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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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2
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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3
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Lee J, Kim B, Woo HM, Kim JW, Jung I, Park SW, Kim YS, Na JH, Jung ST. Enhanced Omicron Variant Neutralization by a Human Antibody Tailored to Wild-Type and Delta-Variant SARS-CoV-2 RBDs. Mol Pharm 2024. [PMID: 39058261 DOI: 10.1021/acs.molpharmaceut.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Given the previous SARS-CoV-2 pandemic and the inherent unpredictability of viral antigenic drift and shift, preemptive development of diverse neutralizing antibodies targeting a broad spectrum of epitopes is essential to ensure immediate therapeutic and prophylactic interventions during emerging outbreaks. In this study, we present a monoclonal antibody engineered for cross-reactivity to both wild-type and Delta RBDs, which, surprisingly, demonstrates enhanced neutralizing activity against the Omicron variant despite a significant number of mutations. Using an Escherichia coli inner membrane display of a human naïve antibody library, we identified antibodies specific to the wild-type SARS-CoV-2 receptor binding domain (RBD). Subsequent directed evolution via yeast surface display yielded JS18.1, an antibody with high binding affinity for both the Delta and Kappa RBDs, as well as enhanced binding to other RBDs (wild-type, Alpha, Beta, Gamma, Kappa, and Mu). Notably, JS18.1 (engineered for wild-type and Delta RBDs) exhibits enhanced neutralizing capability against the Omicron variant and binds to RBDs noncompetitively with ACE2, distinguishing it from other previously reported antibodies. This underscores the potential of pre-existing antibodies to neutralize emerging SARS-CoV-2 strains and offers insights into strategies to combat emerging viruses.
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Affiliation(s)
- Jisun Lee
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Bomi Kim
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hye-Min Woo
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Jun-Won Kim
- Division of Emerging Virus and Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Centers for Disease Control and Prevention Agency, Osong, Cheongju 28159, Republic of Korea
| | - Inji Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Seong-Wook Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Yong-Sung Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-do 16499, Republic of Korea
- Department of Allergy and Clinical Immunology, Ajou University Medical School, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Jung-Hyun Na
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Biomedical Research Center, Korea University Anam Hospital, Seoul 02841, Republic of Korea
- Institute of Human Genetics, Korea University College of Medicine, Seoul 02841, Republic of Korea
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Liu Q, Lu Y, Cai C, Huang Y, Zhou L, Guan Y, Fu S, Lin Y, Yan H, Zhang Z, Li X, Yang X, Yang H, Guo H, Lan K, Chen Y, Hou SC, Xiong Y. A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug. Cell Death Dis 2024; 15:458. [PMID: 38937437 PMCID: PMC11211474 DOI: 10.1038/s41419-024-06802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
SARS-CoV-2 infection is initiated by Spike glycoprotein binding to the human angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain. Blocking this interaction has been proven to be an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody named VHH60, which was directly produced from an engineering nanobody library based on a commercialized nanobody within a very short period. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein at S351, S470-471and S493-494 as determined by structural analysis, with an affinity of 2.56 nM. It inhibits infections of both ancestral SARS-CoV-2 strain and pseudotyped viruses harboring SARS-CoV-2 wildtype, key mutations or variants at the nanomolar level. Furthermore, VHH60 suppressed SARS-CoV-2 infection and propagation 50-fold better and protected mice from death for twice as long as the control group after SARS-CoV-2 nasal infections in vivo. Therefore, VHH60 is not only a powerful nanobody with a promising profile for disease control but also provides evidence for a highly effective and rapid approach to generating therapeutic nanobodies.
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Affiliation(s)
- Qianyun Liu
- State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Lingang Laboratory, Shanghai, 200031, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | | | - Yanyan Huang
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
- Animal Biosafety Level-III Laboratory/Institute for Vaccine Research, Wuhan University, Wuhan, 430071, China
| | - Yanbin Guan
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China
| | - Shiying Fu
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China
| | - Youyou Lin
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China
| | - Huan Yan
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Zhen Zhang
- Animal Biosafety Level-III Laboratory/Institute for Vaccine Research, Wuhan University, Wuhan, 430071, China
| | - Xiang Li
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China.
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
- Animal Biosafety Level-III Laboratory/Institute for Vaccine Research, Wuhan University, Wuhan, 430071, China.
| | - Yu Chen
- State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
| | | | - Yi Xiong
- State Key Laboratory of Virology, Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- Bioduro-sundia LLC., Wuxi, 214174, Jiangsu, China.
- Bayray Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518107, Guangdong, China.
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5
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Wentworth J, Mielcarz DW, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and Functions of Infection-enhancing Antibodies to the N-terminal Domain of SARS-CoV-2. Pathog Immun 2024; 9:1-24. [PMID: 38933606 PMCID: PMC11197847 DOI: 10.20411/pai.v9i2.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024] Open
Abstract
Background Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by N-terminal domain (NTD)-binding monoclonal antibodies (mAbs) has been observed in vitro, but the functional significance of these antibodies in vivo is less clear. Methods We characterized 1,213 SARS-CoV-2 spike (S)-binding mAbs derived from COVID-19 convalescent patients for binding specificity to the SARS-CoV-2 S protein, VH germ-line usage, and affinity maturation. Infection enhancement in a vesicular stomatitis virus (VSV)-SARS-CoV-2 S pseudovirus (PV) assay was characterized in respiratory and intestinal epithelial cell lines, and against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire was used to determine functional attributes of secreted NTD-binding mAbs. Results We identified 72/1213 (5.9%) mAbs that enhanced SARS-CoV-2 infection in a PV assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least 5 months post-infection. Infection enhancement by NTD-binding mAbs was not observed in intestinal and respiratory epithelial cell lines and was diminished or lost against SARS-CoV-2 VOC. Proteomic deconvolution of the serum antibody repertoire from 2 of the convalescent patients identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum. Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Conclusions Functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display functional attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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Affiliation(s)
- Ruth I. Connor
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | | | | | | | | | - Seungmin Shin
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Wendy F. Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
| | - Jordan Wentworth
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Daniel W. Mielcarz
- DartLab, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire
| | - Joshua A. Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | | | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire
| | - Peter F. Wright
- Department of Pediatrics, Geisel School of Medicine, Dartmouth Health, Lebanon, New Hampshire
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6
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Pavia G, Quirino A, Marascio N, Veneziano C, Longhini F, Bruni A, Garofalo E, Pantanella M, Manno M, Gigliotti S, Giancotti A, Barreca GS, Branda F, Torti C, Rotundo S, Lionello R, La Gamba V, Berardelli L, Gullì SP, Trecarichi EM, Russo A, Palmieri C, De Marco C, Viglietto G, Casu M, Sanna D, Ciccozzi M, Scarpa F, Matera G. Persistence of SARS-CoV-2 infection and viral intra- and inter-host evolution in COVID-19 hospitalized patients. J Med Virol 2024; 96:e29708. [PMID: 38804179 DOI: 10.1002/jmv.29708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) persistence in COVID-19 patients could play a key role in the emergence of variants of concern. The rapid intra-host evolution of SARS-CoV-2 may result in an increased transmissibility, immune and therapeutic escape which could be a direct consequence of COVID-19 epidemic currents. In this context, a longitudinal retrospective study on eight consecutive COVID-19 patients with persistent SARS-CoV-2 infection, from January 2022 to March 2023, was conducted. To characterize the intra- and inter-host viral evolution, whole genome sequencing and phylogenetic analysis were performed on nasopharyngeal samples collected at different time points. Phylogenetic reconstruction revealed an accelerated SARS-CoV-2 intra-host evolution and emergence of antigenically divergent variants. The Bayesian inference and principal coordinate analysis analysis showed a host-based genomic structuring among antigenically divergent variants, that might reflect the positive effect of containment practices, within the critical hospital area. All longitudinal antigenically divergent isolates shared a wide range of amino acidic (aa) changes, particularly in the Spike (S) glycoprotein, that increased viral transmissibility (K417N, S477N, N501Y and Q498R), enhanced infectivity (R346T, S373P, R408S, T478K, Q498R, Y505H, D614G, H655Y, N679K and P681H), caused host immune escape (S371L, S375F, T376A, K417N, and K444T/R) and displayed partial or complete resistance to treatments (G339D, R346K/T, S371F/L, S375F, T376A, D405N, N440K, G446S, N460K, E484A, F486V, Q493R, G496S and Q498R). These results suggest that multiple novel variants which emerge in the patient during persistent infection, might spread to another individual and continue to evolve. A pro-active genomic surveillance of persistent SARS-CoV-2 infected patients is recommended to identify genetically divergent lineages before their diffusion.
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Affiliation(s)
- Grazia Pavia
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Angela Quirino
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Claudia Veneziano
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Federico Longhini
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Andrea Bruni
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Eugenio Garofalo
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Marta Pantanella
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Michele Manno
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Simona Gigliotti
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Aida Giancotti
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Giorgio Settimo Barreca
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Carlo Torti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Salvatore Rotundo
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Rosaria Lionello
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Valentina La Gamba
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Lavinia Berardelli
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Sara Palma Gullì
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Alessandro Russo
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Carmela De Marco
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Matera
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
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7
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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [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: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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8
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Leducq V, Zafilaza K, Fauchois A, Ghidaoui E, Sayon S, Dorival C, Meledje ML, Lusivika-Nzinga C, Yordanov Y, Martin-Blondel G, Carrat F, Marcelin AG, Soulie C. Spike Protein Genetic Evolution in Patients at High Risk of Severe Coronavirus Disease 2019 Treated by Monoclonal Antibodies. J Infect Dis 2024; 229:1341-1351. [PMID: 37996072 DOI: 10.1093/infdis/jiad523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND High-risk patients, often immunocompromised and not responding to vaccine, continue to experience severe coronavirus disease 2019 (COVID-19) and death. Monoclonal antibodies (mAbs) were shown to be effective to prevent severe COVID-19 for these patients. Nevertheless, concerns about the emergence of resistance mutations were raised. METHODS We conducted a multicentric prospective cohort study, including 264 patients with mild to moderate COVID-19 at high risk for progression to severe COVID-19 and treated early with casirivimab/imdevimab, sotrovimab, or tixagevimab/cilgavimab. We sequenced the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during follow-up and searched for emerging spike mutations. RESULTS Immunocompromised patients have a 6-fold increased risk of developing mutations, which are associated with a prolonged duration of viral clearance but no clinical worsening. Emerging P337S/R/L/H, E340D/K/A/Q/V/G, and K356T/R substitutions in patients treated with sotrovimab are associated with higher viral RNA loads for up to 14 days post-treatment initiation. Tixagevimab/cilgavimab is associated with a 5-fold increased risk of developing mutations. R346K/I/T/S and K444R/N/M substitutions associated with tixagevimab/cilgavimab have been identified in multiple SARS-CoV-2 lineages, including BQ.1 and XBB. CONCLUSIONS The probability of emerging mutations arising in response to mAbs is significant, emphasizing the crucial need to investigate these mutations thoroughly and assess their impact on patients and the evolutionary trajectory of SARS-CoV-2.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Antoine Fauchois
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Emna Ghidaoui
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Sophie Sayon
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Céline Dorival
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Marie-Laure Meledje
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Clovis Lusivika-Nzinga
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Youri Yordanov
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Service d'Accueil des Urgences, Paris, France
| | - Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Inserm, Université Toulouse III, Toulouse, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Département de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Cathia Soulie
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
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Yu Y, Zhang M, Huang L, Chen Y, Wu X, Li T, Li Y, Wang Y, Huang W. COVID-19 Serum Drives Spike-Mediated SARS-CoV-2 Variation. Viruses 2024; 16:763. [PMID: 38793644 PMCID: PMC11126028 DOI: 10.3390/v16050763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Neutralizing antibodies targeting the spike (S) protein of SARS-CoV-2, elicited either by natural infection or vaccination, are crucial for protection against the virus. Nonetheless, the emergence of viral escape mutants presents ongoing challenges by contributing to breakthrough infections. To define the evolution trajectory of SARS-CoV-2 within the immune population, we co-incubated replication-competent rVSV/SARS-CoV-2/GFP chimeric viruses with sera from COVID-19 convalescents. Our findings revealed that the E484D mutation contributes to increased viral resistant against both convalescent and vaccinated sera, while the L1265R/H1271Y double mutation enhanced viral infectivity in 293T-hACE2 and Vero cells. These findings suggest that under the selective pressure of polyclonal antibodies, SARS-CoV-2 has the potential to accumulate mutations that facilitate either immune evasion or greater infectivity, facilitating its adaption to neutralizing antibody responses. Although the mutations identified in this study currently exhibit low prevalence in the circulating SARS-CoV-2 populations, the continuous and meticulous surveillance of viral mutations remains crucial. Moreover, there is an urgent necessity to develop next-generation antibody therapeutics and vaccines that target diverse, less mutation-prone antigenic sites to ensure more comprehensive and durable immune protection against SARS-CoV-2.
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Affiliation(s)
- Yuanling Yu
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
- National Institutes for Food and Drug Control, Chinese Academy of Medical Science & Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing 100730, China
| | - Lan Huang
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Yanhong Chen
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Xi Wu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
- State Key Laboratory of Drug Regulatory Science, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Tao Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
| | - Yanbo Li
- Beijing Yunling Biotechnology Co., Ltd., Beijing 100176, China
| | - Youchun Wang
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
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10
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Feng S, Reid GE, Clark NM, Harrington A, Uprichard SL, Baker SC. Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies. Virol J 2024; 21:105. [PMID: 38715113 PMCID: PMC11075269 DOI: 10.1186/s12985-024-02378-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. RESULTS We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. CONCLUSIONS Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Gail E Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Nina M Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan L Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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11
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Ray P, Ledgerwood-Lee M, Brickner H, Clark AE, Garretson A, Graham R, Van Zant W, Carlin AF, Aronoff-Spencer ES. Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels. Viruses 2024; 16:662. [PMID: 38793544 PMCID: PMC11125937 DOI: 10.3390/v16050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.
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Affiliation(s)
- Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron Garretson
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Rishi Graham
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
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12
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Guilbaud R, Franco Yusti AM, Leducq V, Zafilaza K, Bridier-Nahmias A, Todesco E, Soulie C, Fauchois A, Le Hingrat Q, Kramer L, Goulenok T, Salpin M, Daugas E, Dorent R, Ottaviani S, Zalcman G, Ghosn J, Choquet S, Cacoub P, Amoura Z, Barroux B, Pourcher V, Spano JP, Louet M, Marcelin AG, Calvez V, Charpentier C, Descamps D, Marot S, Ferré VM, Coppée R. Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study. J Infect Dis 2024; 229:1041-1049. [PMID: 37956413 DOI: 10.1093/infdis/jiad499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.
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Affiliation(s)
- Romane Guilbaud
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Anna-Maria Franco Yusti
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Valentin Leducq
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Karen Zafilaza
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Bridier-Nahmias
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Eve Todesco
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cathia Soulie
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Fauchois
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Quentin Le Hingrat
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Laura Kramer
- Service de Pharmacie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Tiphaine Goulenok
- Service de Médecine Interne, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Mathilde Salpin
- Service de Pneumologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Eric Daugas
- Service de Néphrologie, Université Paris Cité, Inserm U1149, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Richard Dorent
- Service de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sébastien Ottaviani
- Service de Rhumatologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Gérard Zalcman
- Service d'Oncologie Thoracique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
- Service de Maladies Infectieuses, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sylvain Choquet
- Service d'Hématologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Patrice Cacoub
- Service de Médecine Interne et Immunologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Zahir Amoura
- Service de Médecine Interne 2, Centre National de Référence des Histiocytoses, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Benoit Barroux
- Service d'Urologie et de Transplantation Rénale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valérie Pourcher
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service de Maladies Infectieuses et Tropicales, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service d'Oncologie Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Martine Louet
- Service de Santé au Travail, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Vincent Calvez
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Stéphane Marot
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valentine Marie Ferré
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Romain Coppée
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
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Yang ZH, Song YL, Pei J, Li SZ, Liu RL, Xiong Y, Wu J, Liu YL, Fan HF, Wu JH, Wang ZJ, Guo J, Meng SL, Chen XQ, Lu J, Shen S. Measles Virus-Based Vaccine Expressing Membrane-Anchored Spike of SARS-CoV-2 Inducing Efficacious Systemic and Mucosal Humoral Immunity in Hamsters. Viruses 2024; 16:559. [PMID: 38675901 PMCID: PMC11054861 DOI: 10.3390/v16040559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
As SARS-CoV-2 continues to evolve and COVID-19 cases rapidly increase among children and adults, there is an urgent need for a safe and effective vaccine that can elicit systemic and mucosal humoral immunity to limit the emergence of new variants. Using the Chinese Hu191 measles virus (MeV-hu191) vaccine strain as a backbone, we developed MeV chimeras stably expressing the prefusion forms of either membrane-anchored, full-length spike (rMeV-preFS), or its soluble secreted spike trimers with the help of the SP-D trimerization tag (rMeV-S+SPD) of SARS-CoV-2 Omicron BA.2. The two vaccine candidates were administrated in golden Syrian hamsters through the intranasal or subcutaneous routes to determine the optimal immunization route for challenge. The intranasal delivery of rMeV-S+SPD induced a more robust mucosal IgA antibody response than the subcutaneous route. The mucosal IgA antibody induced by rMeV-preFS through the intranasal routine was slightly higher than the subcutaneous route, but there was no significant difference. The rMeV-preFS vaccine stimulated higher mucosal IgA than the rMeV-S+SPD vaccine through intranasal or subcutaneous administration. In hamsters, intranasal administration of the rMeV-preFS vaccine elicited high levels of NAbs, protecting against the SARS-CoV-2 Omicron BA.2 variant challenge by reducing virus loads and diminishing pathological changes in vaccinated animals. Encouragingly, sera collected from the rMeV-preFS group consistently showed robust and significantly high neutralizing titers against the latest variant XBB.1.16. These data suggest that rMeV-preFS is a highly promising COVID-19 candidate vaccine that has great potential to be developed into bivalent vaccines (MeV/SARS-CoV-2).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jia Lu
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, China; (Z.-H.Y.); (Y.-L.S.); (J.P.); (S.-Z.L.); (R.-L.L.); (Y.X.); (J.W.); (Y.-L.L.); (H.-F.F.); (J.-H.W.); (Z.-J.W.); (J.G.); (S.-L.M.); (X.-Q.C.)
| | - Shuo Shen
- Wuhan Institute of Biological Products Co. Ltd., Wuhan 430207, China; (Z.-H.Y.); (Y.-L.S.); (J.P.); (S.-Z.L.); (R.-L.L.); (Y.X.); (J.W.); (Y.-L.L.); (H.-F.F.); (J.-H.W.); (Z.-J.W.); (J.G.); (S.-L.M.); (X.-Q.C.)
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14
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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15
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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16
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Chen L, He Y, Liu H, Shang Y, Guo G. Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants. Front Immunol 2024; 15:1339660. [PMID: 38464527 PMCID: PMC10924305 DOI: 10.3389/fimmu.2024.1339660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.
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Affiliation(s)
- Luyi Chen
- Chongqing Nankai Secondary School, Chongqing, China
| | - Ying He
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Hongye Liu
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Yongjun Shang
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Guoning Guo
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
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17
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Sussman F, Villaverde DS. The Diverse Nature of the Molecular Interactions That Govern the COV-2 Variants' Cell Receptor Affinity Ranking and Its Experimental Variability. Int J Mol Sci 2024; 25:2585. [PMID: 38473831 DOI: 10.3390/ijms25052585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
A critical determinant of infectivity and virulence of the most infectious and or lethal variants of concern (VOCs): Wild Type, Delta and Omicron is related to the binding interactions between the receptor-binding domain of the spike and its host receptor, the initial step in cell infection. It is of the utmost importance to understand how mutations of a viral strain, especially those that are in the viral spike, affect the resulting infectivity of the emerging VOC, knowledge that could help us understand the variant virulence and inform the therapies applied or the vaccines developed. For this sake, we have applied a battery of computational protocols of increasing complexity to the calculation of the spike binding affinity for three variants of concern to the ACE2 cell receptor. The results clearly illustrate that the attachment of the spikes of the Delta and Omicron variants to the receptor originates through different molecular interaction mechanisms. All our protocols unanimously predict that the Delta variant has the highest receptor-binding affinity, while the Omicron variant displays a substantial variability in the binding affinity of the spike that relates to the structural plasticity of the Omicron spike-receptor complex. We suggest that the latter result could explain (at least in part) the variability of the in vitro binding results for this VOC and has led us to suggest a reason for the lower virulence of the Omicron variant as compared to earlier strains. Several hypotheses have been developed around this subject.
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Affiliation(s)
- Fredy Sussman
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Santiago de Compostela, 15784 Santiago de Compostela, Spain
| | - Daniel S Villaverde
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Santiago de Compostela, 15784 Santiago de Compostela, Spain
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18
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Fournelle D, Mostefai F, Brunet-Ratnasingham E, Poujol R, Grenier JC, Gálvez JH, Pagliuzza A, Levade I, Moreira S, Benlarbi M, Beaudoin-Bussières G, Gendron-Lepage G, Bourassa C, Tauzin A, Grandjean Lapierre S, Chomont N, Finzi A, Kaufmann DE, Craig M, Hussin JG. Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis. Viruses 2024; 16:342. [PMID: 38543708 PMCID: PMC10974702 DOI: 10.3390/v16030342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 05/23/2024] Open
Abstract
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.
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Affiliation(s)
- Dominique Fournelle
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Fatima Mostefai
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Elsa Brunet-Ratnasingham
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Raphaël Poujol
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - Jean-Christophe Grenier
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - José Héctor Gálvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Mehdi Benlarbi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gabrielle Gendron-Lepage
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Catherine Bourassa
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Alexandra Tauzin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Simon Grandjean Lapierre
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Andrés Finzi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Daniel E. Kaufmann
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital and University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Morgan Craig
- Research Centre, Centre Hospitalier UniversitaireSainte-Justine, Montréal, QC H3T 1C5, Canada;
- Département de Mathématiques et de Statistique, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Julie G. Hussin
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mila-Quebec AI Institute, Montréal, QC H2S 3H1, Canada
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19
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Zimmerman O, Altman Doss AM, Ying B, Liang CY, Mackin SR, Davis-Adams HG, Adams LJ, VanBlargan LA, Chen RE, Scheaffer SM, Desai P, Raju S, Mantia TL, O’Shaughnessy CC, Monroy JM, Wedner HJ, Rigell CJ, Kau AL, Dy TB, Ren Z, Turner JS, O’Halloran JA, Presti RM, Kendall PL, Fremont DH, Ellebedy AH, Diamond MS. Immunoglobulin replacement products protect against SARS-CoV-2 infection in vivo despite poor neutralizing activity. JCI Insight 2024; 9:e176359. [PMID: 38175703 PMCID: PMC10967375 DOI: 10.1172/jci.insight.176359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Immunoglobulin (IG) replacement products are used routinely in patients with immune deficiency and other immune dysregulation disorders who have poor responses to vaccination and require passive immunity conferred by commercial antibody products. The binding, neutralizing, and protective activity of intravenously administered IG against SARS-CoV-2 emerging variants remains unknown. Here, we tested 198 different IG products manufactured from December 2019 to August 2022. We show that prepandemic IG had no appreciable cross-reactivity or neutralizing activity against SARS-CoV-2. Anti-spike antibody titers and neutralizing activity against SARS-CoV-2 WA1/2020 D614G increased gradually after the pandemic started and reached levels comparable to vaccinated healthy donors 18 months after the diagnosis of the first COVID-19 case in the United States in January 2020. The average time between production to infusion of IG products was 8 months, which resulted in poor neutralization of the variant strain circulating at the time of infusion. Despite limited neutralizing activity, IG prophylaxis with clinically relevant dosing protected susceptible K18-hACE2-transgenic mice against clinical disease, lung infection, and lung inflammation caused by the XBB.1.5 Omicron variant. Moreover, following IG prophylaxis, levels of XBB.1.5 infection in the lung were higher in FcγR-KO mice than in WT mice. Thus, IG replacement products with poor neutralizing activity against evolving SARS-CoV-2 variants likely confer protection to patients with immune deficiency disorders through Fc effector function mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew L. Kau
- Department of Medicine, and
- Department of Molecular Microbiology
- Center for Women’s Infectious Disease Research
| | | | | | | | | | - Rachel M. Presti
- Department of Medicine, and
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, and
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | | | - Ali H. Ellebedy
- Department of Pathology and Immunology
- Department of Molecular Microbiology
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, and
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S. Diamond
- Department of Medicine, and
- Department of Pathology and Immunology
- Department of Molecular Microbiology
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, and
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
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20
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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21
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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22
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Kim D, Kim M, Kim J, Baek K, Park H, Park S, Kang BM, Kim S, Kim MJ, Mostafa MN, Maharjan S, Shin HE, Lee MH, Il Kim J, Park MS, Kim YS, Choi EK, Lee Y, Kwon HJ. A mouse xenograft long-term replication yields a SARS-CoV-2 Delta mutant with increased lethality. J Med Virol 2024; 96:e29459. [PMID: 38345153 DOI: 10.1002/jmv.29459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
We recently established a long-term SARS-CoV-2 infection model using lung-cancer xenograft mice and identified mutations that arose in the SARS-CoV-2 genome during long-term propagation. Here, we applied our model to the SARS-CoV-2 Delta variant, which has increased transmissibility and immune escape compared with ancestral SARS-CoV-2. We observed limited mutations in SARS-CoV-2 Delta during long-term propagation, including two predominant mutations: R682W in the spike protein and L330W in the nucleocapsid protein. We analyzed two representative isolates, Delta-10 and Delta-12, with both predominant mutations and some additional mutations. Delta-10 and Delta-12 showed lower replication capacity compared with SARS-CoV-2 Delta in cultured cells; however, Delta-12 was more lethal in K18-hACE2 mice compared with SARS-CoV-2 Delta and Delta-10. Mice infected with Delta-12 had higher viral titers, more severe histopathology in the lungs, higher chemokine expression, increased astrocyte and microglia activation, and extensive neutrophil infiltration in the brain. Brain tissue hemorrhage and mild vacuolation were also observed, suggesting that the high lethality of Delta-12 was associated with lung and brain pathology. Our long-term infection model can provide mutant viruses derived from SARS-CoV-2 Delta and knowledge about the possible contributions of emergent mutations to the properties of new variants.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Mo-Jong Kim
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Mohd Najib Mostafa
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Yong-Sun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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23
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Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. J Virol 2024; 98:e0161823. [PMID: 38174928 PMCID: PMC10805032 DOI: 10.1128/jvi.01618-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.
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Affiliation(s)
- Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Michael A. Martin
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Laura L. Gibson
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kimberly K. O. Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J. Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Fadi G. Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C. Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca L. Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David D. McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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24
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Cianfarini C, Hassler L, Wysocki J, Hassan A, Nicolaescu V, Elli D, Gula H, Ibrahim AM, Randall G, Henkin J, Batlle D. Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant. Cells 2024; 13:203. [PMID: 38334597 PMCID: PMC10854654 DOI: 10.3390/cells13030203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/10/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) utilizes angiotensin-converting enzyme 2 (ACE2) as its main receptor for cell entry. We bioengineered a soluble ACE2 protein termed ACE2 618-DDC-ABD that has increased binding to SARS-CoV-2 and prolonged duration of action. Here, we investigated the protective effect of this protein when administered intranasally to k18-hACE2 mice infected with the aggressive SARS-CoV-2 Delta variant. k18-hACE2 mice were infected with the SARS-CoV-2 Delta variant by inoculation of a lethal dose (2 × 104 PFU). ACE2 618-DDC-ABD (10 mg/kg) or PBS was administered intranasally six hours prior and 24 and 48 h post-viral inoculation. All animals in the PBS control group succumbed to the disease on day seven post-infection (0% survival), whereas, in contrast, there was only one casualty in the group that received ACE2 618-DDC-ABD (90% survival). Mice in the ACE2 618-DDC-ABD group had minimal disease as assessed using a clinical score and stable weight, and both brain and lung viral titers were markedly reduced. These findings demonstrate the efficacy of a bioengineered soluble ACE2 decoy with an extended duration of action in protecting against the aggressive Delta SARS-CoV-2 variant. Together with previous work, these findings underline the universal protective potential against current and future emerging SARS-CoV-2 variants.
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Affiliation(s)
- Cosimo Cianfarini
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
- Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Luise Hassler
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Jan Wysocki
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Abdelsabour Hassan
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Vlad Nicolaescu
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Derek Elli
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Haley Gula
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Amany M. Ibrahim
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Glenn Randall
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Jack Henkin
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Daniel Batlle
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
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25
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Wang Y, Zhang Z, Yang M, Xiong X, Yan Q, Cao L, Wei P, Zhang Y, Zhang L, Lv K, Chen J, Liu X, Zhao X, Xiao J, Zhang S, Zhu A, Gan M, Zhang J, Cai R, Zhuo J, Zhang Y, Rao H, Qu B, Zhang Y, Chen L, Dai J, Cheng L, Hu Q, Chen Y, Lv H, So RTY, Peiris M, Zhao J, Liu X, Mok CKP, Wang X, Zhao J. Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain. Cell Rep 2024; 43:113653. [PMID: 38175758 DOI: 10.1016/j.celrep.2023.113653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/11/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the subgenus Sarbecovirus, members of which share high sequence similarity. Herein, we report one sarbecovirus antibody, 5817, which has broad-spectrum neutralization capacity against SARS-CoV-2 variants of concern (VOCs) and SARS-CoV, as well as related bat and pangolin viruses. 5817 can hardly compete with six classes of receptor-binding-domain-targeted antibodies grouped by structural classifications. No obvious impairment in the potency is detected against SARS-CoV-2 Omicron and subvariants. The cryoelectron microscopy (cryo-EM) structure of neutralizing antibody 5817 in complex with Omicron spike reveals a highly conserved epitope, only existing at the receptor-binding domain (RBD) open state. Prophylactic and therapeutic administration of 5817 potently protects mice from SARS-CoV-2 Beta, Delta, Omicron, and SARS-CoV infection. This study reveals a highly conserved cryptic epitope targeted by a broad sarbecovirus neutralizing antibody, which would be beneficial to meet the potential threat of pre-emergent SARS-CoV-2 VOCs.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China; Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinyi Xiong
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lei Cao
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Peilan Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China
| | - Yuting Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lu Zhang
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jiantao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuesong Liu
- Department of Critical Care Medicine, State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaochu Zhao
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Juxue Xiao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruoxi Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haiyue Rao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Qu
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuanyuan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lei Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jun Dai
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Linling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yaoqing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ray T Y So
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China
| | - Xiaoqing Liu
- Department of Critical Care Medicine, State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chris Ka Pun Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; S.H. Ho Research Centre for Infectious Diseases, Chinese University of Hong Kong, Hong Kong, China.
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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26
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Zhang L, Li J. Molecular Dynamics Simulations on Spike Protein Mutants Binding with Human β Defensin Type 2. J Phys Chem B 2024; 128:415-428. [PMID: 38189674 DOI: 10.1021/acs.jpcb.3c05460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Human β defensin type 2 (hBD-2), a cationic cysteine-rich peptide secreted from the human innate immune system, can bind Spike-RBD at the same site as receptor ACE2, thus blocking viral entry into ACE2-expressing cells. In order to find out the impact of CoV-2 mutations on hBD-2's antiviral activity, it is important to investigate the binding and interaction of hBD-2 with RBD mutants. All-atom molecular dynamics simulations were conducted on typical RBD mutants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N, and N501Y-E484K-K417N, binding with hBD-2. Starting from the stable binding structure of hBD-2 and wt-RBD and ClusPro and HADDOCK docking-predicted initial structures, the RBD variants bound with hBD-2 simulations were set up, and NAMD simulations were conducted. Based on the structure and dynamics analysis, it was found that most RBD variants can still form a similar number of hydrogen bonds with hBD-2, in addition to having a similar-sized buried surface area (BSA) and a similar binding interface to the RBD wildtype. However, the RBD triple mutant formed a less stable binding structure with hBD-2 than other variants. Additionally, the free energy perturbation (FEP) method was applied to calculate the contribution of key mutant residues to the binding and the free energy change caused by the mutations. The result shows that N439K, K417N, and the trimutation increase the binding free energy of RBD with hBD-2; thus, RBD should bind less stably with hBD-2. E484K decreases the binding free energy, thus it should bind more stably with hBD-2, while N501Y, S477N, T478I, and P479S almost do not change the binding free energy with hBD-2. The MM-GBSA method predicted the binding interaction energy which shows that the trimutant should be able to escape the binding with hBD-2 but N501Y should not. The result can provide insight into understanding the functional mechanism of hBD-2 combating SARS-CoV-2 mutants.
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Affiliation(s)
- Liqun Zhang
- Chemical Engineering Department, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Jadeson Li
- Newton North High School, 457 Walnut Street, Newton, Massachusetts 02460, United States
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Atanasoff KE, Brambilla L, Adelsberg DC, Kowdle S, Stevens CS, Slamanig S, Hung CT, Fu Y, Lim R, Tran L, Allen R, Sun W, Duty JA, Bajic G, Lee B, Tortorella D. An in vitro experimental pipeline to characterize the epitope of a SARS-CoV-2 neutralizing antibody. mBio 2024; 15:e0247723. [PMID: 38054729 PMCID: PMC10870823 DOI: 10.1128/mbio.02477-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/17/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread so long as they recognize and interact with circulating variants. The epitope and binding specificity of a neutralizing anti-SARS-CoV-2 Spike receptor-binding domain antibody clone against many SARS-CoV-2 variants of concern were characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis and VSV-spike neutralization studies. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines.
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Affiliation(s)
- Kristina E. Atanasoff
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luca Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniel C. Adelsberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christian S. Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stefan Slamanig
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Chuan-Tien Hung
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yanwen Fu
- Sorrento Therapeutics, Inc., San Diego, California, USA
| | - Reyna Lim
- Sorrento Therapeutics, Inc., San Diego, California, USA
| | - Linh Tran
- Sorrento Therapeutics, Inc., San Diego, California, USA
| | - Robert Allen
- Sorrento Therapeutics, Inc., San Diego, California, USA
| | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - J. Andrew Duty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Therapeutic Antibody Development, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Conway MJ, Yang H, Revord LA, Novay MP, Lee RJ, Ward AS, Abel JD, Williams MR, Uzarski RL, Alm EW. Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater. BMC Genomics 2024; 25:59. [PMID: 38218804 PMCID: PMC10787452 DOI: 10.1186/s12864-024-09977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. RESULTS One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and contained predominately a derivative of Alpha variant lineage B.1.1.7, detected from fall 2021 through summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage sequence over time, including numerous mutations in the Spike RBD and NTD. CONCLUSIONS We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.
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Affiliation(s)
- Michael J Conway
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA.
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA.
| | - Hannah Yang
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Lauren A Revord
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Michael P Novay
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Rachel J Lee
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Avery S Ward
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Jackson D Abel
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Maggie R Williams
- School of Engineering & Technology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
| | - Rebecca L Uzarski
- Department of Biology and Herbert H. and Grace A. Dow College of Health, Professions, Central Michigan University, Mt. Pleasant, MI, USA
| | - Elizabeth W Alm
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
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Singh P, Anand A, Rana S, Kumar A, Goel P, Kumar S, Gouda KC, Singh H. Impact of COVID-19 vaccination: a global perspective. Front Public Health 2024; 11:1272961. [PMID: 38274537 PMCID: PMC10808156 DOI: 10.3389/fpubh.2023.1272961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction The COVID-19 pandemic has caused widespread morbidity, mortality, and socio-economic disruptions worldwide. Vaccination has proven to be a crucial strategy in controlling the spread of the virus and mitigating its impact. Objective The study focuses on assessing the effectiveness of COVID-19 vaccination in reducing the incidence of positive cases, hospitalizations, and ICU admissions. The presented study is focused on the COVID-19 fully vaccinated population by considering the data from the first positive case reported until 20 September 2021. Methods Using data from multiple countries, time series analysis is deployed to investigate the variations in the COVID-19 positivity rates, hospitalization rates, and ICU requirements after successful vaccination campaigns at the country scale. Results Analysis of the COVID-19 positivity rates revealed a substantial decline in countries with high pre-vaccination rates. Within 1-3 months of vaccination campaigns, these rates decreased by 20-44%. However, certain countries experienced an increase in positivity rates with the emergence of the new Delta variant, emphasizing the importance of ongoing monitoring and adaptable vaccination strategies. Similarly, the analysis of hospitalization rates demonstrated a steady decline as vaccination drive rates rose in various countries. Within 90 days of vaccination, several countries achieved hospitalization rates below 200 per million. However, a slight increase in hospitalizations was observed in some countries after 180 days of vaccination, underscoring the need for continued vigilance. Furthermore, the ICU patient rates decreased as vaccination rates increased across most countries. Within 120 days, several countries achieved an ICU patient rate of 20 per million, highlighting the effectiveness of vaccination in preventing severe cases requiring intensive care. Conclusion COVID-19 vaccination has proven to be very much effective in reducing the incidence of cases, hospitalizations, and ICU admissions. However, ongoing surveillance, variant monitoring, and adaptive vaccination strategies are crucial for maximizing the benefits of vaccination and effectively controlling the spread of the virus.
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Affiliation(s)
- Priya Singh
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India
| | - Aditya Anand
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India
| | - Shweta Rana
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India
| | - Amit Kumar
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India
| | - Prabudh Goel
- Department of Pediatrics Surgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sujeet Kumar
- Centre for Proteomics and Drug Discovery, Amity University Maharashtra, Mumbai, India
| | - Krushna Chandra Gouda
- Earth and Engineering Sciences Division, CSIR Fourth Paradigm Institute, Bangalore, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India
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Pérez-Massón B, Quintana-Pérez Y, Tundidor Y, Pérez-Martínez D, Castro-Martínez C, Pupo-Meriño M, Orosa I, Relova-Hernández E, Villegas R, Guirola O, Rojas G. Studying SARS-CoV-2 interactions using phage-displayed receptor binding domain as a model protein. Sci Rep 2024; 14:712. [PMID: 38184672 PMCID: PMC10771503 DOI: 10.1038/s41598-023-50450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
SARS-CoV-2 receptor binding domain (RBD) mediates viral entry into human cells through its interaction with angiotensin converting enzyme 2 (ACE2). Most neutralizing antibodies elicited by infection or vaccination target this domain. Such a functional relevance, together with large RBD sequence variability arising during viral spreading, point to the need of exploring the complex landscape of interactions between RBD-derived variants, ACE2 and antibodies. The current work was aimed at developing a simple platform to do so. Biologically active and antigenic Wuhan-Hu-1 RBD, as well as mutated RBD variants found in nature, were successfully displayed on filamentous phages. Mutational scanning confirmed the global plasticity of the receptor binding motif within RBD, highlighted residues playing a critical role in receptor binding, and identified mutations strengthening the interaction. The ability of vaccine-induced antibodies to inhibit ACE2 binding of many mutated RBD variants, albeit at different extents, was shown. Amino acid replacements which could compromise such inhibitory potential were underscored. The expansion of our approach could be the starting point for a large-scale phage-based exploration of diversity within RBD of SARS-CoV-2 and related coronaviruses, useful to understand structure-function relationships, to engineer RBD proteins, and to anticipate changes to watch during viral evolution.
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Affiliation(s)
- Beatriz Pérez-Massón
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yazmina Quintana-Pérez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yaima Tundidor
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Dayana Pérez-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Camila Castro-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Mario Pupo-Meriño
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Ivette Orosa
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Ernesto Relova-Hernández
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Rosmery Villegas
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Ave 31 E/158 y 190, Cubanacán, Playa, CP 11300, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba.
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Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024; 52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
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Affiliation(s)
- Yuzhou Feng
- Department of Laboratory Medicine and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiahao Yi
- School of Big Health, Guizhou Medical University, Guiyang 550025, China
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Prabhakaran M, Matassoli F, Leggat D, Hoover A, Srikanth A, Wu W, Henry AR, Wang J, Lin BC, Teng IT, Schramm CA, Castro M, Serebryannyy L, Jean-Baptiste N, Moore C, Gajjala S, Todd JPM, McCarthy E, Narpala S, Francica J, Program VP, Corbett-Helaire KS, Douek DC, Kwong PD, Seder RA, Andrews SF, McDermott AB. Adjuvanted SARS-CoV-2 spike protein vaccination elicits long-lived plasma cells in nonhuman primates. Sci Transl Med 2024; 16:eadd5960. [PMID: 38170789 DOI: 10.1126/scitranslmed.add5960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Durable humoral immunity is mediated by long-lived plasma cells (LLPCs) that reside in the bone marrow. It remains unclear whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein vaccination is able to elicit and maintain LLPCs. Here, we describe a sensitive method to identify and isolate antigen-specific LLPCs by tethering antibodies secreted by these cells onto the cell surface. Using this method, we found that two doses of adjuvanted SARS-CoV-2 spike protein vaccination are able to induce spike protein-specific LLPC reservoirs enriched for receptor binding domain specificities in the bone marrow of nonhuman primates that are detectable for several months after vaccination. Immunoglobulin gene sequencing confirmed that several of these LLPCs were clones of memory B cells elicited 2 weeks after boost that had undergone further somatic hypermutation. Many of the antibodies secreted by these LLPCs also exhibited improved neutralization and cross-reactivity compared with earlier time points. These findings establish our method as a means to sensitively and reliably detect rare antigen-specific LLPCs and demonstrate that adjuvanted SARS-CoV-2 spike protein vaccination establishes spike protein-specific LLPC reservoirs.
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Affiliation(s)
- Madhu Prabhakaran
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Flavio Matassoli
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Leggat
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Walter Reed Army Institute of Research, Military HIV Research Program, Silver Spring, MD 20910, USA
| | - Abigayle Hoover
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abhinaya Srikanth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Weiwei Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mike Castro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonid Serebryannyy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nazaire Jean-Baptiste
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Moore
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suprabhath Gajjala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Astrazeneca, Washington, DC 20004, USA
| | | | - Kizzmekia S Corbett-Helaire
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Jia J, Garbarino E, Wang Y, Li J, Song M, Zhang X, Wang X, Li L, Chi J, Cui L, Tang H. Generation of SARS-CoV-2 spike receptor binding domain mutants and functional screening for immune evaders using a novel lentivirus-based system. J Med Virol 2024; 96:e29425. [PMID: 38258313 DOI: 10.1002/jmv.29425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The emergence of rapid and continuous mutations of severe acute respiratory syndrome 2 (SARS-CoV-2) spike glycoprotein that increased with the Omicron variant points out the necessity to anticipate such mutations for conceiving specific and adaptable therapies to avoid another pandemic. The crucial target for the antibody treatment and vaccine design is the receptor binding domain (RBD) of the SARS-CoV-2 spike. It is also the site where the virus has shown its high ability to mutate and consequently escape immune response. We developed a robust and simple method for generating a large number of functional SARS-CoV-2 spike RBD mutants by error-prone PCR and a novel nonreplicative lentivirus-based system. We prepared anti-RBD wild type (WT) polyclonal antibodies and used them to screen and select for mutant libraries that escape inhibition of virion entry into recipient cells expressing human angiotensin-converting enzyme 2 and transmembrane serine protease 2. We isolated, cloned, and sequenced six mutants totally bearing nine mutation sites. Eight mutations were found in successive WT variants, including Omicron and other recombinants, whereas one is novel. These results, together with the detailed functional analyses of two mutants provided the proof of concept for our approach.
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Affiliation(s)
- Junli Jia
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Emanuela Garbarino
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuhang Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Blood Transfusion, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaming Li
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Minmin Song
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xinjie Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Lingyun Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Jing Chi
- Department of Microbiological Laboratory, Baoan District Center for Disease Control and Prevention, Shenzhen, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huamin Tang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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Alfaleh MA, Alsulaiman RM, Almahboub SA, Nezamuldeen L, Zawawi A, Aljehani ND, Yasir M, Abdulal RH, Alkhaldi R, Helal A, Alamri SS, Malki J, Alhabbab RY, Abujamel TS, Alhakamy NA, Alnami A, Algaissi A, Hassanain M, Hashem AM. ACE2-Fc and DPP4-Fc decoy receptors against SARS-CoV-2 and MERS-CoV variants: a quick therapeutic option for current and future coronaviruses outbreaks. Antib Ther 2024; 7:53-66. [PMID: 38371953 PMCID: PMC10873275 DOI: 10.1093/abt/tbad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic human coronaviruses (CoVs). Anti-CoVs mAbs and vaccines may be effective, but the emergence of neutralization escape variants is inevitable. Angiotensin-converting enzyme 2 and dipeptidyl peptidase 4 enzyme are the getaway receptors for SARS-CoV-2 and MERS-CoV, respectively. Thus, we reformatted these receptors as Fc-fusion decoy receptors. Then, we tested them in parallel with anti-SARS-CoV (ab1-IgG) and anti-MERS-CoV (M336-IgG) mAbs against several variants using pseudovirus neutralization assay. The generated Fc-based decoy receptors exhibited a strong inhibitory effect against all pseudotyped CoVs. Results showed that although mAbs can be effective antiviral drugs, they might rapidly lose their efficacy against highly mutated viruses. We suggest that receptor traps can be engineered as Fc-fusion proteins for highly mutating viruses with known entry receptors, for a faster and effective therapeutic response even against virus harboring antibodies escape mutations.
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Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Reem M Alsulaiman
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sarah A Almahboub
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Leena Nezamuldeen
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Najwa D Aljehani
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Muhammad Yasir
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rwaa H Abdulal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rami Alkhaldi
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Assala Helal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Sawsan S Alamri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Jana Malki
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Rowa Y Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Nabil A Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Aisha Alnami
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21859, Saudi Arabia
| | - Abdullah Algaissi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mazen Hassanain
- Department of Surgery, Faculty of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21859, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21859, Saudi Arabia
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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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Adams LJ, VanBlargan LA, Liu Z, Gilchuk P, Zhao H, Chen RE, Raju S, Chong Z, Whitener BM, Shrihari S, Jethva PN, Gross ML, Crowe JE, Whelan SPJ, Diamond MS, Fremont DH. A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med 2023; 4:101305. [PMID: 38039973 PMCID: PMC10772349 DOI: 10.1016/j.xcrm.2023.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Most neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) target the receptor binding domain (RBD) of the spike (S) protein. Here, we characterize a panel of mAbs targeting the N-terminal domain (NTD) or other non-RBD epitopes of S. A subset of NTD mAbs inhibits SARS-CoV-2 entry at a post-attachment step and avidly binds the surface of infected cells. One neutralizing NTD mAb, SARS2-57, protects K18-hACE2 mice against SARS-CoV-2 infection in an Fc-dependent manner. Structural analysis demonstrates that SARS2-57 engages an antigenic supersite that is remodeled by deletions common to emerging variants. In neutralization escape studies with SARS2-57, this NTD site accumulates mutations, including a similar deletion, but the addition of an anti-RBD mAb prevents such escape. Thus, our study highlights a common strategy of immune evasion by SARS-CoV-2 variants and how targeting spatially distinct epitopes, including those in the NTD, may limit such escape.
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Affiliation(s)
- Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prashant N Jethva
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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Ameratunga R, Mears E, Leung E, Snell R, Woon ST, Kelton W, Medlicott N, Jordan A, Abbott W, Steele R, Rolleston W, Longhurst H, Lehnert K. Soluble wild-type ACE2 molecules inhibit newer SARS-CoV-2 variants and are a potential antiviral strategy to mitigate disease severity in COVID-19. Clin Exp Immunol 2023; 214:289-295. [PMID: 37565297 PMCID: PMC10719217 DOI: 10.1093/cei/uxad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease of 2019 (COVID-19), has caused havoc around the world. While several COVID-19 vaccines and drugs have been authorized for use, these antiviral drugs remain beyond the reach of most low- and middle-income countries. Rapid viral evolution is reducing the efficacy of vaccines and monoclonal antibodies and contributing to the deaths of some fully vaccinated persons. Others with normal immunity may have chosen not to be vaccinated and remain at risk if they contract the infection. Vaccines may not protect some immunodeficient patients from SARS-CoV-2, who are also at increased risk of chronic COVID-19 infection, a dangerous stalemate between the virus and a suboptimal immune response. Intra-host viral evolution could rapidly lead to the selection and dominance of vaccine and monoclonal antibody-resistant clades of SARS-CoV-2. There is thus an urgent need to develop new treatments for COVID-19. The NZACE2-Pātari project, comprising modified soluble angiotensin-converting enzyme 2 (ACE2) molecules, seeks to intercept and block SARS-CoV-2 infection of the respiratory mucosa. In vitro data presented here show that soluble wild-type ACE2 molecules retain the ability to effectively block the Spike (S) glycoprotein of SARS-CoV-2 variants including the ancestral Wuhan, delta (B.1.617.2) and omicron (B.1.1.529) strains. This therapeutic strategy may prove effective if implemented early during the nasal phase of the infection and may act synergistically with other antiviral drugs such as Paxlovid to further mitigate disease severity.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical immunology, Auckland Hospital, AucklandNew Zealand
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Emily Mears
- Applied Translational Genetic Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Russell Snell
- Applied Translational Genetic Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton, New Zealand
- Te Aka Mātuatua School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Anthony Jordan
- Department of Clinical immunology, Auckland Hospital, AucklandNew Zealand
| | - William Abbott
- Department of Surgery, Auckland Hospital, Auckland, New Zealand
| | - Richard Steele
- Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | | | - Hilary Longhurst
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetic Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Li H, Ding L, Liao R, Li N, Hong X, Jiang Z, Liu D. Global genomic diversity and conservation of SARS-CoV-2 since the COVID-19 outbreak. Microbiol Spectr 2023; 11:e0282623. [PMID: 37909759 PMCID: PMC10714991 DOI: 10.1128/spectrum.02826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Our results indicate that most severe acute respiratory syndrome coronavirus 2 genomes sampled from patients had a mutation rate ≤1.07 ‰ and genome-tail proteins (including S protein) were the main sources of genetic polymorphism. The analysis of the virus-host interaction network of genome-tail proteins showed that they shared some antiviral signaling pathways, especially the intracellular protein transport pathway.
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Affiliation(s)
- Heng Li
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
- Department of Geriatrics, Geriatric Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Liping Ding
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Rui Liao
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Nini Li
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiaoping Hong
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
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Schoefbaenker M, Neddermeyer R, Guenther T, Mueller MM, Romberg ML, Classen N, Hennies MT, Hrincius ER, Ludwig S, Kuehn JE, Lorentzen EU. Surrogate Virus Neutralisation Test Based on Nanoluciferase-Tagged Antigens to Quantify Inhibitory Antibodies against SARS-CoV-2 and Characterise Omicron-Specific Reactivity in a Vaccination Cohort. Vaccines (Basel) 2023; 11:1832. [PMID: 38140236 PMCID: PMC10748151 DOI: 10.3390/vaccines11121832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Virus-specific antibodies are crucial for protective immunity against SARS-CoV-2. Assessing functional antibodies through conventional or pseudotyped virus neutralisation tests (pVNT) requires high biosafety levels. Alternatively, the virus-free surrogate virus neutralisation test (sVNT) quantifies antibodies interfering with spike binding to angiotensin-converting enzyme 2. We evaluated secreted nanoluciferase-tagged spike protein fragments as diagnostic antigens in the sVNT in a vaccination cohort. Initially, spike fragments were tested in a capture enzyme immunoassay (EIA), identifying the receptor binding domain (RBD) as the optimal diagnostic antigen. The sensitivity of the in-house sVNT applying the nanoluciferase-labelled RBD equalled or surpassed that of a commercial sVNT (cPass, GenScript Diagnostics) and an in-house pVNT four weeks after the first vaccination (98% vs. 94% and 72%, respectively), reaching 100% in all assays four weeks after the second and third vaccinations. When testing serum reactivity with Omicron BA.1 spike, the sVNT and pVNT displayed superior discrimination between wild-type- and variant-specific serum reactivity compared to a capture EIA. This was most pronounced after the first and second vaccinations, with the third vaccination resulting in robust, cross-reactive BA.1 construct detection. In conclusion, utilising nanoluciferase-labelled antigens permits the quantification of SARS-CoV-2-specific inhibitory antibodies. Designed as flexible modular systems, the assays can be readily adjusted for monitoring vaccine efficacy.
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Affiliation(s)
- Michael Schoefbaenker
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Rieke Neddermeyer
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Theresa Guenther
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marlin M. Mueller
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marie-Luise Romberg
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Nica Classen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
- Institute of Pharmaceutical Biology and Phytochemistry, University of Muenster, Corrensstr. 48, D-48149 Muenster, Germany
| | - Marc T. Hennies
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eike R. Hrincius
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Joachim E. Kuehn
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eva U. Lorentzen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
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Kistler KE, Bedford T. An atlas of continuous adaptive evolution in endemic human viruses. Cell Host Microbe 2023; 31:1898-1909.e3. [PMID: 37883977 DOI: 10.1016/j.chom.2023.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Through antigenic evolution, viruses such as seasonal influenza evade recognition by neutralizing antibodies. This means that a person with antibodies well tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. To expand our understanding of which endemic human viruses evolve in this fashion, we assess adaptive evolution across the genome of 28 endemic viruses spanning a wide range of viral families and transmission modes. Surface proteins consistently show the highest rates of adaptation, and ten viruses in this panel are estimated to undergo antigenic evolution to selectively fix mutations that enable the escape of prior immunity. Thus, antibody evasion is not an uncommon evolutionary strategy among human viruses, and monitoring this evolution will inform future vaccine efforts. Additionally, by comparing overall amino acid substitution rates, we show that SARS-CoV-2 is accumulating protein-coding changes at substantially faster rates than endemic viruses.
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Affiliation(s)
- Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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41
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Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023; 10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.
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Affiliation(s)
- Kim Le
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
- School of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
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Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023; 71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India.
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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023; 127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
Abstract
SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.
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Affiliation(s)
- Mariem Ghoula
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Audrey Deyawe Kongmeneck
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Rita Eid
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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45
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Guruprasad L, Naresh GKRS, Boggarapu G. Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic. Curr Res Struct Biol 2023; 6:100107. [PMID: 37841365 PMCID: PMC10569959 DOI: 10.1016/j.crstbi.2023.100107] [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: 09/10/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose lineages were either 'not classified' or were 'unclassifiable' indicated the virus could still be evolving.
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46
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Costacurta F, Dodaro A, Bante D, Schöppe H, Sprenger B, Moghadasi SA, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (M pro) inhibitor-resistant mutants selected in a VSV-based system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558628. [PMID: 37808638 PMCID: PMC10557589 DOI: 10.1101/2023.09.22.558628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Bernhard Sprenger
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Rainer Schneider
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and functions of infection-enhancing antibodies to the N-terminal domain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558444. [PMID: 37786672 PMCID: PMC10541592 DOI: 10.1101/2023.09.19.558444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Characterization of functional antibody responses to the N-terminal domain (NTD) of the SARS-CoV-2 spike (S) protein has included identification of both potent neutralizing activity and putative enhancement of infection. Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by NTD-binding monoclonal antibodies (mAbs) has been observed in vitro , but the functional significance of these antibodies in vivo is not clear. Here we studied 1,213 S-binding mAbs derived from longitudinal sampling of B-cells collected from eight COVID-19 convalescent patients and identified 72 (5.9%) mAbs that enhanced infection in a VSV-SARS-CoV-2-S-Wuhan pseudovirus (PV) assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least five months post-infection. Enhancement of PV infection by NTD-binding mAbs was not observed using intestinal (Caco-2) and respiratory (Calu-3) epithelial cells as infection targets and was diminished or lost against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire from two of the convalescent subjects identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum ( i.e ., functionally secreted antibody). Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Taken together, these findings suggest functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display diverse attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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Curtis NC, Shin S, Hederman AP, Connor RI, Wieland-Alter WF, Ionov S, Boylston J, Rose J, Sakharkar M, Dorman DB, Dessaint JA, Gwilt LL, Crowley AR, Feldman J, Hauser BM, Schmidt AG, Ashare A, Walker LM, Wright PF, Ackerman ME, Lee J. Characterization of SARS-CoV-2 Convalescent Patients' Serological Repertoire Reveals High Prevalence of Iso-RBD Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556349. [PMID: 37745524 PMCID: PMC10515772 DOI: 10.1101/2023.09.08.556349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
While our understanding of SARS-CoV-2 pathogenesis and antibody responses following infection and vaccination has improved tremendously since the outbreak in 2019, the sequence identities and relative abundances of the individual constituent antibody molecules in circulation remain understudied. Using Ig-Seq, we proteomically profiled the serological repertoire specific to the whole ectodomain of SARS-CoV-2 prefusion-stabilized spike (S) as well as to the receptor binding domain (RBD) over a 6-month period in four subjects following SARS-CoV-2 infection before SARS-CoV-2 vaccines were available. In each individual, we identified between 59 and 167 unique IgG clonotypes in serum. To our surprise, we discovered that ∼50% of serum IgG specific for RBD did not recognize prefusion-stabilized S (referred to as iso-RBD antibodies), suggesting that a significant fraction of serum IgG targets epitopes on RBD inaccessible on the prefusion-stabilized conformation of S. On the other hand, the abundance of iso-RBD antibodies in nine individuals who received mRNA-based COVID-19 vaccines encoding prefusion-stabilized S was significantly lower (∼8%). We expressed a panel of 12 monoclonal antibodies (mAbs) that were abundantly present in serum from two SARS-CoV-2 infected individuals, and their binding specificities to prefusion-stabilized S and RBD were all in agreement with the binding specificities assigned based on the proteomics data, including 1 iso-RBD mAb which bound to RBD but not to prefusion-stabilized S. 2 of 12 mAbs demonstrated neutralizing activity, while other mAbs were non-neutralizing. 11 of 12 mAbs also bound to S (B.1.351), but only 1 maintained binding to S (B.1.1.529). This particular mAb binding to S (B.1.1.529) 1) represented an antibody lineage that comprised 43% of the individual's total S-reactive serum IgG binding titer 6 months post-infection, 2) bound to the S from a related human coronavirus, HKU1, and 3) had a high somatic hypermutation level (10.9%), suggesting that this antibody lineage likely had been elicited previously by pre-pandemic coronavirus and was re-activated following the SARS-CoV-2 infection. All 12 mAbs demonstrated their ability to engage in Fc-mediated effector function activities. Collectively, our study provides a quantitative overview of the serological repertoire following SARS-CoV-2 infection and the significant contribution of iso-RBD antibodies, demonstrating how vaccination strategies involving prefusion-stabilized S may have reduced the elicitation of iso-RBD serum antibodies which are unlikely to contribute to protection.
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50
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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