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Machado RRG, Candido ÉD, Aguiar AS, Chalup VN, Sanches PR, Dorlass EG, Amgarten DE, Pinho JRR, Durigon EL, Oliveira DBL. Immune Evasion of SARS-CoV-2 Omicron Subvariants XBB.1.5, XBB.1.16 and EG.5.1 in a Cohort of Older Adults after ChAdOx1-S Vaccination and BA.4/5 Bivalent Booster. Vaccines (Basel) 2024; 12:144. [PMID: 38400128 PMCID: PMC10892985 DOI: 10.3390/vaccines12020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The recently emerged SARS-CoV-2 Omicron sublineages, including the BA.2-derived XBB.1.5 (Kraken), XBB.1.16 (Arcturus), and EG.5.1 (Eris), have accumulated several spike mutations that may increase immune escape, affecting vaccine effectiveness. Older adults are an understudied group at significantly increased risk of severe COVID-19. Here we report the neutralizing activities of 177 sera samples from 59 older adults, aged 62-97 years, 1 and 4 months after vaccination with a 4th dose of ChAdOx1-S (Oxford/AstraZeneca) and 3 months after a 5th dose of Comirnaty Bivalent Original/Omicron BA.4/BA.5 vaccine (Pfizer-BioNTech). The ChAdOx1-S vaccination-induced antibodies neutralized efficiently the ancestral D614G and BA.4/5 variants, but to a much lesser extent the XBB.1.5, XBB.1.16, and EG.5.1 variants. The results showed similar neutralization titers between XBB.1.16 and EG.5.1 and were lower compared to XBB.1.5. Sera from the same individuals boosted with the bivalent mRNA vaccine contained higher neutralizing antibody titers, providing a better cross-protection against Omicron XBB.1.5, XBB.1.16 and EG.5.1 variants. Previous history of infection during the epidemiological waves of BA.1/BA.2 and BA.4/BA.5, poorly enhanced neutralization activity of serum samples against XBBs and EG.5.1 variants. Our data highlight the continued immune evasion of recent Omicron subvariants and support the booster administration of BA.4/5 bivalent vaccine, as a continuous strategy of updating future vaccine booster doses to match newly emerged SARS-CoV-2 variants.
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Affiliation(s)
- Rafael Rahal Guaragna Machado
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Érika Donizetti Candido
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Andressa Simoes Aguiar
- Dom Pedro II Geriatric and Convalescent Hospital, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo 02265-002, SP, Brazil
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Vanessa Nascimento Chalup
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Patricia Romão Sanches
- Dom Pedro II Geriatric and Convalescent Hospital, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo 02265-002, SP, Brazil
| | - Erick Gustavo Dorlass
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
| | | | - João Renato Rebello Pinho
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
- Laboratório de Medicina Laboratorial (LIM03), Department of Pathology, School of Medicine, University of São Paulo, São Paulo 01246-903, SP, Brazil
- Laboratório de Gastroenterologia Clínica e Experimental (LIM07), Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo 01246-903, SP, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
- Scientific Platform Pasteur-USP, São Paulo 05508-020, SP, Brazil
| | - Danielle Bruna Leal Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
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2
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Guo L, Zhang Q, Zhong J, Chen L, Jiang W, Huang T, Li Y, Zhang Y, Xu L, Wang X, Xiao Y, Wang Y, Dong X, Dong T, Peng Y, Zhang B, Xie Y, Gao H, Shen Z, Ren L, Cheng T, Wang J. Omicron BA.1 breakthrough infections in inactivated COVID-19 vaccine recipients induced distinct pattern of antibody and T cell responses to different Omicron sublineages. Emerg Microbes Infect 2023; 12:2202263. [PMID: 37037791 PMCID: PMC10155635 DOI: 10.1080/22221751.2023.2202263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
The adaptive immunity against SARS-CoV-2 prototype strain and Omicron sublineages induced by BA.1 breakthrough infection in vaccinees of inactivated COVID-19 vaccines have not been well characterized. Here, we report that BA.1 breakthrough infection induced mucosal sIgA and resulted in higher IgG titers against prototype strain and Omicron sublineages in vaccinees than in vaccine naïve-infected individuals. BA.1 breakthrough infection boosted antibody-dependent cellular cytotoxicity and antibody-dependent cellular phagocytosis to prototype strain and BA.1, BA.1.1, BA.2, BA.2.12.1, and BA.2.75 but not BA.4/5 and induced neutralization against prototype strain and BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5 but not BF.7, BQ.1, and XBB. In total, BA.1 breakthrough infection individuals produced less extensive sIgA, plasma IgG and NAb responses against Omicron sublineages compared with those against prototype strain. Further, BA.1 breakthrough infection induced recall B cell response to prototype strain and Omicron variant, primarily targeting memory B cells producing conserved epitopes. Memory T cell responses against Omicron is largely preserved. Individuals with vaccine booster did not induce more beneficial immune responses to Omicron sublineages upon BA.1 breakthrough infection than those with primary vaccine dose only. The breakthrough infection individuals produced stronger adaptive immunity than those of inactivated vaccine-healthy individuals. These data have important implications for understanding the vaccine effectiveness and adaptive immunity to breakthrough infection in individuals fully immunized with inactivated vaccines. Omicron sublineages, especially for those emerged after BA.4/5 strain, evade NAb responses induced by BA.1 breakthrough infection. It is urgent to optimize the vaccine immunogen design and formulations to SARS-CoV-2 variants.
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Affiliation(s)
- Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Haihe Laboratory of Cell Ecosystem, Tianjin, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Qiao Zhang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Jingchuan Zhong
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Wentao Jiang
- Organ Transplant Center, Tianjin First Center Hospital, Tianjin, People’s Republic of China
- Laboratory of Molecular and Treatment of Liver Cancer, Tianjin First Center Hospital, Tianjin, People’s Republic of China
- Research Institute of Transplant Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Tingxuan Huang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Yanan Li
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Yin Zhang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Liuhui Xu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaojing Dong
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford, United Kingdom
- MRC Human Immunology Unit, MRC Weatherall Institute of Medicine, Oxford University, Oxford, United Kingdom
| | - Yanchun Peng
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford, United Kingdom
- MRC Human Immunology Unit, MRC Weatherall Institute of Medicine, Oxford University, Oxford, United Kingdom
| | - Biao Zhang
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, People’s Republic of China
| | - Yan Xie
- Organ Transplant Center, Tianjin First Center Hospital, Tianjin, People’s Republic of China
- Laboratory of Molecular and Treatment of Liver Cancer, Tianjin First Center Hospital, Tianjin, People’s Republic of China
- Research Institute of Transplant Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Hongmei Gao
- Intensive Care Unit, Emergency Medical Research Institute, Tianjin First Center Hospital, Tianjin, People’s Republic of China
| | - Zhongyang Shen
- Organ Transplant Center, Tianjin First Center Hospital, Tianjin, People’s Republic of China
- Research Institute of Transplant Medicine, Nankai University, Tianjin, People’s Republic of China
- NHC Key Laboratory for Critical Care Medicine, Tianjin First Center Hospital, Tianjin, People’s Republic of China
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Tao Cheng
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, People’s Republic of China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
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Trombetta CM, Marchi S, Leonardi M, Coppola C, Benincasa L, Marotta MG, Buonvino N, Maes P, Stufano A, Pontrelli D, Vasinioti VI, Manenti A, Camero M, Montomoli E, Decaro N, Lovreglio P. Evaluation of immune response to SARS-CoV-2 Omicron sublineages six months after different vaccination regimens in Italy. Acta Trop 2023; 248:107042. [PMID: 37863379 DOI: 10.1016/j.actatropica.2023.107042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The Omicron variant is the most divergent, displaying more mutations than previous SARS-CoV-2 variants, particularly in the gene that encodes the spike protein. This study aimed to assess the persistence of neutralizing antibodies towards the SARS-CoV-2 Omicron sublineages (BA.2, BA.5, BQ.1, XBB and XBB1.5) six months after the third dose in different vaccination regimens. Subjects who received 3 doses of mRNA vaccine retained their neutralization activity against BA.2 and BA.5, even though 56.3% and 66.7% showed a ≥ 2-fold reduction in the neutralizing antibody titre, respectively. Subjects who had received the adenovirus-based vaccine plus a booster dose of mRNA vaccine retained their neutralization activity especially against BA.2. With regard to BQ.1, XBB and XBB.1.5, the majority of the subjects showed a ≥ 2-fold reduction in neutralizing antibody titre, with the greatest evasion being observed in the case of XBB. Overall, our results provide further evidence that triple homologous/heterologous vaccination and hybrid immunity result in detectable neutralizing antibodies against the ancestral virus; however, emerging Omicron sublineages, such as XBB and XBB.1.5, show a great evasive capacity, which compromises the effectiveness of current COVID-19 vaccines.
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Affiliation(s)
- Claudia Maria Trombetta
- Department of Molecular and Developmental Medicine, University of Siena, via Aldo Moro 2, Siena 53100, Italy.
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | | | - Chiara Coppola
- Department of Molecular and Developmental Medicine, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | | | - Maria Giovanna Marotta
- Department of Molecular and Developmental Medicine, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | | | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, via Aldo Moro 2, Siena 53100, Italy; VisMederi Research Srl, Siena, Italy; VisMederi Srl, Siena, Italy
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4
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Shen F, Yang CX, Lu Y, Zhang M, Tian RR, Dong XQ, Li AQ, Zheng YT, Pang W. Significant neutralizing escapes of Omicron and its sublineages in SARS-CoV-2-infected individuals vaccinated with inactivated vaccines. J Med Virol 2023; 95:e28516. [PMID: 36680413 DOI: 10.1002/jmv.28516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/13/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
In China, most SARS-CoV-2-infected individuals had been vaccinated with inactivated vaccines. However, little is known about their immune resistances to the previous variants of concerns (VOCs) and the current Omicron sublineages. Here, we collected convalescent serum samples from SARS-CoV-2-infected individuals during the ancestral, Delta, and Omicron BA.1 waves, and evaluated their cross-neutralizing antibodies (nAbs) against the previous VOCs and the current Omicron sublineages using VSV-based pseudoviruses. In the convalescents who had been unvaccinated and vaccinated with two doses of inactivated vaccines, we found infections from either the ancestral or the Delta strain elicited moderate cross-nAbs to previous VOCs, but very few cross-nAbs to the Omicron sublineages, including BA.1, BA.2, BA.3, and BA.4/5. The individuals who had been vaccinated with two doses of inactivated vaccines before Omicron BA.1 infection had moderate nAbs to Omicron BA.1, but weak cross-nAbs to the other Omicron sublineages. While three doses of inactivated vaccines followed Omicron BA.1 infection induced elevated and still weak cross-nAbs to other Omicron sublineages. Our results indicate that the Omicron sublineages show significant immune escape in the previously SARS-CoV-2-infected individuals and thus highlights the importance of vaccine boosters in this population.
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Affiliation(s)
- Fan Shen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cui-Xian Yang
- Yunnan Provincial Infectious Disease Hospital, Kunming, China
| | - Ying Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mi Zhang
- Yunnan Provincial Infectious Disease Hospital, Kunming, China
| | - Ren-Rong Tian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xing-Qi Dong
- Yunnan Provincial Infectious Disease Hospital, Kunming, China
| | - An-Qi Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
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5
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Miyakawa K, Kato H, Ohtake N, Jeremiah SS, Ryo A. Enhancement of Humoral and Cellular Immunity Against Severe Acute Respiratory Syndrome Coronavirus 2 by a Third Dose of BNT162b2 Vaccine in Japanese Healthcare Workers. J Infect Dis 2023; 227:221-225. [PMID: 35978486 DOI: 10.1093/infdis/jiac344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 01/14/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns regarding vaccine effectiveness. We investigated humoral and cellular immune responses against SARS-CoV-2 in healthcare workers before and after a third (booster) dose of the BNT162b2 messenger RNA vaccine. It significantly enhanced both humoral and cellular immunity in previously uninfected individuals. However, cellular immunity was not enhanced in previously infected persons, suggesting that 3 antigenic stimuli by vaccination or natural infection reached a plateau of cellular immunity. Even with reinforced immunity to SARS-CoV-2, we confirmed several postbooster breakthrough cases caused by the Omicron variant.
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Affiliation(s)
- Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Kanagawa, Japan
| | - Norihisa Ohtake
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan.,Bioscience Division, Research and Development Department, Tosoh Corporation, Tokyo Research Center, Kanagawa, Japan
| | | | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan
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6
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Zhu Y, Hu Y, Liu N, Chong H, He Y. Potent inhibition of diverse Omicron sublineages by SARS-CoV-2 fusion-inhibitory lipopeptides. Antiviral Res 2022; 208:105445. [PMID: 36265805 PMCID: PMC9574594 DOI: 10.1016/j.antiviral.2022.105445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
The emergence and rapid spreading of SARS-CoV-2 variants of concern (VOCs) have posed a great challenge to the efficacy of vaccines and therapeutic antibodies, calling for antivirals that can overcome viral evasion. We recently reported that SARS-CoV-2 fusion-inhibitory lipopeptides, IPB02V3 and IPB24, possessed the potent activities against divergent VOCs, including Alpha, Beta, Gamma, Delta, and the initial Omicron strain (B.1.1.529); however, multiple Omicron sublineages have emerged and BA.4/5 is now becoming predominant globally. In this study, we focused on characterizing the functionality of the spike (S) proteins derived from Omicron sublineages and their susceptibility to the inhibition of IPB02V3 and IPB24. We first found that the S proteins of BA.2, BA.2.12.1, BA.3, and BA.4/5 exhibited significantly increased cell fusion capacities compared to BA.1, whereas the pseudoviruses of BA.2.12.1, BA.3, and BA.4/5 had significantly increased infectivity relative to BA.1 or BA.2. Next, we verified that IPB02V3 and IPB24 also maintained their very high potent activities in inhibiting diverse Omicron sublineages, even with enhanced potencies relative to the inhibition on ancestral virus. Moreover, we demonstrated that evolved Omicron mutations in the inhibitor-binding heptad repeat 1 (HR1) site could impair the S protein-driven cell fusogenicity and infectivity, but none of single or combined mutations affected the antiviral activity of IPB02V3 and IPB24. Therefore, we believe that viral fusion inhibitors possess high potential to be developed as effective drugs for fighting SARS-CoV-2 variants including diverse Omicron sublineages.
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Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yue Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Nian Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huihui Chong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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7
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Spratt AN, Kannan SR, Sharma K, Sachdev S, Kandasamy SL, Sönnerborg A, Lorson CL, Singh K. Continued Complexity of Mutations in Omicron Sublineages. Biomedicines 2022; 10:biomedicines10102593. [PMID: 36289855 PMCID: PMC9599772 DOI: 10.3390/biomedicines10102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The latest SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529), has diversified into more than 300 sublineages. With an expanding number of newly emerging sublineages, the mutation profile is also becoming complicated. There exist mutually exclusive and revertant mutations in different sublineages. Omicron sublineages share some common mutations with previous VOCs (Alpha, Beta, Gamma, and Delta), indicating an evolutionary relationship between these VOCs. A diverse mutation profile at the spike–antibody interface, flexibility of the regions harboring mutations, mutation types, and coexisting mutations suggest that SARS-CoV-2’s evolution is far from over.
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Affiliation(s)
- Austin N. Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Saathvik R. Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Kalicharan Sharma
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Shree L. Kandasamy
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Anders Sönnerborg
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, 17177 Stockholm, Sweden
- Correspondence: or
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Luna N, Muñoz M, Ramírez AL, Patiño LH, Castañeda SA, Ballesteros N, Ramírez JD. Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries. Viruses 2022; 14:v14061234. [PMID: 35746705 PMCID: PMC9230695 DOI: 10.3390/v14061234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/21/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage's genomic and epidemiological characteristics. However, in South America, this variant's arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.
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Affiliation(s)
- Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Angie L. Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Luz H. Patiño
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Sergio Andres Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or
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Li Q, Zhang M, Liang Z, Zhang L, Wu X, Yang C, An Y, Tong J, Liu S, Li T, Cui Q, Nie J, Wu J, Huang W, Wang Y. Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. MedComm (Beijing) 2022; 3:e130. [PMID: 35434713 PMCID: PMC8994617 DOI: 10.1002/mco2.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, particularly those with multiple mutations in receptor-binding domain (RBD), pose a critical challenge to the efficacy of coronavirus disease 2019 (COVID-19) vaccines and therapeutic neutralizing monoclonal antibodies (mAbs). Omicron sublineages BA.1, BA.2, BA.3, as well as the recent emergence of C.1.2, B.1.630, B.1.640.1, and B.1.640.2, have multiple mutations in RBD and may lead to severe neutralizing antibody evasion. It is urgent to evaluate the antigenic change of the above seven variants against mAbs and sera from guinea pigs immunized with variants of concern (VOCs) (Alpha, Beta, Gamma, Delta, Omicron) and variants of interest (VOIs) (Lambda, Mu) immunogens. Only seven out of the 24 mAbs showed no reduction in neutralizing activity against BA.1, BA.2, and BA.3. However, among these seven mAbs, the neutralization activity of XGv337 and XGv338 against C.1.2, B.1.630, B.1.640.1, and B.1.640.2 were decreased. Therefore, only five neutralizing mAbs showed no significant change against these seven variants. Using VOCs and VOIs as immunogens, we found that the antigenicity of variants could be divided into three clusters, and each cluster showed similar antigenicity to different immunogens. Among them, D614G, B.1.640.1, and B.1.630 formed a cluster, C.1.2 and B.1.640.2 formed a cluster, and BA.1, BA.2, and BA.3 formed a cluster.
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Affiliation(s)
- Qianqian Li
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
- Jiangsu Recbio Technology Co., Ltd.TaizhouChina
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Ziteng Liang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
- Graduate School of Peking Union Medical CollegeBeijingChina
| | - Li Zhang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Xi Wu
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Chaoying Yang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Yimeng An
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Jincheng Tong
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Shuo Liu
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Tao Li
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Qianqian Cui
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Jianhui Nie
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Jiajing Wu
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Weijin Huang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
| | - Youchun Wang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlWHO Collaborating Center for Standardization and Evaluation of BiologicalsNHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological ProductsNational Institutes for Food and Drug Control (NIFDC)BeijingChina
- Graduate School of Peking Union Medical CollegeBeijingChina
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