1
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. Cell 2024; 187:5468-5482.e11. [PMID: 39303692 PMCID: PMC11427129 DOI: 10.1016/j.cell.2024.08.010] [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: 09/13/2023] [Revised: 05/01/2024] [Accepted: 08/07/2024] [Indexed: 09/22/2024]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.
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Affiliation(s)
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Jonathan E Pekar
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Av. da República, Oeiras, Lisbon 2780-157, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Robert F Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P G Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas P Peacock
- The Pirbright Institute, Woking GU24 0NF, Surrey, UK; Department of Infectious Disease, Imperial College London, London W2 1P, UK
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK
| | - Marc A Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA.
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Florence Débarre
- Institut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.
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2
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Holmes EC. The Emergence and Evolution of SARS-CoV-2. Annu Rev Virol 2024; 11:21-42. [PMID: 38631919 DOI: 10.1146/annurev-virology-093022-013037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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3
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Mallapaty S. Fur farming a 'viral highway' that could spark next pandemic, say scientists. Nature 2024; 633:506. [PMID: 39242956 DOI: 10.1038/d41586-024-02871-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2024]
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4
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Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Xiong Q, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukari A, Starr T, Yan H, Veesler D. Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.608351. [PMID: 39253417 PMCID: PMC11383307 DOI: 10.1101/2024.08.28.608351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity with which merbecoviruses engage ACE2 and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. These results show that several merbecovirus clades independently evolved ACE2 utilization, which appears to be a broadly shared property among these pathogens, through an extraordinary diversity of ACE2 recognition modes. We show that MERS-CoV and HKU5 have markedly distinct antigenicity, due to extensive genetic divergence, and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution and pave the way for developing countermeasures against viruses poised for human emergence.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Chen Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Jimin Lee
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Chen-Bao Ma
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Peng Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Cameron Stewart
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Caroline J Craig
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Abeer Alshukari
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Tyler Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
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5
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Du W, Debski-Antoniak O, Drabek D, van Haperen R, van Dortmondt M, van der Lee J, Drulyte I, van Kuppeveld FJM, Grosveld F, Hurdiss DL, Bosch BJ. Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun 2024; 15:5330. [PMID: 38909062 PMCID: PMC11193727 DOI: 10.1038/s41467-024-49693-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Oliver Debski-Antoniak
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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6
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Yang Y, Li F, Du L. Therapeutic nanobodies against SARS-CoV-2 and other pathogenic human coronaviruses. J Nanobiotechnology 2024; 22:304. [PMID: 38822339 PMCID: PMC11140877 DOI: 10.1186/s12951-024-02573-7] [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: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
Nanobodies, single-domain antibodies derived from variable domain of camelid or shark heavy-chain antibodies, have unique properties with small size, strong binding affinity, easy construction in versatile formats, high neutralizing activity, protective efficacy, and manufactural capacity on a large-scale. Nanobodies have been arisen as an effective research tool for development of nanobiotechnologies with a variety of applications. Three highly pathogenic coronaviruses (CoVs), SARS-CoV-2, SARS-CoV, and MERS-CoV, have caused serious outbreaks or a global pandemic, and continue to post a threat to public health worldwide. The viral spike (S) protein and its cognate receptor-binding domain (RBD), which initiate viral entry and play a critical role in virus pathogenesis, are important therapeutic targets. This review describes pathogenic human CoVs, including viral structures and proteins, and S protein-mediated viral entry process. It also summarizes recent advances in development of nanobodies targeting these CoVs, focusing on those targeting the S protein and RBD. Finally, we discuss potential strategies to improve the efficacy of nanobodies against emerging SARS-CoV-2 variants and other CoVs with pandemic potential. It will provide important information for rational design and evaluation of therapeutic agents against emerging and reemerging pathogens.
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MESH Headings
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/pharmacology
- Single-Domain Antibodies/therapeutic use
- Single-Domain Antibodies/chemistry
- Humans
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- Animals
- COVID-19/virology
- COVID-19/immunology
- COVID-19/therapy
- Coronavirus Infections/drug therapy
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Middle East Respiratory Syndrome Coronavirus/immunology
- Virus Internalization/drug effects
- Pandemics
- Betacoronavirus/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Pneumonia, Viral/immunology
- Severe acute respiratory syndrome-related coronavirus/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
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Affiliation(s)
- Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN, USA.
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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7
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Sohrab SS, Alsaqaf F, Hassan AM, Tolah AM, Bajrai LH, Azhar EI. Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses. BIOLOGY 2024; 13:282. [PMID: 38666894 PMCID: PMC11048170 DOI: 10.3390/biology13040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
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Chaudhury S, Kaur P, Gupta D, Anand P, Chaudhary M, Tiwari S, Mittal A, Gupta J, Kaur S, Singh VD, Dhawan D, Singh P, Sahu SK. Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak. Curr Mol Med 2024; 24:712-733. [PMID: 37312440 DOI: 10.2174/1566524023666230613141746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/15/2023]
Abstract
The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.
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Affiliation(s)
- Soumik Chaudhury
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Paranjeet Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Deepali Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Palak Anand
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Manish Chaudhary
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Siddhita Tiwari
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Amit Mittal
- Faculty of Pharmaceutical Sciences, Desh Bhagat University, Amloh Road, Mandi Gobindgarh, 147301, Punjab, India
| | - Jeena Gupta
- School of Bioscience, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sukhmeen Kaur
- Department of Opthalmology, Punjab Institute of Medical Sciences, Jalandhar, 144001, Punjab, India
| | - Varsh Deep Singh
- American University of Barbados, Wildey, St. Michael, BB11100, Barbados
| | - Dakshita Dhawan
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Princejyot Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sanjeev Kumar Sahu
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
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9
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Rabaan AA, Alenazy MF, Alshehri AA, Alshahrani MA, Al-Subaie MF, Alrasheed HA, Al Kaabi NA, Thakur N, Bouafia NA, Alissa M, Alsulaiman AM, AlBaadani AM, Alhani HM, Alhaddad AH, Alfouzan WA, Ali BMA, Al-Abdulali KH, Khamis F, Bayahya A, Al Fares MA, Sharma M, Dhawan M. An updated review on pathogenic coronaviruses (CoVs) amid the emergence of SARS-CoV-2 variants: A look into the repercussions and possible solutions. J Infect Public Health 2023; 16:1870-1883. [PMID: 37839310 DOI: 10.1016/j.jiph.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2, responsible for COVID-19, shares 79% and 50% of its identity with SARS-CoV-1 and MERS-CoV, respectively. It uses the same main cell attachment and entry receptor as SARS-CoV-1, which is the ACE-2 receptor. However, key residues in the receptor-binding domain of its S-protein seem to give it a stronger affinity for the receptor and a better ability to hide from the host immune system. Like SARS-CoV-1 and MERS-CoV, cytokine storms in critically ill COVID-19 patients cause ARDS, neurological pathology, multiorgan failure, and increased death. Though many issues remain, the global research effort and lessons from SARS-CoV-1 and MERS-CoV are hopeful. The emergence of novel SARS-CoV-2 variants and subvariants raised serious concerns among the scientific community amid the emergence of other viral diseases like monkeypox and Marburg virus, which are major concerns for healthcare settings worldwide. Hence, an updated review on the comparative analysis of various coronaviruses (CoVs) has been developed, which highlights the evolution of CoVs and their repercussions.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan.
| | - Maha Fahad Alenazy
- Department of Physiology, College of Medicine, King Khalid university hospital, King Saud University, Riyadh 4545, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia; Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Hayam A Alrasheed
- Department of pharmacy Practice, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; Pharmacy Department, King Abdullah Bin Abdulaziz University Hospital, Riyadh 11671, Saudi Arabia
| | - Nawal A Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates; College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Nabiha A Bouafia
- Infection prevention and control centre of Excellence, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Abeer M AlBaadani
- Internal Medicine Department, Infectious Disease Division, London health science Center, London, Ontario N6G0X2, Canada
| | - Hatem M Alhani
- Department of Pediatric Infectious Disease, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Department of Infection Control, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Preventive Medicine and Infection Prevention and Control Department, Directorate of Ministry of Health, Dammam 32245, Saudi Arabia
| | - Ali H Alhaddad
- Assistant Agency for Hospital Affairs, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Batool Mohammed Abu Ali
- Infectious disease section, Department of internal medicine, King Fahad Hospital Hofuf, Hofuf 36365, Saudi Arabia
| | - Khadija H Al-Abdulali
- Nursing Department, Home health care, Qatif Health Network, Qatif 31911, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Ali Bayahya
- Microbiology Department, Alqunfudah General Hospital, Alqunfudah 28813, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
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10
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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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11
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Tamayo-Ordóñez MC, Rosas-García NM, Ayil-Gutiérrez BA, Bello-López JM, Tamayo-Ordóñez FA, Anguebes-Franseschi F, Damas-Damas S, Tamayo-Ordóñez YDJ. Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families. Pathogens 2023; 12:1185. [PMID: 37764993 PMCID: PMC10537875 DOI: 10.3390/pathogens12091185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10-5 and 10-3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain's differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies.
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Affiliation(s)
- María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Ninfa María Rosas-García
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
| | - Benjamín Abraham Ayil-Gutiérrez
- CONAHCYT-Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamaulipas, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Campeche, Mexico
| | - Francisco Alberto Tamayo-Ordóñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Francisco Anguebes-Franseschi
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Siprian Damas-Damas
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Yahaira de Jesús Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
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12
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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13
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Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023; 11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.
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Affiliation(s)
- Mervat E. Hamdy
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Ayman H. El Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Naglaa M. Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Momtaz A. Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Osama Alaidi
- Biocomplexity for Research and Consulting Co., Cairo, Egypt
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hussein A. Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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14
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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15
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Esposito MM, Turku S, Lehrfield L, Shoman A. The Impact of Human Activities on Zoonotic Infection Transmissions. Animals (Basel) 2023; 13:1646. [PMID: 37238075 PMCID: PMC10215220 DOI: 10.3390/ani13101646] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
As humans expand their territories across more and more regions of the planet, activities such as deforestation, urbanization, tourism, wildlife exploitation, and climate change can have drastic consequences for animal movements and animal-human interactions. These events, especially climate change, can also affect the arthropod vectors that are associated with the animals in these scenarios. As the COVID-19 pandemic and other various significant outbreaks throughout the centuries have demonstrated, when animal patterns and human interactions change, so does the exposure of humans to zoonotic pathogens potentially carried by wildlife. With approximately 60% of emerging human pathogens and around 75% of all emerging infectious diseases being categorized as zoonotic, it is of great importance to examine the impact of human activities on the prevalence and transmission of these infectious agents. A better understanding of the impact of human-related factors on zoonotic disease transmission and prevalence can help drive the preventative measures and containment policies necessary to improve public health.
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Affiliation(s)
- Michelle Marie Esposito
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Ph.D. Program in Biology, The Graduate Center, City University of New York, New York, NY 10314, USA
- Macaulay Honors College, City University of New York, New York, NY 10314, USA
| | - Sara Turku
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Macaulay Honors College, City University of New York, New York, NY 10314, USA
| | - Leora Lehrfield
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Macaulay Honors College, City University of New York, New York, NY 10314, USA
| | - Ayat Shoman
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
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16
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Ray AS, Bhattacharya K. An Overview on the Zoonotic Aspects of COVID-19. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, INDIA. SECTION B 2023; 94:1-5. [PMID: 37360152 PMCID: PMC10132798 DOI: 10.1007/s40011-023-01445-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 01/24/2023] [Indexed: 06/28/2023]
Abstract
Disruption of pristine natural habitat has a strong positive correlation with this increase in pandemics and thus, the zoonotic aspects are the most important part to uncover scientifically. On the other hand, containment and mitigation are the two basic strategies to stop a pandemic. The route of infection is of utmost importance for any pandemic and often left behind in combating the fatalities in real time. The increase in recent pandemics, from ebola outbreak to ongoing COVID-19 havoc, exerts implicit significance in the search of zoonotic transmissions of the diseases. Thus, a conceptual summary has been made through this article in understanding the basic zoonotic mechanism of the disease COVID-19 based on available published data and schematic presentation has been drawn on the route of transmission, so far discovered.
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Affiliation(s)
- Anushree Singha Ray
- Former Research Fellow, Department of Zoology, The University of Burdwan, Golapbag Purba Burdwan, Burdwan, West Bengal 713104 India
| | - Kuntal Bhattacharya
- Department of Zoology, Durgapur Government College, Paschim Bardhaman, Durgapur, West Bengal 713214 India
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17
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Dunowska M. Cross-species transmission of coronaviruses with a focus on severe acute respiratory syndrome coronavirus 2 infection in animals: a review for the veterinary practitioner. N Z Vet J 2023:1-13. [PMID: 36927253 DOI: 10.1080/00480169.2023.2191349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
AbstractIn 2019 a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from an unidentified source and spread rapidly among humans worldwide. While many human infections are mild, some result in severe clinical disease that in a small proportion of infected people is fatal. The pandemic spread of SARS-CoV-2 has been facilitated by efficient human-to-human transmission of the virus, with no data to indicate that animals contributed to this global health crisis. However, a range of domesticated and wild animals are also susceptible to SARS-CoV-2 infection under both experimental and natural conditions. Humans are presumed to be the source of most animal infections thus far, although natural transmission between mink and between free-ranging deer has occurred, and occasional natural transmission between cats cannot be fully excluded. Considering the ongoing circulation of the virus among people, together with its capacity to evolve through mutation and recombination, the risk of the emergence of animal-adapted variants is not negligible. If such variants remain infectious to humans, this could lead to the establishment of an animal reservoir for the virus, which would complicate control efforts. As such, minimising human-to-animal transmission of SARS-CoV-2 should be considered as part of infection control efforts. The aim of this review is to summarise what is currently known about the species specificity of animal coronaviruses, with an emphasis on SARS-CoV-2, in the broader context of factors that facilitate cross-species transmission of viruses.
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Affiliation(s)
- M Dunowska
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
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18
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de-Dios T, Scheib CL, Houldcroft CJ. An Adagio for Viruses, Played Out on Ancient DNA. Genome Biol Evol 2023; 15:evad047. [PMID: 36930529 PMCID: PMC10063219 DOI: 10.1093/gbe/evad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.
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Affiliation(s)
- Toni de-Dios
- Institute of Genomics, University of Tartu, Estonia
| | - Christiana L Scheib
- Institute of Genomics, University of Tartu, Estonia
- St. John's College, University of Cambridge, United Kingdom
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19
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Mahroum N, Seida I, Esirgün SN, Bragazzi NL. The COVID-19 pandemic - How many times were we warned before? Eur J Intern Med 2022; 105:8-14. [PMID: 35864073 PMCID: PMC9289047 DOI: 10.1016/j.ejim.2022.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/01/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
Abstract
Infectious diseases are known to act in both predictable and unpredictable ways, which leads to the notions of emerging and reemerging infectious diseases. Emerging diseases with their disastrous consequences might be surprising and unpredictable, but they could be foreseen. For instance, some emerging diseases and recently the coronavirus disease 2019 (COVID-19) were the reason for papers published by the World Health Organization (WHO) and other researchers addressing the likely pathogens causing future outbreaks, according to the reports of the WHO in 2016 and 2018. Although it might seem like a wisdom in retrospect, several studies had already indicated possible future outbreaks caused by coronaviruses. Announcements, which may be viewed as "warnings," appeared since the emergence of the first coronavirus-related outbreak caused by severe acute respiratory syndrome coronavirus (SARS-CoV) in the winter of 2002-2003 and a later outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012-2013. Therefore, we were curious to review the medical literature prior to the COVID-19 pandemic with an aim to enumerate and evaluate studies addressing and warning against future outbreaks, and surprisingly pandemics, of members of coronaviruses. Interestingly, we found numerous studies that correctly predicted the current pandemic of COVID-19. While this part is highly interesting, how authorities reacted and prepared for warnings, if any, and how will they get prepared for the next warnings are our main messages. Taking these points into serious consideration will certainly aid in analyzing reports regarding possible future outbreaks as well as in developing various strategies for prevention and coping with such epidemics.
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Affiliation(s)
- Naim Mahroum
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey.
| | - Isa Seida
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey
| | - Sevval Nil Esirgün
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Canada
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20
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Ellwanger JH, Fearnside PM, Ziliotto M, Valverde-Villegas JM, Veiga ABGDA, Vieira GF, Bach E, Cardoso JC, Müller NFD, Lopes G, Caesar L, Kulmann-Leal B, Kaminski VL, Silveira ES, Spilki FR, Weber MN, Almeida SEDEM, Hora VPDA, Chies JAB. Synthesizing the connections between environmental disturbances and zoonotic spillover. AN ACAD BRAS CIENC 2022; 94:e20211530. [PMID: 36169531 DOI: 10.1590/0001-3765202220211530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Philip Martin Fearnside
- Instituto Nacional de Pesquisas da Amazônia/INPA, Avenida André Araújo, 2936, Aleixo, 69067-375 Manaus, AM, Brazil
| | - Marina Ziliotto
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jacqueline María Valverde-Villegas
- Institut de Génétique Moléculaire de Montpellier/IGMM, Centre National de la Recherche Scientifique/CNRS, Laboratoire coopératif IGMM/ABIVAX, 1919, route de Mende, 34090 Montpellier, Montpellier, France
| | - Ana Beatriz G DA Veiga
- Universidade Federal de Ciências da Saúde de Porto Alegre/UFCSPA, Departamento de Ciências Básicas de Saúde, Rua Sarmento Leite, 245, Centro Histórico, 90050-170 Porto Alegre, RS, Brazil
| | - Gustavo F Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Laboratório de Saúde Humana in silico, Avenida Victor Barreto, 2288, Centro, 92010-000 Canoas, RS, Brazil
| | - Evelise Bach
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jáder C Cardoso
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Nícolas Felipe D Müller
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Gabriel Lopes
- Fundação Oswaldo Cruz/FIOCRUZ, Casa de Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Lílian Caesar
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Indiana University/IU, Department of Biology, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Bruna Kulmann-Leal
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Valéria L Kaminski
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal de São Paulo/UNIFESP, Instituto de Ciência e Tecnologia/ICT, Laboratório de Imunologia Aplicada, Rua Talim, 330, Vila Nair, 12231-280 São José dos Campos, SP, Brazil
| | - Etiele S Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Fernando R Spilki
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Matheus N Weber
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Sabrina E DE Matos Almeida
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Vanusa P DA Hora
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal do Rio Grande/FURG, Faculdade de Medicina, Rua Visconde de Paranaguá, 102, Centro, 96203-900, Rio Grande, RS, Brazil
| | - José Artur B Chies
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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21
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Kaur I, Behl T, Sehgal A, Singh S, Sharma N, Subramanian V, Fuloria S, Fuloria NK, Sekar M, Dailah HG, Alsubayiel AM, Bhatia S, Al-Harrasi A, Aleya L, Bungau S. A motley of possible therapies of the COVID-19: reminiscing the origin of the pandemic. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67685-67703. [PMID: 35933528 PMCID: PMC9362373 DOI: 10.1007/s11356-022-22345-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/28/2022] [Indexed: 05/20/2023]
Abstract
The 2019 outbreak of corona virus disease began from Wuhan (China), transforming into a leading pandemic, posing an immense threat to the global population. The WHO coined the term nCOVID-19 for the disease on 11th February, 2020 and the International Committee of Taxonomy of Viruses named it SARS-CoV-2, on account of its similarity with SARS-CoV-1 of 2003. The infection is associated with fever, cough, pneumonia, lung damage, and ARDS along with clinical implications of lung opacities. Brief understanding of the entry target of virus, i.e., ACE2 receptors has enabled numerous treatment options as discussed in this review. The manuscript provides a holistic picture of treatment options in COVID-19, such as non-specific anti-viral drugs, immunosuppressive agents, anti-inflammatory candidates, anti-HCV, nucleotide inhibitors, antibodies and anti-parasitic, RNA-dependent RNA polymerase inhibitors, anti-retroviral, vitamins and hormones, JAK inhibitors, and blood plasma therapy. The text targets to enlist the investigations conducted on all the above categories of drugs, with respect to the COVID-19 pandemic, to accelerate their significance in hindering the disease progression. The data collected primarily targets recently published articles and most recent records of clinical trials, focusing on the last 10-year database. The current review provides a comprehensive view on the critical need of finding a suitable treatment for the currently prevalent COVID-19 disease, and an opportunity for the researchers to investigate the varying possibilities to find and optimized treatment approach to mitigate and ameliorate the chaos created by the pandemic worldwide.
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Affiliation(s)
- Ishnoor Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, 133207, India
| | - Neelam Sharma
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, 133207, India
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy & Center of Excellence for Biomaterials Engineering, AIMST University, Bedong, Kedah, Malaysia
| | - Neeraj Kumar Fuloria
- Faculty of Pharmacy & Center of Excellence for Biomaterials Engineering, AIMST University, Bedong, Kedah, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine, Perak, Ipoh, Malaysia
| | - Hamed Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan, Saudi Arabia
| | - Amal M Alsubayiel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah, Kingdom of Saudi Arabia
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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22
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Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science 2022; 377:960-966. [PMID: 35881005 PMCID: PMC9348752 DOI: 10.1126/science.abp8337] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/18/2022] [Indexed: 01/08/2023]
Abstract
Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.
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Affiliation(s)
- Jonathan E. Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Katherine Izhikevich
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer L. Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Nathaniel L. Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jade C. Wang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA
| | - Scott Hughes
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY 11101, USA
| | - Jungmin Lee
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul, South Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | | | - Raymond Tzer Pin Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Mohd Noor Mat Isa
- Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Yusuf Muhammad Noor
- Malaysia Genome and Vaccine Institute, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Tetyana I. Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA
- Zalgen Labs, LCC, Frederick, MD 21703 USA
- Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK
| | - Marc A. Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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23
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Lan J, Chen P, Liu W, Ren W, Zhang L, Ding Q, Zhang Q, Wang X, Ge J. Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2. Structure 2022; 30:1432-1442.e4. [PMID: 35917815 PMCID: PMC9341007 DOI: 10.1016/j.str.2022.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and human coronavirus (hCoV)-NL63 utilize ACE2 as the functional receptor for cell entry, which leads to zoonotic infection. Horses (Equus caballus) attracted our attention because the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 and SARS-CoV-2-related coronaviruses bind equine ACE2 (eACE2) with high affinity. Here we show that eACE2 binds the RBDs of these three coronaviruses and also SARS-CoV-2 variants but with lower affinities compared with human ACE2 (hACE2). Structural analysis and mutation assays indicated that eACE2-H41 accounts for the lower binding affinity of eACE2 to the RBDs of SARS-CoV-2 variants (Alpha, Beta, and Gamma), SARS-CoV, and hCoV-NL63. Pseudovirus infection assays showed that the SARS-CoV-2 Delta strain (B.1.617.2) displayed a significantly increased infection efficiency in eACE2-expressing HeLa cells. Our results reveal the molecular basis of eACE2 binding to the RBDs of SARS-CoV, SARS-CoV-2, and hCoV-NL63, which provides insights into the potential animal transmission of these ACE2-dependent coronaviruses.
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Affiliation(s)
- Jun Lan
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weiming Liu
- Department of Critical Care Medicine, Beijing Boai Hospital, China Rehabilitation Research Centre, No. 10 Jiaomen Beilu, Fengtai District, Beijing 100068, China
| | - Wenlin Ren
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Qiang Ding
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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24
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Abstract
Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should also be considered. Results: Here we show that the genomes of SARS-CoV-2 and SARS-CoV-1 significantly diverge from other SARS-like coronaviruses through short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for host cell invasion, virus replication, and host immune response. For SARS-CoV-1, we identify two sites: one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain; for SARS-CoV-2, one at the start of the viral replicase domain, and the other toward the end of the spike gene past its domain junction. At this junction, we detect a highly specific stretch of yeast origin covering the critical furin cleavage site insert PRRA, which has not been seen in other lineage b betacoronaviruses. As yeast is not a natural host for this virus family, we propose an artificial synthesis model for viral constructs in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential yeast sequence patterns congruent with chromosomes harboring specific auxotrophic markers further support yeast artificial synthesis. Conclusions: These results provide evidence that the genomes of SARS-CoV-1 and SARS-CoV-2 contain sequence information that points to their artificial synthesis in genetically modified yeast cells. Our data specifically allow the identification of the yeast S. cerevisiae as a potential recombination donor for the critical furin cleavage site in SARS-CoV-2.
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25
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Li S, Yang R, Zhang D, Han P, Xu Z, Chen Q, Zhao R, Zhao X, Qu X, Zheng A, Wang L, Li L, Hu Y, Zhang R, Su C, Niu S, Zhang Y, Qi J, Liu K, Wang Q, Gao GF. Cross-species recognition and molecular basis of SARS-CoV-2 and SARS-CoV binding to ACE2s of marine animals. Natl Sci Rev 2022; 9:nwac122. [PMID: 36187898 PMCID: PMC9517163 DOI: 10.1093/nsr/nwac122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/04/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has an extremely broad host range that includes hippopotami, which are phylogenetically closely related to whales. The cellular ACE2 receptor is one of the key determinants of the host range. Here, we found that ACE2s from several marine mammals and hippopotami could efficiently bind to the receptor-binding domain (RBD) of both SARS-CoV and SARS-CoV-2 and facilitate the transduction of SARS-CoV and SARS-CoV-2 pseudoviruses into ACE2-expressing cells. We further resolved the cryo-electron microscopy complex structures of the minke whale ACE2 and sea lion ACE2, respectively, bound to the RBDs, revealing that they have similar binding modes to human ACE2 when it comes to the SARS-CoV-2 RBD and SARS-CoV RBD. Our results indicate that marine mammals could potentially be new victims or virus carriers of SARS-CoV-2, which deserves further careful investigation and study. It will provide an early warning for the prospective monitoring of marine mammals.
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Affiliation(s)
| | | | | | | | - Zepeng Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Faculty of Health Sciences, University of Macau, Macau, China
| | - Qian Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Institute of Physical Science and Information, Anhui University, Hefei230039, China
| | - Runchu Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Institute of Physical Science and Information, Anhui University, Hefei230039, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing100101, China
| | - Xiao Qu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Anqi Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing100101, China
| | - Linjie Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Savaid Medical School, University of Chinese Academy of Sciences, Beijing100049, China
| | - Yu Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,School of Life Sciences, University of Science and Technology of China, Hefei230026, China
| | - Rong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning530004, China
| | - Chao Su
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Sheng Niu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong030801, China
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China,Savaid Medical School, University of Chinese Academy of Sciences, Beijing100049, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing100101, China
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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Affiliation(s)
- Jin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 678 Haping Road, Harbin 150069, China.
| | - Jiumeng Sun
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Dongyan Li
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Ningning Wang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Lifang Wang
- College of Veterinary Medicine, China Agricultural University, No. 17 Qinghua Donglu, Beijing 100083, China
| | - Chang Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Xiaorong Meng
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St., Charles Avenue, New Orleans, LA 70118, USA
| | - Marc A Suchard
- Departments of Biomathematics, Human Genetics and Biostatistics, David Geffen School of Medicine and Fielding School of Public Health, University of California, Los Angeles, Geffen Hall 885 Tiverton Drive, Los Angeles, CA 90095, USA
| | - Xu Zhang
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, 400 East Main St., Frankfort, KY 40601, USA
| | - Shuo Su
- College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany.
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27
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Wang W, Tian JH, Chen X, Hu RX, Lin XD, Pei YY, Lv JX, Zheng JJ, Dai FH, Song ZG, Chen YM, Zhang YZ. Coronaviruses in Wild Animals Sampled in and Around Wuhan in the Beginning of COVID-19 Emergence. Virus Evol 2022; 8:veac046. [PMID: 35769892 PMCID: PMC9214087 DOI: 10.1093/ve/veac046] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/22/2022] Open
Abstract
Over the last several decades, no emerging virus has had a profound impact on the world as the SARS-CoV-2 that emerged at the end of 2019 has done. To know where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated from and how it jumped into human population, we immediately started a surveillance investigation in wild mammals in and around Wuhan when we determined the agent. Herein, coronaviruses were screened in the lung, liver, and intestinal tissue samples from fifteen raccoon dogs, seven Siberian weasels, three hog badgers, and three Reeves’s muntjacs collected in Wuhan and 334 bats collected around Wuhan. Consequently, eight alphacoronaviruses were identified in raccoon dogs, while nine betacoronaviruses were found in bats. Notably, the newly discovered alphacoronaviruses shared a high whole-genome sequence similarity (97.9 per cent) with the canine coronavirus (CCoV) strain 2020/7 sampled from domestic dog in the UK. Some betacoronaviruses identified here were closely related to previously known bat SARS-CoV-related viruses sampled from Hubei province and its neighbors, while the remaining betacoronaviruses exhibited a close evolutionary relationship with SARS-CoV-related bat viruses in the RdRp gene tree and clustered together with SARS-CoV-2-related bat coronaviruses in the M, N and S gene trees, but with relatively low similarity. Additionally, these newly discovered betacoronaviruses seem unlikely to bind angiotensin-converting enzyme 2 because of the deletions in the two key regions of their receptor-binding motifs. Finally, we did not find SARS-CoV-2 or its progenitor virus in these animal samples. Due to the high circulation of CCoVs in raccoon dogs in Wuhan, more scientific efforts are warranted to better understand their diversity and evolution in China and the possibility of a potential human agent.
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Affiliation(s)
- Wen Wang
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, 102206, China
| | - Jun-Hua Tian
- Hubei Key Laboratory of Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University , Wuhan, 430070, Hubei Province, China
- Wuhan Center for Disease Control and Prevention , Wuhan, Hubei Province, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University , Guangzhou, Guangdong Province, China
| | - Rui-Xue Hu
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention , Wenzhou, Zhejiang Province, China
| | - Yuan-Yuan Pei
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Jia-Xin Lv
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Jiao-Jiao Zheng
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Fa-Hui Dai
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Zhi-Gang Song
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, Shanghai key laboratory of organ transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University , Shanghai, China
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28
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Li Z, Jiang J, Tong Y, Ruan X, Xu J. COVID-19 is a natural infectious disease. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022; 4:38-42. [PMID: 34927018 PMCID: PMC8664692 DOI: 10.1016/j.jobb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Jiafu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Xiangdong Ruan
- Academy of Forest Inventory and Planning, State Forestry and Grassland Administration, Beijing 100714, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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29
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Siddiqui S, Alhamdi HWS, Alghamdi HA. Recent Chronology of COVID-19 Pandemic. Front Public Health 2022; 10:778037. [PMID: 35602161 PMCID: PMC9114873 DOI: 10.3389/fpubh.2022.778037] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/16/2022] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is highly contagious and is caused by severe acute respiratory syndrome coronavirus 2. It spreads by means of respiratory droplets and close contact with infected persons. With the progression of disease, numerous complications develop, particularly among persons with chronic illnesses. Pathological investigations indicate that it affects multiple organs and can induce acute respiratory distress syndrome. Prevention is vital and self-isolation is the best means of containing this virus. Good community health practices like maintaining sufficient distance from other people, wearing protective face masks and regular hand washing should be adopted. Convalescent plasma transfusion and the administration of the antiviral Remdesivir have been found to be effective. Vaccines offer lifesaving protecting against COVID-19 which has killed millions and our best bet for staying safe. Screening, suppression/containment as well as mitigation are the strategies implemented for controlling COVID-19 pandemic. Vaccination is essential to end the COVID-19 pandemic and everyone should have an access to them. The current COVID-19 pandemic brought the global economy to a standstill and has exacted an enormous human and financial toll.
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Affiliation(s)
- Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
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30
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Varret M, Martin FX, Varret F. A tentative tracking of the SARS-Cov2 pandemic in France, based on a corrected SIR model including vaccination effects. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202226301002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed successive extensions of the SIR model in order to track the dynamics of the SARS-Cov2 disease. The analysis of health system available data is published in a chronicle accessible on the net: https://corona-circule.github.io/lettres/. This chronicle was initiated on late march 2020 and up to now contains 50 issues. A constant concern was the reliability of the data: for instance, we very soon evidenced that the number of confirmed cases, because of the asymptomatic carriers and the erratic testing policy, was hugely underestimated. By the end of 2020 we made a basic change in the model which consisted in accounting for a constant contagiousness time (SIR-tcc) instead of the probabilistic evolution of the end of the infection assumed so far. Recently we completed this SIR-tcc model for the vaccination effects in order to properly track the evolution of the group immunity threshold. Calculations were performed using the Excel facility (Microsoft), allowing a manual fitting of the model parameters. The results have dealt with a large number of countries, but we focus here on the data regarding France. Further pieces of information are also presented, in order to help elucidating some the factors responsible for the complex history of the pandemic dynamics. (submitted dec 14th 2021)
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31
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Färber I, Krüger J, Rocha C, Armando F, von Köckritz-Blickwede M, Pöhlmann S, Braun A, Baumgärtner W, Runft S, Krüger N. Investigations on SARS-CoV-2 Susceptibility of Domestic and Wild Animals Using Primary Cell Culture Models Derived from the Upper and Lower Respiratory Tract. Viruses 2022; 14:v14040828. [PMID: 35458558 PMCID: PMC9032458 DOI: 10.3390/v14040828] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Several animal species are susceptible to SARS-CoV-2 infection, as documented by case reports and serological and in vivo infection studies. However, the susceptibility of many animal species remains unknown. Furthermore, the expression patterns of SARS-CoV-2 entry factors, such as the receptor angiotensin-converting enzyme 2 (ACE2), as well as transmembrane protease serine subtype 2 (TMPRSS2) and cathepsin L (CTSL), cellular proteases involved in SARS-CoV-2 spike protein activation, are largely unexplored in most species. Here, we generated primary cell cultures from the respiratory tract of domestic and wildlife animals to assess their susceptibility to SARS-CoV-2 infection. Additionally, the presence of ACE2, TMPRSS2 and CTSL within respiratory tract compartments was investigated in a range of animals, some with unknown susceptibility to SARS-CoV-2. Productive viral replication was observed in the nasal mucosa explants and precision-cut lung slices from dogs and hamsters, whereas culture models from ferrets and multiple ungulate species were non-permissive to infection. Overall, whereas TMPRSS2 and CTSL were equally expressed in the respiratory tract, the expression levels of ACE2 were more variable, suggesting that a restricted availability of ACE2 may contribute to reduced susceptibility. Summarized, the experimental infection of primary respiratory tract cell cultures, as well as an analysis of entry-factor distribution, enable screening for SARS-CoV-2 animal reservoirs.
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Affiliation(s)
- Iris Färber
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Johannes Krüger
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Maren von Köckritz-Blickwede
- Department of Biochemistry, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
- Faculty of Biology and Psychology, Georg-August-University, 37073 Göttingen, Germany
| | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 30625 Hannover, Germany;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
- Correspondence: ; Tel.: +49-511-953-8620; Fax: +49-511-953-8675
| | - Sandra Runft
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Nadine Krüger
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
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32
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Akinnusi PA, Olubode SO, Salaudeen WA. Molecular binding studies of anthocyanins with multiple antiviral activities against SARS-CoV-2. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:102. [PMID: 35431537 PMCID: PMC9006501 DOI: 10.1186/s42269-022-00786-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/30/2022] [Indexed: 05/11/2023]
Abstract
Background The search for ideal drugs with absolute antiviral activity against SARS-CoV-2 is still in place, and attention has been recently drawn to natural products. Several molecular targets have been identified as points of therapeutic intervention. The targets used in this study include SARS-CoV-2 helicase, spike protein, RNA-dependent RNA polymerase, main protease, and human ACE-2. An integrative computer-aided approach, which includes molecular docking, pharmacophore modeling, and pharmacokinetic profiling, was employed to identify anthocyanins with robust multiple antiviral activities against these SARS-CoV-2 targets. Result Four anthocyanins (Delphinidin 3-O-glucosyl-glucoside, Cyanidin 3-O-glucosyl-rutinoside, Cyanidin 3-(p-coumaroyl)-diglucoside-5-glucoside), and Nasunin) with robust multiple inhibitory interactions were identified from a library of 118 anthocyanins using computer-aided techniques. These compounds exhibited very good binding affinity to the protein targets and moderate pharmacokinetic profiles. However, Cyanidin 3-O-glucosyl-rutinoside is reported to be the most suitable drug candidate with multiple antiviral effects against SARS-CoV-2 due to its good binding affinity to all five protein targets engaged in the study. Conclusions The anthocyanins reported in this study exhibit robust binding affinities and strong inhibitory molecular interactions with the target proteins and could be well exploited as potential drug candidates with potent multiple antiviral effects against COVID-19.
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Haley PJ. From bats to pangolins: new insights into species differences in the structure and function of the immune system. Innate Immun 2022; 28:107-121. [PMID: 35506564 PMCID: PMC9136466 DOI: 10.1177/17534259221093120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 01/08/2023] Open
Abstract
Species differences in the structure and function of the immune system of laboratory animals are known to exist and have been reviewed extensively. However, the number and diversity of wild and exotic species, along with their associated viruses, that come into contact with humans has increased worldwide sometimes with lethal consequences. Far less is known about the immunobiology of these exotic and wild species. Data suggest that species differences of the mechanisms of inflammation, innate immunity and adaptive immunity are all involved in the establishment and maintenance of viral infections across reservoir hosts. The current review attempts to collect relevant data concerning the basics of innate and adaptive immune functions of exotic and wild species followed by identification of those differences that may play a role in the maintenance of viral infections in reservoir hosts.
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Affiliation(s)
- Patrick J. Haley
- Haley Tox/Path Consulting LLC, 104 Cypress Springs Way, 78633, Georgetown Texas, United States
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Govind Kumar V, Ogden DS, Isu UH, Polasa A, Losey J, Moradi M. Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1. J Biol Chem 2022; 298:101814. [PMID: 35278433 PMCID: PMC8907130 DOI: 10.1016/j.jbc.2022.101814] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/01/2023] Open
Abstract
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.
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Affiliation(s)
- Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dylan S Ogden
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - James Losey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA.
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Yépez Y, Marcano-Ruiz M, Bezerra RS, Fam B, Ximenez JPB, Silva WA, Bortolini MC. Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Genet Mol Biol 2022; 45:e20210309. [PMID: 35266951 PMCID: PMC8908351 DOI: 10.1590/1678-4685-gmb-2021-0309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.
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Affiliation(s)
- Yuri Yépez
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Mariana Marcano-Ruiz
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Rafael S Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Bibiana Fam
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - João PB Ximenez
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Wilson A Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Departamento de Genética, Ribeirão Preto, SP, Brazil
- Instituto de Pesquisa do Câncer de Guarapuava, Guarapuava, PR,
Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
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36
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Lohrasbi-Nejad A. Detection of homologous recombination events in SARS-CoV-2. Biotechnol Lett 2022; 44:399-414. [PMID: 35037234 PMCID: PMC8761517 DOI: 10.1007/s10529-021-03218-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/07/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE The COVID-19 disease with acute respiratory symptoms emerged in 2019. The causal agent of the disease, the SARS-CoV-2 virus, is classified into the Betacoronaviruses family. Coronaviruses (CoVs) are a huge family of viruses. Therefore, homologous recombination studies can help recognize the phylogenetic relationships among these viruses. METHODS In order to detect possible recombination events in SASRS-CoV-2, the genome sequences of Betacoronaviruses were obtained from the GenBank. The nucleotide sequences with the identity ≥ 60% to SARS-CoV-2 genome sequence were selected and then analyzed using different algorithms. RESULTS The results showed two recombination events at the beginning and the end of the genome sequence of SARS-CoV-2. Bat-SL-CoVZC21 (GenBank accession number MG772934) was specified as the minor parent for both events with p-values of 8.66 × 10-87 and 3.29 × 10-48, respectively. Furthermore, two recombination regions were detected at the beginning and the middle of the SARS-CoV-2 spike gene. Pangolin-CoV (PCoV_GX-P4L) and Rattus CoV (ChRCoV-HKU24) were determined as the potential parents with the GenBank accession number MT040333 and KM349742, respectively. Analysis of the spike gene revealed more similarity and less nucleotide diversity between SARS-CoV-2 and pangolin-CoVs. CONCLUSION Detection of the ancestors of SARS-CoV-2 in the coronaviruses family can help identify and define the phylogenetic relationships of the family Coronaviridae. Furthermore, constructing a phylogenetic tree based on the recombination regions made changes in the phylogenetic relationships of Betacoronaviruses.
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Affiliation(s)
- Azadeh Lohrasbi-Nejad
- Department of Agricultural Biotechnology, Shahid Bahonar University of Kerman, Kerman, Iran.
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37
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Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Roy S, Ayukekbong JA, Saylors KE, Joly DO, Wolfe ND, Rubin EM, Lange CE. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110. [PMID: 35233291 PMCID: PMC8867583 DOI: 10.1093/ve/veab110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/05/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
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Affiliation(s)
- Nkom F Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Amethyst Gillis
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Centre Region Route de Kribi, Yaoundé, BP 1364, Cameroon
| | - Joseph Le Doux Diffo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Jean-Michel Takuo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Julius Nwobegahay
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
| | | | - Anne W Rimoin
- Department of Epidemiology, University of California, 71-254 Center for Health Sciences, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bradley S Schneider
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Mosaic, Yaoundé, Centre Region, BP 35353, Cameroon
| | | | - David J McIver
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
- One Health Institute, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Sanjit Roy
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- University of Victoria, 3800 Finnerty Road, Victoria BC V8P 5C2, Canada
| | | | - Karen E Saylors
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
| | - Damien O Joly
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | | | - Edward M Rubin
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | - Christian E Lange
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
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Abstract
Since the outbreak in late December 2019, the coronavirus disease 2019 (COVID-19) pandemic has spread across the globe, causing great damage to human life and property. A lot of researchers around the world have devoted themselves to the study of its origin, pathogenic mechanism, and transmission route, and this article gives a summary. First, both humans and animals can act as the host of coronavirus. In indoor environments, the virus may exist in aerosols, droplets, saliva, etc., from the nose and mouth connected to the respiratory system, as well as feces, urine, etc., from the digestive and urinary systems. In addition, other substances, such as breast milk, eye feces, and blood, released from the host can carry viruses. The virus transmitted indoors is affected by indoor machinery, natural forces, and human activities, and spreads in different distances. Second, the virus spreads outdoors through three kinds of media: solid, liquid, and gas, and is affected by their survival time, the temperature, and humidity in the environment.
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Rahbar MR, Jahangiri A, Khalili S, Zarei M, Mehrabani-Zeinabad K, Khalesi B, Pourzardosht N, Hessami A, Nezafat N, Sadraei S, Negahdaripour M. Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis. Sci Rep 2021; 11:23622. [PMID: 34880279 PMCID: PMC8654821 DOI: 10.1038/s41598-021-01655-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Spike glycoprotein (Sgp) is liable for binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the host receptors. Since Sgp is the main target for vaccine and drug designing, elucidating its mutation pattern could help in this regard. This study is aimed at investigating the correspondence of specific residues to the SgpSARS-CoV-2 functionality by explorative interpretation of sequence alignments. Centrality analysis of the Sgp dissects the importance of these residues in the interaction network of the RBD-ACE2 (receptor-binding domain) complex and furin cleavage site. Correspondence of RBD to threonine500 and asparagine501 and furin cleavage site to glutamine675, glutamine677, threonine678, and alanine684 was observed; all residues are exactly located at the interaction interfaces. The harmonious location of residues dictates the RBD binding property and the flexibility, hydrophobicity, and accessibility of the furin cleavage site. These species-specific residues can be assumed as real targets of evolution, while other substitutions tend to support them. Moreover, all these residues are parts of experimentally identified epitopes. Therefore, their substitution may affect vaccine efficacy. Higher rate of RBD maintenance than furin cleavage site was predicted. The accumulation of substitutions reinforces the probability of the multi-host circulation of the virus and emphasizes the enduring evolutionary events.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Mehrabani-Zeinabad
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine, and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saman Sadraei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.
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40
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Díaz AV, Walker M, Webster JP. Surveillance and control of SARS-CoV-2 in mustelids: An evolutionary perspective. Evol Appl 2021; 14:2715-2725. [PMID: 34899977 PMCID: PMC8652926 DOI: 10.1111/eva.13310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/18/2023] Open
Abstract
The relevance of mustelids in SARS-CoV-2 transmission has become increasingly evident. Alongside experimental demonstration of airborne transmission among ferrets, the major animal model for human respiratory diseases, transmission of SARS-CoV-2 within- and/or between-commercial mink farms has occurred and continues to occur. The number of mink reared for the luxury fur trade is approximately 60.5 million, across 36 mustelid-farming countries. By July 2021, SARS-CoV-2 outbreaks have been reported in 12 of these countries, at 412 European and 20 North American mink farms. Reverse zoonotic transmission events (from humans to mink) have introduced the virus to farms with subsequent extensive mink-to-mink transmission as well as further zoonotic (mink-to-human) transmission events generating cases among both farm workers and the broader community. Overcrowded housing conditions inherent within intensive mink farms, often combined with poor sanitation and welfare, both guarantee spread of SARS-CoV-2 and facilitate opportunities for viral variants, thereby effectively representing biotic hubs for viral transmission and evolution of virulence. Adequate preventative, surveillance and control measures within the mink industry are imperative both for the control of the current global pandemic and to mitigate against future outbreaks.
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Affiliation(s)
- Adriana V Díaz
- Department of Pathobiology and Population Sciences Royal Veterinary College University of London Herts UK
| | - Martin Walker
- Department of Pathobiology and Population Sciences Royal Veterinary College University of London Herts UK
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences Royal Veterinary College University of London Herts UK
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41
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Geng R, Zhou P. Severe acute respiratory syndrome (SARS) related coronavirus in bats. ANIMAL DISEASES 2021; 1:4. [PMID: 34778877 PMCID: PMC8062212 DOI: 10.1186/s44149-021-00004-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/06/2021] [Indexed: 11/25/2022] Open
Abstract
Three major human coronavirus disease outbreaks, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and 2019 coronavirus disease (COVID-19), occurred in the twenty-first century and were caused by different coronaviruses (CoVs). All these viruses are considered to have originated from bats and transmitted to humans through intermediate hosts. SARS-CoV-1 and SARS-CoV-2, disease agent of COVID-19, shared around 80% genomic similarity, and thus belong to SARS-related CoVs. As a natural reservoir of viruses, bats harbor numerous other SARS-related CoVs that could potentially infect humans around the world, causing SARS or COVID-19 like outbreaks in the future. In this review, we summarized the current knowledge of CoVs on geographical distribution, genetic diversity, cross-species transmission potential and possible pathogenesis in humans, aiming for a better understanding of bat SARS-related CoVs in the context of prevention and control.
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Affiliation(s)
- Rong Geng
- CAS key laboratory of special pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhou
- CAS key laboratory of special pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
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42
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Wong ACP, Lau SKP, Woo PCY. Interspecies Jumping of Bat Coronaviruses. Viruses 2021; 13:2188. [PMID: 34834994 PMCID: PMC8620431 DOI: 10.3390/v13112188] [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: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.
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Affiliation(s)
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
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43
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Nova N. Cross-Species Transmission of Coronaviruses in Humans and Domestic Mammals, What Are the Ecological Mechanisms Driving Transmission, Spillover, and Disease Emergence? Front Public Health 2021; 9:717941. [PMID: 34660513 PMCID: PMC8514784 DOI: 10.3389/fpubh.2021.717941] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022] Open
Abstract
Coronaviruses cause respiratory and digestive diseases in vertebrates. The recent pandemic, caused by the novel severe acute respiratory syndrome (SARS) coronavirus 2, is taking a heavy toll on society and planetary health, and illustrates the threat emerging coronaviruses can pose to the well-being of humans and other animals. Coronaviruses are constantly evolving, crossing host species barriers, and expanding their host range. In the last few decades, several novel coronaviruses have emerged in humans and domestic animals. Novel coronaviruses have also been discovered in captive wildlife or wild populations, raising conservation concerns. The evolution and emergence of novel viruses is enabled by frequent cross-species transmission. It is thus crucial to determine emerging coronaviruses' potential for infecting different host species, and to identify the circumstances under which cross-species transmission occurs in order to mitigate the rate of disease emergence. Here, I review (broadly across several mammalian host species) up-to-date knowledge of host range and circumstances concerning reported cross-species transmission events of emerging coronaviruses in humans and common domestic mammals. All of these coronaviruses had similar host ranges, were closely related (indicative of rapid diversification and spread), and their emergence was likely associated with high-host-density environments facilitating multi-species interactions (e.g., shelters, farms, and markets) and the health or well-being of animals as end- and/or intermediate spillover hosts. Further research is needed to identify mechanisms of the cross-species transmission events that have ultimately led to a surge of emerging coronaviruses in multiple species in a relatively short period of time in a world undergoing rapid environmental change.
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Affiliation(s)
- Nicole Nova
- Department of Biology, Stanford University, Stanford, CA, United States
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44
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Glidden CK, Nova N, Kain MP, Lagerstrom KM, Skinner EB, Mandle L, Sokolow SH, Plowright RK, Dirzo R, De Leo GA, Mordecai EA. Human-mediated impacts on biodiversity and the consequences for zoonotic disease spillover. Curr Biol 2021; 31:R1342-R1361. [PMID: 34637744 PMCID: PMC9255562 DOI: 10.1016/j.cub.2021.08.070] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human-mediated changes to natural ecosystems have consequences for both ecosystem and human health. Historically, efforts to preserve or restore 'biodiversity' can seem to be in opposition to human interests. However, the integration of biodiversity conservation and public health has gained significant traction in recent years, and new efforts to identify solutions that benefit both environmental and human health are ongoing. At the forefront of these efforts is an attempt to clarify ways in which biodiversity conservation can help reduce the risk of zoonotic spillover of pathogens from wild animals, sparking epidemics and pandemics in humans and livestock. However, our understanding of the mechanisms by which biodiversity change influences the spillover process is incomplete, limiting the application of integrated strategies aimed at achieving positive outcomes for both conservation and disease management. Here, we review the literature, considering a broad scope of biodiversity dimensions, to identify cases where zoonotic pathogen spillover is mechanistically linked to changes in biodiversity. By reframing the discussion around biodiversity and disease using mechanistic evidence - while encompassing multiple aspects of biodiversity including functional diversity, landscape diversity, phenological diversity, and interaction diversity - we work toward general principles that can guide future research and more effectively integrate the related goals of biodiversity conservation and spillover prevention. We conclude by summarizing how these principles could be used to integrate the goal of spillover prevention into ongoing biodiversity conservation initiatives.
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Affiliation(s)
| | - Nicole Nova
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Morgan P Kain
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Natural Capital Project, Stanford University, Stanford, CA 94305, USA
| | | | - Eloise B Skinner
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Centre for Planetary Health and Food Security, Griffith University, Gold Coast, QLD 4222, Australia
| | - Lisa Mandle
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Natural Capital Project, Stanford University, Stanford, CA 94305, USA; Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Susanne H Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA; Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Raina K Plowright
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Giulio A De Leo
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA; Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Erin A Mordecai
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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45
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Singh SK, Singh S, Singh R. Targeting novel coronavirus SARS-CoV-2 spike protein with phytoconstituents of Momordica charantia. J Ovarian Res 2021; 14:126. [PMID: 34579761 PMCID: PMC8474883 DOI: 10.1186/s13048-021-00872-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Infections by the SARS-CoV-2 virus causing COVID-19 are presently a global emergency. The current vaccination effort may reduce the infection rate, but strain variants are emerging under selection pressure. Thus, there is an urgent need to find drugs that treat COVID-19 and save human lives. Hence, in this study, we identified phytoconstituents of an edible vegetable, Bitter melon (Momordica charantia), that affect the SARS-CoV-2 spike protein. METHODS Components of Momordica charantia were tested to identify the compounds that bind to the SARS-CoV-2 spike protein. An MTiOpenScreen web-server was used to perform docking studies. The Lipinski rule was utilized to evaluate potential interactions between the drug and other target molecules. PyMol and Schrodinger software were used to identify the hydrophilic and hydrophobic interactions. Surface plasmon resonance (SPR) was employed to assess the interaction between an extract component (erythrodiol) and the spike protein. RESULTS Our in-silico evaluations showed that phytoconstituents of Momordica charantia have a low binding energy range, -5.82 to -5.97 kcal/mol. A docking study revealed two sets of phytoconstituents that bind at the S1 and S2 domains of SARS-CoV-2. SPR showed that erythrodiol has a strong binding affinity (KD = 1.15 μM) with the S2 spike protein of SARS-CoV-2. Overall, docking, ADME properties, and SPR displayed strong interactions between phytoconstituents and the active site of the SARS-CoV-2 spike protein. CONCLUSION This study reveals that phytoconstituents from bitter melon are potential agents to treat SARS-CoV-2 viral infections due to their binding to spike proteins S1 and S2.
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Affiliation(s)
- Santosh Kumar Singh
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
- Cancer Health Equity Institute, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
| | - Shailesh Singh
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
- Cancer Health Equity Institute, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
| | - Rajesh Singh
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
- Cancer Health Equity Institute, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310 USA
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46
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Gupta P, Singh MP, Goyal K, Tripti P, Ansari MI, Obli Rajendran V, Dhama K, Malik YS. Bats and viruses: a death-defying friendship. Virusdisease 2021; 32:467-479. [PMID: 34518804 PMCID: PMC8426161 DOI: 10.1007/s13337-021-00716-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 01/10/2023] Open
Abstract
Bats have a primeval evolutionary origin and have adopted various survival methods. They have played a central role in the emergence of various viral diseases. The sustenance of a plethora of virus species inside them has been an earnest area of study. This review explains how the evolution of viruses in bats has been linked to their metabolic pathways, flight abilities, reproductive abilities and colonization behaviors. The utilization of host immune response by DNA and RNA viruses is a commencement of the understanding of differences in the impact of viral infection in bats from other mammals. Rabies virus and other lyssa viruses have had long documented history as bat viruses. While many others like Ebola virus, Nipah virus, Hantavirus, SARS-CoV, MERS-CoV and other new emerging viruses like Sosuga virus, Menangle and Tioman virus are now being studied extensively for their transmission in new hosts. The ongoing pandemic SARS-CoV-2 virus has also been implicated to be originated from bats. Certain factors have been linked to spillover events while the scope of entitlement of other conditions in the spread of diseases from bats still exists. However, certain physiological and ecological parameters have been linked to specific transmission patterns, and more definite proofs are awaited for establishing these connections.
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Affiliation(s)
- Parakriti Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mini P. Singh
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pande Tripti
- Biological Standardization Division, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Dasauli, Kursi Road, Lucknow, Uttar Pradesh 226026 India
| | - Vinodhkumar Obli Rajendran
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab 141 004 India
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47
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Kayode AJ, Banji-Onisile FO, Olaniran AO, Okoh AI. An Overview of the Pathogenesis, Transmission, Diagnosis, and Management of Endemic Human Coronaviruses: A Reflection on the Past and Present Episodes and Possible Future Outbreaks. Pathogens 2021; 10:1108. [PMID: 34578140 PMCID: PMC8470645 DOI: 10.3390/pathogens10091108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the 2019 coronavirus pandemic caught the world by surprise in late 2019 and has held it hostage for months with an increasing number of infections and deaths. Although coronavirus was first discovered in the 1960s and was known to cause respiratory infection in humans, no information was available about the epidemic pattern of the virus until the past two decades. This review addresses the pathogenesis, transmission dynamics, diagnosis, management strategies, the pattern of the past and present events, and the possibility of future outbreaks of the endemic human coronaviruses. Several studies have described bats as presumptive natural reservoirs of coronaviruses. In essence, the identification of a diverse group of similar SARS coronaviruses in bats suggests the possibility of a future epidemic due to severe acute respiratory syndrome (SARS-like) coronaviruses originating from different reservoir hosts. The study also identified a lack of vaccines to prevent human coronavirus infections in humans in the past, however, the recent breakthrough in vaccine discovery and approval for emergency use for the treatment of Severe Acute Respiratory Syndrome Coronavirus 2 is commendable. The high rates of genomic substitution and recombination due to errors in RNA replication and the potential for independent species crossing suggest the chances of an entirely new strain evolving. Therefore, rapid research efforts should be deployed for vaccination to combat the COVID-19 pandemic and prevent a possible future outbreak. More sensitization and enlightenment on the need to adopt good personal hygiene practices, social distancing, and scientific evaluation of existing medications with promising antiviral effects against SARS-CoV-2 is required. In addition, intensive investigations to unravel and validate the possible reservoirs, the intermediate host, as well as insight into the ability of the virus to break the species barrier are needed to prevent future viral spillover and possible outbreaks.
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Affiliation(s)
- Adeoye J. Kayode
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
| | - Folasade O. Banji-Onisile
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Ademola O. Olaniran
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Department of Environmental Health Sciences, College Health Sciences, University of Sharjah, Sharjah 555588, United Arab Emirates
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48
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Islam MS, Hasib FMY, Nath C, Ara J, Nu MS, Fazal MA, Chowdhury S. Coronavirus disease 2019 and its potential animal reservoirs: A review. INTERNATIONAL JOURNAL OF ONE HEALTH 2021. [DOI: 10.14202/ijoh.2021.171-181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the 21st century, the world has been plagued by coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus of the family Coronaviridae epidemiologically suspected to be linked to a wet market in Wuhan, China. The involvement of wildlife and wet markets with the previous outbreaks simultaneously has been brought into sharp focus. Although scientists are yet to ascertain the host range and zoonotic potential of SARS-CoV-2 rigorously, information about its two ancestors, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), is a footprint for research on COVID-19. A 96% genetic similarity with bat coronaviruses and SARS-CoV-2 indicates that the bat might be a potential reservoir of SARS-CoV-2 just like SARS-CoV and MERS-CoV, where civets and dromedary camels are considered the potential intermediate host, respectively. Perceiving the genetic similarity between pangolin coronavirus and SARS-CoV-2, many scientists also have given the scheme that the pangolin might be the intermediate host. The involvement of SARS-CoV-2 with other animals, such as mink, snake, and turtle has also been highlighted in different research articles based on the interaction between the key amino acids of S protein in the receptor-binding domain and angiotensin-converting enzyme II (ACE2). This study highlights the potential animal reservoirs of SARS-CoV-2 and the role of wildlife in the COVID-19 pandemic. Although different causes, such as recurring viral genome recombination, wide genetic assortment, and irksome food habits, have been blamed for this emergence, basic research studies and literature reviews indicate an enormous consortium between humans and animals for the COVID-19 pandemic.
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Affiliation(s)
- Md. Sirazul Islam
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - F. M. Yasir Hasib
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Chandan Nath
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Jahan Ara
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Mong Sing Nu
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md. Abul Fazal
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Sharmin Chowdhury
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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49
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Kulikowski CA. Pandemics: Historically Slow "Learning Curve" Leading to Biomedical Informatics and Vaccine Breakthroughs. Yearb Med Inform 2021; 30:290-301. [PMID: 33882592 PMCID: PMC8416199 DOI: 10.1055/s-0041-1726482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The worldwide tragedy of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic vividly demonstrates just how inadequate mitigation and control of the spread of infectious diseases can be when faced with a new microorganism with unknown pathogenic effects. Responses by governments in charge of public health, and all other involved organizations, have proved largely wanting. Data infrastructure and the information and communication systems needed to deal with the pandemic have likewise not been up to the task. Nevertheless, after a year of the worldwide outbreak, hope arises from this being the first major pandemic event in history where genomic and related biosciences - relying on biomedical informatics - have been essential in decoding the viral sequence data and producing the mRNA and other biotechnologies that unexpectedly rapidly have led to investigation, design, development, and testing of useful vaccines. Medical informatics may also help support public health actions and clinical interventions - but scalability and impact will depend on overcoming ingrained human shortcomings to deal with complex socio-economic, political, and technological disruptions together with the many ethical challenges presented by pandemics. OBJECTIVES The principal goal is to review the history of biomedical information and healthcare practices related to past pandemics in order to illustrate just how exceptional and dependent on biomedical informatics are the recent scientific insights into human immune responses to viral infection, which are enabling rapid antiviral vaccine development and clinical management of severe cases - despite the many societal challenges ahead. METHODS This paper briefly reviews some of the key historical antecedents leading up to modern insights into epidemic and pandemic processes with their biomedical and healthcare information intended to guide practitioners, agencies, and the lay public in today's ongoing pandemic events. CONCLUSIONS Poor scientific understanding and excessively slow learning about infectious disease processes and mitigating behaviors have stymied effective treatment until the present time. Advances in insights about immune systems, genomes, proteomes, and all the other -omes, became a reality thanks to the key sequencing technologies and biomedical informatics that enabled the Human Genome Project, and only now, 20 years later, are having an impact in ameliorating devastating zoonotic infectious pandemics, including the present SARS-CoV-2 event through unprecedently rapid vaccine development. In the future these advances will hopefully also enable more targeted prevention and treatment of disease. However, past and present shortcomings of most of the COVID-19 pandemic responses illustrate just how difficult it is to persuade enough people - and especially political leaders - to adopt societally beneficial risk-avoidance behaviors and policies, even as these become better understood.
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50
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Berber E, Sumbria D, Çanakoğlu N. Meta-analysis and comprehensive study of coronavirus outbreaks: SARS, MERS and COVID-19. J Infect Public Health 2021; 14:1051-1064. [PMID: 34174535 PMCID: PMC8214867 DOI: 10.1016/j.jiph.2021.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Zoonotic coronaviruses have caused several endemic and pandemic situations around the world. SARS caused the first epidemic alert at the beginning of this century, followed by MERS. COVID-19 appeared to be highly contagious, with human-to-human transmission by aerosol droplets, and reached nearly all countries around the world. A plethora of studies were performed, with reports being published within a short period of time by scientists and medical physicians. It has been difficult to find the relevant data to create an overview of the situation according to studies from accumulated findings and reports. In the present study we aimed to perform a comprehensive study in the context of the case fatality ratios (CFRs) of three major human Coronavirus outbreaks which occurred during the first twenty years of 21st century. METHODS In this study, we performed meta-analyses on SARS, MERS and COVID-19 outbreak events from publicly available records. Study analyses were performed with the help of highly reputable scientific databases such as PubMed, WOS and Scopus to evaluate and present current knowledge on zoonotic coronavirus outbreaks, starting from 2000 to the end of 2020. RESULTS A total of 250,194 research studies and records were identified with specific keywords and synonyms for the three viruses in order to cover all publications. In the end, 41 records were selected and included after applying several exclusion and inclusion criteria on identified datasets. SARS was found to have a nearly 11% case fatality ratio (CFR), which means the estimated number of deaths as a proportion of confirmed positive cases; Taiwan was the country most affected by the SARS outbreak based on the CFR analysis. MERS had CFRs of 35.8 and 26 in Saudi Arabia during the 2012 and 2015 outbreaks, respectively. COVID-19 resulted in a 2.2 CFR globally, and the USA reported the highest mortality ratio in the world in the end of first year of COVID-19 pandemic. CONCLUSION Some members of the Coronaviridae family can cause highly contagious and devastating infections among humans. Within the last two decades, the whole world has witnessed several deadly emerging infectious diseases, which are most commonly zoonotic in nature. We conclude that pre-existing immunity during the early stages of a pandemic might be important, but case control and management strategies should be improved to decrease CFRs. Finally, we have addressed several concerns in relation to outbreak events in this study.
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Affiliation(s)
- Engin Berber
- University of Tennessee, Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, Knoxville, TN, USA; Erciyes University, College of Veterinary Medicine, Department of Virology, Kayseri, Turkey.
| | - Deepak Sumbria
- University of Tennessee, Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, Knoxville, TN, USA; Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Department of Silviculture and Agroforestry, College of Forestry, Solan, Himachal Pradesh, India
| | - Nurettin Çanakoğlu
- Muğla Sıtkı Koçman University, Milas Faculty of Veterinary Science, Department of Virology, Muğla, Turkey
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