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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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202
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Rahman S, Rahman MM, Miah M, Begum MN, Sarmin M, Mahfuz M, Hossain ME, Rahman MZ, Chisti MJ, Ahmed T, Arifeen SE, Rahman M. COVID-19 reinfections among naturally infected and vaccinated individuals. Sci Rep 2022; 12:1438. [PMID: 35082344 PMCID: PMC8792012 DOI: 10.1038/s41598-022-05325-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/03/2022] [Indexed: 12/17/2022] Open
Abstract
The protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited due to the current vaccination or natural infection is a global concern. We aimed to investigate the rate of SARS-CoV-2 infection and its clinical features among infection-naïve, infected, vaccinated, and post-infection-vaccinated individuals. A cohort was designed among icddr,b staff registered for COVID-19 testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). Reinfection cases were confirmed by whole-genome sequencing. From 19 March 2020 to 31 March 2021, 1644 (mean age, 38.4 years and 57% male) participants were enrolled; where 1080 (65.7%) were tested negative and added to the negative cohort. The positive cohort included 750 positive patients (564 from baseline and 186 from negative cohort follow-up), of whom 27.6% were hospitalized and 2.5% died. Among hospitalized patients, 45.9% had severe to critical disease and 42.5% required oxygen support. Hypertension and diabetes mellitus were found significantly higher among the hospitalised patients compared to out-patients; risk ratio 1.3 and 1.6 respectively. The risk of infection among positive cohort was 80.2% lower than negative cohort (95% CI 72.6-85.7%; p < 0.001). Genome sequences showed that genetically distinct SARS-CoV-2 strains were responsible for reinfections. Naturally infected populations were less likely to be reinfected by SARS-CoV-2 than the infection-naïve and vaccinated individuals. Although, reinfected individuals did not suffer severe disease, a remarkable proportion of naturally infected or vaccinated individuals were (re)-infected by the emerging variants.
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Affiliation(s)
- Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - M Mahfuzur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mojnu Miah
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mst Noorjahan Begum
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Monira Sarmin
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammad Enayet Hossain
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammed Ziaur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Shams El Arifeen
- Maternal and Child Health Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division, icddr,b: International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.
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203
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Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.21.477288. [PMID: 35118471 PMCID: PMC8811904 DOI: 10.1101/2022.01.21.477288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-CoV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the cilgavimab (AZD1061) mAb. Here, we show that this residue substitution remodels the ACE2-binding site allosterically, thereby dampening receptor recognition severely and altering the epitopes recognized by these three mAbs. Although vaccine-elicited neutralizing antibody titers are decreased similarly against the E406 mutant and the Delta or Epsilon variants, broadly neutralizing sarbecovirus mAbs, including a clinical mAb, inhibit the E406W spike mutant.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Tyler Starr
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Sasha W. Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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204
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Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031127. [PMID: 35162151 PMCID: PMC8834809 DOI: 10.3390/ijerph19031127] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/07/2023]
Abstract
Few studies have assessed incubation periods of the severe acute respiratory syndrome coronavirus 2 Delta variant. This study aimed to elucidate the transmission dynamics, especially the incubation period, for the Delta variant compared with non-Delta strains. We studied unvaccinated coronavirus disease 2019 patients with definite single exposure date from August 2020 to September 2021 in Japan. The incubation periods were calculated and compared by Mann-Whitney U test for Delta (with L452R mutation) and non-Delta cases. We estimated mean and percentiles of incubation period by fitting parametric distribution to data in the Bayesian statistical framework. We enrolled 214 patients (121 Delta and 103 non-Delta cases) with one specific date of exposure to the virus. The mean incubation period was 3.7 days and 4.9 days for Delta and non-Delta cases, respectively (p-value = 0.000). When lognormal distributions were fitted, the estimated mean incubation periods were 3.7 (95% credible interval (CI) 3.4-4.0) and 5.0 (95% CI 4.5-5.6) days for Delta and non-Delta cases, respectively. The estimated 97.5th percentile of incubation period was 6.9 (95% CI 5.9-8.0) days and 10.4 (95% CI 8.6-12.7) days for Delta and non-Delta cases, respectively. Unvaccinated Delta variant cases had shorter incubation periods than non-Delta variant cases.
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205
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Jiang Y, Wu Q, Song P, You C. The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines. Front Med (Lausanne) 2022; 8:806641. [PMID: 35118097 PMCID: PMC8804231 DOI: 10.3389/fmed.2021.806641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.
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Affiliation(s)
| | | | | | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
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206
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Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. MICROMACHINES 2022; 13:mi13020145. [PMID: 35208270 PMCID: PMC8879704 DOI: 10.3390/mi13020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022]
Abstract
Purpose: This study aims to establish a competitive allele-specific PCR based on penta-primer amplification refractory mutation system (PARMS) technology to detect the key mutation sites of variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus for rapid typing. Methods: Competitive allele-specific primers and universal primers were designed for the key gene mutation sites N501Y, E484K, L452R, and K417N of SARS-CoV-2 VOCs, respectively.Using the principle of allele-specific polymerase chain reaction and fluorescence energy resonance transfer, different VOCs can be differentiated. Results: Using reverse transcribed cDNA of different VOCs as specimens, through double-blind detection, different VOC types can be effectively identified, with an accuracy rate of 100%. Through the identification and detection of different VOCs, effective differentiation can be achieved. Conclusions: The system has high specificity and sensitivity, with a detection limit of 1.28 copies/reaction.PARMS technology is fast, efficient, and low-cost. It is used for the identification and detection of the popular SARS-CoV-2 VOCs, which is helpful for the rapid and accurate prevention and control of COVID-19 epidemic.
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207
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Chatterjee D, Tauzin A, Laumaea A, Gong SY, Bo Y, Guilbault A, Goyette G, Bourassa C, Gendron-Lepage G, Medjahed H, Richard J, Moreira S, Côté M, Finzi A. Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Viruses 2022; 14:v14010144. [PMID: 35062348 PMCID: PMC8780535 DOI: 10.3390/v14010144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants is fueling the recent waves of the COVID-19 pandemic. Here, we assessed ACE2 binding and antigenicity of Mu (B.1.621) and A.2.5 Spikes. Both these variants carry some mutations shared by other emerging variants. Some of the pivotal mutations such as N501Y and E484K in the receptor-binding domain (RBD) detected in B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) are now present within the Mu variant. Similarly, the L452R mutation of B.1.617.2 (Delta) variant is present in A.2.5. In this study, we observed that these Spike variants bound better to the ACE2 receptor in a temperature-dependent manner. Pseudoviral particles bearing the Spike of Mu were similarly neutralized by plasma from vaccinated individuals than those carrying the Beta (B.1.351) and Delta (B.1.617.2) Spikes. Altogether, our results indicate the importance of measuring critical parameters such as ACE2 interaction, plasma recognition and neutralization ability of each emerging variant.
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Affiliation(s)
- Debashree Chatterjee
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Annemarie Laumaea
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (Y.B.); (M.C.)
| | - Aurélie Guilbault
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (A.G.); (S.M.)
| | - Guillaume Goyette
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Catherine Bourassa
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Gabrielle Gendron-Lepage
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Halima Medjahed
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (A.G.); (S.M.)
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (Y.B.); (M.C.)
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G4, Canada
- Correspondence:
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208
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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209
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Salazar-García M, Acosta-Contreras S, Rodríguez-Martínez G, Cruz-Rangel A, Flores-Alanis A, Patiño-López G, Luna-Pineda VM. Pseudotyped Vesicular Stomatitis Virus-Severe Acute Respiratory Syndrome-Coronavirus-2 Spike for the Study of Variants, Vaccines, and Therapeutics Against Coronavirus Disease 2019. Front Microbiol 2022; 12:817200. [PMID: 35095820 PMCID: PMC8795712 DOI: 10.3389/fmicb.2021.817200] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
World Health Organization (WHO) has prioritized the infectious emerging diseases such as Coronavirus Disease (COVID-19) in terms of research and development of effective tests, vaccines, antivirals, and other treatments. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2), the etiological causative agent of COVID-19, is a virus belonging to risk group 3 that requires Biosafety Level (BSL)-3 laboratories and the corresponding facilities for handling. An alternative to these BSL-3/-4 laboratories is to use a pseudotyped virus that can be handled in a BSL-2 laboratory for study purposes. Recombinant Vesicular Stomatitis Virus (VSV) can be generated with complementary DNA from complete negative-stranded genomic RNA, with deleted G glycoprotein and, instead, incorporation of other fusion protein, like SARS-CoV-2 Spike (S protein). Accordingly, it is called pseudotyped VSV-SARS-CoV-2 S. In this review, we have described the generation of pseudotyped VSV with a focus on the optimization and application of pseudotyped VSV-SARS-CoV-2 S. The application of this pseudovirus has been addressed by its use in neutralizing antibody assays in order to evaluate a new vaccine, emergent SARS-CoV-2 variants (delta and omicron), and approved vaccine efficacy against variants of concern as well as in viral fusion-focused treatment analysis that can be performed under BSL-2 conditions.
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Affiliation(s)
- Marcela Salazar-García
- Laboratorio de Biología del Desarrollo y Teratogénesis Experimental, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
| | - Samyr Acosta-Contreras
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
| | | | - Armando Cruz-Rangel
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Alejandro Flores-Alanis
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Genaro Patiño-López
- Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
| | - Victor M. Luna-Pineda
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
- Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
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210
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Nie C, Sahoo AK, Herrmann A, Ballauff M, Netz RR, Haag R. Charge Matters: Mutations in Omicron variant favor Binding to Cells. Chembiochem 2022; 23:e202100681. [PMID: 35020256 PMCID: PMC9015620 DOI: 10.1002/cbic.202100681] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Indexed: 11/13/2022]
Abstract
Evidence is strengthening to suggest that the novel SARS‐CoV‐2 mutant Omicron, with its more than 60 mutations, will spread and dominate worldwide. Although the mutations in the spike protein are known, the molecular basis for why the additional mutations in the spike protein that have not previously occurred account for Omicron's higher infection potential, is not understood. We propose, based on chemical rational and molecular dynamics simulations, that the elevated occurrence of positively charged amino acids in certain domains of the spike protein (Delta: +4; Omicron: +5 vs. wild type) increases binding to cellular polyanionic receptors, such as heparan sulfate due to multivalent charge‐charge interactions. This observation is a starting point for targeted drug development.
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Affiliation(s)
- Chuanxiong Nie
- Freie Universität Berlin Fachbereich Biologie Chemie Pharmazie: Freie Universitat Berlin Fachbereich Biologie Chemie Pharmazie, Institute of Chemistry and Biochemistry, Takustr. 3, 14195, Berlin, GERMANY
| | - Anil Kumar Sahoo
- Freie Universitat Berlin, Fachbereich Physik, Arnimallee, 14, 14195, Berlin, GERMANY
| | - Andreas Herrmann
- Freie Universität Berlin Fachbereich Biologie Chemie Pharmazie: Freie Universitat Berlin Fachbereich Biologie Chemie Pharmazie, Institute of Chemistry and Biochemistry, Takustr. 3, 14195, Berlin, GERMANY
| | - Matthias Ballauff
- Freie Universität Berlin Fachbereich Biologie Chemie Pharmazie: Freie Universitat Berlin Fachbereich Biologie Chemie Pharmazie, Institute of Chemistry and Biochemistry, Takustr. 3, 14195, Berlin, GERMANY
| | - Roland R Netz
- Freie Universitat Berlin, Fachbereich Physik, Arnimallee, 14, 14195, Berlin, GERMANY
| | - Rainer Haag
- Freie Universität Berlin: Freie Universitat Berlin, Takustr. 3, Institute of Chemistry and Biochemistry, 14195, Berlin, GERMANY
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Zhang M, Liang Y, Yu D, Du B, Cheng W, Li L, Yu Z, Luo S, Zhang Y, Wang H, Zhang X, Zhang W. A systematic review of Vaccine Breakthrough Infections by SARS-CoV-2 Delta Variant. Int J Biol Sci 2022; 18:889-900. [PMID: 35002532 PMCID: PMC8741840 DOI: 10.7150/ijbs.68973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Vaccines are proving to be highly effective in controlling hospitalization and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as shown by clinical trials and real-world evidence. However, a deadly second wave of coronavirus disease 2019 (COVID-19), infected by SARS-CoV-2 variants, especially the Delta (B.1.617.2) variant, with an increased number of post-vaccination breakthrough infections were reported in the world recently. Actually, Delta variant not only resulted in a severe surge of vaccine breakthrough infections which was accompanied with high viral load and transmissibility, but also challenged the development of effective vaccines. Therefore, the biological characteristics and epidemiological profile of Delta variant, the current status of Delta variant vaccine breakthrough infections and the mechanism of vaccine breakthrough infections were discussed in this article. In addition, the significant role of the Delta variant spike (S) protein in the mechanism of immune escape of SARS-CoV-2 was highlighted in this article. In particular, we further discussed key points on the future SARS-CoV-2 vaccine research and development, hoping to make a contribution to the early, accurate and rapid control of the COVID-19 epidemic.
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Affiliation(s)
- Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Shuying Luo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
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212
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In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
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Servellita V, Morris MK, Sotomayor-Gonzalez A, Gliwa AS, Torres E, Brazer N, Zhou A, Hernandez KT, Sankaran M, Wang B, Wong D, Wang C, Zhang Y, Reyes KR, Glasner D, Deng X, Streithorst J, Miller S, Frias E, Rodgers M, Cloherty G, Hackett J, Hanson C, Wadford D, Philip S, Topper S, Sachdev D, Chiu CY. Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. Nat Microbiol 2022; 7:277-288. [PMID: 35013591 DOI: 10.1038/s41564-021-01041-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 01/19/2023]
Abstract
Associations between vaccine breakthrough cases and infection by different SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analysed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from 1 February to 30 June 2021, of which 125 (9.1%) were vaccine breakthrough infections. Vaccine breakthrough infections were more commonly associated with circulating antibody-resistant variants carrying ≥1 mutation associated with decreased antibody neutralization (L452R/Q, E484K/Q and/or F490S) than infections in unvaccinated individuals (78% versus 48%, P = 1.96 × 10-8). Differences in viral loads were non-significant between unvaccinated and fully vaccinated cases overall (P = 0.99) and according to lineage (P = 0.09-0.78). Symptomatic vaccine breakthrough infections had comparable viral loads (P = 0.64), whereas asymptomatic breakthrough infections had decreased viral loads (P = 0.023) compared with infections in unvaccinated individuals. In 5 cases with serial samples available for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to an immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results show that vaccine breakthrough infections are overrepresented by antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may be as efficient in spreading COVID-19 as unvaccinated infections, regardless of the infecting lineage.
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Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Noah Brazer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | - Baolin Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Daniel Wong
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin Glasner
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | | | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Susan Philip
- San Francisco Department of Public Health, San Francisco, CA, USA
| | | | - Darpun Sachdev
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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214
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The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges. J Infect Public Health 2022; 15:228-240. [PMID: 35042059 PMCID: PMC8730674 DOI: 10.1016/j.jiph.2021.12.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/13/2021] [Accepted: 12/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background The SARS-CoV-2 coronavirus epidemic is hastening the discovery of the most efficient vaccines. The development of cost-effective vaccines seems to be the only solution to terminate this pandemic. However, the vaccines’ effectiveness has been questioned due to recurrent mutations in the SARS-CoV-2 genome. Most of the mutations are associated with the spike protein, a vital target for several marketed vaccines. Many countries were highly affected by the 2nd wave of the SARS-CoV-2, like the UK, India, Brazil and France. Experts are also alarming the further COVID-19 wave with the emergence of Omicron, which is highly affecting the South African populations. This review encompasses the detailed description of all vaccine candidates and COVID-19 mutants that will add value to design further studies to combat the COVID-19 pandemic. Methods The information was generated using various search engines like google scholar, PubMed, clinicaltrial.gov.in, WHO database, ScienceDirect, and news portals by using keywords SARS-CoV-2 mutants, COVID-19 vaccines, efficacy of SARS-CoV-2 vaccines, COVID-19 waves. Results This review has highlighted the evolution of SARS-CoV-2 variants and the vaccine efficacy. Currently, various vaccine candidates are undergoing several phases of development. Their efficacy still needs to check for newly emerged variants. We have focused on the evolution, multiple mutants, waves of the SARS-CoV-2, and different marketed vaccines undergoing various clinical trials and the design of the trials to determine vaccine efficacy. Conclusion Various mutants of SARS-CoV-2 arrived, mainly concerned with the spike protein, a key component to design the vaccine candidates. Various vaccines are undergoing clinical trial and show impressive results, but their efficacy still needs to be checked in different SARS-CoV-2 mutants. We discussed all mutants of SARS-CoV-2 and the vaccine’s efficacy against them. The safety concern of these vaccines is also discussed. It is important to understand how coronavirus gets mutated to design better new vaccines, providing long-term protection and neutralizing broad mutant variants. A proper study approach also needs to be considered while designing the vaccine efficacy trials, which further improved the study outcomes. Taking preventive measures to protect from the virus is also equally important, like vaccine development.
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215
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Afrin SZ, Islam MT, Paul SK, Kobayashi N, Parvin R. Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021. Virology 2022; 565:29-37. [PMID: 34700068 PMCID: PMC8531988 DOI: 10.1016/j.virol.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023]
Abstract
Bangladesh is the second-worst-affected country in South Asia by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The aim of this study is to examine genome sequences from Bangladesh from January 2021 to June 2021 in order to monitor the SARS-CoV-2 VOC and the clades or lineages that are prevalent in the country. Within the study timeframe, at least eight Nextstrain clades were found: 20A, 20B, 20C, 20H (Beta, V2), 20I (Alpha, V1), 20 J (Gamma, V3), 21A (Delta), 21D (Eta), and six GISAID clades: four main (G, GH, GR, GRY) and two minors (GV, O) with an introduction of VOC B.1.1.7/Alpha, B.1.351/Beta and B.1.617.2/Delta. The introduction and recent occurrence of VOCs with substantial alterations in the receptor binding site of spike protein (K417 N, K417T, L452R, T478K, E484K, S494P, N501Y) are of particular importance. Specifically, VOC B.1.617.2/Delta has surpassed all prior VOCs in Bangladesh, posing a challenge to the existing disease management.
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Affiliation(s)
| | - Md Taohidul Islam
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Shyamal Kumar Paul
- Department of Microbiology, Netrokona Medical College, Netrokona, Bangladesh
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Rokshana Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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216
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Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Microb Pathog 2022; 164:105404. [PMID: 35065253 PMCID: PMC8769534 DOI: 10.1016/j.micpath.2022.105404] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/07/2023]
Abstract
COVID-19 pandemic 2nd wave catastrophic effect in the state of Chhattisgarh, India, from where no exclusive genomic data yet published, has prompted us to undertake this study to unearth the causative variant. Whole-genome sequencing of SARS-CoV-2 isolated from COVID-19 infected nine vaccinated healthcare workers (HCW), thirty mild/moderate, seventeen severe, and twenty-seven deceased patients, was performed. The significant predominance of the SARS-CoV-2 variant of concern (VOC), Delta (lineage B.1.617.2) identified in sixty-four (77.1%) cases in contrast to B.1 and its sublineage in eleven (13.2%), variant under monitoring (VUM), Kappa (lineage B.1.617.1) in five (6.0%) and another VOC Alpha (lineage B.1.1.7) in three (3.6%) cases respectively (p < 0.05, χ2 = 162.49). 88.8% vaccine breakthrough, 60% mild/moderate, 94.4% severe and 81.5% dead patients were infected by Delta. Kappa presents exclusively in mild/moderate, Alpha in vaccine breakthrough, mild/moderate, and dead patient and B.1 and its sublineages in mild, severe, and dead patient categories. Delta variant spike mutation of T19R, G142D, E156G, L452R, and deletion (F157 and R158) helps in escaping antibody response, T478K and D614G enhance viral affinity with ACE2 receptor while P681R and D950N result in higher replication and transmissibility by cleaving S1/S2 at furin site. We conclude that Delta variant predominant role along with co-occurrence of Kappa, Alpha, and B.1 variant during COVID-19 2nd wave pandemic in Chhattisgarh may pose a potential threat of future outbreak through hybrid variant evolution. Thus, intensive genomic surveillance for monitoring variant evolution and a more efficacious vaccine against the Delta and Alpha variants are required.
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217
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Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, Wu J, Luo Z. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2022; 20:824-837. [PMID: 35126885 PMCID: PMC8802458 DOI: 10.1016/j.csbj.2022.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
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218
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Tang J, Grubbs G, Lee Y, Wu H, Luke TC, Egland KA, Bausch CL, Sullivan EJ, Khurana S. OUP accepted manuscript. J Infect Dis 2022; 226:655-663. [PMID: 35106573 PMCID: PMC8903330 DOI: 10.1093/infdis/jiac031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/26/2022] [Indexed: 12/01/2022] Open
Abstract
Passive antibody immunotherapeutics directed against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are promising countermeasures for protection and treatment of coronavirus disease 2019 (COVID-19). SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) can impact the clinical efficacy of immunotherapeutics. A fully human polyclonal antibody immunotherapeutic purified from plasma of transchromosomic (Tc) bovines hyperimmunized with SARS-CoV-2 WA-1 spike (SAB-185) is being assessed for efficacy in a phase 2/3 clinical trial when different circulating SARS-CoV-2 variants predominated. We evaluated antibody binding, avidity maturation, and SARS-CoV-2 VOCs/VOIs virus-neutralizing capacity of convalescent plasma compared with different lots of SAB-185 and individual Tc bovine sera sequentially obtained after each vaccination against Alpha, Epsilon, Iota, Gamma, Beta, Kappa, and Delta variants. In contrast to convalescent plasma, sera and SAB-185 derived from hyperimmunized Tc bovines demonstrated higher antibody avidity and more potent cross-neutralizing activity of VOCs/VOIs. Thus, SAB-185 is a potential promising therapeutic candidate for the treatment of patients infected with SARS-CoV-2 variants.
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Affiliation(s)
- Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Youri Lee
- Division of Viral Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hua Wu
- SAB Biotherapeutics, Sioux Falls, South Dakota, USA
| | | | | | | | | | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, USA
- Correspondence: Surender Khurana, PhD, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA ()
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219
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Abstract
The unprecedented public health and economic impact of the COVID-19 pandemic caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been met with an equally unprecedented scientific response. Much of this response has focused, appropriately, on the mechanisms of SARS-CoV-2 entry into host cells, and in particular the binding of the spike (S) protein to its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequent membrane fusion. This Review provides the structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the S protein with ACE2, engagement of the receptor-binding domain of the S protein with ACE2, proteolytic activation of the S protein, endocytosis and membrane fusion. We define the roles of furin-like proteases, transmembrane protease, serine 2 (TMPRSS2) and cathepsin L in these processes, and delineate the features of ACE2 orthologues in reservoir animal species and S protein adaptations that facilitate efficient human transmission. We also examine the utility of vaccines, antibodies and other potential therapeutics targeting SARS-CoV-2 entry mechanisms. Finally, we present key outstanding questions associated with this critical process.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA.
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220
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Showers WM, Leach SM, Kechris K, Strong M. Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105153. [PMID: 34801754 PMCID: PMC8600767 DOI: 10.1016/j.meegid.2021.105153] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 01/18/2023]
Abstract
Amid the ongoing COVID-19 pandemic, it has become increasingly important to monitor the mutations that arise in the SARS-CoV-2 virus, to prepare public health strategies and guide the further development of vaccines and therapeutics. The spike (S) protein and the proteins comprising the RNA-Dependent RNA Polymerase (RdRP) are key vaccine and drug targets, respectively, making mutation surveillance of these proteins of great importance. Full protein sequences were downloaded from the GISAID database, aligned, and the variants identified. 437,006 unique viral genomes were analyzed. Polymorphisms in the protein sequence were investigated and examined longitudinally to identify sequence and strain variants appearing between January 5th, 2020 and January 16th, 2021. A structural analysis was also performed to investigate mutations in the receptor binding domain and the N-terminal domain of the spike protein. Within the spike protein, there were 766 unique mutations observed in the N-terminal domain and 360 in the receptor binding domain. Four residues that directly contact ACE2 were mutated in more than 100 sequences, including positions K417, Y453, S494, and N501. Within the furin cleavage site of the spike protein, a high degree of conservation was observed, but the P681H mutation was observed in 10.47% of sequences analyzed. Within the RNA dependent RNA polymerase complex proteins, 327 unique mutations were observed in Nsp8, 166 unique mutations were observed in Nsp7, and 1157 unique mutations were observed in Nsp12. Only 4 sequences analyzed contained mutations in the 9 residues that directly interact with the therapeutic Remdesivir, suggesting limited mutations in drug interacting residues. The identification of new variants emphasizes the need for further study on the effects of the mutations and the implications of increased prevalence, particularly for vaccine or therapeutic efficacy.
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Affiliation(s)
- William M Showers
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA.
| | - Sonia M Leach
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA
| | - Katerina Kechris
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA
| | - Michael Strong
- University of Colorado Anschutz Medical Campus, 13001 East 17th Place, Aurora, CO, USA; Center for Genes, Environment, and Health, National Jewish Health, Smith Building, Room A651, 1400 Jackson Street, Denver, CO, USA
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Gao F, Huang J, Li T, Hu C, Shen M, Mu S, Luo F, Song S, Hao Y, Wang W, Han X, Qian C, Wang Y, Wu R, Li L, Li S, Jin A. A Highly Conserved Peptide Vaccine Candidate Activates Both Humoral and Cellular Immunity Against SARS-CoV-2 Variant Strains. Front Immunol 2021; 12:789905. [PMID: 34950151 PMCID: PMC8688401 DOI: 10.3389/fimmu.2021.789905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Facing the imminent need for vaccine candidates with cross-protection against globally circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutants, we present a conserved antigenic peptide RBD9.1 with both T-cell and B-cell epitopes. RBD9.1 can be recognized by coronavirus disease 2019 (COVID-19) convalescent serum, particularly for those with high neutralizing potency. Immunization with RBD9.1 can successfully induce the production of the receptor-binding domain (RBD)-specific antibodies in Balb/c mice. Importantly, the immunized sera exhibit sustained neutralizing efficacy against multiple dominant SARS-CoV-2 variant strains, including B.1.617.2 that carries a point mutation (SL452R) within the sequence of RBD9.1. Specifically, SY451 and SY454 are identified as the key amino acids for the binding of the induced RBD-specific antibodies to RBD9.1. Furthermore, we have confirmed that the RBD9.1 antigenic peptide can induce a S448-456 (NYNYLYRLF)-specific CD8+ T-cell response. Both RBD9.1-specific B cells and the S448-456-specific T cells can still be activated more than 3 months post the last immunization. This study provides a potential vaccine candidate that can generate long-term protective efficacy over SARS-CoV-2 variants, with the unique functional mechanism of activating both humoral and cellular immunity.
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Affiliation(s)
- Fengxia Gao
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Jingjing Huang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Tingting Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Chao Hu
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Meiying Shen
- Department of Endocrine Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song Mu
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Feiyang Luo
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Shuyi Song
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yanan Hao
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Wang Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaojian Han
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Chen Qian
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yingming Wang
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Ruixin Wu
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Luo Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Shenglong Li
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
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Abstract
The field of molecular epidemiology responded to the SARS-CoV-2 pandemic with an unrivaled amount of whole viral genome sequencing. By the time this sentence is published we will have well surpassed 1.5 million whole genomes, more than 4 times the number of all microbial whole genomes deposited in GenBank and 35 times the total number of viral genomes. This extraordinary dataset that accrued in near real time has also given us an opportunity to chart the global and local evolution of a virus as it moves through the world population. The data itself presents challenges that have never been dealt with in molecular epidemiology, and tracking a virus that is changing so rapidly means that we are often running to catch up. Here we review what is known about the evolution of the virus, and the critical impact that whole genomes have had on our ability to trace back and track forward the spread of lineages of SARS-CoV-2. We then review what whole genomes have told us about basic biological properties of the virus such as transmissibility, virulence, and immune escape with a special emphasis on pediatric disease. We couch this discussion within the framework of systematic biology and phylogenetics, disciplines that have proven their worth again and again for identifying and deciphering the spread of epidemics, though they were largely developed in areas far removed from infectious disease and medicine.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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223
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Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
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Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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224
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Zhang L, Dutta S, Xiong S, Chan M, Chan KK, Fan TM, Bailey KL, Lindeblad M, Cooper LM, Rong L, Gugliuzza AF, Shukla D, Procko E, Rehman J, Malik AB. Engineered High-Affinity ACE2 Peptide Mitigates ARDS and Death Induced by Multiple SARS-CoV-2 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.21.473668. [PMID: 34981059 PMCID: PMC8722596 DOI: 10.1101/2021.12.21.473668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Vaccine hesitancy and continuing emergence of SARS-CoV-2 variants of concern that may escape vaccine-induced immune responses highlight the urgent need for effective COVID-19 therapeutics. Monoclonal antibodies used in the clinic have varying efficacies against distinct SARS-CoV-2 variants; thus, there is considerable interest in engineered ACE2 peptides with augmented binding affinities for SARS-CoV-2 Spike protein. These could have therapeutic benefit against multiple viral variants. Using molecular dynamics simulations, we show how three amino acid substitutions in an engineered soluble ACE2 peptide (sACE2 2 .v2.4-IgG1) markedly increase affinity for the SARS-CoV-2 Spike (S) protein. We demonstrate high binding affinity to S protein of the early SARS-CoV-2 WA-1/2020 isolate and also to multiple variants of concern: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) SARS-CoV-2 variants. In humanized K18-hACE2 mice, prophylactic and therapeutic administration of sACE2 2 .v2.4-IgG1 peptide prevented acute lung vascular endothelial injury and lung edema (essential features of ARDS) and significantly improved survival after infection by SARS-CoV-2 WA-1/2020 as well as P.1 variant of concern. These studies demonstrate for the first time broad efficacy in vivo of an ACE2 decoy peptide against multiple SARS-CoV-2 variants and point to its therapeutic potential.
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Affiliation(s)
- Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, USA
| | - Shiqin Xiong
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Matthew Chan
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, USA
| | - Kui K. Chan
- Cyrus Biotechnology, Inc., Seattle, WA 98101, USA
| | - Timothy M. Fan
- Department of Veterinary Clinical Medicine, University of Illinois College of Veterinary Medicine, Urbana, IL 61802, USA
| | - Keith L. Bailey
- Department of Veterinary Clinical Medicine, University of Illinois College of Veterinary Medicine, Urbana, IL 61802, USA
| | - Matthew Lindeblad
- Toxicology Research Laboratory, Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Laura M. Cooper
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Anthony F. Gugliuzza
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL 61801, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Asrar B. Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL 60612, USA
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225
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Zhao LP, Lybrand TP, Gilbert PB, Hawn TR, Schiffer JT, Stamatatos L, Payne TH, Carpp LN, Geraghty DE, Jerome KR. Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Viruses 2021; 14:9. [PMID: 35062214 PMCID: PMC8777887 DOI: 10.3390/v14010009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022] Open
Abstract
The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from coronavirus disease 2019 (COVID-19) cases in the United States (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from 19 January 2020 to 15 March 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics and to identify VRVs with significant and substantial dynamics (false discovery rate q-value < 0.01; maximum VRV proportion >10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modeling was performed to gain insight into the potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which had not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identified 17 VRVs ~91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of four VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported a potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods.
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Affiliation(s)
- Lue Ping Zhao
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109, USA
| | - Terry P. Lybrand
- Quintepa Computing LLC, Nashville, TN 37205, USA;
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Peter B. Gilbert
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
| | - Thomas R. Hawn
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Joshua T. Schiffer
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
| | - Lindsay N. Carpp
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
| | - Daniel E. Geraghty
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA;
| | - Keith R. Jerome
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
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226
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Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep 2021; 37:110156. [PMID: 34914928 PMCID: PMC8642162 DOI: 10.1016/j.celrep.2021.110156] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 12/01/2021] [Indexed: 12/25/2022] Open
Abstract
The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Beta (B.1.351) and Gamma (P.1) variants of concern (VoCs) include a key mutation (N501Y) found in the Alpha (B.1.1.7) variant that enhances affinity of the spike protein for its receptor, angiotensin-converting enzyme 2 (ACE2). Additional mutations are found in these variants at residues 417 and 484 that appear to promote antibody evasion. In contrast, the Epsilon variants (B.1.427/429) lack the N501Y mutation yet exhibit antibody evasion. We have engineered spike proteins to express these receptor binding domain (RBD) VoC mutations either in isolation or in different combinations and analyze the effects using biochemical assays and cryoelectron microscopy (cryo-EM) structural analyses. Overall, our findings suggest that the emergence of new SARS-CoV-2 variant spikes can be rationalized as the result of mutations that confer increased ACE2 affinity, increased antibody evasion, or both, providing a framework to dissect the molecular factors that drive VoC evolution.
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227
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Kuzmina A, Wattad S, Khalaila Y, Ottolenghi A, Rosental B, Engel S, Rosenberg E, Taube R. SARS CoV-2 Delta variant exhibits enhanced infectivity and a minor decrease in neutralization sensitivity to convalescent or post-vaccination sera. iScience 2021; 24:103467. [PMID: 34805783 PMCID: PMC8591850 DOI: 10.1016/j.isci.2021.103467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/19/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Since their identification, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Kappa and Delta have rapidly spread to become globally dominant. However, their infectivity and sensitivity to administered vaccines have not been documented. We monitored the neutralization potential of convalescent or BNT162b2 post-vaccination sera against Kappa and Delta SARS-CoV-2 pseudoviruses. We show that both variants were successfully neutralized by convalescent and post-vaccination sera, exhibiting a mild decrease in their neutralization sensitivity. Of the two variants, Delta presented enhanced infectivity levels compared with Kappa or wild-type SARS-CoV-2. Nevertheless, both variants were not as infectious or resistant to post-vaccination sera as the Beta variant of concern. Interestingly, the Delta plus variant (AY.1/B.1.617.2.1) exhibited high resistance to post-vaccination sera, similar to that of the Beta SARS-CoV-2. However, its infectivity levels were close to those of wild-type SARS-CoV-2. These results account for the worldwide prevalence of Delta variant of concern and confirm the efficacy of the BNT162b2 vaccine against circulating other Delta variants.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Seraj Wattad
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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228
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Wu K, Choi A, Koch M, Elbashir S, Ma L, Lee D, Woods A, Henry C, Palandjian C, Hill A, Jani H, Quinones J, Nunna N, O'Connell S, McDermott AB, Falcone S, Narayanan E, Colpitts T, Bennett H, Corbett KS, Seder R, Graham BS, Stewart-Jones GBE, Carfi A, Edwards DK. Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice. Vaccine 2021; 39:7394-7400. [PMID: 34815117 PMCID: PMC8572694 DOI: 10.1016/j.vaccine.2021.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/04/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.
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Affiliation(s)
- Kai Wu
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA.
| | - Angela Choi
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Matthew Koch
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Sayda Elbashir
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - LingZhi Ma
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Diana Lee
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Angela Woods
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Carole Henry
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | | | - Anna Hill
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Hardik Jani
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Julian Quinones
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Naveen Nunna
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | | | | | - Tonya Colpitts
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | | | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Robert Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA
| | | | - Andrea Carfi
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA
| | - Darin K Edwards
- Moderna, Inc., 200 Technology Square, Cambridge, MA 02139, USA.
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229
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Dubey A, Choudhary S, Kumar P, Tomar S. Emerging SARS-CoV-2 Variants: Genetic Variability and Clinical Implications. Curr Microbiol 2021; 79:20. [PMID: 34905108 PMCID: PMC8669229 DOI: 10.1007/s00284-021-02724-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
Abstract
The sudden rise in COVID-19 cases in 2020 and the incessant emergence of fast-spreading variants have created an alarming situation worldwide. Besides the continuous advancements in the design and development of vaccines to combat this deadly pandemic, new variants are frequently reported, possessing mutations that rapidly outcompeted an existing population of circulating variants. As concerns grow about the effects of mutations on the efficacy of vaccines, increased transmissibility, immune escape, and diagnostic failures are few other apprehensions liable for more deadly waves of COVID-19. Although the phenomenon of antigenic drift in new variants of SARS-CoV-2 is still not validated, it is conceived that the virus is acquiring new mutations as a fitness advantage for rapid transmission or to overcome immunological resistance of the host cell. Considerable evolution of SARS-CoV-2 has been observed since its first appearance in 2019, and despite the progress in sequencing efforts to characterize the mutations, their impacts in many variants have not been analyzed. The present article provides a substantial review of literature explaining the emerging variants of SARS-CoV-2 circulating globally, key mutations in viral genome, and the possible impacts of these new mutations on prevention and therapeutic strategies currently administered to combat this pandemic. Rising infections, mortalities, and hospitalizations can possibly be tackled through mass vaccination, social distancing, better management of available healthcare infrastructure, and by prioritizing genome sequencing for better serosurveillance studies and community tracking.
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Affiliation(s)
- Aakriti Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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230
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Viruses 2021; 13:2485. [PMID: 34960755 PMCID: PMC8707919 DOI: 10.3390/v13122485] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. Here, we compared B.1.617 variants for neutralization resistance by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. B.1.617.1, B.1.617.2, and AY.1 pseudoviruses showed a modest 1.5- to 4.4-fold reduction in neutralization by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for C.37, P.1, R.1, and B.1.526 pseudoviruses, but 7- and 16-fold reductions for vaccine-elicited and convalescent sera, respectively, were seen for B.1.351 pseudoviruses. Among twenty-three therapeutic antibodies tested, four antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses and six antibodies showed either complete or partial loss of neutralization against B.1.617.1 and AY.1 pseudoviruses. Our results indicate that the current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants. Finally, the P681R substitution confers efficient cleavage of B.1.617 variants' spike proteins and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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Affiliation(s)
- Sabari Nath Neerukonda
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Russell Vassell
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Richard Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Lisa Bentley
- Office of the Assistance Secretary for Preparedness and Response, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Ann E. Eakin
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD 20892, USA;
| | - Karl J. Erlandson
- Influenza and Emerging Infectious Diseases Division, Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Carol D. Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
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231
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Xiao Y, Lidsky PV, Shirogane Y, Aviner R, Wu CT, Li W, Zheng W, Talbot D, Catching A, Doitsh G, Su W, Gekko CE, Nayak A, Ernst JD, Brodsky L, Brodsky E, Rousseau E, Capponi S, Bianco S, Nakamura R, Jackson PK, Frydman J, Andino R. A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell 2021; 184:6037-6051.e14. [PMID: 34852237 PMCID: PMC8598942 DOI: 10.1016/j.cell.2021.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.
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Affiliation(s)
- Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ranen Aviner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chien-Ting Wu
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Weiyi Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weihao Zheng
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Dale Talbot
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Aleph Therapeutics, Inc., Stanford, CA 94305, USA
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gilad Doitsh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; School of Life Sciences, Jilin University, Changchun, China
| | - Colby E Gekko
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center and Department of Evolutionary & Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - Elsa Rousseau
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Sara Capponi
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | | | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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232
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Ahouidi AD, Rodgers MA, Padane A, Leye N, Olivo A, Mbow M, Mboup A, Diaw PA, Dia A, Harris B, Padane YAD, Lo G, Meyer TV, Diedhiou CK, Diagne D, Kane NCT, Cloherty G, Mboup S. Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Sci Rep 2021; 11:23644. [PMID: 34880295 PMCID: PMC8655062 DOI: 10.1038/s41598-021-02874-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that carry mutations in the spike gene are of concern for potential impact to treatment and prevention efforts. To monitor for new SARS-CoV-2 mutations, a panel of specimens were sequenced from both wave one (N = 96), and wave two (N = 117) of the pandemic in Senegal by whole genome next generation sequencing. Amongst these genomes, new combinations of SARS-CoV-2 spike mutations were identified, with E484K + N501T, L452R + N501Y, and L452M + S477N exclusively found in second wave specimens. These sequences are evidence of local diversification over the course of the pandemic and parallel evolution of escape mutations in different lineages.
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Affiliation(s)
- Ambroise D Ahouidi
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal.
| | - Mary A Rodgers
- Abbott Global Surveillance Program, Abbott Laboratories, Abbott Park, IL, USA.
| | - Abdou Padane
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Nafissatou Leye
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Ana Olivo
- Abbott Global Surveillance Program, Abbott Laboratories, Abbott Park, IL, USA
| | - Moustapha Mbow
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Aminata Mboup
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Papa Alassane Diaw
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Aminata Dia
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Barbara Harris
- Abbott Global Surveillance Program, Abbott Laboratories, Abbott Park, IL, USA
| | - Yacine Amet Dia Padane
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Gora Lo
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Todd V Meyer
- Abbott Global Surveillance Program, Abbott Laboratories, Abbott Park, IL, USA
| | - Cyrille K Diedhiou
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Diabou Diagne
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Ndeye Coumba Toure Kane
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Gavin Cloherty
- Abbott Global Surveillance Program, Abbott Laboratories, Abbott Park, IL, USA
| | - Souleymane Mboup
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
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233
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Melo-González F, Soto JA, González LA, Fernández J, Duarte LF, Schultz BM, Gálvez NMS, Pacheco GA, Ríos M, Vázquez Y, Rivera-Pérez D, Moreno-Tapia D, Iturriaga C, Vallejos OP, Berríos-Rojas RV, Hoppe-Elsholz G, Urzúa M, Bruneau N, Fasce RA, Mora J, Grifoni A, Sette A, Weiskopf D, Zeng G, Meng W, González-Aramundiz JV, González PA, Abarca K, Ramírez E, Kalergis AM, Bueno SM. Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Front Immunol 2021; 12:747830. [PMID: 34858404 PMCID: PMC8630786 DOI: 10.3389/fimmu.2021.747830] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible of the current pandemic ongoing all around the world. Since its discovery in 2019, several circulating variants have emerged and some of them are associated with increased infections and death rate. Despite the genetic differences among these variants, vaccines approved for human use have shown a good immunogenic and protective response against them. In Chile, over 70% of the vaccinated population is immunized with CoronaVac, an inactivated SARS-CoV-2 vaccine. The immune response elicited by this vaccine has been described against the first SARS-CoV-2 strain isolated from Wuhan, China and the D614G strain (lineage B). To date, four SARS-CoV-2 variants of concern described have circulated worldwide. Here, we describe the neutralizing capacities of antibodies secreted by volunteers in the Chilean population immunized with CoronaVac against variants of concern Alpha (B.1.1.7), Beta (B.1.351) Gamma (P.1) and Delta (B.617.2). Methods Volunteers enrolled in a phase 3 clinical trial were vaccinated with two doses of CoronaVac in 0-14 or 0-28 immunization schedules. Sera samples were used to evaluate the capacity of antibodies induced by the vaccine to block the binding between Receptor Binding Domain (RBD) from variants of concern and the human ACE2 receptor by an in-house ELISA. Further, conventional microneutralization assays were used to test neutralization of SARS-CoV-2 infection. Moreover, interferon-γ-secreting T cells against Spike from variants of concern were evaluated in PBMCs from vaccinated subjects using ELISPOT. Results CoronaVac promotes the secretion of antibodies able to block the RBD of all the SARS-CoV-2 variants studied. Seropositivity rates of neutralizing antibodies in the population evaluated were over 97% for the lineage B strain, over 80% for Alpha and Gamma variants, over 75% for Delta variant and over 60% for the Beta variant. Geometric means titers of blocking antibodies were reduced when tested against SARS-CoV-2 variants as compared to ancestral strain. We also observed that antibodies from vaccinated subjects were able to neutralize the infection of variants D614G, Alpha, Gamma and Delta in a conventional microneutralization assay. Importantly, after SARS-CoV-2 infection, we observed that the blocking capacity of antibodies from vaccinated volunteers increased up to ten times for all the variants tested. We compared the number of interferon-γ-secreting T cells specific for SARS-CoV-2 Spike WT and variants of concern from vaccinated subjects and we did not detect significant differences. Conclusion Immunization with CoronaVac in either immunization schedule promotes the secretion of antibodies able to block SARS-CoV-2 variants of concern and partially neutralizes SARS-CoV-2 infection. In addition, it stimulates cellular responses against all variants of concern.
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Affiliation(s)
- Felipe Melo-González
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge A Soto
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Liliana A González
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Fernández
- Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Luisa F Duarte
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara M Schultz
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicolás M S Gálvez
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gaspar A Pacheco
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mariana Ríos
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yaneisi Vázquez
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela Rivera-Pérez
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela Moreno-Tapia
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Iturriaga
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Omar P Vallejos
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roslye V Berríos-Rojas
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Guillermo Hoppe-Elsholz
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Urzúa
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Bruneau
- Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Rodrigo A Fasce
- Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Judith Mora
- Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, United States
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | | | | | - José V González-Aramundiz
- Departamento de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A González
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Katia Abarca
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eugenio Ramírez
- Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Endocrinología, Facultad de Medicina, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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234
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Hu J, Wei XY, Xiang J, Peng P, Xu FL, Wu K, Luo FY, Jin AS, Fang L, Liu BZ, Wang K, Tang N, Huang AL. Reduced neutralization of SARS-CoV-2 B.1.617 variant by convalescent and vaccinated sera. Genes Dis 2021; 9:1290-1300. [PMID: 34877393 PMCID: PMC8639289 DOI: 10.1016/j.gendis.2021.11.007] [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: 07/11/2021] [Revised: 09/26/2021] [Accepted: 11/05/2021] [Indexed: 01/10/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Spike protein that mediates coronavirus entry into host cells is a major target for COVID-19 vaccines and antibody therapeutics. However, multiple variants of SARS-CoV-2 have emerged, which may potentially compromise vaccine effectiveness. Using a pseudovirus-based assay, we evaluated SARS-CoV-2 cell entry mediated by the viral Spike B.1.617 and B.1.1.7 variants. We also compared the neutralization ability of monoclonal antibodies from convalescent sera and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine) and ZF2001 (RBD-subunit vaccine) against B.1.617 and B.1.1.7 variants. Our results showed that, compared to D614G and B.1.1.7 variants, B.1.617 shows enhanced viral entry and membrane fusion, as well as more resistant to antibody neutralization. These findings have important implications for understanding viral infectivity and for immunization policy against SARS-CoV-2 variants.
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Affiliation(s)
- Jie Hu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Xiao-Yu Wei
- Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402177, PR China
| | - Jin Xiang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Pai Peng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Feng-Li Xu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Kang Wu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Fei-Yang Luo
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Ai-Shun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Liang Fang
- Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402177, PR China
| | - Bei-Zhong Liu
- Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402177, PR China
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, PR China
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235
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Edwards LJ, Fowlkes AL, Wesley MG, Kuntz JL, Odean MJ, Caban-Martinez AJ, Dunnigan K, Phillips AL, Grant L, Herring MK, Groom HC, Respet K, Beitel S, Zunie T, Hegmann KT, Kumar A, Joseph G, Poe B, Louzado-Feliciano P, Smith ME, Thiese MS, Schaefer-Solle N, Yoo YM, Silvera CA, Mayo Lamberte J, Mak J, McDonald LC, Stuckey MJ, Kutty P, Arvay ML, Yoon SK, Tyner HL, Burgess JL, Hunt DR, Meece J, Gaglani M, Naleway AL, Thompson MG. Research on the Epidemiology of SARS-CoV-2 in Essential Response Personnel (RECOVER): Protocol for a Multisite Longitudinal Cohort Study. JMIR Res Protoc 2021; 10:e31574. [PMID: 34662287 PMCID: PMC8647972 DOI: 10.2196/31574] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Workers critical to emergency response and continuity of essential services during the COVID-19 pandemic are at a disproportionally high risk of SARS-CoV-2 infection. Prospective cohort studies are needed for enhancing the understanding of the incidence of symptomatic and asymptomatic SARS-CoV-2 infections, identifying risk factors, assessing clinical outcomes, and determining the effectiveness of vaccination. OBJECTIVE The Research on the Epidemiology of SARS-CoV-2 in Essential Response Personnel (RECOVER) prospective cohort study was designed to estimate the incidence of symptomatic and asymptomatic SARS-CoV-2 infections, examine the risk factors for infection and clinical spectrum of illness, and assess the effectiveness of vaccination among essential workers. METHODS The RECOVER multisite network was initiated in August 2020 and aims to enroll 3000 health care personnel (HCP), first responders, and other essential and frontline workers (EFWs) at 6 US locations. Data on participant demographics, medical history, and vaccination history are collected at baseline and throughout the study. Active surveillance for the symptoms of COVID-19-like illness (CLI), access of medical care, and symptom duration is performed by text messages, emails, and direct participant or medical record reports. Participants self-collect a mid-turbinate nasal swab weekly, regardless of symptoms, and 2 additional respiratory specimens at the onset of CLI. Blood is collected upon enrollment, every 3 months, approximately 28 days after a reverse transcription polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection, and 14 to 28 days after a dose of any COVID-19 vaccine. From February 2021, household members of RT-PCR-confirmed participants are self-collecting mid-turbinate nasal swabs daily for 10 days. RESULTS The study observation period began in August 2020 and is expected to continue through spring 2022. There are 2623 actively enrolled RECOVER participants, including 280 participants who have been found to be positive for SARS-CoV-2 by RT-PCR. Enrollment is ongoing at 3 of the 6 study sites. CONCLUSIONS Data collected through the cohort are expected to provide important public health information for essential workers at high risk for occupational exposure to SARS-CoV-2 and allow early evaluation of COVID-19 vaccine effectiveness. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/31574.
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Affiliation(s)
| | - Ashley L Fowlkes
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Jennifer L Kuntz
- Kaiser Permanente Northwest Center for Health Research, Portland, OR, United States
| | - Marilyn J Odean
- Whiteside Institute for Clinical Research, Duluth, MN, United States
- St. Luke's Regional Health Care System, Duluth, MN, United States
| | | | - Kayan Dunnigan
- Baylor Scott and White Health, Temple, TX, United States
| | | | - Lauren Grant
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Holly C Groom
- Kaiser Permanente Northwest Center for Health Research, Portland, OR, United States
| | - Karley Respet
- St. Luke's Regional Health Care System, Duluth, MN, United States
| | - Shawn Beitel
- University of Arizona, Tucson, AZ, United States
| | - Tnelda Zunie
- Baylor Scott and White Health, Temple, TX, United States
| | | | - Archana Kumar
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gregory Joseph
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Brandon Poe
- Abt Associates, Inc, Atlanta, GA, United States
| | | | | | | | | | - Young M Yoo
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Josephine Mak
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Matthew J Stuckey
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Preeta Kutty
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Melissa L Arvay
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sarang K Yoon
- University of Utah, Salt Lake City, UT, United States
| | - Harmony L Tyner
- St. Luke's Regional Health Care System, Duluth, MN, United States
| | | | | | - Jennifer Meece
- Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Manjusha Gaglani
- Baylor Scott and White Health, Temple, TX, United States
- Texas A&M University College of Medicine, Temple, TX, United States
| | - Allison L Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, OR, United States
| | - Mark G Thompson
- Centers for Disease Control and Prevention, Atlanta, GA, United States
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236
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-7989. [PMID: 34731254 PMCID: PMC11073194 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India.
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237
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 613] [Impact Index Per Article: 204.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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238
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Kumar A, Parashar R, Kumar S, Faiq MA, Kumari C, Kulandhasamy M, Narayan RK, Jha RK, Singh HN, Prasoon P, Pandey SN, Kant K. Emerging SARS-CoV-2 variants can potentially break set epidemiological barriers in COVID-19. J Med Virol 2021; 94:1300-1314. [PMID: 34811761 PMCID: PMC9011477 DOI: 10.1002/jmv.27467] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/19/2021] [Indexed: 12/29/2022]
Abstract
Young age, female sex, absence of comorbidities, and prior infection or vaccination are known epidemiological barriers for contracting the new infection and/or increased disease severity. Demographic trends from the recent coronavirus disease 2019 waves, which are believed to be driven by newer severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants, indicate that the aforementioned epidemiological barriers are being breached and a larger number of younger and healthy individuals are developing severe disease. The new SARS‐CoV‐2 variants have key mutations that can induce significant changes in the virus‐host interactions. Recent studies report that, some of these mutations, singly or in a group, enhance key mechanisms, such as binding of the receptor‐binding domain (RBD) of the viral spike protein with the angiotensin‐converting enzyme 2 (ACE2) receptor in the host‐cells, increase the glycosylation of spike protein at the antigenic sites, and enhance the proteolytic cleavage of the spike protein, thus leading to improved host‐cell entry and the replication of the virus. The putative changes in the virus–host interactions imparted by the mutations in the RBD sequence can potentially be the reason behind the breach of the observed epidemiological barriers. Susceptibility for contracting SARS‐CoV‐2 infection and the disease outcomes are known to be influenced by host‐cell expressions of ACE2 and other proteases. The new variants can act more efficiently, and even with the lesser availability of the viral entry‐receptor and the associated proteases, can have more efficient host‐cell entry and greater replication resulting in high viral loads and prolonged viral shedding, widespread tissue‐injury, and severe inflammation leading to increased transmissibility and lethality. Furthermore, the accumulating evidence shows that multiple new variants have reduced neutralization by both, natural and vaccine‐acquired antibodies, indicating that repeated and vaccine breakthrough infections may arise as serious health concerns in the ongoing pandemic. Emerging SARS‐CoV‐2 variants:
Harbor key mutations altering the virus‐host interactions. Show more efficient host‐cell entry and greater replication resulting in higher viral loads, prolonged viral shedding, and greater tissue injury. Show reduced neutralization by natural and vaccine acquired antibodies. Causing symptomatic illness in increasing number of young, women, and healthy individuals.
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Affiliation(s)
- Ashutosh Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Rakesh Parashar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,India Health Lead, Oxford Policy Management Limited, Oxford, UK
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,New York University (NYU) Langone Health Center, NYU Robert I Grossman School of Medicine, New York, New York, USA
| | - Chiman Kumari
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Biochemistry, Maulana Azad Medical College (MAMC), New Delhi, India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Rakesh K Jha
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Systems Biology, Columbia University Irving Medical Center, New York, USA
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Zoology, Banaras Hindu University (BHU), Varanasi, India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bathinda, India
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239
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Tada T, Zhou H, Dcosta BM, Samanovic MI, Mulligan MJ, Landau NR. Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera. iScience 2021; 24:103341. [PMID: 34723159 PMCID: PMC8541826 DOI: 10.1016/j.isci.2021.103341] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/13/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
Highly transmissible SARS-CoV-2 variants identified in India and designated B.1.617, Kappa (B.1.617.1), Delta (B.1.617.2), B.1.618, and B.1.36.29 contain spike mutations L452R, T478K, E484K, E484Q, and N440K located within the spike receptor-binding domain and thus could contribute to increased transmissibility and potentially allow re-infection or cause resistance to vaccine-elicited antibody. To address these issues, we used lentiviruses pseudotyped by variant spikes to measure their neutralization by convalescent sera, vaccine-elicited and Regeneron therapeutic antibodies, and ACE2 affinity. Convalescent sera and vaccine-elicited antibodies neutralized viruses with Delta spike with 2- to 5-fold decrease in titer in different donors. Regeneron antibody cocktail neutralized virus with the Delta spike with a 2.6-fold decrease in titer. Neutralization resistance to serum antibodies and monoclonal antibodies was mediated by L452R mutation. These relatively modest decreases in antibody neutralization titer for viruses with variant spike proteins suggest that current vaccines will remain protective against the family of Delta variants. Vaccine-elicited antibodies neutralize Delta spike with 4- to 5-fold decrease in titer Delta variant is resistant to REGN10933 monoclonal antibody Neutralization resistance is mediated by L452R
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, New York, NY 10016, USA
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240
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Oliveira MM, Schemberger MO, Suzukawa AA, Riediger IN, do Carmo Debur M, Becker G, Resende PC, Gräf T, Balsanelli E, de Baura VA, de Souza EM, Pedrosa FO, Alves LR, Blanes L, Nardelli SC, Aguiar AM, Albrecht L, Zanette D, Ávila AR, Morello LG, Marchini FK, Dos Santos HG, Passetti F, Dallagiovanna B, Faoro H. Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Virol J 2021; 18:222. [PMID: 34789293 PMCID: PMC8596384 DOI: 10.1186/s12985-021-01690-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/01/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil. METHODS The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil. RESULTS Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná. CONCLUSIONS Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.
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Affiliation(s)
- Mauro M Oliveira
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Michelle O Schemberger
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Andreia A Suzukawa
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Irina N Riediger
- Laboratório Central do Estado do Paraná, LACEN, Curitiba, Paraná, Brazil
| | | | - Guilherme Becker
- Laboratório Central do Estado do Paraná, LACEN, Curitiba, Paraná, Brazil
| | - Paola Cristina Resende
- Laboratórios de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, FIOCRUZ, Salvador, Bahia, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Valter Antônio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal Do Paraná, Curitiba, Paraná, Brazil
| | - Lysangela R Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Sheila Cristina Nardelli
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Alessandra M Aguiar
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Letusa Albrecht
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Dalila Zanette
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Andréa R Ávila
- Laboratório de Pesquisa em Apicomplexa, Carlos Chagas Institute, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Luis Gustavo Morello
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Fabricio K Marchini
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | | | - Fabio Passetti
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Bruno Dallagiovanna
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil
| | - Helisson Faoro
- Laboratório de Ciências e Tecnologias Aplicadas Em Saúde, Instituto Carlos Chagas, FIOCRUZ, Curitiba, Paraná, Brazil.
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241
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Abstract
Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of proteins encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we describe the use of a convenient bacterial cell-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identified 16 distinct intraviral protein-protein interactions (PPIs), involving 16 proteins. We found that many of the identified proteins interact with more than one partner. Further, our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm, and we used this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examined how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
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Cross-Neutralization of Emerging SARS-CoV-2 Variants of Concern by Antibodies Targeting Distinct Epitopes on Spike. mBio 2021; 12:e0297521. [PMID: 34781736 PMCID: PMC8593667 DOI: 10.1128/mbio.02975-21] [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] [Indexed: 12/23/2022] Open
Abstract
Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have arisen that exhibit increased viral transmissibility and partial evasion of immunity induced by natural infection and vaccination. To address the specific antibody targets that were affected by recent viral variants, we generated 43 monoclonal antibodies (mAbs) from 10 convalescent donors that bound three distinct domains of the SARS-CoV-2 spike. Viral variants harboring mutations at K417, E484, and N501 could escape most of the highly potent antibodies against the receptor binding domain (RBD). Despite this, we identified 12 neutralizing mAbs against three distinct regions of the spike protein that neutralize SARS-CoV-2 and variants of concern (VOCs), including B.1.1.7 (alpha), P.1 (gamma), and B.1.617.2 (delta). Notably, antibodies targeting distinct epitopes could neutralize discrete variants, suggesting that different variants may have evolved to disrupt the binding of particular neutralizing antibody classes. These results underscore that humans exposed to the first pandemic wave of prototype SARS-CoV-2 possess neutralizing antibodies against current variants and that it is critical to induce antibodies targeting multiple distinct epitopes of the spike that can neutralize emerging variants of concern.
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Liu Z, Skowron K, Grudlewska-Buda K, Wiktorczyk-Kapischke N. The existence, spread, and strategies for environmental monitoring and control of SARS-CoV-2 in environmental media. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148949. [PMID: 34252782 PMCID: PMC8262394 DOI: 10.1016/j.scitotenv.2021.148949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is the most influential infectious disease to emerge in the early 21st century. The outbreak of COVID-19 has caused a great many deaths and has had a negative impact on the world's economic development. The etiological agent of COVID-19 is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2, which is highly infectious and variable, can be transmitted through different environmental media (gaseous, liquid, and solid). There are many unanswered questions surrounding this virus. This review summarizes the current knowledge on the latest global COVID-19 epidemic situation, SARS-CoV-2 variants, the progress in SARS-CoV-2 vaccine use, and the existence and spread of SARS-CoV-2 in gaseous, liquid, and solid media, with particular emphasis on the prevention and control of further spread of the disease. This review aims to help people worldwide to become more familiar with the transmission characteristics of SARS-CoV-2 in environmental media, so as targeted measures to fight the epidemic, reduce deaths, and restore the economy can be implemented under the pressure of global SARS-CoV-2 vaccine shortages.
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Affiliation(s)
- Zhongchuang Liu
- Green Intelligence Environmental School, Yangtze Normal University, 16 Juxian Rd. Lidu, Fuling District of Chongqing, China; Chongqing Multiple-source Technology Engineering Research Center for Ecological Environment Monitoring, Yangtze Normal University, 16 Juxian Rd. Lidu, Fuling District of Chongqing, China.
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, 9 M. Skłodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, 9 M. Skłodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz, 9 M. Skłodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
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Al-Karmalawy AA, Soltane R, Abo Elmaaty A, Tantawy MA, Antar SA, Yahya G, Chrouda A, Pashameah RA, Mustafa M, Abu Mraheil M, Mostafa A. Coronavirus Disease (COVID-19) Control between Drug Repurposing and Vaccination: A Comprehensive Overview. Vaccines (Basel) 2021; 9:1317. [PMID: 34835248 PMCID: PMC8622998 DOI: 10.3390/vaccines9111317] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 02/06/2023] Open
Abstract
Respiratory viruses represent a major public health concern, as they are highly mutated, resulting in new strains emerging with high pathogenicity. Currently, the world is suffering from the newly evolving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus is the cause of coronavirus disease 2019 (COVID-19), a mild-to-severe respiratory tract infection with frequent ability to give rise to fatal pneumonia in humans. The overwhelming outbreak of SARS-CoV-2 continues to unfold all over the world, urging scientists to put an end to this global pandemic through biological and pharmaceutical interventions. Currently, there is no specific treatment option that is capable of COVID-19 pandemic eradication, so several repurposed drugs and newly conditionally approved vaccines are in use and heavily applied to control the COVID-19 pandemic. The emergence of new variants of the virus that partially or totally escape from the immune response elicited by the approved vaccines requires continuous monitoring of the emerging variants to update the content of the developed vaccines or modify them totally to match the new variants. Herein, we discuss the potential therapeutic and prophylactic interventions including repurposed drugs and the newly developed/approved vaccines, highlighting the impact of virus evolution on the immune evasion of the virus from currently licensed vaccines for COVID-19.
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Affiliation(s)
- Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Department of Biology, Faculty of Sciences, Tunis El Manar University, Tunis 1068, Tunisia
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Mohamed A Tantawy
- Hormones Department, Medical Research and Clinical Studies Research Institute, National Research Centre, Dokki 12622, Egypt
- Stem Cells Laboratory, Center of Excellence for Advanced Sciences, National Research Centre, Dokki 12622, Egypt
| | - Samar A Antar
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Amani Chrouda
- Department of Chemistry, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11932, Saudi Arabia
- Laboratory of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University, Monastir 5000, Tunisia
- Institute of Analytical Sciences, UMR CNRS-UCBL-ENS 5280, 5 Rue la Doua, CEDEX, 69100 Villeurbanne, France
| | - Rami Adel Pashameah
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Muhamad Mustafa
- Department of Medicinal Chemistry, Deraya University, Minia 61111, Egypt
| | - Mobarak Abu Mraheil
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
| | - Ahmed Mostafa
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki 12622, Egypt
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.05.467523. [PMID: 34790980 PMCID: PMC8597883 DOI: 10.1101/2021.11.05.467523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antibodies and current vaccines. Here we compared B.1.617 variants, and their single and double RBD substitutions for resistance to neutralization by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. Pseudoviruses with the B.1.617.1, B.1.617.2, and AY.1 spike showed a modest 1.5 to 4.4-fold reduction in neutralization titer by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for pseudoviruses with C.37, P.1, R.1, and B.1.526 spikes, but seven- and sixteen-fold reduction for vaccine-elicited and convalescent sera, respectively, was seen for pseudoviruses with the B.1.351 spike. Four of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses due to the L452R substitution, whereas six of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.1 pseudoviruses due to either the E484Q or L452R substitution. Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution. The modest resistance of B.1.617 variants to vaccine-elicited sera suggest that current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants, but the therapeutic antibodies need to be carefully selected based on their resistance profiles. Finally, the spike proteins of B.1.617 variants are more efficiently cleaved due to the P681R substitution, and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model. EBioMedicine 2021; 73:103675. [PMID: 34758415 PMCID: PMC8572342 DOI: 10.1016/j.ebiom.2021.103675] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background Following the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread throughout the world, new viral variants of concern (VOC) have emerged. There is a critical need to understand the impact of the emerging variants on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Methods Syrian golden hamsters are the leading small animal model that recapitulates key aspects of severe coronavirus disease 2019 (COVID-19). We performed intranasal inoculation of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1-2020) or VOC first identified in the United Kingdom (B.1.1.7, alpha) and South Africa (B.1.351, beta) and analyzed viral loads and host responses. Findings Similar gross and histopathologic pulmonary lesions were observed after infection with all three variants. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of challenged animals, infectious titers in the lungs were comparable between the variants. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Transcriptional profiling of lung samples 4 days post-challenge (DPC) indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.1.7 infection. Furthermore, no additional mutations in the spike protein were detected at 4 DPC. Interpretations Although disease severity and viral shedding were not significantly different, the emerging VOC induced distinct humoral responses and transcriptional profiles compared to the ancestral virus. These observations suggest potential differences in acute early responses or alterations in immune modulation by VOC. Funding Intramural Research Program, NIAID, NIH; National Center for Research Resources, NIH; National Center for Advancing Translational Sciences, NIH.
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Deb P, Molla MMA, Saif-Ur-Rahman KM, Das MC, Das D. A review of epidemiology, clinical features and disease course, transmission dynamics, and neutralization efficacy of SARS-CoV-2 variants. THE EGYPTIAN JOURNAL OF BRONCHOLOGY 2021. [PMCID: PMC8571979 DOI: 10.1186/s43168-021-00090-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background After the first detection in November 2019, SARS-CoV-2 has spread rapidly over the continents and started the pandemic of the millennium. In addition to several novels and repurposed monoclonal antibodies (mAbs) as a therapeutic option against COVID-19, scientists from across the world have developed several candidate vaccines, developed mainly targeting the Wuhan strain, with very promising results to combat this pandemic. Unfortunately like any RNA viruses, SARS CoV-2 has also gone through the accumulation of hundreds and thousands of mutations in their genome lead to the development of several variants of concerns (VOC) and variants of interests (VOI), resulting in increased transmissibility and virulence of the virus, along with their capacity to escape cross-protection. Seemingly, the main hindrance of containing this pandemic right now is the effectiveness of currently available vaccines and mAbs against newly emerging variants. Therefore, it is important to monitor variants epidemiology, transmission dynamics, clinical characteristics, as well as their immune evasion capacity to implement appropriate vaccine strategy and other containment measures. Body In this review, we tried to focus on variants characteristics and to what extent they can escape immunity, provided by both available vaccinated sera and convalescent sera. A stringent literature review was performed using various databases, mentioned in the methodology portion. The current geographical distribution of these variants of SARS CoV-2 has been presented using a heat map. Findings from published articles comparing these variants, in terms of genome epidemiology, transmissibility, viral load dynamics, and association with different waves have been described briefly. Due strength was given while describing variants neutralization potency against current vaccines, mAbs, and also against convalescent sera. Data from both clinical trials and in vitro/ex-vivo studies have been discussed here. Comparative findings from several articles were brought into one concise paper. After careful reviewing of all the available data, it was clear that, without hesitation, we should strengthen our vaccination strategy, because the severity of COVID 19 is reasonably lower, irrespective of variants and vaccine used. Conclusion We hope that many falsified myths and beliefs regarding vaccine immunity and emerging variants will be clarified in light of this available evidence, which we summarized in our paper.
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Lou F, Li M, Pang Z, Jiang L, Guan L, Tian L, Hu J, Fan J, Fan H. Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape. Front Immunol 2021; 12:744242. [PMID: 34804024 PMCID: PMC8602852 DOI: 10.3389/fimmu.2021.744242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
The global pandemic of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), places a heavy burden on global public health. Four SARS-CoV-2 variants of concern including B.1.1.7, B.1.351, B.1.617.2, and P.1, and two variants of interest including C.37 and B.1.621 have been reported to have potential immune escape, and one or more mutations endow them with worrisome epidemiologic, immunologic, or pathogenic characteristics. This review introduces the latest research progress on SARS-CoV-2 variants of interest and concern, key mutation sites, and their effects on virus infectivity, mortality, and immune escape. Moreover, we compared the effects of various clinical SARS-CoV-2 vaccines and convalescent sera on epidemic variants, and evaluated the neutralizing capability of several antibodies on epidemic variants. In the end, SARS-CoV-2 evolution strategies in different transmission stages, the impact of different vaccination strategies on SARS-CoV-2 immune escape, antibody therapy strategies and COVID-19 epidemic control prospects are discussed. This review will provide a systematic and comprehensive understanding of the secret of SARS-CoV-2 variants of interest/concern and immune escape.
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Affiliation(s)
- Fuxing Lou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Jiang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Guan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiaming Hu
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Ahmad L. Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Front Immunol 2021; 12:742167. [PMID: 34804022 PMCID: PMC8596465 DOI: 10.3389/fimmu.2021.742167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/14/2021] [Indexed: 11/20/2022] Open
Abstract
COVID-19 pandemic remains an on-going global health and economic threat that has amassed millions of deaths. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of this disease and is constantly under evolutionary pressures that drive the modification of its genome which may represent a threat to the efficacy of current COVID-19 vaccines available. This article highlights the pressures that facilitate the rise of new SARS-CoV-2 variants and the key mutations of the viral spike protein - L452R, E484K, N501Y and D614G- that promote immune escape mechanism and warrant a cautionary point for clinical and public health responses in terms of re-infection, vaccine breakthrough infection and therapeutic values.
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Affiliation(s)
- Liyana Ahmad
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB) Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
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Xiong S, Zhang L, Qadir AS, Richner JM, Class J, Rehman J, Malik AB. Interleukin-1RA Mitigates SARS-CoV-2-Induced Inflammatory Lung Vascular Leakage and Mortality in Humanized K18-hACE-2 Mice. Arterioscler Thromb Vasc Biol 2021; 41:2773-2785. [PMID: 34496633 PMCID: PMC8545251 DOI: 10.1161/atvbaha.121.316925] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/27/2021] [Indexed: 01/02/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Shiqin Xiong
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology (S.X., L.Z., A.S.Q., J.R., A.B.M.), University of Illinois College of Medicine at Chicago
- Now with Department of Cardiometabolic Diseases, Merck Research Laboratories, South San Francisco, CA (S.X.)
| | - Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology (S.X., L.Z., A.S.Q., J.R., A.B.M.), University of Illinois College of Medicine at Chicago
| | - Abdul S. Qadir
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology (S.X., L.Z., A.S.Q., J.R., A.B.M.), University of Illinois College of Medicine at Chicago
| | - Justin M. Richner
- Department of Microbiology and Immunology (J.M.R., J.C.), University of Illinois College of Medicine at Chicago
- Division of Cardiology, Department of Medicine (J.R.), University of Illinois College of Medicine at Chicago
| | - Jake Class
- Department of Microbiology and Immunology (J.M.R., J.C.), University of Illinois College of Medicine at Chicago
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology (S.X., L.Z., A.S.Q., J.R., A.B.M.), University of Illinois College of Medicine at Chicago
| | - Asrar B. Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology (S.X., L.Z., A.S.Q., J.R., A.B.M.), University of Illinois College of Medicine at Chicago
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