affiliation(s)
- Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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12
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Akaishi T, Fujiwara K, Ishii T. Genetic Recombination Sites Away from the Insertion/Deletion Hotspots in SARS-Related Coronaviruses. TOHOKU J EXP MED 2023; 259:17-26. [PMID: 36351613 DOI: 10.1620/tjem.2022.j093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Affiliation(s)
| | - Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University
| | - Tadashi Ishii
- Department of Education and Support for Regional Medicine, Tohoku University
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13
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Nabi F, Ahmad O, Khan YA, Nabi A, Md Amiruddin H, Abul Qais F, Masroor A, Hisamuddin M, Uversky VN, Khan RH. Computational studies on phylogeny and drug designing using molecular simulations for COVID-19. J Biomol Struct Dyn 2022; 40:10753-10762. [PMID: 34278954 DOI: 10.1080/07391102.2021.1947895] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since the first appearance of a novel coronavirus pneumonia (NCP) caused by a novel human coronavirus, and especially after the infection started its rapid spread over the world causing the COVID-19 (coronavirus disease 2019) pandemics, a very substantial part of the scientific community is engaged in the intensive research dedicated to finding of the potential therapeutics to cure this disease. As repurposing of existing drugs represents the only instant solution for those infected with the virus, we have been working on utilization of the structure-based virtual screening method to find some potential medications. In this study, we screened a library of 646 FDA approved drugs against the receptor-binding domain of the SARS-CoV-2 spike (S) protein and the main protease of this virus. Scoring functions revealed that some of the anticancer drugs (such as Pazopanib, Irinotecan, and Imatinib), antipsychotic drug (Risperidone), and antiviral drug (Raltegravir) have a potential to interact with both targets with high efficiency. Further we performed molecular dynamics simulations to understand the evolution in protein upon interaction with drug. Also, we have performed a phylogenetic analysis of 43 different coronavirus strains infecting 12 different mammalian species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Yawar Ali Khan
- Department of Bioengeenering, Intergral University, Lucknow, India
| | - Anas Nabi
- Department of Computer Science, Vivekanand College of Technology and Management, Aligarh, India
| | - Hashmi Md Amiruddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Aiman Masroor
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia.,Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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14
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Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017. Cell Rep 2022; 41:111831. [PMID: 36493785 PMCID: PMC9705200 DOI: 10.1016/j.celrep.2022.111831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/27/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, multiple SARS-CoV-2-related viruses have been characterized, including pangolin-origin GD/1/2019 and GX/P2V/2017. Our previous study indicated that both viruses have the potential to infect humans. Here, we find that CB6 (commercial name etesevimab), a COVID-19 therapeutic monoclonal antibody (MAb) developed by our group, efficiently inhibits GD/1/2019 but not GX/P2V/2017. A total of 50 SARS-CoV-2 MAbs divided into seven groups based on their receptor-binding domain (RBD) epitopes, together with the COVID-19 convalescent sera, are systematically screened for their cross-binding and cross-neutralizing properties against GX/P2V/2017. We find that GX/P2V/2017 displays substantial immune difference from SARS-CoV-2. Furthermore, we solve two complex structures of the GX/P2V/2017 RBD with MAbs belonging to RBD-1 and RBD-5, providing a structural basis for their different antigenicity. These results highlight the necessity for broad anti-coronavirus countermeasures and shed light on potential therapeutic targets.
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15
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Murakami S, Kitamura T, Matsugo H, Kamiki H, Oyabu K, Sekine W, Takenaka-Uema A, Sakai-Tagawa Y, Kawaoka Y, Horimoto T. Isolation of Bat Sarbecoviruses, Japan. Emerg Infect Dis 2022; 28:2500-2503. [PMID: 36417954 PMCID: PMC9707576 DOI: 10.3201/eid2812.220801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Surveillance of bat betacoronaviruses is crucial for understanding their spillover potential. We isolated bat sarbecoviruses from Rhinolophus cornutus bats in multiple locations in Japan. These viruses grew efficiently in cells expressing R. cornutus angiotensin converting enzyme-2, but not in cells expressing human angiotensin converting enzyme-2, suggesting a narrow host range.
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16
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Ouyang WO, Tan TJ, Lei R, Song G, Kieffer C, Andrabi R, Matreyek KA, Wu NC. Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning. SCIENCE ADVANCES 2022; 8:eadd7221. [PMID: 36417523 PMCID: PMC9683733 DOI: 10.1126/sciadv.add7221] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Increasing the expression level of the SARS-CoV-2 spike (S) protein has been critical for COVID-19 vaccine development. While previous efforts largely focused on engineering the receptor-binding domain (RBD) and the S2 subunit, the amino-terminal domain (NTD) has been long overlooked because of the limited understanding of its biophysical constraints. In this study, the effects of thousands of NTD single mutations on S protein expression were quantified by deep mutational scanning. Our results revealed that in terms of S protein expression, the mutational tolerability of NTD residues was inversely correlated with their proximity to the RBD and S2. We also identified NTD mutations at the interdomain interface that increased S protein expression without altering its antigenicity. Overall, this study not only advances the understanding of the biophysical constraints of the NTD but also provides invaluable insights into S-based immunogen design.
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Affiliation(s)
- Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Collin Kieffer
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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17
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Li Y, Merbah M, Wollen-Roberts S, Beckman B, Mdluli T, Swafford I, Mayer SV, King J, Corbitt C, Currier JR, Liu H, Esber A, Pinyakorn S, Parikh A, Francisco LV, Phanuphak N, Maswai J, Owuoth J, Kibuuka H, Iroezindu M, Bahemana E, Vasan S, Ake JA, Modjarrad K, Gromowski G, Paquin-Proulx D, Rolland M. Coronavirus Antibody Responses before COVID-19 Pandemic, Africa and Thailand. Emerg Infect Dis 2022; 28:2214-2225. [PMID: 36220131 PMCID: PMC9622245 DOI: 10.3201/eid2811.221041] [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] [Indexed: 11/19/2022] Open
Abstract
Prior immune responses to coronaviruses might affect human SARS-CoV-2 response. We screened 2,565 serum and plasma samples collected from 2013 through early 2020, before the COVID-19 pandemic began, from 2,250 persons in 4 countries in Africa (Kenya, Nigeria, Tanzania, and Uganda) and in Thailand, including persons living with HIV-1. We detected IgG responses to SARS-CoV-2 spike (S) subunit 2 protein in 1.8% of participants. Profiling against 23 coronavirus antigens revealed that responses to S, subunit 2, or subunit 1 proteins were significantly more frequent than responses to the receptor-binding domain, S-Trimer, or nucleocapsid proteins (p<0.0001). We observed similar responses in persons with or without HIV-1. Among all coronavirus antigens tested, SARS-CoV-2, SARS-CoV-1, and Middle East respiratory syndrome coronavirus antibody responses were much higher in participants from Africa than in participants from Thailand (p<0.01). We noted less pronounced differences for endemic coronaviruses. Serosurveys could affect vaccine and monoclonal antibody distribution across global populations.
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18
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Allen JD, Ivory D, Ge Song S, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505118. [PMID: 36052375 PMCID: PMC9435400 DOI: 10.1101/2022.08.24.505118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the impact of SARS-CoV-2. Vaccines remain successful at limiting severe disease and death, however the continued emergence of SARS-CoV-2 variants, together with the potential for further coronavirus zoonosis, motivates the search for pan-coronavirus vaccines that induce broadly neutralizing antibodies. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of several sarbecovirus glycan shields. Many N-linked glycan attachment sites are shared by all sarbecoviruses, and the processing state of certain sites is highly conserved. However, there are significant differences in the processing state at several glycan sites that surround the receptor binding domain. Our studies reveal similarities and differences in the glycosylation of sarbecoviruses and show how subtle changes in the protein sequence can have pronounced impacts on the glycan shield.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dylan Ivory
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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19
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Hassanin A. Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19. Gene X 2022; 835:146641. [PMID: 35700806 PMCID: PMC9200079 DOI: 10.1016/j.gene.2022.146641] [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: 01/15/2022] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degenerate codons. The results show evidence for the eight following groups: (i) SARS-CoV related coronaviruses (SCoVrC including many bat viruses from China), (ii) SARS-CoV-2 related coronaviruses (SCoV2rC; including five bat viruses from Cambodia, Thailand and Yunnan), (iii) pangolin sarbecoviruses, (iv) three bat sarbecoviruses showing evidence of recombination between SCoVrC and SCoV2rC genomes, (v) two highly divergent bat sarbecoviruses from Yunnan, (vi) the bat sarbecovirus from Japan, (vii) the bat sarbecovirus from Bulgaria, and (viii) the bat sarbecovirus from Kenya. All these groups can be diagnosed by specific nucleotide compositional features except the one concerned by recombination between SCoVrC and SCoV2rC. In particular, SCoV2rC genomes have less cytosines and more uracils at third codon-positions than other sarbecoviruses, whereas the genomes of pangolin sarbecoviruses show more adenines at third codon-positions. I suggest that taxonomic differences in the imbalanced nucleotide pools available in host cells during viral replication can explain the eight groups of SNC here detected among Sarbecovirus genomes. A related effect due to hibernating bats and their latitudinal distribution is also discussed. I conclude that the two independent host switches from Rhinolophus bats to pangolins resulted in convergent mutational constraints and that SARS-CoV-2 emerged directly from a horseshoe bat sarbecovirus.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, EPHE, MNHN, UA, Paris, France.
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20
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Inactivated SARS-CoV-2 Vaccine Shows Cross-Protection against Bat SARS-Related Coronaviruses in Human ACE2 Transgenic Mice. J Virol 2022; 96:e0016922. [PMID: 35343762 PMCID: PMC9044931 DOI: 10.1128/jvi.00169-22] [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] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-1) and SARS-CoV-2 are highly pathogenic to humans and have caused pandemics in 2003 and 2019, respectively. Genetically diverse SARS-related coronaviruses (SARSr-CoVs) have been detected or isolated from bats, and some of these viruses have been demonstrated to utilize human angiotensin-converting enzyme 2 (ACE2) as a receptor and to have the potential to spill over to humans. A pan-sarbecovirus vaccine that provides protection against SARSr-CoV infection is urgently needed. In this study, we evaluated the protective efficacy of an inactivated SARS-CoV-2 vaccine against recombinant SARSr-CoVs carrying two different spike proteins (named rWIV1 and rRsSHC014S, respectively). Although serum neutralizing assays showed limited cross-reactivity between the three viruses, the inactivated SARS-CoV-2 vaccine provided full protection against SARS-CoV-2 and rWIV1 and partial protection against rRsSHC014S infection in human ACE2 transgenic mice. Passive transfer of SARS-CoV-2-vaccinated mouse sera provided low protection for rWIV1 but not for rRsSHC014S infection in human ACE2 mice. A specific cellular immune response induced by WIV1 membrane protein peptides was detected in the vaccinated animals, which may explain the cross-protection of the inactivated vaccine. This study shows the possibility of developing a pan-sarbecovirus vaccine against SARSr-CoVs for future preparedness. IMPORTANCE The genetic diversity of SARSr-CoVs in wildlife and their potential risk of cross-species infection highlight the necessity of developing wide-spectrum vaccines against infection of various SARSr-CoVs. In this study, we tested the protective efficacy of the SARS-CoV-2 inactivated vaccine (IAV) against two SARSr-CoVs with different spike proteins in human ACE2 transgenic mice. We demonstrate that the SARS-CoV-2 IAV provides full protection against rWIV1 and partial protection against rRsSHC014S. The T-cell response stimulated by the M protein may account for the cross protection against heterogeneous SARSr-CoVs. Our findings suggest the feasibility of the development of pan-sarbecovirus vaccines, which can be a strategy of preparedness for future outbreaks caused by novel SARSr-CoVs from wildlife.
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21
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Hassanin A, Rambaud O, Klein D. Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses. Viruses 2022; 14:v14020440. [PMID: 35216033 PMCID: PMC8879460 DOI: 10.3390/v14020440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/07/2022] [Accepted: 02/18/2022] [Indexed: 01/22/2023] Open
Abstract
Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.
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22
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- *Correspondence: Cara E. Brook
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23
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Peng MS, Li JB, Cai ZF, Liu H, Tang X, Ying R, Zhang JN, Tao JJ, Yin TT, Zhang T, Hu JY, Wu RN, Zhou ZY, Zhang ZG, Yu L, Yao YG, Shi ZL, Lu XM, Lu J, Zhang YP. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zool Res 2021; 42:834-844. [PMID: 34766482 PMCID: PMC8645874 DOI: 10.24272/j.issn.2095-8137.2021.334] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 11/07/2022] Open
Abstract
Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. E-mail:
| | - Jian-Bo Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Zheng-Fei Cai
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Hang Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruochen Ying
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jia-Nan Zhang
- Molbreeding Biotechnology Co., Ltd., Shijiazhuang, Hebei 050035, China
| | - Jia-Jun Tao
- Molbreeding Biotechnology Co., Ltd., Shijiazhuang, Hebei 050035, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Tao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Ru-Nian Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhong-Yin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Gang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650201, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Xue-Mei Lu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. E-mail:
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24
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Islam MS, Hasib FMY, Nath C, Ara J, Nu MS, Fazal MA, Chowdhury S. Coronavirus disease 2019 and its potential animal reservoirs: A review. INTERNATIONAL JOURNAL OF ONE HEALTH 2021. [DOI: 10.14202/ijoh.2021.171-181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the 21st century, the world has been plagued by coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus of the family Coronaviridae epidemiologically suspected to be linked to a wet market in Wuhan, China. The involvement of wildlife and wet markets with the previous outbreaks simultaneously has been brought into sharp focus. Although scientists are yet to ascertain the host range and zoonotic potential of SARS-CoV-2 rigorously, information about its two ancestors, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), is a footprint for research on COVID-19. A 96% genetic similarity with bat coronaviruses and SARS-CoV-2 indicates that the bat might be a potential reservoir of SARS-CoV-2 just like SARS-CoV and MERS-CoV, where civets and dromedary camels are considered the potential intermediate host, respectively. Perceiving the genetic similarity between pangolin coronavirus and SARS-CoV-2, many scientists also have given the scheme that the pangolin might be the intermediate host. The involvement of SARS-CoV-2 with other animals, such as mink, snake, and turtle has also been highlighted in different research articles based on the interaction between the key amino acids of S protein in the receptor-binding domain and angiotensin-converting enzyme II (ACE2). This study highlights the potential animal reservoirs of SARS-CoV-2 and the role of wildlife in the COVID-19 pandemic. Although different causes, such as recurring viral genome recombination, wide genetic assortment, and irksome food habits, have been blamed for this emergence, basic research studies and literature reviews indicate an enormous consortium between humans and animals for the COVID-19 pandemic.
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Affiliation(s)
- Md. Sirazul Islam
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - F. M. Yasir Hasib
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Chandan Nath
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Jahan Ara
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Mong Sing Nu
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md. Abul Fazal
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Sharmin Chowdhury
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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25
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Vale FF, Vítor JMB, Marques AT, Azevedo-Pereira JM, Anes E, Goncalves J. Origin, phylogeny, variability and epitope conservation of SARS-CoV-2 worldwide. Virus Res 2021; 304:198526. [PMID: 34339772 PMCID: PMC8323504 DOI: 10.1016/j.virusres.2021.198526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses innumerous challenges, like understanding what triggered the emergence of this new human virus, how this RNA virus is evolving or how the variability of viral genome may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at GenBank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Additionally, we analyzed 199,984 spike glycoprotein sequences. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide variants (SNVs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNVs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. Additionally, all predicted epitopes for the structural E, M and N proteins are highly conserved. The amino acid changes present in the spike glycoprotein of variables of concern (VOCs) comprise between 3.4% and 20.7% of the predicted epitopes of this protein. These results favors the continuous efficacy of the available vaccines targeting the spike protein, and other structural proteins. Multiple epitopes vaccines should sustain vaccine efficacy since at least some of the epitopes present in variability regions of VOCs are conserved and thus recognizable by antibodies.
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Affiliation(s)
- Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal.
| | - Jorge M B Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy, Pharmacology and Health Technologies Department, Faculty of Pharmacy, Universidade de Lisboa, Lisbon 1649-003, Portugal
| | - Andreia T Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Joao Goncalves
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
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26
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Hassanin A, Tu VT, Curaudeau M, Csorba G. Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species. Sci Rep 2021; 11:14276. [PMID: 34253798 PMCID: PMC8275577 DOI: 10.1038/s41598-021-93738-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023] Open
Abstract
The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as reservoirs of viruses closely related to SARS-CoV-2. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia and China. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of bat viruses closely related to SARS-CoV-2 was predicted using the four localities in which bat viruses were recently discovered and the localities where bats showed the same CO1 haplotypes than virus-positive bats. The ecological niche of bat viruses related to SARS-CoV was deduced from the localities where bat viruses were previously detected. The results show that the ecological niche of bat viruses related to SARS-CoV2 includes several regions of mainland Southeast Asia whereas the ecological niche of bat viruses related to SARS-CoV is mainly restricted to China. In agreement with these results, human populations in Laos, Vietnam, Cambodia, and Thailand appear to be much less affected by the COVID-19 pandemic than other countries of Southeast Asia. In the climatic transitional zone between the two ecological niches (southern Yunnan, northern Laos, northern Vietnam), genomic recombination between highly divergent viruses is more likely to occur. Considering the limited data and the risk of recombinant bat-CoVs emergence as the source of new pandemics in humans, the bat populations in these regions should be under surveillance.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), SU, MNHN, CNRS, EPHE, UA, Sorbonne Université, Paris, France.
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
| | - Manon Curaudeau
- Institut de Systématique, Évolution, Biodiversité (ISYEB), SU, MNHN, CNRS, EPHE, UA, Sorbonne Université, Paris, France
| | - Gabor Csorba
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13, Budapest, H-1088, Hungary
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27
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Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations. Viruses 2021; 13:v13050936. [PMID: 34070175 PMCID: PMC8158508 DOI: 10.3390/v13050936] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/13/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.
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28
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. Science 2021; 371:735-741. [PMID: 33436524 PMCID: PMC7928838 DOI: 10.1126/science.abf6840] [Citation(s) in RCA: 275] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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29
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Wells HL, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba DK, Navarrete-Macias I, Liang E, Cranfield M, Han BA, Tingley MW, Diuk-Wasser M, Goldstein T, Johnson CK, Mazet JAK, Chandran K, Munster VJ, Gilardi K, Anthony SJ. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. Virus Evol 2021; 7:veab007. [PMID: 33754082 PMCID: PMC7928622 DOI: 10.1093/ve/veab007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S. 4th St, Hamilton, MT 59840, USA.,Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - D K Byarugaba
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,Makerere University, College of Veterinary Medicine, Living Stone Road, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, 125 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - B A Han
- Cary Institute of Ecosystem Studies, 2801 Sharon Turnpike, Millbrook, NY 12545, USA
| | - M W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - M Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - C K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - V J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - S J Anthony
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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30
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Wells H, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba D, Navarrete-Macias I, Liang E, Cranfield M, Han B, Tingley M, Diuk-Wasser M, Goldstein T, Johnson C, Mazet J, Chandran K, Munster V, Gilardi K, Anthony S. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.07.07.190546. [PMID: 32676605 PMCID: PMC7359528 DOI: 10.1101/2020.07.07.190546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H.L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - D.K Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- Makerere University, College of Veterinary Medicine, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - B.A Han
- Cary Institute of Ecosystem Studies, Millbrook, New York, USA
| | - M.W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - M Diuk-Wasser
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - C.K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - J Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - K Chandran
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - V.J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Kampala, Uganda
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - S.J Anthony
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, California, USA
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31
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Kia GSN, Tao Y, Umoh JU, Kwaga JKP, Tong S. Identification of Coronaviruses, Paramyxoviruses, Reoviruses, and Rotaviruses among Bats in Nigeria. Am J Trop Med Hyg 2021; 104:1106-1110. [PMID: 33534762 DOI: 10.4269/ajtmh.19-0872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/04/2020] [Indexed: 11/07/2022] Open
Abstract
Bats are often consumed by some ethnic groups in Nigeria despite association of bats with many important emerging viruses. More than 300 bats representing eight species were captured during 2010-2011 in eight locations of northern Nigeria. Available fecal swabs (n = 95) were screened for the presence of arenaviruses, CoVs, paramyxoviruses (PMVs), reoviruses, rhabdoviruses, and influenza viruses using generic reverse transcription-polymerase chain reaction assays. Here, we document the detection of CoVs, PMVs, reoviruses, and rotaviruses (RVs) in Nigerian bats. The Nigerian bat CoVs are grouped within other bat SARS-CoV-like viruses identified from Ghana in a sister clade next to the human SARS-CoV clade. The phylogenetic analysis indicated a broad range of RVs present in Nigerian bats, some cluster with human RVs and some represent novel species. Our study adds that continuing global surveillance for viruses in bats to understand their origin, adaptation, and evolution is important to prevent and control future zoonotic disease outbreaks.
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Affiliation(s)
| | - Ying Tao
- 2Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Suxiang Tong
- 2Centers for Disease Control and Prevention, Atlanta, Georgia
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32
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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33
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33236016 PMCID: PMC7685334 DOI: 10.1101/2020.11.17.387092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protection against SARS-CoV-2 and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor-binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles; 4–8 distinct RBDs). Mice immunized with RBD-nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic-RBD-nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs compared to sera from immunizations with homotypic SARS-CoV-2–RBD-nanoparticles or COVID-19 convalescent human plasmas. Moreover, sera from mosaic-RBD–immunized mice neutralized heterologous pseudotyped coronaviruses equivalently or better after priming than sera from homotypic SARS-CoV-2–RBD-nanoparticle immunizations, demonstrating no immunogenicity loss against particular RBDs resulting from co-display. A single immunization with mosaic-RBD-nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses. One sentence summary: Nanoparticle strategy for pan-sarbecovirus vaccine Immunizing with nanoparticles displaying diverse coronavirus RBDs elicits cross-reactive and neutralizing antibody responses.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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34
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The zoonotic potential of bat-borne coronaviruses. Emerg Top Life Sci 2020; 4:353-369. [PMID: 33258903 DOI: 10.1042/etls20200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Seven zoonoses - human infections of animal origin - have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.
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35
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Murakami S, Kitamura T, Suzuki J, Sato R, Aoi T, Fujii M, Matsugo H, Kamiki H, Ishida H, Takenaka-Uema A, Shimojima M, Horimoto T. Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan. Emerg Infect Dis 2020; 26:3025-3029. [PMID: 33219796 PMCID: PMC7706965 DOI: 10.3201/eid2612.203386] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epidemiology of bat Betacoronavirus, subgenus Sarbecovirus is largely unknown, especially outside China. We detected a sarbecovirus phylogenetically related to severe acute respiratory syndrome coronavirus 2 from Rhinolophus cornutus bats in Japan. The sarbecovirus' spike protein specifically recognizes angiotensin-converting enzyme 2 of R. cornutus, but not humans, as an entry receptor.
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36
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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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37
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Tiwari M, Mishra D. Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design. J Clin Virol 2020; 128:104441. [PMID: 32425659 PMCID: PMC7227581 DOI: 10.1016/j.jcv.2020.104441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Novel coronavirus has wrecked medical and health care facilities claiming ∼5% death tollsglobally. All efforts to contain the pathogenesis either using inhibitory drugs or vaccines largelyremained futile due to a lack of better understanding of the genomic feature of this virus. In thepresent study, we compared the 2019-nCoV with other coronaviruses, which indicated that batSARS like coronavirus could be a probable ancestor of the novel coronavirus. The proteinsequence similarity of pangolin-hCoV and bat-hCoV with human coronavirus was higher ascompared to their nucleotide similarity denoting the occurrence of more synonymous mutationsin the genome. Phylogenetic and alignment analysis of 591 novel coronaviruses of differentclades from Group I to Group V revealed several mutations and concomitant amino acidchanges. Detailed investigation on nucleotide substitution unfolded 100 substitutions in thecoding region of which 43 were synonymous and 57 were of non-synonymous type. The nonsynonymous substitutions resulting into 57 amino acid changes were found to be distributed overdifferent hCoV proteins with maximum on spike protein. An important di-amino acid change RGto KR was observed in ORF9 protein. Additionally, several interesting features of the novelcoronavirus genome have been highlighted in respect to various other human infecting viruseswhich may explain extreme pathogenicity, infectivity and simultaneously the reason behindfailure of the antiviral therapies. SUMMARY: This study presents a comprehensive phylogenetic analysis of SARS-CoV2 isolates to understand discrete mutations that are occurring between patient samples. The analysis unravel various amino acid mutations in the viral proteins which may provide an explanation for varying treatment efficacies of different inhibitory drugs and a future direction towards a combinatorial treatment therapies based on the kind of mutation in the viral genome.
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Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Divya Mishra
- Department of Plant Pathology, Kansas State University, 66506, Kansas, United States.
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38
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1101/2020.02.13.945485] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 05/24/2023]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China.
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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39
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Abstract
Abstract
Viruses similar to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been discovered in bats of the genus Rhinolophus and in the Sunda pangolin, Manis javanica Desmarest, 1822, suggesting that these animals have played a key role in the emergence of the Covid-19 outbreak in the city of Wuhan, China. In this paper, we review the available data for sarbecoviruses (viruses related to SARS-CoV [2002–2003 outbreak] and SARS-CoV-2) to propose all possible hypotheses on the origin of Covid-19, i. e., involving direct transmission from horseshoe bats to humans, indirect transmission via the pangolin or another animal, with interspecies contamination between either wild animals or animals kept in cage. Present evidence indicates that Rhinolophus bats are the natural reservoir of all sarbecoviruses, and that two divergent SARS-CoV-2-like viruses have circulated in southern China (at least in Guangxi and Guangdong provinces) between August 2017 and March 2019 in captive pangolins destined for sale in wildlife markets. We performed a genetic analysis of seven seized pangolins found to be positive for SARS-CoV-2-like virus using mitochondrial DNA sequences extracted from Sequence Reads Archive data. The results reveal that the same SARS-CoV-2-like virus can be found in animals with distinct haplotypes, which means that they were probably captured in different Southeast Asian regions. Our interpretation is that some pangolins were contaminated in captivity (by other pangolins or by another species to be determined), suggesting that illegal trade of living wild mammals is at the origin of the Covid-19 outbreak. To definitely validate this hypothesis, it is however necessary to discover a virus almost identical to SARS CoV-2 (at least 99% of identity) in animals sold in wet markets. Although pangolins are good candidates, other mammals, such as small carnivores, should not be overlooked.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN , Sorbonne Université, EPHE, Université des Antilles, Muséum National d’Histoire Naturelle , CP 51, 57 rue Cuvier, 75231 , Paris Cedex 05 , France
| | - Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN , Sorbonne Université, EPHE, Université des Antilles, Muséum National d’Histoire Naturelle , CP 51, 57 rue Cuvier, 75231 , Paris Cedex 05 , France
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN , Sorbonne Université, EPHE, Université des Antilles, Muséum National d’Histoire Naturelle , CP 51, 57 rue Cuvier, 75231 , Paris Cedex 05 , France
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40
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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020. [PMID: 32123347 DOI: 10.1038/s41564-020-0695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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41
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Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LL, Samborskiy D, Sidorov IA, Sola I, Ziebuhr J. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5:536-544. [PMID: 32123347 DOI: 10.1101/2020.02.07.937862] [Citation(s) in RCA: 399] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 05/21/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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42
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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020. [PMID: 32123347 DOI: 10.1038/s41564-020-0598-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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43
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020. [DOI: 10.1038/s41586-020-2169-0 10.1101/2020.02.13.945485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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44
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1038/s41586-020-2169-0] [Citation(s) in RCA: 1137] [Impact Index Per Article: 284.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 11/09/2022]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China. .,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China. .,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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