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Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell 2021; 184:4848-4856. [PMID: 34480864 PMCID: PMC8373617 DOI: 10.1016/j.cell.2021.08.017] [Citation(s) in RCA: 267] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 01/11/2023]
Abstract
Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94704, USA
| | - Joel O Wertheim
- Department of Medicine, University of California-San Diego, La Jolla, CA 92093, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter C Doherty
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - Julian L Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX 77807, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
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Khalid S, Siddique R, Shaheen S, Shahid MN, Shamim Z, Khan MKA, Serçe ÇU. Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). BRAZ J BIOL 2021; 83:e247237. [PMID: 34495154 DOI: 10.1590/1519-6984.247237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/09/2021] [Indexed: 11/22/2022] Open
Abstract
Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.
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Affiliation(s)
- S Khalid
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - R Siddique
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - S Shaheen
- Lahore College for Women University, Department of Botany, Jail Road, Lahore, Pakistan
| | - M N Shahid
- University of Education, Township, Department of Botany, Division of Science and Technology, Lahore, Pakistan
| | - Z Shamim
- Mirpur University of Science and Technology, Department of Biotechnology, Mirpur, Azad Kashmir, Pakistan
| | - M K A Khan
- University of Okara, Department of Zoology, Okara, Pakistan
| | - Ç Ulubaş Serçe
- Niğde Ömer Halisdemir Üniversitesi, Tarım Bilimleri ve Teknolojileri Fakültesi, Bitkisel Üretim ve Teknolojileri Bölümü, Niğde, Turkey
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53
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Jamwal VL, Kumar N, Bhat R, Jamwal PS, Singh K, Dogra S, Kulkarni A, Bhadra B, Shukla MR, Saran S, Dasgupta S, Vishwakarma RA, Gandhi SG. Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant. Virol J 2021; 18:178. [PMID: 34461941 PMCID: PMC8404189 DOI: 10.1186/s12985-021-01642-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/12/2021] [Indexed: 01/12/2023] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, has infected more than 179 million people worldwide. Testing of infected individuals is crucial for identification and isolation, thereby preventing further spread of the disease. Presently, Taqman™ Reverse Transcription Real Time PCR is considered gold standard, and is the most common technique used for molecular testing of COVID-19, though it requires sophisticated equipments, expertise and is also relatively expensive. Objective Development and optimization of an alternate molecular testing method for the diagnosis of COVID-19, through a two step Reverse Transcription Loop-mediated isothermal AMPlification (RT-LAMP). Results Primers for LAMP were carefully designed for discrimination from other closely related human pathogenic coronaviruses. Care was also taken that primer binding sites are present in conserved regions of SARS-CoV2. Our analysis shows that the primer binding sites are well conserved in all the variants of concern (VOC) and variants of interest (VOI), notified by World Health Organization (WHO). These lineages include B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526 and B.1.617.1. Various DNA polymerases with strand displacement activity were evaluated and conditions were optimized for LAMP amplification and visualization. Different LAMP primer sets were also evaluated using synthetic templates as well as patient samples. Conclusion In a double blind study, the RT-LAMP assay was validated on more than 150 patient samples at two different sites. The RT-LAMP assay appeared to be 89.2% accurate when compared to the Taqman™ rt-RT-PCR assay. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01642-9.
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Affiliation(s)
- Vijay Lakshmi Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Natish Kumar
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rahul Bhat
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Piyush Singh Jamwal
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Kaurab Singh
- Higher Education Department, Union Territory of Jammu and Kashmir, Jammu, India
| | - Sandeep Dogra
- Department of Microbiology, Government Medical College, Jammu, 180001, India
| | - Abhishek Kulkarni
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Bhaskar Bhadra
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Manish R Shukla
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Saurabh Saran
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Santanu Dasgupta
- A2O - Biology, Reliance Technology Group, Reliance Industries Limited, RCP, Navi Mumbai, 400701, India
| | - Ram A Vishwakarma
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sumit G Gandhi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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54
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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55
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Liang J, Zhu C, Zhang L. Cospeciation of coronavirus and paramyxovirus with their bat hosts in the same geographical areas. BMC Ecol Evol 2021; 21:148. [PMID: 34325659 PMCID: PMC8319908 DOI: 10.1186/s12862-021-01878-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Bat-borne viruses are relatively host specific. We hypothesize that this host specificity is due to coevolution of the viruses with their hosts. To test this hypothesis, we investigated the coevolution of coronavirus and paramyxovirus with their bat hosts. Published nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) gene of 60 coronavirus strains identified from 37 bat species, the RNA polymerase large (L) gene of 36 paramyxovirus strains from 29 bat species, and the cytochrome B (cytB) gene of 35 bat species were analyzed for coevolution signals. Each coevolution signal detected was tested and verified by global-fit cophylogenic analysis using software ParaFit, PACo, and eMPRess. Results Significant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry closely related viruses. Conclusions Our results suggest that paramyxovirus and coronavirus coevolve with their hosts.
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Affiliation(s)
- Jie Liang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Chunchao Zhu
- Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
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56
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Malik YS, Kumar P, Ansari MI, Hemida MG, El Zowalaty ME, Abdel-Moneim AS, Ganesh B, Salajegheh S, Natesan S, Sircar S, Safdar M, Vinodhkumar OR, Duarte PM, Patel SK, Klein J, Rahimi P, Dhama K. SARS-CoV-2 Spike Protein Extrapolation for COVID Diagnosis and Vaccine Development. Front Mol Biosci 2021; 8:607886. [PMID: 34395515 PMCID: PMC8355592 DOI: 10.3389/fmolb.2021.607886] [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: 09/18/2020] [Accepted: 04/09/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) led to coronavirus disease 2019 (COVID-19) pandemic affecting nearly 71.2 million humans in more than 191 countries, with more than 1.6 million mortalities as of 12 December, 2020. The spike glycoprotein (S-protein), anchored onto the virus envelope, is the trimer of S-protein comprised of S1 and S2 domains which interacts with host cell receptors and facilitates virus-cell membrane fusion. The S1 domain comprises of a receptor binding domain (RBD) possessing an N-terminal domain and two subdomains (SD1 and SD2). Certain regions of S-protein of SARS-CoV-2 such as S2 domain and fragment of the RBD remain conserved despite the high selection pressure. These conserved regions of the S-protein are extrapolated as the potential target for developing molecular diagnostic techniques. Further, the S-protein acts as an antigenic target for different serological assay platforms for the diagnosis of COVID-19. Virus-specific IgM and IgG antibodies can be used to detect viral proteins in ELISA and lateral flow immunoassays. The S-protein of SARS-CoV-2 has very high sequence similarity to SARS-CoV-1, and the monoclonal antibodies (mAbs) against SARS-CoV-1 cross-react with S-protein of SARS-CoV-2 and neutralize its activity. Furthermore, in vitro studies have demonstrated that polyclonal antibodies targeted against the RBD of S-protein of SARS-CoV-1 can neutralize SARS-CoV-2 thus inhibiting its infectivity in permissive cell lines. Research on coronaviral S-proteins paves the way for the development of vaccines that may prevent SARS-CoV-2 infection and alleviate the current global coronavirus pandemic. However, specific neutralizing mAbs against SARS-CoV-2 are in clinical development. Therefore, neutralizing antibodies targeting SARS-CoV-2 S-protein are promising specific antiviral therapeutics for pre-and post-exposure prophylaxis and treatment of SARS-CoV-2 infection. We hereby review the approaches taken by researchers across the world to use spike gene and S-glycoprotein for the development of effective diagnostics, vaccines and therapeutics against SARA-CoV-2 infection the COVID-19 pandemic.
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Affiliation(s)
- Yashpal S. Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Mohd Ikram Ansari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
- Department of Biosciences, Integral University, Lucknow, India
| | - Maged G. Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Hofuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Shaikh, Egypt
| | - Mohamed E. El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, Al-Taif, Saudi Arabia
- Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Balasubramanian Ganesh
- Laboratory Division, Indian Council of Medical Research - National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, India
| | - Sina Salajegheh
- Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Muhammad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur, Pakistan
| | - O. R. Vinodhkumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Phelipe M. Duarte
- Veterinarian, Professor at the Faculty of Biological and Health Sciences, Universidade de Cuiabá, Primavera do Leste, Brazil
| | - Shailesh K. Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Jörn Klein
- Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Parastoo Rahimi
- Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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57
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429646. [PMID: 33564759 PMCID: PMC7872347 DOI: 10.1101/2021.02.03.429646] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
| | - Joe Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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58
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Canessa E. Uncovering Signals from the Coronavirus Genome. Genes (Basel) 2021; 12:genes12070973. [PMID: 34202172 PMCID: PMC8303286 DOI: 10.3390/genes12070973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 01/21/2023] Open
Abstract
A signal analysis of the complete genome sequenced for coronavirus variants of concern—B.1.1.7 (Alpha), B.1.135 (Beta) and P1 (Gamma)—and coronavirus variants of interest—B.1.429–B.1.427 (Epsilon) and B.1.525 (Eta)—is presented using open GISAID data. We deal with a certain new type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases. Our method provides additional information to conventional similarity comparisons via alignment methods and Fourier Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of complete genomics sequences according to its progression along the nucleotide bases position. The present new method could be useful for the bioinformatics surveillance and dynamics of coronavirus genome variants.
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Affiliation(s)
- Enrique Canessa
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Science Dissemination Unit (SDU), 34151 Trieste, Italy
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59
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Beyrampour-Basmenj H, Milani M, Ebrahimi-Kalan A, Ben Taleb Z, Ward KD, Dargahi Abbasabad G, Aliyari-serej Z, Ebrahimi Kalan M. An Overview of the Epidemiologic, Diagnostic and Treatment Approaches of COVID-19: What do We Know? Public Health Rev 2021; 42:1604061. [PMID: 34381626 PMCID: PMC8245675 DOI: 10.3389/phrs.2021.1604061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 01/08/2023] Open
Abstract
Background: In late December 2019, a new infectious respiratory disease (COVID-19) was reported in a number of patients with a history of exposure to the Huanan seafood market in China. The World Health Organization officially announced the COVID-19 pandemic on March 11, 2020. Here, we provided an overview of the epidemiologic, diagnostic and treatment approaches associated with COVID-19. Methods: We reviewed the publications indexed in major biomedical databases by December 20, 2020 or earlier (updated on May 16, 2021). Search keywords included a combination of: COVID-19, Coronavirus disease 2019, SARS-CoV-2, Epidemiology, Prevention, Diagnosis, Vaccine, and Treatment. We also used available information about COVID-19 from valid sources such as WHO. Results and Conclusion: At the time of writing this review, while most of the countries authorized COVID-19 vaccines for emergency use starting December 8, 2020, there is no a definite cure for it. This review synthesizes current knowledge of virology, epidemiology, clinical symptoms, diagnostic approaches, common treatment strategies, novel potential therapeutic options for control and prevention of COVID-19 infection, available vaccines, public health and clinical implications.
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Affiliation(s)
| | | | | | - Ziyad Ben Taleb
- University of Texas at Arlington, Arlington, VA, United States
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60
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Suleman S, Shukla SK, Malhotra N, Bukkitgar SD, Shetti NP, Pilloton R, Narang J, Nee Tan Y, Aminabhavi TM. Point of care detection of COVID-19: Advancement in biosensing and diagnostic methods. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 414:128759. [PMID: 33551668 PMCID: PMC7847737 DOI: 10.1016/j.cej.2021.128759] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 05/08/2023]
Abstract
The recent outbreak of COVID-19 has created much inconvenience and fear that the virus can seriously affect humans, causing health hazards and death. This pandemic has created much worry and as per the report by World Health Organization (WHO), more than 43 million individuals in 215 countries and territories were affected. People around the world are still struggling to overcome the problems associated with this pandemic. Of all the available methods, reverse-transcriptase polymerase chain reaction (RT-PCR) has been widely practiced for the pandemic detection even though several diagnostic tools are available having varying accuracy and sensitivity. The method offers many advantages making it a life-saving tool, but the method has the limitation of transporting to the nearest pathology lab, thus limiting its application in resource limited settings. This has a risen a crucial need for point-of-care devices for on-site detection. In this venture, biosensors have been used, since they can be applied immediately at the point-of-care. This review will discuss about the available diagnostic methods and biosensors for COVID-19 detection.
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Affiliation(s)
- Shariq Suleman
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Sudheesh K Shukla
- Institute of Advanced Materials, IAAM. Gammalkilsvagen 18, 590 53, Ulrika, Sweden
| | - Nitesh Malhotra
- Department of Physiotherapy, Faculty of Applied Health Sciences (FAHS), Manav Rachana International Institute of Research and Studies, Faridabad, Haryana, India
| | - Shikandar D Bukkitgar
- Center for Electrochemical Science & Materials, Department of Chemistry, K.L.E. Institute of Technology, Opposite to Airport, Hubballi 580 027, India
| | - Nagaraj P Shetti
- Center for Electrochemical Science & Materials, Department of Chemistry, K.L.E. Institute of Technology, Opposite to Airport, Hubballi 580 027, India
| | - Roberto Pilloton
- Institute of Crystallography of National Research Council (IC-CNR), Rome, Italy
| | - Jagriti Narang
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Yen Nee Tan
- Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
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61
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Goraichuk IV, Arefiev V, Stegniy BT, Gerilovych AP. Zoonotic and Reverse Zoonotic Transmissibility of SARS-CoV-2. Virus Res 2021; 302:198473. [PMID: 34118360 PMCID: PMC8188804 DOI: 10.1016/j.virusres.2021.198473] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent detections of this virus in pet, zoo, wild, and farm animals have compelled inquiry regarding the zoonotic (animal-to-human) and reverse zoonotic (human-to-animal) transmissibility of SARS-CoV-2 with the potential of COVID-19 pandemic evolving into a panzootic. It is important to monitor the global spread of disease and to assess the significance of genomic changes to support prevention and control efforts during a pandemic. An understanding of the SARS-CoV-2 epidemiology provides opportunities to prevent the risk of repeated re-infection of humans and requires a robust One Health-based investigation. This review paper describes the known properties and the existing gaps in scientific knowledge about the zoonotic and reverse zoonotic transmissibility of the novel virus SARS-CoV-2 and the COVID-19 disease it causes.
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Affiliation(s)
- Iryna V Goraichuk
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Vasiliy Arefiev
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Borys T Stegniy
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Anton P Gerilovych
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
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62
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Structural basis for broad coronavirus neutralization. Nat Struct Mol Biol 2021; 28:478-486. [PMID: 33981021 DOI: 10.1038/s41594-021-00596-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/21/2021] [Indexed: 02/03/2023]
Abstract
Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.
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63
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Fedry J, Hurdiss DL, Wang C, Li W, Obal G, Drulyte I, Du W, Howes SC, van Kuppeveld FJM, Förster F, Bosch BJ. Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11. SCIENCE ADVANCES 2021; 7:eabf5632. [PMID: 33958322 PMCID: PMC8172134 DOI: 10.1126/sciadv.abf5632] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/26/2021] [Indexed: 05/05/2023]
Abstract
The emergence of SARS-CoV-2 antibody escape mutations highlights the urgent need for broadly neutralizing therapeutics. We previously identified a human monoclonal antibody, 47D11, capable of cross-neutralizing SARS-CoV-2 and SARS-CoV and protecting against the associated respiratory disease in an animal model. Here, we report cryo-EM structures of both trimeric spike ectodomains in complex with the 47D11 Fab. 47D11 binds to the closed receptor-binding domain, distal to the ACE2 binding site. The CDRL3 stabilizes the N343 glycan in an upright conformation, exposing a mutationally constrained hydrophobic pocket, into which the CDRH3 loop inserts two aromatic residues. 47D11 stabilizes a partially open conformation of the SARS-CoV-2 spike, suggesting that it could be used effectively in combination with other antibodies targeting the exposed receptor-binding motif. Together, these results reveal a cross-protective epitope on the SARS-CoV-2 spike and provide a structural roadmap for the development of 47D11 as a prophylactic or postexposure therapy for COVID-19.
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Affiliation(s)
- Juliette Fedry
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Daniel L Hurdiss
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - Gonzalo Obal
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, Netherlands
| | - Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - Stuart C Howes
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands.
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64
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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65
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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66
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Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations. Viruses 2021; 13:v13050936. [PMID: 34070175 PMCID: PMC8158508 DOI: 10.3390/v13050936] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/13/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.
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67
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Millet JK, Jaimes JA, Whittaker GR. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol Rev 2021; 45:fuaa057. [PMID: 33118022 PMCID: PMC7665467 DOI: 10.1093/femsre/fuaa057] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
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Affiliation(s)
- Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
- Cornell Feline Health Center, Ithaca, NY 14853, USA
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68
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Kaina B. On the Origin of SARS-CoV-2: Did Cell Culture Experiments Lead to Increased Virulence of the Progenitor Virus for Humans? In Vivo 2021; 35:1313-1326. [PMID: 33910809 DOI: 10.21873/invivo.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/17/2022]
Abstract
We are currently in a rapidly expanding pandemic of the SARS-CoV-2 virus, which originated in the city of Wuhan in central China. The disease COVID-19 is now spread worldwide and has tremendous socio-economic consequences. The origin of the virus can be reconstructed through epidemiological studies and, even more so, from genome comparisons. How the evolution of the virus and the transition to humans might have happened is the subject of much speculation. It is considered certain that the virus is of animal origin and very likely passed from bats to humans in a zoonotic event. An intermediate host was postulated, but many SARS-like bat viruses have the ability to infect human cells directly, which has been shown experimentally by scientists in the Wuhan Institute of Virology using collected specimens containing virus material from horseshoe bats. The propagation of SARS-like bat viruses in cell culture allowed experiments aimed at increasing the infectivity of the virus and adaptation to human cells. This article summarizes the unique properties of SARS-CoV-2 and focusses on a specific sequence encoding the spike protein. Possible scenarios of virus evolution are discussed, with particular emphasis on the hypothesis that the virus could have emerged unintentionally through routine culture or gain-of-function experiments in a laboratory, where it was optimally adapted to human cells and caused cryptic infections among workers who finally spread the virus causing the pandemic.
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Affiliation(s)
- Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
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69
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Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti A, Tambone V, Sagnelli C, Pascarella S, Riva A, Ceccarelli G, Marcello A, Azarian T, Wilkinson E, de Oliveira T, Alcantara LCJ, Cauda R, Caruso A, Dean NE, Browne C, Lourenco J, Salemi M, Zella D, Ciccozzi M. SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy. Commun Biol 2021; 4:489. [PMID: 33883675 PMCID: PMC8060392 DOI: 10.1038/s42003-021-02025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/03/2021] [Indexed: 01/08/2023] Open
Abstract
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as "hidden reservoirs" during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brittany Rife Magalis
- Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
| | - Silvia Fabris
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Giovanni Campisi
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alessandra Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | | | | | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Rome, Italy
| | - Alberto Riva
- ICBR, University of Florida, Gainesville, FL, USA
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Policlinico Umberto I Università 'Sapienza', Rome, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Cauda
- Department Infectious Diseases, - Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Natalie E Dean
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Cameron Browne
- Department of Mathematics, University of Lafayette, Lafayette, LA, USA
| | - Jose Lourenco
- Department of Zoology, University of Oxford, Oxford, UK
| | - Marco Salemi
- Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.
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70
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Lei J, Ma-Lauer Y, Han Y, Thoms M, Buschauer R, Jores J, Thiel V, Beckmann R, Deng W, Leonhardt H, Hilgenfeld R, von Brunn A. The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation. EMBO J 2021; 40:e102277. [PMID: 33876849 PMCID: PMC8167360 DOI: 10.15252/embj.2019102277] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
The ongoing outbreak of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS‐CoV‐2) demonstrates the continuous threat of emerging coronaviruses (CoVs) to public health. SARS‐CoV‐2 and SARS‐CoV share an otherwise non‐conserved part of non‐structural protein 3 (Nsp3), therefore named as “SARS‐unique domain” (SUD). We previously found a yeast‐2‐hybrid screen interaction of the SARS‐CoV SUD with human poly(A)‐binding protein (PABP)‐interacting protein 1 (Paip1), a stimulator of protein translation. Here, we validate SARS‐CoV SUD:Paip1 interaction by size‐exclusion chromatography, split‐yellow fluorescent protein, and co‐immunoprecipitation assays, and confirm such interaction also between the corresponding domain of SARS‐CoV‐2 and Paip1. The three‐dimensional structure of the N‐terminal domain of SARS‐CoV SUD (“macrodomain II”, Mac2) in complex with the middle domain of Paip1, determined by X‐ray crystallography and small‐angle X‐ray scattering, provides insights into the structural determinants of the complex formation. In cellulo, SUD enhances synthesis of viral but not host proteins via binding to Paip1 in pBAC‐SARS‐CoV replicon‐transfected cells. We propose a possible mechanism for stimulation of viral translation by the SUD of SARS‐CoV and SARS‐CoV‐2.
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Ma-Lauer
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - Yinze Han
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Matthias Thoms
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Robert Buschauer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wen Deng
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Heinrich Leonhardt
- Department of Biology and Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck- Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
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71
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Malik YS, Ansari MI, Kattoor JJ, Kaushik R, Sircar S, Subbaiyan A, Tiwari R, Dhama K, Ghosh S, Tomar S, Zhang KYJ. Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Brief Bioinform 2021; 22:1006-1022. [PMID: 33377145 PMCID: PMC7953982 DOI: 10.1093/bib/bbaa383] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.
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Affiliation(s)
| | | | | | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Japan
| | | | | | - Ruchi Tiwari
- Department of Vet erinary Microbiology, DUVASU, Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Souvik Ghosh
- Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | | | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Japan
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72
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, di iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SP, Bloom JD, Corti D, Veesler D, Pizzuto MS. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.07.438818. [PMID: 33851169 PMCID: PMC8043460 DOI: 10.1101/2021.04.07.438818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2X259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2X259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2X259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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Affiliation(s)
- M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Michael A. Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | | | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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73
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Ijaz MK, Nims RW, Zhou SS, Whitehead K, Srinivasan V, Kapes T, Fanuel S, Epstein JH, Daszak P, Rubino JR, McKinney J. Microbicidal actives with virucidal efficacy against SARS-CoV-2 and other beta- and alpha-coronaviruses and implications for future emerging coronaviruses and other enveloped viruses. Sci Rep 2021; 11:5626. [PMID: 33707476 PMCID: PMC7952405 DOI: 10.1038/s41598-021-84842-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Mitigating the risk of acquiring coronaviruses including SARS-CoV-2 requires awareness of the survival of virus on high-touch environmental surfaces (HITES) and skin, and frequent use of targeted microbicides with demonstrated efficacy. The data on stability of infectious SARS-CoV-2 on surfaces and in suspension have been put into perspective, as these inform the need for hygiene. We evaluated the efficacies of formulated microbicidal actives against alpha- and beta-coronaviruses, including SARS-CoV-2. The coronaviruses SARS-CoV, SARS-CoV-2, human coronavirus 229E, murine hepatitis virus-1, or MERS-CoV were deposited on prototypic HITES or spiked into liquid matrices along with organic soil loads. Alcohol-, quaternary ammonium compound-, hydrochloric acid-, organic acid-, p-chloro-m-xylenol-, and sodium hypochlorite-based microbicidal formulations were evaluated per ASTM International and EN standard methodologies. All evaluated formulated microbicides inactivated SARS-CoV-2 and other coronaviruses in suspension or on prototypic HITES. Virucidal efficacies (≥ 3 to ≥ 6 log10 reduction) were displayed within 30 s to 5 min. The virucidal efficacy of a variety of commercially available formulated microbicides against SARS-CoV-2 and other coronaviruses was confirmed. These microbicides should be useful for targeted surface and hand hygiene and disinfection of liquids, as part of infection prevention and control for SARS-CoV-2 and emerging mutational variants, and other emerging enveloped viruses.
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Affiliation(s)
- M Khalid Ijaz
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA.
- Medgar Evers College of the City University of New York (CUNY), 1650 Bedford Ave, Brooklyn, NY, 11225, USA.
| | - Raymond W Nims
- RMC Pharmaceutical Solutions, Inc, 1851 Lefthand Circle, Suite A, Longmont, CO, 80501, USA
| | - Sifang Steve Zhou
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Kelly Whitehead
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Vanita Srinivasan
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Tanya Kapes
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Semhar Fanuel
- Microbac Laboratories, Inc, 105 Carpenter Drive, Sterling, VA, 20164, USA
| | - Jonathan H Epstein
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018-6507, USA
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018-6507, USA
| | - Joseph R Rubino
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
| | - Julie McKinney
- Reckitt Benckiser LLC, Global Research and Development for Lysol and Dettol, One Philips Parkway, Montvale, NJ, 07645, USA
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74
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Dixson JD, Azad RK. A novel predictor of ACE2-binding ability among betacoronaviruses. Evol Med Public Health 2021; 9:360-373. [PMID: 34858595 PMCID: PMC8634463 DOI: 10.1093/emph/eoab032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/05/2021] [Indexed: 11/21/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in ~4.8 million deaths worldwide as of this writing. Almost all conceivable aspects of SARS-CoV-2 have been explored since the virus began spreading in the human population. Despite numerous proposals, it is still unclear how and when the virus gained the ability to efficiently bind to and infect human cells. In an effort to understand the evolution of receptor binding domain (RBD) of the spike protein of SARS-CoV-2, and specifically, how the ability of RBD to bind to angiotensin-converting enzyme 2 receptor (ACE2) of humans evolved in coronaviruses, we have applied an alignment-free technique to infer functional relatedness among betacoronaviruses. This technique, concurrently being optimized for identifying novel prions, was adapted to gain new insights into coronavirus evolution, specifically in the context of the ongoing COVID-19 pandemic. Novel methods for predicting the capacity for coronaviruses, in general, to infect human cells are urgently needed. Methodology proposed method utilizes physicochemical properties of amino acids to develop fully dynamic waveform representations of proteins that encode both the amino acid content and the context of amino acids. These waveforms are then subjected to dynamic time warping (DTW) and distance evaluation to develop a distance metric that is relatively less sensitive to variation in sequence length and primary amino acid composition. Results and Conclusions Using our proposed method, we show that in contrast to alignment-based maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic analyses, all bat betacoronavirus spike protein RBDs known to bind to the ACE2 receptor are found within a single physicochemical cluster. Further, other RBDs within that cluster are from pangolin coronaviruses, two of which have already been shown to bind to ACE2 while the others are suspected, yet unverified ACE2 binding domains. This finding is important because both severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 use the host ACE2 receptor for cell entry. Surveillance for coronaviruses belonging to this cluster could potentially guide efforts to stifle or curtail potential and/or early zoonotic outbreaks with their associated deaths and financial devastation. Lay Summary Robust methods for predicting human ACE2 receptor binding by the spike protein of coronaviruses are needed for the early detection of zoonotic coronaviruses and biosurveillance to prevent future outbreaks. Here we present a new waveform-based approach that utilizes the physicochemical properties of amino acids to determine the propensity of betacoronaviruses to infect humans. Comparison with the established phylogenetic methods demonstrates the usefulness of this new approach in the biosurveillance of coronaviruses.
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Affiliation(s)
- Jamie D Dixson
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
- Department of Mathematics, University of North Texas, Denton, TX 76203, USA
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75
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Jin T, Yin J. Patterns of virus growth across the diversity of life. Integr Biol (Camb) 2021; 13:44-59. [PMID: 33616184 DOI: 10.1093/intbio/zyab001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
Although viruses in their natural habitats add up to less than 10% of the biomass, they contribute more than 90% of the genome sequences [1]. These viral sequences or 'viromes' encode viruses that populate the Earth's oceans [2, 3] and terrestrial environments [4, 5], where their infections impact life across diverse ecological niches and scales [6, 7], including humans [8-10]. Most viruses have yet to be isolated and cultured [11-13], and surprisingly few efforts have explored what analysis of available data might reveal about their nature. Here, we compiled and analyzed seven decades of one-step growth and other data for viruses from six major families, including their infections of archaeal, bacterial and eukaryotic hosts [14-191]. We found that the use of host cell biomass for virus production was highest for archaea at 10%, followed by bacteria at 1% and eukarya at 0.01%, highlighting the degree to which viruses of archaea and bacteria exploit their host cells. For individual host cells, the yield of virus progeny spanned a relatively narrow range (10-1000 infectious particles per cell) compared with the million-fold difference in size between the smallest and largest cells. Furthermore, healthy and infected host cells were remarkably similar in the time they needed to multiply themselves or their virus progeny. Specifically, the doubling time of healthy cells and the delay time for virus release from infected cells were not only correlated (r = 0.71, p < 10-10, n = 101); they also spanned the same range from tens of minutes to about a week. These results have implications for better understanding the growth, spread and persistence of viruses in complex natural habitats that abound with diverse hosts, including humans and their associated microbes.
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Affiliation(s)
- Tianyi Jin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
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76
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Alipoor SD, Mortaz E, Jamaati H, Tabarsi P, Bayram H, Varahram M, Adcock IM. COVID-19: Molecular and Cellular Response. Front Cell Infect Microbiol 2021; 11:563085. [PMID: 33643932 PMCID: PMC7904902 DOI: 10.3389/fcimb.2021.563085] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
In late December 2019, a vtiral pneumonia with an unknown agent was reported in Wuhan, China. A novel coronavirus was identified as the causative agent. Because of the human-to-human transmission and rapid spread; coronavirus disease 2019 (COVID-19) has rapidly increased to an epidemic scale and poses a severe threat to human health; it has been declared a public health emergency of international concern (PHEIC) by the World Health Organization (WHO). This review aims to summarize the recent research progress of COVID-19 molecular features and immunopathogenesis to provide a reference for further research in prevention and treatment of SARS coronavirus2 (SARS-CoV-2) infection based on the knowledge from researches on SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV).
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Affiliation(s)
- Shamila D. Alipoor
- Molecular Medicine Department, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Jamaati
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hasan Bayram
- Department of Pulmonary Medicine, Koc University School of Medicine, Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Mohammad Varahram
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the NIHR Imperial Biomedical Research Centre, London, United Kingdom
- Priority Research Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
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77
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Animal Coronaviruses and SARS-COV-2 in Animals, What Do We Actually Know? Life (Basel) 2021; 11:life11020123. [PMID: 33562645 PMCID: PMC7914637 DOI: 10.3390/life11020123] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses (CoVs) are a well-known group of viruses in veterinary medicine. We currently know four genera of Coronavirus, alfa, beta, gamma, and delta. Wild, farmed, and pet animals are infected with CoVs belonging to all four genera. Seven human respiratory coronaviruses have still been identified, four of which cause upper-respiratory-tract diseases, specifically, the common cold, and the last three that have emerged cause severe acute respiratory syndromes, SARS-CoV-1, MERS-CoV, and SARS-CoV-2. In this review we briefly describe animal coronaviruses and what we actually know about SARS-CoV-2 infection in farm and domestic animals.
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78
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Wells HL, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba DK, Navarrete-Macias I, Liang E, Cranfield M, Han BA, Tingley MW, Diuk-Wasser M, Goldstein T, Johnson CK, Mazet JAK, Chandran K, Munster VJ, Gilardi K, Anthony SJ. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. Virus Evol 2021; 7:veab007. [PMID: 33754082 PMCID: PMC7928622 DOI: 10.1093/ve/veab007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S. 4th St, Hamilton, MT 59840, USA.,Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - D K Byarugaba
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,Makerere University, College of Veterinary Medicine, Living Stone Road, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, 125 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - B A Han
- Cary Institute of Ecosystem Studies, 2801 Sharon Turnpike, Millbrook, NY 12545, USA
| | - M W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - M Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - C K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - V J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - S J Anthony
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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79
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Bouwman KM, Tomris I, Turner HL, van der Woude R, Shamorkina TM, Bosman GP, Rockx B, Herfst S, Snijder J, Haagmans BL, Ward AB, Boons GJ, de Vries RP. Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins. PLoS Pathog 2021; 17:e1009282. [PMID: 33556147 PMCID: PMC7895411 DOI: 10.1371/journal.ppat.1009282] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/19/2021] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Receptor binding studies on sarbecoviruses would benefit from an available toolkit of recombinant spike proteins, or domains thereof, that recapitulate receptor binding properties of native viruses. We hypothesized that trimeric Receptor Binding Domain (RBD) proteins would be suitable candidates to study receptor binding properties of SARS-CoV-1 and -2. Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI-/- mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. The results demonstrate that trimeric, complex glycosylated proteins are superior in receptor binding compared to monomeric and immaturely glycosylated variants. Although differences in binding to commonly used cell lines were minimal between the different RBD preparations, substantial differences were observed when respiratory tissues of experimental animals were stained. The RBD trimers demonstrated distinct ACE2 expression profiles in bronchiolar ducts and confirmed the higher binding affinity of SARS-CoV-2 over SARS-CoV-1. Our results show that complex glycosylated trimeric RBD proteins are attractive to analyze sarbecovirus receptor binding and explore ACE2 expression profiles in tissues.
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Affiliation(s)
- Kim M Bouwman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gerlof P Bosman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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80
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Janabi AHD. Molecular Docking Analysis of Anti-Severe Acute Respiratory Syndrome-Coronavirus 2 Ligands against Spike Glycoprotein and the 3-Chymotrypsin-Like Protease. JOURNAL OF MEDICAL SIGNALS & SENSORS 2021; 11:31-36. [PMID: 34026588 PMCID: PMC8043116 DOI: 10.4103/jmss.jmss_25_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/26/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022]
Abstract
Background: The severe acute respiratory syndrome-like disease coronavirus disease 2019 (COVID-19) is a disastrous global pandemic with 16,288,490 infected cases and 649,884 deaths. Until now, no effective treatments are found. Methods: The virus uses the 3-chymotrypsin-like protease for inducing the activity of the viral polyproteins and the spike (S) glycoprotein for human cell entry through the human angiotensin-converting enzyme 2 receptor. Blocking the active binding sites of these molecules might be beneficial for decreasing the activity of the virus and suppressing the viral entry to the human cells. Here, docking methods were used to identify a group of ligands may perform the blocking operations. Results: The results revealed the strongest binding affinities, sorted high to low, for tadalafil (Cialis) (phosphodiesterase type 5 inhibitor, tirofiban (antiplatelet), paraxanthine (central nervous system stimulant), dexamethasone, gentian violet cation (triphenylmethane), salbutamol, and amlodipine (calcium channel blocker). Conclusion: These substances may provide vital help for further clinical investigation in fighting against the current global pandemic of the COVID-19.
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Affiliation(s)
- Ali Hassan Daghir Janabi
- Department of Veterinary Microbiology, College of Veterinary Medicine, University of Al-Qadisiyah, Diwaniyah City, Iraq
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81
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Biodiversity loss and COVID-19 pandemic: The role of bats in the origin and the spreading of the disease. Biochem Biophys Res Commun 2021; 538:2-13. [PMID: 33092787 PMCID: PMC7566801 DOI: 10.1016/j.bbrc.2020.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
The loss of biodiversity in the ecosystems has created the general conditions that have favored and, in fact, made possible, the insurgence of the COVID-19 pandemic. A lot of factors have contributed to it: deforestation, changes in forest habitats, poorly regulated agricultural surfaces, mismanaged urban growth. They have altered the composition of wildlife communities, greatly increased the contacts of humans with wildlife, and altered niches that harbor pathogens, increasing their chances to come in contact with humans. Among the wildlife, bats have adapted easily to anthropized environments such as houses, barns, cultivated fields, orchards, where they found the suitable ecosystem to prosper. Bats are major hosts for αCoV and βCoV: evolution has shaped their peculiar physiology and their immune system in a way that makes them resistant to viral pathogens that would instead successfully attack other species, including humans. In time, the coronaviruses that bats host as reservoirs have undergone recombination and other modifications that have increased their ability for inter-species transmission: one modification of particular importance has been the development of the ability to use ACE2 as a receptor in host cells. This particular development in CoVs has been responsible for the serious outbreaks in the last two decades, and for the present COVID-19 pandemic.
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Wells H, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba D, Navarrete-Macias I, Liang E, Cranfield M, Han B, Tingley M, Diuk-Wasser M, Goldstein T, Johnson C, Mazet J, Chandran K, Munster V, Gilardi K, Anthony S. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.07.07.190546. [PMID: 32676605 PMCID: PMC7359528 DOI: 10.1101/2020.07.07.190546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H.L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - D.K Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- Makerere University, College of Veterinary Medicine, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - B.A Han
- Cary Institute of Ecosystem Studies, Millbrook, New York, USA
| | - M.W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - M Diuk-Wasser
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - C.K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - J Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - K Chandran
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - V.J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Kampala, Uganda
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - S.J Anthony
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, California, USA
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83
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Li JY, Wang Q, Liao CH, Qiu Y, Ge XY. The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses. Virus Res 2021; 295:198307. [PMID: 33476695 PMCID: PMC7813513 DOI: 10.1016/j.virusres.2021.198307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 11/24/2022]
Abstract
Bats carry diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). The suspected interspecies transmission of SARSr-CoVs from bats to humans has caused two severe CoV pandemics, the SARS pandemic in 2003 and the recent COVID-19 pandemic. The receptor utilization of SARSr-CoV plays the key role in determining the host range and the interspecies transmission ability of the virus. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as their receptor. Previous studies showed that WIV1 strain, the first living coronavirus isolated from bat using ACE2 as its receptor, is the prototype of SARS-CoV. The receptor-binding domain (RBD) in the spike protein (S) of SARS-CoV and WIV1 is responsible for ACE2 binding and medicates the viral entry. Comparing to SARS-CoV, WIV1 has three distinct amino acid residues (442, 472, and 487) in its RBD. This study aimed at exploring whether these three residues could alter the receptor utilization of SARSr-CoVs. We replaced the three residues in SARS-CoV (BJ01 strain) S with their counterparts in WIV1 S, and then evaluated the change of their utilization of bat, civet, and human ACE2s using a lentivirus-based pseudovirus infection system. To further validate the S-ACE2 interactions, the binding affinity between the RBDs of these S proteins and the three ACE2s were verified by flow cytometry. The results showed that the single amino acid substitution Y442S in the RBD of BJ01 S enhanced its utilization of bat ACE2 and its binding affinity to bat ACE2. On the contrary, the reverse substitution in WIV1 S (S442Y) significantly attenuated the pseudovirus utilization of bat, civet and human ACE2s for cell entry, and reduced its binding affinity with the three ACE2s. These results suggest that the S442 is critical for WIV1 adapting to bats as its natural hosts. These findings will enhance our understanding of host adaptations and cross-species infections of coronaviruses, contributing to the prediction and prevention of coronavirus epidemics.
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Affiliation(s)
- Jin-Yan Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ce-Heng Liao
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
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84
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Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE, Bloom JD. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe 2021; 29:44-57.e9. [PMID: 33259788 PMCID: PMC7676316 DOI: 10.1016/j.chom.2020.11.007] [Citation(s) in RCA: 716] [Impact Index Per Article: 238.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies. They further enable the design of escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same RBD surface but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea N Loes
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Sarah K Hilton
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Huddleston
- Molecular and Cell Biology, University of Washington, Seattle, WA 98195 USA
| | - Rachel Eguia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S Dingens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel E Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert H Carnahan
- Howard Hughes Medical Institute, Seattle, WA 98109, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- Howard Hughes Medical Institute, Seattle, WA 98109, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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85
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Isolation of MERS-related coronavirus from lesser bamboo bats that uses DPP4 and infects human-DPP4-transgenic mice. Nat Commun 2021; 12:216. [PMID: 33431849 PMCID: PMC7801609 DOI: 10.1038/s41467-020-20458-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
While a number of human coronaviruses are believed to be originated from ancestral viruses in bats, it remains unclear if bat coronaviruses are ready to cause direct bat-to-human transmission. Here, we report the isolation of a MERS-related coronavirus, Tylonycteris-bat-CoV-HKU4, from lesser bamboo bats. Tylonycteris-bat-CoV-HKU4 replicates efficiently in human colorectal adenocarcinoma and hepatocarcinoma cells with cytopathic effects, and can utilize human-dipeptidyl-peptidase-4 and dromedary camel-dipeptidyl-peptidase-4 as the receptors for cell entry. Flow cytometry, co-immunoprecipitation and surface plasmon resonance assays show that Tylonycteris-bat-CoV-HKU4-receptor-binding-domain can bind human-dipeptidyl-peptidase-4, dromedary camel-dipeptidyl-peptidase-4, and Tylonycteris pachypus-dipeptidyl-peptidase-4. Tylonycteris-bat-CoV-HKU4 can infect human-dipeptidyl-peptidase-4-transgenic mice by intranasal inoculation with self-limiting disease. Positive virus and inflammatory changes were detected in lungs and brains of infected mice, associated with suppression of antiviral cytokines and activation of proinflammatory cytokines and chemokines. The results suggest that MERS-related bat coronaviruses may overcome species barrier by utilizing dipeptidyl-peptidase-4 and potentially emerge in humans by direct bat-to-human transmission. Several human coronaviruses (CoV) have been proposed to emerge from bats but evidence of direct bat-to-human transmission is slim. In this work, the authors isolate a MERS-related CoV strain directly from bats and show that it infects target cells in vitro and engineered mice through the human DDP4 receptor.
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86
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Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D. Structural basis for broad coronavirus neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.12.29.424482. [PMID: 33398277 PMCID: PMC7781312 DOI: 10.1101/2020.12.29.424482] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
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Affiliation(s)
- Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. Alexandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur, Unité de Virologie Structurale, Paris, France; CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Leah Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Oliver Acton
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Chunyan Wang
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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87
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Kianmehr A, Faraoni I, Kucuk O, Mahrooz A. Epigenetic alterations and genetic variations of angiotensin-converting enzyme 2 (ACE2) as a functional receptor for SARS-CoV-2: potential clinical implications. Eur J Clin Microbiol Infect Dis 2021; 40:1587-1598. [PMID: 33939044 PMCID: PMC8091148 DOI: 10.1007/s10096-021-04264-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
Receptor recognition is a crucial step in viral infection and is a critical factor for cell entry and tissue tropism. In several recent studies, angiotensin-converting enzyme 2 (ACE2) has been demonstrated to be the cellular receptor of SARS-CoV-2 as it was previously well known as the receptor of SARS-CoV. SARS-CoV-2 can bind with high affinity to human ACE2 and engages it as an entry receptor. It seems that the genetic, notably epigenetic variations of ACE2 are less known in different populations, indicating the need for its further investigation. These variations have the potential to affect its contribution to the pathogenicity of COVID-19. The contribution of epigenetics in the interindividual variability of ACE2 merits more attention because epigenetic processes can play important roles in ACE2 alterations in various tissues and different people and populations. Analyzing different DNA methylation patterns and microRNAs, contributing to the ACE2 modulation in the lungs will have a high priority. The epigenetic and genetic variations of ACE2 become even more important when considering that some people have mild clinical symptoms despite having COVID-19. The pathogenicity of SARS-CoV-2 infection is complex; therefore, a better understanding of the underlying pathobiology, especially binding the virus to its receptors, could help improve therapeutic and preventive approaches. This review aims to highlight the importance of evaluating both the epigenetic and genetic variations of ACE2 as a receptor for the deadly SARS-CoV-2.
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Affiliation(s)
- Anvarsadat Kianmehr
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran ,Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Isabella Faraoni
- Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rom, Italy
| | - Omer Kucuk
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA USA
| | - Abdolkarim Mahrooz
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran ,Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Km 17 Khazarabad Road, Sari, Iran
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88
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Ou Z, Ouzounis C, Wang D, Sun W, Li J, Chen W, Marlière P, Danchin A. A Path toward SARS-CoV-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution. Genome Biol Evol 2020; 12:2467-2485. [PMID: 33125064 PMCID: PMC7665462 DOI: 10.1093/gbe/evaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
In the context of the COVID-19 pandemic, we describe here the singular metabolic background that constrains enveloped RNA viruses to evolve toward likely attenuation in the long term, possibly after a step of increased pathogenicity. Cytidine triphosphate (CTP) is at the crossroad of the processes allowing SARS-CoV-2 to multiply, because CTP is in demand for four essential metabolic steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope, it is a critical building block of the host transfer RNAs synthesis and it is required for synthesis of dolichol-phosphate, a precursor of viral protein glycosylation. The CCA 3'-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. This unique metabolic setup allowed us to highlight and provide a raison d'être to viperin, an enzyme of innate antiviral immunity, which synthesizes 3'-deoxy-3',4'-didehydro-CTP as an extremely efficient antiviral nucleotide.
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Affiliation(s)
- Zhihua Ou
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Christos Ouzounis
- Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, Greece
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Weijun Chen
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, Paris, France
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, Paris, France.,School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, Hong Kong
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89
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The zoonotic potential of bat-borne coronaviruses. Emerg Top Life Sci 2020; 4:353-369. [PMID: 33258903 DOI: 10.1042/etls20200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Seven zoonoses - human infections of animal origin - have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.
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90
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Yaghoubi A, Amel Jamehdar S, Movaqar A, Milani N, Soleimanpour S. An effective drug against COVID-19: reality or dream? Expert Rev Respir Med 2020; 15:505-518. [PMID: 33215942 DOI: 10.1080/17476348.2021.1854092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is well known as a novel member of the coronavirus family which caused a sudden outbreak of Coronavirus disease-2019 (COVID-19) in China that quickly developed into a global pandemic. No effective approaches are found as yet for the therapy and epidemiological control of this new virus. We searched the literature in PubMed, Scopus, Web of Knowledge, Google Scholar, and MeSH, for articles and abstracts describing SARS-CoV-2, COVID-19, pneumonia, clinical trials, drug, treatment, and medicine.Areas covered: The present study aimed to comprehensively overview the current literature on effective anti-SARS-CoV-2 drugs.Expert opinion: Since the beginning of this pandemic disease, many studies have been conducted to find effective drugs to prevent COVID-19, because there are no specific drugs for the treatment of this disease. Most of these drugs with the antiviral potential effect toward COVID-19 are already used as the treatment of other infectious diseases. Some drugs that show the promising therapeutic potential in the initial clinical studies include remdesivir as an inhibitor of RNA-dependent RNA polymerase and favipiravir as an inhibitor of virus replication. Currently, remdesivir received the FDA authorizes to use as an experimental drug for emergency use in COVID-19 patients.
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Affiliation(s)
- Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeid Amel Jamehdar
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aref Movaqar
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nasrin Milani
- Internal Medicine Specialist, Department of Internal Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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91
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Murakami S, Kitamura T, Suzuki J, Sato R, Aoi T, Fujii M, Matsugo H, Kamiki H, Ishida H, Takenaka-Uema A, Shimojima M, Horimoto T. Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan. Emerg Infect Dis 2020; 26:3025-3029. [PMID: 33219796 PMCID: PMC7706965 DOI: 10.3201/eid2612.203386] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epidemiology of bat Betacoronavirus, subgenus Sarbecovirus is largely unknown, especially outside China. We detected a sarbecovirus phylogenetically related to severe acute respiratory syndrome coronavirus 2 from Rhinolophus cornutus bats in Japan. The sarbecovirus' spike protein specifically recognizes angiotensin-converting enzyme 2 of R. cornutus, but not humans, as an entry receptor.
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92
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Xiao Y, Xu H, Guo W, Zhao Y, Luo Y, Wang M, He Z, Ding Z, Liu J, Deng L, Sha F, Ma X. Update on treatment and preventive interventions against COVID-19: an overview of potential pharmacological agents and vaccines. MOLECULAR BIOMEDICINE 2020; 1:16. [PMID: 34765999 PMCID: PMC7711057 DOI: 10.1186/s43556-020-00017-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) triggered by the new member of the coronaviridae family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created an unprecedented challenge for global health. In addition to mild to moderate clinical manifestations such as fever, cough, and fatigue, severe cases often developed lethal complications including acute respiratory distress syndrome (ARDS) and acute lung injury. Given the alarming rate of infection and increasing trend of mortality, the development of underlying therapeutic and preventive treatment, as well as the verification of its effectiveness, are the top priorities. Current research mainly referred to and evaluated the application of the empirical treatment based on two precedents, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), including antiviral drugs targeting different stages of virus replication, immunotherapy modulating the overactivated inflammation response, and other therapies such as herbal medicine and mesenchymal stem cells. Besides, the ongoing development of inventing prophylactic interventions such as various vaccines by companies and institutions worldwide is crucial to decline morbidity and mortality. This review mainly focused on promising candidates for the treatment of COVID-19 and collected recently updated evidence relevant to its feasibility in clinical practice in the near future.
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Affiliation(s)
- Yinan Xiao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Hanyue Xu
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Wen Guo
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yunuo Zhao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yuling Luo
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Ming Wang
- Infectious Diseases Center, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Zhiyao He
- Department of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Zhenyu Ding
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Jiyan Liu
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Lei Deng
- Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, New York, 10465 USA
| | - Fushen Sha
- Department of Internal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York, 11203 USA
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 China
- West China Hospital, Sichuan University, Chengdu, 610041 China
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93
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Zekri ARN, Easa Amer K, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, Bahnasy AA, Abdel Hamid W, Gad A, Ali M, Ali Hassan W, Samir Madboly M, Abdel Raouf A, Khattab AA, Salah El Din Hamdy M, Sherif Soliman M, Hamdi El Sissy M, Mohamed El Khateeb S, Hosny Ezzelarab M, Fathalla LA, Abouelhoda M. Genomic characterization of SARS-CoV-2 in Egypt. J Adv Res 2020; 30:123-132. [PMID: 33262895 PMCID: PMC7688418 DOI: 10.1016/j.jare.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Khaled Easa Amer
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Abeer A Bahnasy
- Surgical Pathology Department National Cancer Institute, Cairo University, 11796, Egypt
| | | | - Ahmad Gad
- Military Central Laboratories, Egypt
| | - Mahmoud Ali
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Wael Ali Hassan
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | | | - Ayman A Khattab
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | - May Sherif Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Maha Hamdi El Sissy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | | | | | - Lamiaa A Fathalla
- Clinical Pathology Department, National Cancer Institute, Cairo University 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
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94
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Pimentel AC, Beraldo CS, Cogni R. Host-shift as the cause of emerging infectious diseases: Experimental approaches using Drosophila-virus interactions. Genet Mol Biol 2020; 44:e20200197. [PMID: 33237151 PMCID: PMC7731900 DOI: 10.1590/1678-4685-gmb-2020-0197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
Host shifts, when a cross-species transmission of a pathogen can lead to successful infections, are the main cause of emerging infectious diseases, such as COVID-19. A complex challenge faced by the scientific community is to address the factors that determine whether the cross-species transmissions will result in spillover or sustained onwards infections. Here we review recent literature and present a perspective on current approaches we are using to understand the mechanisms underlying host shifts. We highlight the usefulness of the interactions between Drosophila species and viruses as an ideal study model. Additionally, we discuss how cross-infection experiments - when pathogens from a natural reservoir are intentionally injected in novel host species- can test the effect cross-species transmissions may have on the fitness of virus and host, and how the host phylogeny may influence this response. We also discuss experiments evaluating how cooccurrence with other viruses or the presence of the endosymbiont bacteria Wolbachia may affect the performance of new viruses in a novel host. Finally, we discuss the need of surveys of virus diversity in natural populations using next-generation sequencing technologies. In the long term, these approaches can contribute to a better understanding of the basic biology of host shifts.
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Affiliation(s)
- André C. Pimentel
- Universidade de São Paulo, Instituto de Biociências, Departamento de
Ecologia, São Paulo, SP, Brazil
| | - Camila S. Beraldo
- Universidade de São Paulo, Instituto de Biociências, Departamento de
Ecologia, São Paulo, SP, Brazil
- University of Helsinki, Organismal and Evolutionary Biology Research
Program, Helsinki, Finland
| | - Rodrigo Cogni
- Universidade de São Paulo, Instituto de Biociências, Departamento de
Ecologia, São Paulo, SP, Brazil
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95
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Lokugamage KG, Hage A, de Vries M, Valero-Jimenez AM, Schindewolf C, Dittmann M, Rajsbaum R, Menachery VD. Type I Interferon Susceptibility Distinguishes SARS-CoV-2 from SARS-CoV. J Virol 2020; 94:e01410-20. [PMID: 32938761 PMCID: PMC7654262 DOI: 10.1128/jvi.01410-20] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and an arsenal of immune antagonists. In this report, we evaluate type I interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication to SARS-CoV, the novel CoV is much more sensitive to IFN-I. In Vero E6 and in Calu3 cells, SARS-CoV-2 is substantially attenuated in the context of IFN-I pretreatment, whereas SARS-CoV is not. In line with these findings, SARS-CoV-2 fails to counteract phosphorylation of STAT1 and expression of ISG proteins, while SARS-CoV is able to suppress both. Comparing SARS-CoV-2 and influenza A virus in human airway epithelial cultures, we observe the absence of IFN-I stimulation by SARS-CoV-2 alone but detect the failure to counteract STAT1 phosphorylation upon IFN-I pretreatment, resulting in near ablation of SARS-CoV-2 infection. Next, we evaluated IFN-I treatment postinfection and found that SARS-CoV-2 was sensitive even after establishing infection. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonists. The absence of an equivalent open reading frame 3b (ORF3b) and genetic differences versus ORF6 suggest that the two key IFN-I antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to IFN-I responses between SARS-CoV and SARS-CoV-2 that may help inform disease progression, treatment options, and animal model development.IMPORTANCE With the ongoing outbreak of COVID-19, differences between SARS-CoV-2 and the original SARS-CoV could be leveraged to inform disease progression and eventual treatment options. In addition, these findings could have key implications for animal model development as well as further research into how SARS-CoV-2 modulates the type I IFN response early during infection.
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Affiliation(s)
- Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Adam Hage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Maren de Vries
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Ana M Valero-Jimenez
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Meike Dittmann
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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96
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Kumar D, Chauhan G, Kalra S, Kumar B, Gill MS. A perspective on potential target proteins of COVID-19: Comparison with SARS-CoV for designing new small molecules. Bioorg Chem 2020; 104:104326. [PMID: 33142431 PMCID: PMC7524440 DOI: 10.1016/j.bioorg.2020.104326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.
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Affiliation(s)
- Devendra Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico
| | - Sourav Kalra
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India.
| | - Manjinder Singh Gill
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India.
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97
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Evolutionary Arms Race between Virus and Host Drives Genetic Diversity in Bat Severe Acute Respiratory Syndrome-Related Coronavirus Spike Genes. J Virol 2020; 94:JVI.00902-20. [PMID: 32699095 PMCID: PMC7527062 DOI: 10.1128/jvi.00902-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/17/2020] [Indexed: 01/03/2023] Open
Abstract
Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoVs in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS-CoV and SARSr-CoV infection but with different binding affinities to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity for spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease. The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of the human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiencies in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS-CoV and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with that of their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that some key residues were under positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics. IMPORTANCE Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoVs in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS-CoV and SARSr-CoV infection but with different binding affinities to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity for spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease.
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98
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Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KH, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SP, Carnahan RH, Crowe JE, Bloom JD. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.10.292078. [PMID: 32935107 PMCID: PMC7491521 DOI: 10.1101/2020.09.10.292078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and make a major contribution to the neutralizing antibody response elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding, and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same RBD surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies, and enable us to design escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same surface of the RBD but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth J. Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Sarah K. Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Huddleston
- Molecular and Cell Biology, University of Washington, Seattle, WA, 98195 USA
| | - Rachel Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S. Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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99
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Platto S, Xue T, Carafoli E. COVID19: an announced pandemic. Cell Death Dis 2020; 11:799. [PMID: 32973152 PMCID: PMC7513903 DOI: 10.1038/s41419-020-02995-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/22/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
A severe upper respiratory tract syndrome caused by the new coronavirus has now spread to the entire world as a highly contagious pandemic. The large scale explosion of the disease is conventionally traced back to January of this year in the Chinese province of Hubei, the wet markets of the principal city of Wuhan being assumed to have been the specific causative locus of the sudden explosion of the infection. A number of findings that are now coming to light show that this interpretation of the origin and history of the pandemic is overly simplified. A number of variants of the coronavirus would in principle have had the ability to initiate the pandemic well before January of this year. However, even if the COVID-19 had become, so to say, ready, conditions in the local environment would have had to prevail to induce the loss of the biodiversity's "dilution effect" that kept the virus under control, favoring its spillover from its bat reservoir to the human target. In the absence of these appropriate conditions only abortive attempts to initiate the pandemic could possibly occur: a number of them did indeed occur in China, and probably elsewhere as well. These conditions were unfortunately present at the wet marked in Wuhan at the end of last year.
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Affiliation(s)
- Sara Platto
- China Biodiversity Conservation and Green Development Foundation, Beijing, China.
- Department of Biotechnology, College of Life Sciences, Jianghan University, Wuhan, China.
| | - Tongtong Xue
- Department of Biotechnology, College of Life Sciences, Jianghan University, Wuhan, China
| | - Ernesto Carafoli
- Venetian Institute of molecular Medicine, University of Padova, Padova, Italy
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100
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Xue M, Zheng P, Bian X, Huang Z, Huang H, Zeng Y, Hu H, Liu X, Zhou L, Sun B, Wu JL, Zhong N. Exploration and correlation analysis of changes in Krebs von den Lungen-6 levels in COVID-19 patients with different types in China. Biosci Trends 2020; 14:290-296. [PMID: 32565512 DOI: 10.5582/bst.2020.03197] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study aimed to determine the clinical significance of Krebs von den Lungen-6 (KL-6) in patients with COVID-19, so as to find a marker with high sensitivity, specificity and easy detection to evaluate the lung injury and inflammation of COVID-19. Sixty-three COVID-19 patients and 43 non-COVID-19 patients with similar clinical phenotypes and/or imaging findings were enrolled to test the levels of KL-6 using chemiluminescent immunoassay. In addition, the blood gas, imaging and lymphocyte factors tests were collected from all participants. The data was finally analyzed using multivariate statistical analysis. The results showed KL-6 levels in COVID-19 patients were higher than those in non-COVID-19 patients (P < 0.001). Moreover, the KL-6 levels in severe and critically severe patients were significantly upregulated compared with patients with mild and common type (P < 0.05). Meanwhile, the imaging evaluation showed a significant correlation between KL-6 and pulmonary lesion area (P < 0.05). KL-6 was also found to be significantly correlated with oxygenation index and oxygen partial pressure difference of alveolar artery (PA-aDO2) (Both P < 0.01). In conclusion, KL-6 could be an indicator to evaluate the progression of COVID-19, which is parallel to the level of lung injury and inflammation in patients. Moreover, it can also reflect the pulmonary ventilation function.
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Affiliation(s)
- Mingshan Xue
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peiyan Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiqing Bian
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, China
| | - Zhifeng Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huimin Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yifeng Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haisheng Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Luqian Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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