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Xia S, Wang L, Jiao F, Yu X, Xu W, Huang Z, Li X, Wang Q, Zhu Y, Man Q, Jiang S, Lu L. SARS-CoV-2 Omicron subvariants exhibit distinct fusogenicity, but similar sensitivity, to pan-CoV fusion inhibitors. Emerg Microbes Infect 2023; 12:2178241. [PMID: 36748716 PMCID: PMC9970205 DOI: 10.1080/22221751.2023.2178241] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Continuous emergence of the Omicron variant, along with its subvariants, has caused an increasing number of infections, reinfections, and vaccine-breakthrough infections, seriously threatening human health. Recently, several new Omicron subvariants, such as BA.5, BA.2.75, BA.4.6, and BF.7, bearing distinct mutation profiles in their spike (S) proteins, have significantly increased their capacity to evade vaccine-induced immunity and have shown enhanced infectivity and transmissibility, quickly becoming dominant sublineages. In this study, we found the S proteins of these Omicron subvariants to have 2- to 4-fold more efficient membrane fusion kinetics than that of the original Omicron variant (BA.1), indicating that these novel Omicron subvariants might possess increased pathogenicity. We also identified that peptide-based pan-CoV fusion inhibitors, EK1 and EK1C4, showed equal efficacy against membrane fusion mediated by S proteins of the noted Omicron subvariants and infection by their pseudoviruses. Additionally, either immune sera induced by wild-type (WT) SARS-CoV-2 RBD-based vaccine or BA.2 convalescent sera showed potent synergism with EK1 against both WT SARS-CoV-2 and various Omicron subvariants, further suggesting that EK1-based fusion inhibitors are promising candidates for development as clinical antiviral agents against the currently circulating Omicron subvariants.
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Affiliation(s)
- Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China,Shuai Xia Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Lijue Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Fanke Jiao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Xueying Yu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Ziqi Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Xicheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Qiuhong Man
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China,Qiuhong Man Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China,Shibo Jiang Department of Clinical Laboratory, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China, Lu Lu Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
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Keeshan A, Galipeau Y, Heiskanen A, Collins E, McCluskie PS, Arnold C, Saginur R, Booth R, Little J, McGuinty M, Buchan CA, Crawley A, Langlois MA, Cooper C. Results of the Stop the Spread Ottawa (SSO) cohort study: a Canadian urban-based prospective evaluation of antibody responses and neutralisation efficiency to SARS-CoV-2 infection and vaccination. BMJ Open 2023; 13:e077714. [PMID: 37907304 PMCID: PMC10619119 DOI: 10.1136/bmjopen-2023-077714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Predictors of COVID-19 vaccine immunogenicity and the influence of prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection require elucidation. METHODS Stop the Spread Ottawa is a prospective cohort of individuals at-risk for or who have been infected with SARS-CoV-2, initially enrolled for 10 months beginning October 2020. This cohort was enriched for public-facing workers. This analysis focuses on safety and immunogenicity of the initial two doses of COVID-19 vaccine. RESULTS Post-vaccination data with blood specimens were available for 930 participants. 22.8% were SARS-CoV2 infected prior to the first vaccine dose. Cohort characteristics include: median age 44 (IQR: 22-56), 66.6% women, 89.0% white, 83.2% employed. 38.1% reported two or more comorbidities and 30.8% reported immune compromising condition(s). Over 95% had detectable IgG levels against the spike and receptor binding domain (RBD) 3 months post second vaccine dose. By multivariable analysis, increasing age and high-level immune compromise predicted diminishing IgG spike and RBD titres at month 3 post second dose. IgG spike and RBD titres were higher immediately post vaccination in those with SARS-CoV-2 infection prior to first vaccination and spike titres were higher at 6 months in those with wider time intervals between dose 1 and 2. IgG spike and RBD titres and neutralisation were generally similar by sex, weight and whether receiving homogeneous or heterogeneous combinations of vaccines. Common symptoms post dose 1 vaccine included fatigue (64.7%), injection site pain (47.5%), headache (27.2%), fever/chills (26.2%) and body aches (25.3%). These symptoms were similar with subsequent doses. CONCLUSION The initial two COVID-19 vaccine doses are safe, well-tolerated and highly immunogenic across a broad spectrum of vaccine recipients including those working in public facing environments.
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Affiliation(s)
- Alexa Keeshan
- Dept of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Yannick Galipeau
- Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - Aliisa Heiskanen
- Dept of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Erin Collins
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Pauline S McCluskie
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Corey Arnold
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Raphael Saginur
- Department of Medicine, Ottawa Hospital, Ottawa, Ontario, Canada
| | - Ronald Booth
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Michaeline McGuinty
- Division of Infectious Diseases, Department of Medicine, Ottawa Hospital, Ottawa, Ontario, Canada
| | - C Arianne Buchan
- Dept of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Division of Infectious Diseases, Department of Medicine, Ottawa Hospital, Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Anglea Crawley
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Coronavirus Variants Rapid Response Network, Ottawa, Ontario, Canada
| | - Marc-Andre Langlois
- Coronavirus Variants Rapid Response Network, Ottawa, Ontario, Canada
- Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Curtis Cooper
- Dept of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Coronavirus Variants Rapid Response Network, Ottawa, Ontario, Canada
- Division of Infectious Diseases, Ottawa Hospital Research Institute Clinical Epidemiology Program, Ottawa,Canada, Ontario, Canada
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3
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Ali H, Naseem A, Siddiqui ZI. SARS-CoV-2 Syncytium under the Radar: Molecular Insights of the Spike-Induced Syncytia and Potential Strategies to Limit SARS-CoV-2 Replication. J Clin Med 2023; 12:6079. [PMID: 37763019 PMCID: PMC10531702 DOI: 10.3390/jcm12186079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 infection induces non-physiological syncytia when its spike fusogenic protein on the surface of the host cells interacts with the ACE2 receptor on adjacent cells. Spike-induced syncytia are beneficial for virus replication, transmission, and immune evasion, and contribute to the progression of COVID-19. In this review, we highlight the properties of viral fusion proteins, mainly the SARS-CoV-2 spike, and the involvement of the host factors in the fusion process. We also highlight the possible use of anti-fusogenic factors as an antiviral for the development of therapeutics against newly emerging SARS-CoV-2 variants and how the fusogenic property of the spike could be exploited for biomedical applications.
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Affiliation(s)
- Hashim Ali
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Zaheenul Islam Siddiqui
- Diabetes and Obesity Research Center, NYU Grossman Long Island School of Medicine, New York, NY 11501, USA
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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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5
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Bello SO, Yunusa A, Adamu AA, Imam MU, Bello MB, Shuaibu A, Igumbor EU, Habib ZG, Popoola MA, Ochu CL, Bello AY, Deeni YY, Okoye I. Innovative, rapid, high-throughput method for drug repurposing in a pandemic-A case study of SARS-CoV-2 and COVID-19. Front Pharmacol 2023; 14:1130828. [PMID: 36937851 PMCID: PMC10014809 DOI: 10.3389/fphar.2023.1130828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Several efforts to repurpose drugs for COVID-19 treatment have largely either failed to identify a suitable agent or agents identified did not translate to clinical use. Reasons that have been suggested to explain the failures include use of inappropriate doses, that are not clinically achievable, in the screening experiments, and the use of inappropriate pre-clinical laboratory surrogates to predict efficacy. In this study, we used an innovative algorithm, that incorporates dissemination and implementation considerations, to identify potential drugs for COVID-19 using iterative computational and wet laboratory methods. The drugs were screened at doses that are known to be achievable in humans. Furthermore, inhibition of viral induced cytopathic effect (CPE) was used as the laboratory surrogate to predict efficacy. Erythromycin, pyridoxine, folic acid and retapamulin were found to inhibit SARS-CoV-2 induced CPE in Vero cells at concentrations that are clinically achievable. Additional studies may be required to further characterize the inhibitions of CPE and the possible mechanisms.
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Affiliation(s)
- Shaibu Oricha Bello
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- *Correspondence: Shaibu Oricha Bello,
| | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Adamu Ahmed Adamu
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Medical Biochemistry, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abdulmalik Shuaibu
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of veterinary Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Ehimario Uche Igumbor
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Zaiyad Garba Habib
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Medicine, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Mustapha Ayodele Popoola
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
| | - Chinwe Lucia Ochu
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Nigerian Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Aishatu Yahaya Bello
- Department of Clinical pharmacy and Pharmacy Practice, Faculty of Pharmaceutical sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Yusuf Yahaya Deeni
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Abuja, Nigeria
- Department of Microbiology and Biotechnology, Federal University of Dutse, Dutse, Nigeria
- Centre for Environmental and Public Health Research and Development, Kano, Nigeria
| | - Ifeoma Okoye
- University of Nigeria Centre for Clinical Trials, University of Nigeria Teaching Hospital, Enugu, Ituku Ozalla, Nigeria
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6
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Li M, Ge H, Sun Z, Fu J, Cao L, Feng X, Meng G, Peng Y, Liu Y, Zhao C. A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review. Front Cell Infect Microbiol 2022; 12:1068015. [PMID: 36619749 PMCID: PMC9816412 DOI: 10.3389/fcimb.2022.1068015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.
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Affiliation(s)
- Mingna Li
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Hongjuan Ge
- College of public health, Jilin Medical University, Jilin, China
| | - Zhe Sun
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Jangshan Fu
- College of public health, Jilin Medical University, Jilin, China
| | - Lele Cao
- College of public health, Jilin Medical University, Jilin, China
| | - Xinrui Feng
- College of public health, Jilin Medical University, Jilin, China,Medical college, Yanbian University, Jilin, China
| | - Guixian Meng
- College of medical laboratory, Jilin Medical University, Jilin, China
| | - Yubo Peng
- Business School, The University of Adelaide, Adelaide, SA, Australia
| | - Yan Liu
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
| | - Chen Zhao
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
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7
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Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, Fournier PE, La Scola B, Raoult D. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Sci Rep 2022; 12:18721. [PMID: 36333340 PMCID: PMC9636146 DOI: 10.1038/s41598-022-22060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants' genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
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Affiliation(s)
- Pierre Dudouet
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Anthony Levasseur
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Mamadou Beye
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Emilie Burel
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Lavrard
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Wahiba Bader
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Bernard La Scola
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
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8
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Sokhansanj BA, Rosen GL. Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. Comput Biol Med 2022; 149:105969. [PMID: 36041271 PMCID: PMC9384346 DOI: 10.1016/j.compbiomed.2022.105969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.
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Affiliation(s)
- Bahrad A Sokhansanj
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
| | - Gail L Rosen
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Maljkovic Berry I, Conte MA. Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses 2022; 14:2128. [PMID: 36298683 PMCID: PMC9609618 DOI: 10.3390/v14102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022] Open
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Montgomery Blair High School, Silver Spring, MD 20901, USA
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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10
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The Spike-Stabilizing D614G Mutation Interacts with S1/S2 Cleavage Site Mutations To Promote the Infectious Potential of SARS-CoV-2 Variants. J Virol 2022; 96:e0130122. [PMID: 36121299 PMCID: PMC9555207 DOI: 10.1128/jvi.01301-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained genetically stable during the first 3 months of the pandemic, before acquiring a D614G spike mutation that rapidly spread worldwide and then generating successive waves of viral variants with increasingly high transmissibility. We set out to evaluate possible epistatic interactions between the early-occurring D614G mutation and the more recently emerged cleavage site mutations present in spike of the Alpha, Delta, and Omicron variants of concern. The P681H/R mutations at the S1/S2 cleavage site increased spike processing and fusogenicity but limited its incorporation into pseudoviruses. In addition, the higher cleavage rate led to higher shedding of the spike S1 subunit, resulting in a lower infectivity of the P681H/R-carrying pseudoviruses compared to those expressing the Wuhan wild-type spike. The D614G mutation increased spike expression at the cell surface and limited S1 shedding from pseudovirions. As a consequence, the D614G mutation preferentially increased the infectivity of P681H/R-carrying pseudoviruses. This enhancement was more marked in cells where the endosomal route predominated, suggesting that more stable spikes could better withstand the endosomal environment. Taken together, these findings suggest that the D614G mutation stabilized S1/S2 association and enabled the selection of mutations that increased S1/S2 cleavage, leading to the emergence of SARS-CoV-2 variants expressing highly fusogenic spikes. IMPORTANCE The first SARS-CoV-2 variant that spread worldwide in early 2020 carried a D614G mutation in the viral spike, making this protein more stable in its cleaved form at the surface of virions. The Alpha and Delta variants, which spread in late 2020 and early 2021, respectively, proved increasingly transmissible and pathogenic compared to the original strain. Interestingly, Alpha and Delta both carried the mutations P681H/R in a cleavage site that made the spike more cleaved and more efficient at mediating viral fusion. We show here that variants with increased spike cleavage due to P681H/R were even more dependent on the stabilizing effect of the D614G mutation, which limited the shedding of cleaved S1 subunits from viral particles. These findings suggest that the worldwide spread of the D614G mutation was a prerequisite for the emergence of more pathogenic SARS-CoV-2 variants with highly fusogenic spikes.
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11
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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12
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Berry IM, Conte MA. Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.16.504117. [PMID: 36032969 PMCID: PMC9413717 DOI: 10.1101/2022.08.16.504117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Montgomery Blair High School, Silver Spring, MD, USA
| | - Migun Shakya
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick S G Chain
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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13
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Castonguay N, Zhang W, Langlois MA. Meta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2. Front Microbiol 2021; 12:676314. [PMID: 34267735 PMCID: PMC8276313 DOI: 10.3389/fmicb.2021.676314] [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: 03/05/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China, and is the causative agent for the worldwide COVID-19 pandemic. SARS-CoV-2 is a positive-sense single-stranded RNA virus belonging to the betacoronavirus genus. Due to the error-prone nature of the viral RNA-dependent polymerase complex, coronaviruses are known to acquire new mutations at each cycle of genome replication. This constitutes one of the main factors driving the evolution of its relatively large genome and the emergence of new genetic variants. In the past few months, the identification of new B.1.1.7 (United Kingdom), B.1.351 (South Africa), and P.1 (Brazil) variants of concern (VOC) has highlighted the importance of tracking the emergence of mutations in the SARS-CoV-2 genome that impact transmissibility, virulence, and immune and neutralizing antibody escape. Here we analyzed the appearance and prevalence trajectory over time of mutations that appeared in all SARS-CoV-2 genes from December 2019 to April 2021. The goal of the study was to identify which genetic modifications are the most frequent and study the dynamics of their propagation, their incorporation into the consensus sequence, and their impact on virus biology. We also analyzed the structural properties of the spike glycoprotein of the B.1.1.7, B.1.351, and P.1 variants for its binding to the host receptor ACE2. This study offers an integrative view of the emergence, disappearance, and consensus sequence integration of successful mutations that constitute new SARS-CoV-2 variants and their impact on neutralizing antibody therapeutics and vaccines.
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Affiliation(s)
- Nicolas Castonguay
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Wandong Zhang
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- uOttawa Center for Infection, Immunity and Inflammation (CI3), Ottawa, ON, Canada
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