1
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Guselnikov SV, Baranov KO, Kulemzin SV, Belovezhets TN, Chikaev AN, Murasheva SV, Volkova OY, Mechetina LV, Najakshin AM, Chikaev NA, Solodkov PP, Sergeeva MV, Smirnov AV, Serova IA, Serov OL, Markhaev AG, Kononova YV, Alekseev AY, Gulyaeva MA, Danilenko DM, Battulin NR, Shestopalov AM, Taranin AV. A potent, broadly neutralizing human monoclonal antibody that efficiently protects hACE2-transgenic mice from infection with the Wuhan, BA.5, and XBB.1.5 SARS-CoV-2 variants. Front Immunol 2024; 15:1442160. [PMID: 39100673 PMCID: PMC11294225 DOI: 10.3389/fimmu.2024.1442160] [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: 06/01/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
The COVID-19 pandemic has uncovered the high genetic variability of the SARS-CoV-2 virus and its ability to evade the immune responses that were induced by earlier viral variants. Only a few monoclonal antibodies that have been reported to date are capable of neutralizing a broad spectrum of SARS-CoV-2 variants. Here, we report the isolation of a new broadly neutralizing human monoclonal antibody, iC1. The antibody was identified through sorting the SARS-CoV-1 RBD-stained individual B cells that were isolated from the blood of a vaccinated donor following a breakthrough infection. In vitro, iC1 potently neutralizes pseudoviruses expressing a wide range of SARS-CoV-2 Spike variants, including those of the XBB sublineage. In an hACE2-transgenic mouse model, iC1 provided effective protection against the Wuhan strain of the virus as well as the BA.5 and XBB.1.5 variants. Therefore, iC1 can be considered as a potential component of the broadly neutralizing antibody cocktails resisting the SARS-CoV-2 mutation escape.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- Humans
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- Mice, Transgenic
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Mice
- Antibodies, Viral/immunology
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Pandemics/prevention & control
- Betacoronavirus/immunology
- Betacoronavirus/genetics
- Broadly Neutralizing Antibodies/immunology
- Disease Models, Animal
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- Pneumonia, Viral/prevention & control
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus Infections/prevention & control
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Affiliation(s)
- Sergey V. Guselnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Konstantin O. Baranov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey V. Kulemzin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana N. Belovezhets
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anton N. Chikaev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana V. Murasheva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Y. Volkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ludmila V. Mechetina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander M. Najakshin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai A. Chikaev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel P. Solodkov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maria V. Sergeeva
- Department of Vaccinology, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Alexander V. Smirnov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina A. Serova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg L. Serov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander G. Markhaev
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Yulia V. Kononova
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Alexander Y. Alekseev
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Marina A. Gulyaeva
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Daria M. Danilenko
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Nariman R. Battulin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander M. Shestopalov
- Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander V. Taranin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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2
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Wang J, Shi B, Chen H, Yu M, Wang P, Qian Z, Hu K, Wang J. Engineered Multivalent Nanobodies Efficiently Neutralize SARS-CoV-2 Omicron Subvariants BA.1, BA.4/5, XBB.1 and BQ.1.1. Vaccines (Basel) 2024; 12:417. [PMID: 38675799 PMCID: PMC11054741 DOI: 10.3390/vaccines12040417] [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: 03/07/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Most available neutralizing antibodies are ineffective against highly mutated SARS-CoV-2 Omicron subvariants. Therefore, it is crucial to develop potent and broad-spectrum alternatives to effectively manage Omicron subvariants. Here, we constructed a high-diversity nanobody phage display library and identified nine nanobodies specific to the SARS-CoV-2 receptor-binding domain (RBD). Five of them exhibited cross-neutralization activity against the SARS-CoV-2 wild-type (WT) strain and the Omicron subvariants BA.1 and BA.4/5, and one nanobody demonstrated marked efficacy even against the Omicron subvariants BQ.1.1 and XBB.1. To enhance the therapeutic potential, we engineered a panel of multivalent nanobodies with increased neutralizing potency and breadth. The most potent multivalent nanobody, B13-B13-B13, cross-neutralized all tested pseudoviruses, with a geometric mean of the 50% inhibitory concentration (GM IC50) value of 20.83 ng/mL. An analysis of the mechanism underlying the enhancement of neutralization breadth by representative multivalent nanobodies demonstrated that the strategic engineering approach of combining two or three nanobodies into a multivalent molecule could improve the affinity between a single nanobody and spike, and could enhance tolerance toward escape mutations such as R346T and N460K. Our engineered multivalent nanobodies may be promising drug candidates for treating and preventing infection with Omicron subvariants and even future variants.
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Affiliation(s)
- Jiali Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Bingjie Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hanyi Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mengyuan Yu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Peipei Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Keping Hu
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Andes Antibody Technology Hengshui LL Company, Hengshui 053000, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen 518118, China
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3
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Arantes I, Gomes M, Ito K, Sarafim S, Gräf T, Miyajima F, Khouri R, de Carvalho FC, de Almeida WAF, Siqueira MM, Resende PC, Naveca FG, Bello G. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiol Spectr 2024; 12:e0383123. [PMID: 38315011 PMCID: PMC10913747 DOI: 10.1128/spectrum.03831-23] [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: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. IMPORTANCE Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
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Affiliation(s)
- Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Sharbilla Sarafim
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | | | | | - Felipe Cotrim de Carvalho
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Walquiria Aparecida Ferreira de Almeida
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - COVID-19 Fiocruz Genomic Surveillance Network
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
- Fiocruz, Fortaleza, Brazil
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
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4
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Solodkov PP, Najakshin AM, Chikaev NA, Kulemzin SV, Mechetina LV, Baranov KO, Guselnikov SV, Gorchakov AA, Belovezhets TN, Chikaev AN, Volkova OY, Markhaev AG, Kononova YV, Alekseev AY, Gulyaeva MA, Shestopalov AM, Taranin AV. Serial Llama Immunization with Various SARS-CoV-2 RBD Variants Induces Broad Spectrum Virus-Neutralizing Nanobodies. Vaccines (Basel) 2024; 12:129. [PMID: 38400113 PMCID: PMC10891761 DOI: 10.3390/vaccines12020129] [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: 12/03/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The emergence of SARS-CoV-2 mutant variants has posed a significant challenge to both the prevention and treatment of COVID-19 with anti-coronaviral neutralizing antibodies. The latest viral variants demonstrate pronounced resistance to the vast majority of human monoclonal antibodies raised against the ancestral Wuhan variant. Less is known about the susceptibility of the evolved virus to camelid nanobodies developed at the start of the pandemic. In this study, we compared nanobody repertoires raised in the same llama after immunization with Wuhan's RBD variant and after subsequent serial immunization with a variety of RBD variants, including that of SARS-CoV-1. We show that initial immunization induced highly potent nanobodies, which efficiently protected Syrian hamsters from infection with the ancestral Wuhan virus. These nanobodies, however, mostly lacked the activity against SARS-CoV-2 omicron-pseudotyped viruses. In contrast, serial immunization with different RBD variants resulted in the generation of nanobodies demonstrating a higher degree of somatic mutagenesis and a broad range of neutralization. Four nanobodies recognizing distinct epitopes were shown to potently neutralize a spectrum of omicron variants, including those of the XBB sublineage. Our data show that nanobodies broadly neutralizing SARS-CoV-2 variants may be readily induced by a serial variant RBD immunization.
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Affiliation(s)
- Pavel P. Solodkov
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Alexander M. Najakshin
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Nikolai A. Chikaev
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Sergey V. Kulemzin
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Ludmila V. Mechetina
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Konstantin O. Baranov
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Sergey V. Guselnikov
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Andrey A. Gorchakov
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Tatyana N. Belovezhets
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Anton N. Chikaev
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Olga Y. Volkova
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
| | - Alexander G. Markhaev
- Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (A.G.M.); (Y.V.K.); (A.Y.A.); (M.A.G.); (A.M.S.)
| | - Yulia V. Kononova
- Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (A.G.M.); (Y.V.K.); (A.Y.A.); (M.A.G.); (A.M.S.)
| | - Alexander Y. Alekseev
- Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (A.G.M.); (Y.V.K.); (A.Y.A.); (M.A.G.); (A.M.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina A. Gulyaeva
- Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (A.G.M.); (Y.V.K.); (A.Y.A.); (M.A.G.); (A.M.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander M. Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (A.G.M.); (Y.V.K.); (A.Y.A.); (M.A.G.); (A.M.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander V. Taranin
- Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.P.S.); (A.M.N.); (N.A.C.); (L.V.M.); (K.O.B.); (S.V.G.); (T.N.B.); (A.N.C.); (O.Y.V.)
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5
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Kulemzin SV, Guselnikov SV, Nekrasov BG, Molodykh SV, Kuvshinova IN, Murasheva SV, Belovezhets TN, Gorchakov AA, Chikaev AN, Chikaev NA, Volkova OY, Yurina AA, Najakshin AM, Taranin AV. Hybrid Immunity from Gam-COVID-Vac Vaccination and Natural SARS-CoV-2 Infection Confers Broader Neutralizing Activity against Omicron Lineage VOCs Than Revaccination or Reinfection. Vaccines (Basel) 2024; 12:55. [PMID: 38250868 PMCID: PMC10818410 DOI: 10.3390/vaccines12010055] [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: 11/02/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
SARS-CoV-2 has a relatively high mutation rate, with the frequent emergence of new variants of concern (VOCs). Each subsequent variant is more difficult to neutralize by the sera of vaccinated individuals and convalescents. Some decrease in neutralizing activity against new SARS-CoV-2 variants has also been observed in patients vaccinated with Gam-COVID-Vac. In the present study, we analyzed the interplay between the history of a patient's repeated exposure to SARS-CoV-2 antigens and the breadth of neutralization activity. Our study includes four cohorts of patients: Gam-COVID-Vac booster vaccinated individuals (revaccinated, RV), twice-infected unvaccinated individuals (reinfected, RI), breakthrough infected (BI), and vaccinated convalescents (VC). We assessed S-protein-specific antibody levels and the ability of sera to neutralize lentiviral particles pseudotyped with Spike protein from the original Wuhan variant, as well as the Omicron variants BA.1 and BA.4/5. Individuals with hybrid immunity (BI and VC cohorts) exhibited significantly higher levels of virus-binding IgG and enhanced breadth of virus-neutralizing activity compared to individuals from either the revaccination or reinfection (RV and RI) cohorts. These findings suggest that a combination of infection and vaccination, regardless of the sequence, results in significantly higher levels of S-protein-specific IgG antibodies and the enhanced neutralization of SARS-CoV-2 variants, thereby underscoring the importance of hybrid immunity in the context of emerging viral variants.
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Affiliation(s)
- Sergey V. Kulemzin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Sergey V. Guselnikov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | | | | | | | - Svetlana V. Murasheva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Tatyana N. Belovezhets
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Andrey A. Gorchakov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Anton N. Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Nikolai A. Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Olga Y. Volkova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Anna A. Yurina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Alexander M. Najakshin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Alexander V. Taranin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
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6
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Li L, Chen X, Wang Z, Li Y, Wang C, Jiang L, Zuo T. Breakthrough infection elicits hypermutated IGHV3-53/3-66 public antibodies with broad and potent neutralizing activity against SARS-CoV-2 variants including the emerging EG.5 lineages. PLoS Pathog 2023; 19:e1011856. [PMID: 38048356 PMCID: PMC10721163 DOI: 10.1371/journal.ppat.1011856] [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: 08/14/2023] [Revised: 12/14/2023] [Accepted: 11/25/2023] [Indexed: 12/06/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants of concern (VOCs) calls for efforts to study broadly neutralizing antibodies elicited by infection or vaccination so as to inform the development of vaccines and antibody therapeutics with broad protection. Here, we identified two convalescents of breakthrough infection with relatively high neutralizing titers against all tested viruses. Among 50 spike-specific monoclonal antibodies (mAbs) cloned from their B cells, the top 6 neutralizing mAbs (KXD01-06) belong to previously defined IGHV3-53/3-66 public antibodies. Although most antibodies in this class are dramatically escaped by VOCs, KXD01-06 all exhibit broad neutralizing capacity, particularly KXD01-03, which neutralize SARS-CoV-2 from prototype to the emerging EG.5.1 and FL.1.5.1. Deep mutational scanning reveals that KXD01-06 can be escaped by current and prospective variants with mutations on D420, Y421, L455, F456, N460, A475 and N487. Genetic and functional analysis further indicates that the extent of somatic hypermutation is critical for the breadth of KXD01-06 and other IGHV3-53/3-66 public antibodies. Overall, the prevalence of broadly neutralizing IGHV3-53/3-66 public antibodies in these two convalescents provides rationale for novel vaccines based on this class of antibodies. Meanwhile, KXD01-06 can be developed as candidates of therapeutics against SARS-CoV-2 through further affinity maturation.
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Affiliation(s)
- Ling Li
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Xixian Chen
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
- University of Science and Technology of China, Hefei, People’s Republic of China
| | - Zuowei Wang
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Yunjian Li
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Chen Wang
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Liwei Jiang
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Teng Zuo
- Laboratory of Immunoengineering, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, People’s Republic of China
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Nagasawa N, Kimura R, Akagawa M, Shirai T, Sada M, Okayama K, Sato-Fujimoto Y, Saito M, Kondo M, Katayama K, Ryo A, Kuroda M, Kimura H. Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants. Microorganisms 2023; 11:2336. [PMID: 37764181 PMCID: PMC10537508 DOI: 10.3390/microorganisms11092336] [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: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.
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Affiliation(s)
- Norika Nagasawa
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Ryusuke Kimura
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi-shi 371-8514, Gunma, Japan
| | - Mao Akagawa
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo-ku, Tokyo 113-8431, Japan;
| | - Tatsuya Shirai
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyourin University School of Medicine, 6-20-2, Shinkawa, Mitaka-shi 181-8611, Tokyo, Japan;
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
| | - Yuka Sato-Fujimoto
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Makoto Saito
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Mayumi Kondo
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku, Tokyo 108-8641, Japan;
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama-shi 208-0011, Tokyo, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan;
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
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