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Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States. J Virol 2023; 97:e0082923. [PMID: 37882520 PMCID: PMC10688340 DOI: 10.1128/jvi.00829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.
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Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, Durham, USA
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, Ithaca, New York, USA
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Muzeniek T, Perera T, Siriwardana S, Bas D, Kaplan F, Öruc M, Becker-Ziaja B, Perera I, Weerasena J, Handunnetti S, Schwarz F, Premawansa G, Premawansa S, Yapa W, Nitsche A, Kohl C. Full Genome of batCoV/MinFul/2018/SriLanka, a Novel Alpha-Coronavirus Detected in Miniopterus fuliginosus, Sri Lanka. Viruses 2022; 14:v14020337. [PMID: 35215931 PMCID: PMC8874963 DOI: 10.3390/v14020337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 02/01/2023] Open
Abstract
Coronaviruses (CoV) are divided into the genera α-CoVs, β-CoVs, γ-CoVs and δ-CoVs. Of these, α-CoVs and β-CoVs are solely capable of causing infections in humans, resulting in mild to severe respiratory symptoms. Bats have been identified as natural reservoir hosts for CoVs belonging to these two genera. Consequently, research on bat populations, CoV prevalence in bats and genetic characterization of bat CoVs is of special interest to investigate the potential transmission risks. We present the genome sequence of a novel α-CoV strain detected in rectal swab samples of Miniopterus fuliginosus bats from a colony in the Wavul Galge cave (Koslanda, Sri Lanka). The novel strain is highly similar to Miniopterus bat coronavirus 1, an α-CoV located in the subgenus of Minunacoviruses. Phylogenetic reconstruction revealed a high identity of the novel strain to other α-CoVs derived from Miniopterus bats, while human-pathogenic α-CoV strains like HCoV-229E and HCoV-NL63 were more distantly related. Comparison with selected bat-related and human-pathogenic strains of the β-CoV genus showed low identities of ~40%. Analyses of the different genes on nucleotide and amino acid level revealed that the non-structural ORF1a/1b are more conserved among α-CoVs and β-CoVs, while there are higher variations in the structural proteins known to be important for host specificity. The novel strain was named batCoV/MinFul/2018/SriLanka and had a prevalence of 50% (66/130) in rectal swab samples and 58% (61/104) in feces samples that were collected from Miniopterus bats in Wavul Galge cave. Based on the differences between strain batCoV/MinFul/2018/SriLanka and human-pathogenic α-CoVs and β-CoVs, we conclude that there is a rather low transmission risk to humans. Further studies in the Wavul Galge cave and at other locations in Sri Lanka will give more detailed information about the prevalence of this virus.
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Affiliation(s)
- Therese Muzeniek
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Thejanee Perera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka; (T.P.); (J.W.); (S.H.)
| | - Sahan Siriwardana
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (I.P.); (S.P.); (W.Y.)
| | - Dilara Bas
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Fatimanur Kaplan
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Mizgin Öruc
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Beate Becker-Ziaja
- Centre for International Health Protection, Public Health Laboratory Support (ZIG 4), Robert Koch Institute, 13353 Berlin, Germany;
| | - Inoka Perera
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (I.P.); (S.P.); (W.Y.)
| | - Jagathpriya Weerasena
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka; (T.P.); (J.W.); (S.H.)
| | - Shiroma Handunnetti
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka; (T.P.); (J.W.); (S.H.)
| | - Franziska Schwarz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | | | - Sunil Premawansa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (I.P.); (S.P.); (W.Y.)
| | - Wipula Yapa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (I.P.); (S.P.); (W.Y.)
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
- Correspondence: ; Tel.: +49-301-8754-2144
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Schaeffer R, Temeeyasen G, Hause BM. Alphacoronaviruses Are Common in Bats in the Upper Midwestern United States. Viruses 2022; 14:v14020184. [PMID: 35215778 PMCID: PMC8877427 DOI: 10.3390/v14020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Bats are a reservoir for coronaviruses (CoVs) that periodically spill over to humans, as evidenced by severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. A collection of 174 bat samples originating from South Dakota, Minnesota, Iowa, and Nebraska submitted for rabies virus testing due to human exposure were analyzed using a pan-coronavirus PCR. A previously partially characterized CoV, Eptesicus bat CoV, was identified in 12 (6.9%) samples by nested RT-PCR. Six near-complete genomes were determined. Genetic analysis found a high similarity between all CoV-positive samples, Rocky Mountain bat CoV 65 and alphacoronavirus HCQD-2020 recently identified in South Korea. Phylogenetic analysis of genome sequences showed EbCoV is closely related to bat CoV HKU2 and swine acute diarrhea syndrome CoV; however, topological incongruences were noted for the spike gene that was more closely related to porcine epidemic diarrhea virus. Similar to some alphaCoVs, a novel gene, ORF7, was discovered downstream of the nucleocapsid, whose protein lacked similarity to known proteins. The widespread circulation of EbCoV with similarities to bat viruses that have spilled over to swine warrants further surveillance.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Do HQ, Nguyen VG, Chung CU, Jeon YS, Shin S, Jang KC, Pham LBH, Kong A, Kim CU, Park YH, Park BK, Chung HC. Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020. Viruses 2021; 13:v13102041. [PMID: 34696471 PMCID: PMC8540747 DOI: 10.3390/v13102041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.
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Affiliation(s)
- Hai-Quynh Do
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam;
| | - Chul-Un Chung
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Yong-Shin Jeon
- Department of Life Science, Dongguk University, Gyeongju 38066, Korea;
| | - Sook Shin
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Kuem-Chan Jang
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Le Bich Hang Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam;
| | - Aeri Kong
- Department of Medical Science, University of California, Los Angeles, CA 90095, USA;
| | - Cheong-Ung Kim
- Department of Veterinary Medicine Microbology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
| | - Yong-Ho Park
- Noah Biotech Research Unit, Noah Biotech Co. Ltd, Suwon 16612, Korea; (S.S.); (K.-C.J.); (Y.-H.P.)
| | - Bong-Kyun Park
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
| | - Hee-Chun Chung
- Virology Lab, Department of Veterinary Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea;
- Correspondence: (C.-U.C.); (B.-K.P.); (H.-C.C.); Tel.: +82-2-880-1255 (C.-U.C., B.-K.P. & H.-C.C.); Fax: +82-2-885-0263 (C.-U.C., B.-K.P. & H.-C.C.)
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6
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Ip HS, Griffin KM, Messer JD, Winzeler ME, Shriner SA, Killian ML, K. Torchetti M, DeLiberto TJ, Amman BR, Cossaboom CM, Harvey RR, Wendling NM, Rettler H, Taylor D, Towner JS, Barton Behravesh C, Blehert DS. An Opportunistic Survey Reveals an Unexpected Coronavirus Diversity Hotspot in North America. Viruses 2021; 13:v13102016. [PMID: 34696445 PMCID: PMC8539472 DOI: 10.3390/v13102016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus. Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified. Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus. Our findings indicate an unexpectedly high prevalence of coronavirus among the domestic and wild free-roaming animals tested on mink farms. These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses.
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Affiliation(s)
- Hon S. Ip
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
- Correspondence: ; Tel.: +1-608-270-2464
| | - Kathryn M. Griffin
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Jeffrey D. Messer
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Megan E. Winzeler
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
| | - Susan A. Shriner
- Wildlife Services, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA; (S.A.S.); (T.J.D.)
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Diagnostic Virology Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.K.T.)
| | - Mia K. Torchetti
- National Veterinary Services Laboratories, Diagnostic Virology Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.K.T.)
| | - Thomas J. DeLiberto
- Wildlife Services, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA; (S.A.S.); (T.J.D.)
| | - Brian R. Amman
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Caitlin M. Cossaboom
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - R. Reid Harvey
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Natalie M. Wendling
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Hannah Rettler
- Utah Department of Health, Salt Lake City, UT 84114, USA;
| | - Dean Taylor
- Utah Department of Agriculture and Food, Salt Lake City, UT 84116, USA;
| | - Jonathan S. Towner
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - Casey Barton Behravesh
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA; (B.R.A.); (C.M.C.); (R.R.H.); (N.M.W.); (J.S.T.); (C.B.B.)
| | - David S. Blehert
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch. Madison, WI 53711, USA; (K.M.G.); (J.D.M.); (M.E.W.); (D.S.B.)
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Lazov CM, Belsham GJ, Bøtner A, Rasmussen TB. Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark. Viruses 2021; 13:1073. [PMID: 34199948 PMCID: PMC8229204 DOI: 10.3390/v13061073] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.
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Affiliation(s)
- Christina M. Lazov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark
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8
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Kimprasit T, Nunome M, Iida K, Murakami Y, Wong ML, Wu CH, Kobayashi R, Hengjan Y, Takemae H, Yonemitsu K, Kuwata R, Shimoda H, Si L, Sohn JH, Asakawa S, Ichiyanagi K, Maeda K, Oh HS, Mizutani T, Kimura J, Iida A, Hondo E. Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia. PLoS One 2021; 16:e0244006. [PMID: 33444317 PMCID: PMC7808576 DOI: 10.1371/journal.pone.0244006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.
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Affiliation(s)
- Thachawech Kimprasit
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Min-Liang Wong
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Hsin Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Lifan Si
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, China
| | - Joon-Hyuk Sohn
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, Korea
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junpei Kimura
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Lokman SM, Rasheduzzaman M, Salauddin A, Barua R, Tanzina AY, Rumi MH, Hossain MI, Siddiki AMAMZ, Mannan A, Hasan MM. Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infect Genet Evol 2020; 84:104389. [PMID: 32502733 PMCID: PMC7266584 DOI: 10.1016/j.meegid.2020.104389] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/31/2020] [Indexed: 12/14/2022]
Abstract
The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the N-terminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.
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Affiliation(s)
- Syed Mohammad Lokman
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md Rasheduzzaman
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Asma Salauddin
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Rocktim Barua
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Meheadi Hasan Rumi
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md Imran Hossain
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - A M A M Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chattogram 4202, Bangladesh
| | - Adnan Mannan
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.
| | - Md Mahbub Hasan
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh; Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
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10
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Uddin MB, Hasan M, Harun-Al-Rashid A, Ahsan MI, Imran MAS, Ahmed SSU. Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective. Infect Genet Evol 2020; 84:104440. [PMID: 32622082 PMCID: PMC7327474 DOI: 10.1016/j.meegid.2020.104440] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2, a new coronavirus strain responsible for COVID-19, has emerged in Wuhan City, China, and continuing its global pandemic nature. The availability of the complete gene sequences of the virus helps to know about the origin and molecular characteristics of this virus. In the present study, we performed bioinformatic analysis of the available gene sequence data of SARS-CoV-2 for the understanding of evolution and molecular characteristics and immunogenic resemblance of the circulating viruses. Phylogenetic analysis was performed for four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings demonstrated that SARS-CoV-2 exhibited convergent evolutionary relation with previously reported SARS-CoV. It was also depicted that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed a lower level of resemblance. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. Descriptive epidemiological analysis on several epidemiological indices was performed on available epidemiological outbreak information from several open databases on COVID-19 (SARS-CoV-2). Satellite-derived imaging data have been employed to understand the role of temperature in the environmental persistence of the virus. Findings of the descriptive analysis were used to describe the global impact of newly emerged SARS-CoV-2, and the risk of an epidemic in Bangladesh.
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MESH Headings
- Alphacoronavirus/classification
- Alphacoronavirus/genetics
- Alphacoronavirus/metabolism
- Amino Acid Sequence
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Bangladesh/epidemiology
- Base Sequence
- Betacoronavirus/classification
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Chiroptera/virology
- Computational Biology
- Coronavirus 229E, Human/classification
- Coronavirus 229E, Human/genetics
- Coronavirus 229E, Human/metabolism
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Coronavirus NL63, Human/classification
- Coronavirus NL63, Human/genetics
- Coronavirus NL63, Human/metabolism
- Coronavirus OC43, Human/classification
- Coronavirus OC43, Human/genetics
- Coronavirus OC43, Human/metabolism
- Genome, Viral
- Humans
- Middle East Respiratory Syndrome Coronavirus/classification
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Mutation
- Nucleoproteins/chemistry
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Interaction Domains and Motifs
- Severe acute respiratory syndrome-related coronavirus/classification
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/metabolism
- SARS-CoV-2
- Sequence Alignment
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Envelope Proteins/chemistry
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Ahmed Harun-Al-Rashid
- Department of Aquatic Resource Management, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Irtija Ahsan
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Abdus Shukur Imran
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
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11
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Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2. Mol Biol Evol 2020; 37:2706-2710. [PMID: 32658964 PMCID: PMC7454803 DOI: 10.1093/molbev/msaa178] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the scope and impact of the COVID-19 pandemic there exists a strong desire to understand where the SARS-CoV-2 virus came from and how it jumped species boundaries to humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness and divergence times of viruses and identifying past selective pressures. However, we must uphold rigorous standards of inference and interpretation on this topic because of the ramifications of being wrong. Here, we dispute the conclusions of Xia (2020. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense. Mol Biol Evol. doi:10.1093/molbev/masa095) that dogs are a likely intermediate host of a SARS-CoV-2 ancestor. We highlight major flaws in Xia's inference process and his analysis of CpG deficiencies, and conclude that there is no direct evidence for the role of dogs as intermediate hosts. Bats and pangolins currently have the greatest support as ancestral hosts of SARS-CoV-2, with the strong caveat that sampling of wildlife species for coronaviruses has been limited.
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Affiliation(s)
- David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases & Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Maciej F Boni
- 5Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA
| | | | - Rhys Parry
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO
| | - James L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pleuni S Pennings
- Department of Biology, San Francisco State University, San Francisco, CA
| | - Richard A Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
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12
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Abstract
Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. The author shows that SARS-CoV-2 has the most extreme CpG deficiency in all known betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (alphacoronavirus) as possessing the most extreme CpG deficiency, comparable with that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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13
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Bittar C, Machado RRG, Comelis MT, Bueno LM, Beguelini MR, Morielle-Versute E, Nogueira ML, Rahal P. Alphacoronavirus Detection in Lungs, Liver, and Intestines of Bats from Brazil. Microb Ecol 2020; 79:203-212. [PMID: 31144002 PMCID: PMC7080140 DOI: 10.1007/s00248-019-01391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/15/2019] [Indexed: 05/08/2023]
Abstract
Bats are flying mammals distributed worldwide known to host several types of Coronavirus (CoV). Since they were reported as the probable source of spillover of highly pathogenic CoV into the human population, investigating the circulation of this virus in bats around the world became of great importance. We analyzed samples from 103 bats from two distinct regions in Brazil. Coronavirus from the Alphacoronavirus genus was detected in 12 animals, 11 from São José do Rio Preto-SP region and 1 from Barreiras-BA region, resulting in a prevalence of 17.18% and 2.56% respectively. The virus was detected not only in intestines but also in lungs and liver. Phylogenetic analysis based on nsP12 genomic region suggests that the sequences group according to host family and sampling location. Studies on the circulation of these viruses in bats remain important to understand the ecology and evolutionary relationship of these pathogens.
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Affiliation(s)
- Cíntia Bittar
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil.
| | - Rafael Rahal Guaragna Machado
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Manuela Tosi Comelis
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Larissa Mayumi Bueno
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Mateus Rodrigues Beguelini
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
- Centro das Ciências Biológicas e da Saúde (CCBS), Universidade Federal do Oeste da Bahia (UFOB), Rua Professor José Seabra de Lemos, 316, Recanto dos Pássaros, Barreiras, BA, 47808-021, Brazil
| | - Eliana Morielle-Versute
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Maurício Lacerda Nogueira
- Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, Vila São Pedro, Sao Jose do Rio Preto, SP, 15090-000, Brazil
| | - Paula Rahal
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
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14
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Yuan P, Yang Z, Song H, Wang K, Yang Y, Xie L, Huang S, Liu J, Ran L, Song Z. Three Main Inducers of Alphacoronavirus Infection of Enterocytes: Sialic Acid, Proteases, and Low pH. Intervirology 2018; 61:53-63. [PMID: 30176660 PMCID: PMC7179561 DOI: 10.1159/000492424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are similar coronaviruses, causing diseases characterized by vomiting, diarrhea, and death from severe dehydration in piglets. Thus, they have caused huge losses to the swine-breeding industry worldwide. Nowadays, they are easily transmitted among the continents via vehicles, equipment, and cargo. Both viruses establish an infection in porcine enterocytes in the small intestine, and their spike (S) proteins play a key role in the virus-cell binding process under unfavorable conditions when the intestine with a low pH is filled with a thick layer of mucus and proteases. Sialic acid, proteases, and low pH are three main inducers of coronavirus infection. However, the details of how sialic acid and low pH affect virus binding to the host cell are not determined, and the functions of the proteases are unknown. This review emphasizes the role of three factors in the invasion of TGEV and PEDV into porcine enterocytes and offers more insights into Alphacoronavirus infection in the intestinal environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhenhui Song
- *Zhenhui Song, PhD, Department of Veterinary Medicine, College of Animal Science, Southwest University, Chongqing 402460 (People's Republic of China), E-Mail
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15
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Zhou P, Fan H, Lan T, Yang XL, Shi WF, Zhang W, Zhu Y, Zhang YW, Xie QM, Mani S, Zheng XS, Li B, Li JM, Guo H, Pei GQ, An XP, Chen JW, Zhou L, Mai KJ, Wu ZX, Li D, Anderson DE, Zhang LB, Li SY, Mi ZQ, He TT, Cong F, Guo PJ, Huang R, Luo Y, Liu XL, Chen J, Huang Y, Sun Q, Zhang XLL, Wang YY, Xing SZ, Chen YS, Sun Y, Li J, Daszak P, Wang LF, Shi ZL, Tong YG, Ma JY. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 2018; 556:255-258. [PMID: 29618817 PMCID: PMC7094983 DOI: 10.1038/s41586-018-0010-9] [Citation(s) in RCA: 464] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/26/2018] [Indexed: 01/03/2023]
Abstract
Cross-species transmission of viruses from wildlife animal reservoirs poses a marked threat to human and animal health 1 . Bats have been recognized as one of the most important reservoirs for emerging viruses and the transmission of a coronavirus that originated in bats to humans via intermediate hosts was responsible for the high-impact emerging zoonosis, severe acute respiratory syndrome (SARS) 2-10 . Here we provide virological, epidemiological, evolutionary and experimental evidence that a novel HKU2-related bat coronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), is the aetiological agent that was responsible for a large-scale outbreak of fatal disease in pigs in China that has caused the death of 24,693 piglets across four farms. Notably, the outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. Furthermore, we identified SADS-related CoVs with 96-98% sequence identity in 9.8% (58 out of 591) of anal swabs collected from bats in Guangdong province during 2013-2016, predominantly in horseshoe bats (Rhinolophus spp.) that are known reservoirs of SARS-related CoVs. We found that there were striking similarities between the SADS and SARS outbreaks in geographical, temporal, ecological and aetiological settings. This study highlights the importance of identifying coronavirus diversity and distribution in bats to mitigate future outbreaks that could threaten livestock, public health and economic growth.
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Affiliation(s)
- Peng Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hang Fan
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tian Lan
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei-Feng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Taishan Medical College, Taian, China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ya-Wei Zhang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qing-Mei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Shailendra Mani
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jin-Man Li
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Qian Pei
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Ping An
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jun-Wei Chen
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Ling Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Kai-Jie Mai
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Zi-Xian Wu
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Di Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Li-Biao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Shi-Yue Li
- School of Public Health, Wuhan University, Wuhan, China
| | - Zhi-Qiang Mi
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tong-Tong He
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Peng-Ju Guo
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Ren Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yun Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xiang-Ling Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jing Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yong Huang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qiang Sun
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yuan-Yuan Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shao-Zhen Xing
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yan-Shan Chen
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Yuan Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Taishan Medical College, Taian, China
| | | | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
| | - Yi-Gang Tong
- Beijing Institute of Microbiology and Epidemiology, Beijing, China.
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.
| | - Jing-Yun Ma
- College of Animal Science, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.
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16
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Gong L, Li J, Zhou Q, Xu Z, Chen L, Zhang Y, Xue C, Wen Z, Cao Y. A New Bat-HKU2-like Coronavirus in Swine, China, 2017. Emerg Infect Dis 2017; 23. [PMID: 28654418 PMCID: PMC5572857 DOI: 10.3201/eid2309.170915] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We identified from suckling piglets with diarrhea in China a new bat-HKU2-like porcine coronavirus (porcine enteric alphacoronavirus). The GDS04 strain of this coronavirus shares high aa identities (>90%) with the reported bat-HKU2 strains in Coronaviridae-wide conserved domains, suggesting that the GDS04 strain belongs to the same species as HKU2.
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