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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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2
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Cohen LE, Fagre AC, Chen B, Carlson CJ, Becker DJ. Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis. Nat Microbiol 2023; 8:1176-1186. [PMID: 37231088 PMCID: PMC10234814 DOI: 10.1038/s41564-023-01375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records of infection prevalence at the finest methodological, spatiotemporal and phylogenetic level of detail possible from public records into an open, static database named datacov, together with metadata on sampling and diagnostic methods. We found substantial heterogeneity in viral prevalence across studies, reflecting spatiotemporal variation in viral dynamics and methodological differences. Meta-analysis identified sample type and sampling design as the best predictors of prevalence, with virus detection maximized in rectal and faecal samples and by repeat sampling of the same site. Fewer than one in five studies collected and reported longitudinal data, and euthanasia did not improve virus detection. We show that bat sampling before the SARS-CoV-2 pandemic was concentrated in China, with research gaps in South Asia, the Americas and sub-Saharan Africa, and in subfamilies of phyllostomid bats. We propose that surveillance strategies should address these gaps to improve global health security and enable the origins of zoonotic coronaviruses to be identified.
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Affiliation(s)
- Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
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3
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Popov IV, Ohlopkova OV, Donnik IM, Zolotukhin PV, Umanets A, Golovin SN, Malinovkin AV, Belanova AA, Lipilkin PV, Lipilkina TA, Popov IV, Logvinov AK, Dubovitsky NA, Stolbunova KA, Sobolev IA, Alekseev AY, Shestopalov AM, Burkova VN, Chikindas ML, Venema K, Ermakov AM. Detection of coronaviruses in insectivorous bats of Fore-Caucasus, 2021. Sci Rep 2023; 13:2306. [PMID: 36759670 PMCID: PMC9909659 DOI: 10.1038/s41598-023-29099-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Coronaviruses (CoVs) pose a huge threat to public health as emerging viruses. Bat-borne CoVs are especially unpredictable in their evolution due to some unique features of bat physiology boosting the rate of mutations in CoVs, which is already high by itself compared to other viruses. Among bats, a meta-analysis of overall CoVs epizootiology identified a nucleic acid observed prevalence of 9.8% (95% CI 8.7-10.9%). The main objectives of our study were to conduct a qPCR screening of CoVs' prevalence in the insectivorous bat population of Fore-Caucasus and perform their characterization based on the metagenomic NGS of samples with detected CoV RNA. According to the qPCR screening, CoV RNA was detected in 5 samples, resulting in a 3.33% (95% CI 1.1-7.6%) prevalence of CoVs in bats from these studied locations. BetaCoVs reads were identified in raw metagenomic NGS data, however, detailed characterization was not possible due to relatively low RNA concentration in samples. Our results correspond to other studies, although a lower prevalence in qPCR studies was observed compared to other regions and countries. Further studies should require deeper metagenomic NGS investigation, as a supplementary method, which will allow detailed CoV characterization.
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Affiliation(s)
- Igor V Popov
- Centre for Healthy Eating and Food Innovation, Maastricht University-Campus Venlo, 5900 AA, Venlo, The Netherlands.
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia.
| | - Olesia V Ohlopkova
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program On the Development of Genetic Technologies, Koltsovo, 630559, Russia
| | - Irina M Donnik
- Ural State Agrarian University, Ekaterinburg, 620075, Russia
| | | | - Alexander Umanets
- Centre for Healthy Eating and Food Innovation, Maastricht University-Campus Venlo, 5900 AA, Venlo, The Netherlands
- Maastricht University, Youth, Food and Health, 5900 AA, Venlo, The Netherlands
| | - Sergey N Golovin
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | - Aleksey V Malinovkin
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | | | - Pavel V Lipilkin
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | - Tatyana A Lipilkina
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | - Ilya V Popov
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | - Alexandr K Logvinov
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
| | - Nikita A Dubovitsky
- Research Institute of Virology, Federal State Budgetary Scientific Institution "Federal Research Center for Fundamental and Translational Medicine", 630117, Novosibirsk, Russia
| | - Kristina A Stolbunova
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, 630559, Koltsovo, Russia
| | - Ivan A Sobolev
- Research Institute of Virology, Federal State Budgetary Scientific Institution "Federal Research Center for Fundamental and Translational Medicine", 630117, Novosibirsk, Russia
| | - Alexander Yu Alekseev
- Research Institute of Virology, Federal State Budgetary Scientific Institution "Federal Research Center for Fundamental and Translational Medicine", 630117, Novosibirsk, Russia
| | - Alexander M Shestopalov
- Research Institute of Virology, Federal State Budgetary Scientific Institution "Federal Research Center for Fundamental and Translational Medicine", 630117, Novosibirsk, Russia
| | - Valentina N Burkova
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia
- National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Michael L Chikindas
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ, 08901, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Koen Venema
- Centre for Healthy Eating and Food Innovation, Maastricht University-Campus Venlo, 5900 AA, Venlo, The Netherlands
| | - Alexey M Ermakov
- Agrobiotechnology Center, Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, Rostov-On-Don, 344000, Russia
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4
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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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5
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Goud VR, Chakraborty R, Chakraborty A, Lavudi K, Patnaik S, Sharma S, Patnaik S. A bioinformatic approach of targeting SARS-CoV-2 replication by silencing a conserved alternative reserve of the orf8 gene using host miRNAs. Comput Biol Med 2022; 145:105436. [PMID: 35366472 PMCID: PMC8942883 DOI: 10.1016/j.compbiomed.2022.105436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 12/16/2022]
Abstract
The causative agent of the COVID-19 pandemic, the SARS-CoV-2 virus has yielded multiple relevant mutations, many of which have branched into major variants. The Omicron variant has a huge similarity with the original viral strain (first COVID-19 strain from Wuhan). Among different genes, the highly variable orf8 gene is responsible for crucial host interactions and has undergone multiple mutations and indels. The sequence of the orf8 gene of the Omicron variant is, however, identical with the gene sequence of the wild type. orf8 modulates the host immunity making it easier for the virus to conceal itself and remain undetected. Variants seem to be deleting this gene without affecting the viral replication. While analyzing, we came across the conserved orf7a gene in the viral genome which exhibits a partial sequence homology as well as functional similarity with the SARS-CoV-2 orf8. Hence, we have proposed here in our hypothesis that, orf7a might be an alternative reserve of orf8 present in the virus which was compensating for the lost gene. A computational approach was adopted where we screened various miRNAs targeted against the orf8 gene. These miRNAs were then docked onto the orf8 mRNA sequences. The same set of miRNAs was then used to check for their binding affinity with the orf7a reference mRNA. Results showed that miRNAs targeting the orf8 had favorable shape complementarity and successfully docked with the orf7a gene as well. These findings provide a basis for developing new therapeutic approaches where both orf8 and orf7a can be targeted simultaneously.
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Affiliation(s)
| | | | | | - Kousalya Lavudi
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Sriram Patnaik
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Swati Sharma
- School of Biotechnology, KIIT University, Bhubaneswar, India,Dept. of Skill Buildings Shri Ramasamy Memorial University, Sikkim, Gangtok, 737102, India
| | - Srinivas Patnaik
- School of Biotechnology, KIIT University, Bhubaneswar, India,Corresponding author. School of Biotechnology, KIIT University, Bhubaneswar, 751024, India
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6
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Urushadze L, Babuadze G, Shi M, Escobar LE, Mauldin MR, Natradeze I, Machablishvili A, Kutateladze T, Imnadze P, Nakazawa Y, Velasco-Villa A. A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia. Viruses 2021; 14:v14010072. [PMID: 35062276 PMCID: PMC8778869 DOI: 10.3390/v14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022] Open
Abstract
Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.
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Affiliation(s)
- Lela Urushadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - George Babuadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Biological Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Main Campus, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Mang Shi
- Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China;
| | - Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601, USA;
| | - Matthew R. Mauldin
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Ioseb Natradeze
- Institute of Zoology, Campus S, Ilia State University, Tbilisi 0162, Georgia;
| | - Ann Machablishvili
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Tamar Kutateladze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
| | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi 0198, Georgia; (L.U.); (G.B.); (A.M.); (T.K.); (P.I.)
- Department of Public Health and Epidemiology, Faculty of Medicine, Main Campus, Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Yoshinori Nakazawa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
| | - Andres Velasco-Villa
- Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; (M.R.M.); (Y.N.)
- Correspondence:
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7
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Cappelle J, Furey N, Hoem T, Ou TP, Lim T, Hul V, Heng O, Chevalier V, Dussart P, Duong V. Longitudinal monitoring in Cambodia suggests higher circulation of alpha and betacoronaviruses in juvenile and immature bats of three species. Sci Rep 2021; 11:24145. [PMID: 34921180 PMCID: PMC8683416 DOI: 10.1038/s41598-021-03169-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/25/2021] [Indexed: 12/28/2022] Open
Abstract
Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46-7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.
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Affiliation(s)
- Julien Cappelle
- CIRAD, UMR ASTRE (Animal, Santé, Territoires, Risques, Ecosystèmes), TA A 117/E, Campus International de Baillarguet, 34398, Montpellier CEDEX 5, France.
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France.
| | - Neil Furey
- Harrison Institute, Sevenoaks, Kent, England
- Fauna and Flora International, Phnom Penh, Cambodia
| | - Thavry Hoem
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Tey Putita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Thona Lim
- Free the Bears, Phnom Penh, Cambodia
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Oudam Heng
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Véronique Chevalier
- CIRAD, UMR ASTRE (Animal, Santé, Territoires, Risques, Ecosystèmes), TA A 117/E, Campus International de Baillarguet, 34398, Montpellier CEDEX 5, France
- ASTRE, CIRAD, INRAE, Univ Montpellier, Montpellier, France
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- Virology Unit, Institut Pasteur de Madagascar, Institut Pasteur International Network, Antananarivo, Madagascar
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
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8
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Hakim MS. SARS-CoV-2, Covid-19, and the debunking of conspiracy theories. Rev Med Virol 2021; 31:e2222. [PMID: 33586302 PMCID: PMC7995093 DOI: 10.1002/rmv.2222] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/25/2022]
Abstract
The emergence of a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has engaged considerable awareness and attention around the world. The associated disease, coronavirus disease 2019 (Covid-19), has now involved virtually all 200 countries. The total number of confirmed cases has been much more than in the two previous outbreaks of human coronaviruses, that is, SARS-CoV and Middle East respiratory syndrome coronavirus. In line with the outbreak escalation, false information about SARS-CoV-2 and its associated disease disseminated globally, particularly through online and social media. Believers in conspiracy theories promote misinformation that the virus is not contagious, is the result of laboratory manipulation or is created to gain profit by distributing new vaccines. The most dangerous effect of this widely disseminated misinformation is it will negatively influence the attitudes and behaviours for preventive measures to contain the outbreak. In this review, I discuss common conspiracy theories associated with SARS-CoV-2 and Covid-19 and consider how we can address and counterbalance these issues based on scientific information and studies.
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Affiliation(s)
- Mohamad S. Hakim
- Department of MicrobiologyFaculty of Medicine, Public Health and NursingUniversitas Gadjah MadaYogyakartaIndonesia
- Center for Child Health—PROFaculty of Medicine, Public Health and NursingUniversitas Gadjah MadaYogyakartaIndonesia
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9
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Jallouli M, Zemni M, Ben Mabrouk A, Mahjoub MA. Toward new multi-wavelets: associated filters and algorithms. Part I: theoretical framework and investigation of biomedical signals, ECG, and coronavirus cases. Soft comput 2021; 25:14059-14079. [PMID: 34512141 PMCID: PMC8419217 DOI: 10.1007/s00500-021-06217-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/29/2022]
Abstract
Biosignals are nowadays important subjects for scientific researches from both theory, and applications, especially, with the appearance of new pandemics threatening the humanity such as the new coronavirus. One aim in the present work is to prove that wavelets may be a successful machinery to understand such phenomena by applying a step forward extension of wavelets to multi-wavelets. We proposed in a first step to improve multi-wavelet notion by constructing more general families using independent components for multi-scaling and multi-wavelet mother functions. A special multi-wavelet is then introduced, continuous, and discrete multi-wavelet transforms are associated, as well as new filters, and algorithms of decomposition, and reconstruction. Applied breakthroughs of the paper may be summarized in three aims. In a first direction, an approximation (reconstruction) of a classical (stationary, periodic) example dealing with Fourier modes has been conducted in order to confirm the efficiency of the HSch multi-wavelets in approximating such signals and in providing fast algorithms. The second experimentation is concerned with the decomposition and reconstruction application of the HSch multi-wavelet on an ECG signal. The last experimentation is concerned with a de-noising application on a strain of coronavirus signal permitting to localize approximately the transmembrane segments of such a series as neighborhoods of the local maxima of an numerized version of the strain. Accuracy of the method has been evaluated by means of error estimates and statistical tests.
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Affiliation(s)
- Malika Jallouli
- LATIS, Laboratory of Advanced Technology, and Intelligent Systems, Université de Sousse, Ecole Nationale d’Ingénieurs de Sousse, 4023 Sousse, Tunisie
| | - Makerem Zemni
- LATIS, Laboratory of Advanced Technology, and Intelligent Systems, Université de Sousse, Ecole Nationale d’Ingénieurs de Sousse, 4023 Sousse, Tunisie
| | - Anouar Ben Mabrouk
- Laboratory of Algebra, Number Theory, and Nonlinear Analysis LR15ES18, Department of Mathematics, Faculty of Sciences, University of Monastir, 5000 Monastir, Tunisia
- Department of Mathematics, Higher Institute of Applied Mathematics, and Computer Science, Street of Assad Ibn Alfourat, University of Kairouan, 3100 Kairouan, Tunisia
- Department of Mathematics, College of Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohamed Ali Mahjoub
- LATIS, Laboratory of Advanced Technology, and Intelligent Systems, Université de Sousse, Ecole Nationale d’Ingénieurs de Sousse, 4023 Sousse, Tunisie
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10
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Liang J, Zhu C, Zhang L. Cospeciation of coronavirus and paramyxovirus with their bat hosts in the same geographical areas. BMC Ecol Evol 2021; 21:148. [PMID: 34325659 PMCID: PMC8319908 DOI: 10.1186/s12862-021-01878-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Bat-borne viruses are relatively host specific. We hypothesize that this host specificity is due to coevolution of the viruses with their hosts. To test this hypothesis, we investigated the coevolution of coronavirus and paramyxovirus with their bat hosts. Published nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) gene of 60 coronavirus strains identified from 37 bat species, the RNA polymerase large (L) gene of 36 paramyxovirus strains from 29 bat species, and the cytochrome B (cytB) gene of 35 bat species were analyzed for coevolution signals. Each coevolution signal detected was tested and verified by global-fit cophylogenic analysis using software ParaFit, PACo, and eMPRess. Results Significant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry closely related viruses. Conclusions Our results suggest that paramyxovirus and coronavirus coevolve with their hosts.
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Affiliation(s)
- Jie Liang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Chunchao Zhu
- Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
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11
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Perveen N, Muzaffar SB, Al-Deeb MA. Exploring human-animal host interactions and emergence of COVID-19: Evolutionary and ecological dynamics. Saudi J Biol Sci 2021; 28:1417-1425. [PMID: 33281479 PMCID: PMC7708805 DOI: 10.1016/j.sjbs.2020.11.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease (COVID-19) that emerged in December 2019 had caused substantial morbidity and mortality at the global level within few months. It affected economies, stopped travel, and isolated individuals and populations around the world. Wildlife, especially bats, serve as reservoirs of coronaviruses from which the variant Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged that causes COVID-19. In this review, we describe the current knowledge on COVID-19 and the significance of wildlife hosts in its emergence. Mammalian and avian coronaviruses have diverse host ranges with distinct lineages of coronaviruses. Recombination and reassortments occur more frequently in mixed-animal markets where diverse viral genotypes intermingle. Human coronaviruses have evolved through gene gains and losses primarily in interfaces where wildlife and humans come in frequent contact. There is a gap in our understanding of bats as reservoirs of coronaviruses and there is a misconception that bats periodically transmit coronaviruses to humans. Future research should investigate bat viral diversity and loads at interfaces between humans and bats. Furthermore, there is an urgent need to evaluate viral strains circulating in mixed animal markets, where the coronaviruses circulated before becoming adapted to humans. We propose and discuss a management intervention plan for COVID-19 and raise questions on the suitability of current containment plans. We anticipate that more virulent coronaviruses could emerge unless proper measures are taken to limit interactions between diverse wildlife and humans in wild animal markets.
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Affiliation(s)
- Nighat Perveen
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Sabir Bin Muzaffar
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Mohammad Ali Al-Deeb
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
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12
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Zhu W, Yang J, Lu S, Lan R, Jin D, Luo XL, Pu J, Wu S, Xu J. Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China. Virol Sin 2020; 36:402-411. [PMID: 33259031 PMCID: PMC7706178 DOI: 10.1007/s12250-020-00325-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/27/2020] [Indexed: 12/02/2022] Open
Abstract
Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world’s high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, 815000, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, China.
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13
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Latinne A, Hu B, Olival KJ, Zhu G, Zhang L, Li H, Chmura AA, Field HE, Zambrana-Torrelio C, Epstein JH, Li B, Zhang W, Wang LF, Shi ZL, Daszak P. Origin and cross-species transmission of bat coronaviruses in China. Nat Commun 2020; 11:4235. [PMID: 32843626 PMCID: PMC7447761 DOI: 10.1038/s41467-020-17687-3] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 07/06/2020] [Indexed: 12/31/2022] Open
Abstract
Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.
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Affiliation(s)
- Alice Latinne
- EcoHealth Alliance, New York, USA
- Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam; Wildlife Conservation Society, Health Program, Bronx, NY, USA
| | - Ben Hu
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Libiao Zhang
- Guangdong Institute of Applied Biological Resources, Guangdong Academy of Sciences, Guangzhou, China
| | | | | | - Hume E Field
- EcoHealth Alliance, New York, USA
- School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia
| | | | | | - Bei Li
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Zheng-Li Shi
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
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14
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Gautam A, Kaphle K, Shrestha B, Phuyal S. Susceptibility to SARS, MERS, and COVID-19 from animal health perspective. Open Vet J 2020; 10:164-177. [PMID: 32821661 PMCID: PMC7419072 DOI: 10.4314/ovj.v10i2.6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/11/2022] Open
Abstract
Viruses are having great time as they seem to have bogged humans down. Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and novel coronavirus (COVID-19) are the three major coronaviruses of present-day global human and animal health concern. COVID-19 caused by SARS-CoV-2 is identified as the newest disease, presumably of bat origin. Different theories on the evolution of viruses are in circulation, yet there is no denying the fact that the animal source is the skeleton. The whole world is witnessing the terror of the COVID-19 pandemic that is following the same path of SARS and MERS, and seems to be more severe. In addition to humans, several species of animals are reported to have been infected with these life-threatening viruses. The possible routes of transmission and their zoonotic potentialities are the subjects of intense research. This review article aims to overview the link of all these three deadly coronaviruses among animals along with their phylogenic evolution and cross-species transmission. This is essential since animals as pets or food are said to pose some risk, and their better understanding is a must in order to prepare a possible plan for future havoc in both human and animal health. Although COVID-19 is causing a human health hazard globally, its reporting in animals are limited compared to SARS and MERS. Non-human primates and carnivores are most susceptible to SARS-coronavirus and SARS-CoV-2, respectively, whereas the dromedary camel is susceptible to MERS-coronavirus. Phylogenetically, the trio viruses are reported to have originated from bats and have special capacity to undergo mutation and genomic recombination in order to infect humans through its reservoir or replication host. However, it is difficult to analyze how the genomic pattern of coronaviruses occurs. Thus, increased possibility of new virus-variants infecting humans and animals in the upcoming days seems to be the biggest challenge for the future of the world. One health approach is portrayed as our best way ahead, and understanding the animal dimension will go a long way in formulating such preparedness plans.
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Affiliation(s)
- Aasish Gautam
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Krishna Kaphle
- Veterinary Teaching Hospital, Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Birendra Shrestha
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Samiksha Phuyal
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
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15
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Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio 2020; 11:e01610-20. [PMID: 32694143 PMCID: PMC7374062 DOI: 10.1128/mbio.01610-20] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/27/2022] Open
Abstract
To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.
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Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Jenny G H Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | - Raphael T C Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
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16
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Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio 2020; 11:mBio.01610-20. [PMID: 32694143 DOI: 10.1101/2020.03.11.987222] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.
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Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Jenny G H Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | - Raphael T C Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
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17
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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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18
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Latinne A, Hu B, Olival KJ, Zhu G, Zhang L, Li H, Chmura AA, Field HE, Zambrana-Torrelio C, Epstein JH, Li B, Zhang W, Wang LF, Shi ZL, Daszak P. Origin and cross-species transmission of bat coronaviruses in China. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32577651 DOI: 10.1101/2020.05.31.116061] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus . Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.
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19
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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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20
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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: 1149] [Impact Index Per Article: 287.3] [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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21
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A new coronavirus associated with human respiratory disease in China. Nature 2020; 579:265-269. [PMID: 32015508 PMCID: PMC7094943 DOI: 10.1038/s41586-020-2008-3] [Citation(s) in RCA: 7099] [Impact Index Per Article: 1774.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/28/2020] [Indexed: 12/02/2022]
Abstract
Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans. Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
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22
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Lim XF, Lee CB, Pascoe SM, How CB, Chan S, Tan JH, Yang X, Zhou P, Shi Z, Sessions OM, Wang LF, Ng LC, Anderson DE, Yap G. Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches. J Gen Virol 2019; 100:1363-1374. [PMID: 31418677 PMCID: PMC7079695 DOI: 10.1099/jgv.0.001307] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bats are important reservoirs and vectors in the transmission of emerging infectious diseases. Many highly pathogenic viruses such as SARS-CoV and rabies-related lyssaviruses have crossed species barriers to infect humans and other animals. In this study we monitored the major roost sites of bats in Singapore, and performed surveillance for zoonotic pathogens in these bats. Screening of guano samples collected during the survey uncovered a bat coronavirus (Betacoronavirus) in Cynopterus brachyotis, commonly known as the lesser dog-faced fruit bat. Using a capture-enrichment sequencing platform, the full-length genome of the bat CoV was sequenced and found to be closely related to the bat coronavirus HKU9 species found in Leschenault’s rousette discovered in the Guangdong and Yunnan provinces.
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Affiliation(s)
- Xiao Fang Lim
- Environmental Health Institute, National Environment Agency, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | | | | | - Choon Beng How
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Sharon Chan
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Jun Hao Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Xinglou Yang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peng Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Zhengli Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - October M Sessions
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Grace Yap
- Environmental Health Institute, National Environment Agency, Singapore
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23
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Kim Y, Son K, Kim YS, Lee SY, Jheong W, Oem JK. Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea. Virus Genes 2019; 55:545-549. [PMID: 31076983 PMCID: PMC7089380 DOI: 10.1007/s11262-019-01668-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/30/2019] [Indexed: 01/05/2023]
Abstract
Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.
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Affiliation(s)
- Yongkwan Kim
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea.,Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Kidong Son
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea
| | - Young-Sik Kim
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Sook-Young Lee
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Weonhwa Jheong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea
| | - Jae-Ku Oem
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea.
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24
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Bat Coronaviruses in China. Viruses 2019; 11:v11030210. [PMID: 30832341 PMCID: PMC6466186 DOI: 10.3390/v11030210] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022] Open
Abstract
During the past two decades, three zoonotic coronaviruses have been identified as the cause of large-scale disease outbreaks–Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Swine Acute Diarrhea Syndrome (SADS). SARS and MERS emerged in 2003 and 2012, respectively, and caused a worldwide pandemic that claimed thousands of human lives, while SADS struck the swine industry in 2017. They have common characteristics, such as they are all highly pathogenic to humans or livestock, their agents originated from bats, and two of them originated in China. Thus, it is highly likely that future SARS- or MERS-like coronavirus outbreaks will originate from bats, and there is an increased probability that this will occur in China. Therefore, the investigation of bat coronaviruses becomes an urgent issue for the detection of early warning signs, which in turn minimizes the impact of such future outbreaks in China. The purpose of the review is to summarize the current knowledge on viral diversity, reservoir hosts, and the geographical distributions of bat coronaviruses in China, and eventually we aim to predict virus hotspots and their cross-species transmission potential.
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25
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Xu L, Wu J, Li Q, Wei Y, Tan Z, Cai J, Guo H, Yang L, Huang X, Chen J, Zhang F, He B, Tu C. Seroprevalence, cross antigenicity and circulation sphere of bat-borne hantaviruses revealed by serological and antigenic analyses. PLoS Pathog 2019; 15:e1007545. [PMID: 30668611 PMCID: PMC6358112 DOI: 10.1371/journal.ppat.1007545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/01/2019] [Accepted: 12/24/2018] [Indexed: 01/06/2023] Open
Abstract
Bats are newly identified reservoirs of hantaviruses (HVs) among which very divergent HVs have been discovered in recent years. However, their significance for public health remains unclear since their seroprevalence as well as antigenic relationship with human-infecting HVs have not been investigated. In the present study archived tissues of 1,419 bats of 22 species from 6 families collected in 5 south and southwest provinces in China were screened by pan-HV RT-PCR following viral metagenomic analysis. As a result nine HVs have been identified in two bat species in two provinces and phylogenetically classified into two species, Laibin virus (LAIV, ICTV approved species, 1 strain) and Xuan son virus (XSV, proposed species, 8 strains). Additionally, 709 serum samples of these bats were also analyzed by ELISA to investigate the seroprevalence and cross-reactivity between different HVs using expressed recombinant nucleocapsid proteins (rNPs) of LAIV, XSV and Seoul virus (SEOV). The cross-reactivity of some bat sera were further confirmed by western blot (WB) using three rNPs followed by fluorescent antibody virus neutralization test (FAVNT) against live SEOV. Results showed that the total HV seropositive rate of bat sera was 18.5% (131/709) with many cross reacting with two or all three rNPs and several able to neutralize SEOV. WB analysis using the three rNPs and their specific hyperimmune sera demonstrated cross-reactivity between XSV/SEOV and LAIV/XSV, but not LAIV/SEOV, indicating that XSV is antigenically closer to human-infecting HVs. In addition a study of the distribution of the viruses identified an area covering the region between Chinese Guangxi and North Vietnam, in which XSV and LAIV circulate within different bat colonies with a high seroprevalence. A circulation sphere of bat-borne HVs has therefore been proposed. Some HVs are life-threatening pathogens predominantly carried and transmitted by rodents. In recent years bat-borne HVs have been identified in a broad range of bat species. To understand their significance to public health the present study conducted extensive investigations on genetic diversity, seroprevalence, distribution and cross antigenicity of bat-borne HVs in south and southwest China. The results provide the first profiling of cross-reactivity between bat-borne and human-infecting HVs, demonstrating that some bat sera can neutralize SEOV in cell culture. They also revealed that divergent bat-borne HVs co-exist and are widely distributed in Chinese Guangxi/Yunnan as well as in north Vietnam, resulting in identification of an area between China and Vietnam in which natural circulation of bat-borne HVs is maintained. Given the existence of bat-borne HVs genetically and antigenically close to human-infecting HVs, the need for extensive future studies is emphasized in order to assess the potential risk of these viruses to public health.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Jianmin Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Qi Li
- Institute for Viral Disease Prevention and Control, Hebei Province Center for Disease Prevention and Control, Shijiazhuang, Hebei, China
| | - Yamei Wei
- Institute for Viral Disease Prevention and Control, Hebei Province Center for Disease Prevention and Control, Shijiazhuang, Hebei, China
| | - Zhizhou Tan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Jianqiu Cai
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Huancheng Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Ling’en Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Xiaohong Huang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jing Chen
- Institute of Animal Health, Guangdong Academy of Agricultural Science, Guangzhou, Guangdong, China
| | - Fuqiang Zhang
- Center for Disease Control and Prevention of Southern Theater Command, Kunming, Yunnan, China
- * E-mail: (FZ); (BH); (CT)
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- * E-mail: (FZ); (BH); (CT)
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, Jilin, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- * E-mail: (FZ); (BH); (CT)
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26
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Lee S, Jo SD, Son K, An I, Jeong J, Wang SJ, Kim Y, Jheong W, Oem JK. Genetic Characteristics of Coronaviruses from Korean Bats in 2016. MICROBIAL ECOLOGY 2018; 75:174-182. [PMID: 28725945 PMCID: PMC7079938 DOI: 10.1007/s00248-017-1033-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/04/2017] [Indexed: 05/31/2023]
Abstract
Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.
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Affiliation(s)
- Saemi Lee
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Seong-Deok Jo
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Kidong Son
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Injung An
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jipseol Jeong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Seung-Jun Wang
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Yongkwan Kim
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Weonhwa Jheong
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jae-Ku Oem
- Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea.
- Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Iksan, Republic of Korea.
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Li W, Luo R, He Q, van Kuppeveld FJM, Rottier PJM, Bosch BJ. Aminopeptidase N is not required for porcine epidemic diarrhea virus cell entry. Virus Res 2017; 235:6-13. [PMID: 28363778 PMCID: PMC7114539 DOI: 10.1016/j.virusres.2017.03.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/14/2022]
Abstract
Overexpression of porcine APN in cells does not confer susceptibility to PEDV. Knockout APN expression in PEDV-susceptible cells has no effect on PEDV infection. Results demonstrate that APN is not essential for PEDV cell entry.
Porcine epidemic diarrhea virus (PEDV) is an emerging pathogenic coronavirus that causes a significant economic burden to the swine industry. The virus infects the intestinal epithelium and causes villous atrophy, resulting in diarrhea and dehydration. Interaction of the viral spike (S) surface glycoprotein − through its S1 subunit − with the host cell receptor is the first step in infection and the main determinant for virus tropism. As for several other alphacoronaviruses including the porcine transmissible gastroenteritis virus (TGEV) and the human coronavirus 229E (HCoV-229E), the aminopeptidase N (APN) protein was reported to be a functional receptor for PEDV. In this study we examined the role of APN as a receptor. We show that overexpression of porcine APN renders MDCK cells susceptible to TGEV, but not to PEDV. Consistently, unlike TGEV-S1, PEDV-S1 exhibited no binding to cell-surface expressed APN or to a soluble version of APN. Moreover, preincubation of these viruses with soluble APN or pretreatment of APN expressing ST cells with soluble TGEV-S1 blocked TGEV infection, but had no effect on infection by PEDV. The combined observations indicated that APN is not required for PEDV infection. To definitively prove this conclusion, we applied CRISPR/Cas9 genome engineering to knock out APN expression in PEDV-susceptible porcine (ST) and human cell lines (Huh7 and HeLa). As a consequence these cells no longer bound TGEV-S1 and HCoV-229E-S1 at their surface and were resistant to infection by the corresponding viruses. However, genetic ablation of APN expression had no effect on their infectability by PEDV, demonstrating that APN is not essential for PEDV cell entry.
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Affiliation(s)
- Wentao Li
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rui Luo
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Qigai He
- State Key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter J M Rottier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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28
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Shi ZL, Guo D, Rottier PJM. Coronavirus: epidemiology, genome replication and the interactions with their hosts. Virol Sin 2016; 31:1-2. [PMID: 26908210 PMCID: PMC7091033 DOI: 10.1007/s12250-016-3746-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Zheng-Li Shi
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Deyin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430070, China.
| | - Peter J M Rottier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, CL, Netherlands.
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29
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Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia. INFECTION GENETICS AND EVOLUTION 2016; 48:10-18. [PMID: 27932284 PMCID: PMC7106194 DOI: 10.1016/j.meegid.2016.11.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 01/01/2023]
Abstract
South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n = 55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii Coronaviruses detected in bats from Lao PDR and Cambodia. High diversity of αCoVs and βCoVs circulating in bats in Cambodia and Lao PDR. One strain of βCoV, a new member of the MERS-CoV sister-clade, detected from Pipistrellus coromandra. A αCoV strain genetically related to PEDV-CoV, detected from Myotis horsfieldii. CoVs detected for the first time in Megaerops niphanae, Myotis horsfieldii and Macroglossus sp.
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