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Piccoli BC, Y Castro TR, Tessele LF, Casarin BC, Seerig AP, Vieira ADA, Santos VT, Schwarzbold AV, Trindade PA. Genomic surveillance and vaccine response to the dominant SARS-CoV-2 XBB lineage in Rio Grande do Sul. Sci Rep 2024; 14:16831. [PMID: 39039137 PMCID: PMC11263389 DOI: 10.1038/s41598-024-67828-7] [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: 02/01/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
The COVID-19 pandemic has been marked by novel viral variants, posing challenges to global public health. Recombination, a viral evolution mechanism, is implicated in SARS-CoV-2's ongoing evolution. The XBB recombinant lineage, known for evading antibody-mediated immunity, exhibits higher transmissibility without increased disease severity. We investigated the prevalence and genomic features of XBB in SARS-CoV-2-positive cases in Rio Grande do Sul (RS), Brazil. We sequenced 357 samples from epidemiological weeks (EW) 47/2022 to 17/2023, and included 389 publicly available sequences. Clinical and epidemiological data were obtained from DATASUS, e-SUS, and SIVEP GRIPE (data recording systems of the Brazilian Ministry of Health). Of these, 143 were classified as XBB and 586 were other Omicron lineages. In March 2023 (EW 10), XBB became dominant, accounting for 83.3% of cases. 97.7% of XBB-infected patients successfully recovered from the infection, with a low mortality rate (2.3%). Even after receiving three vaccine doses and having been previously infected, 59.5% of the patients experienced reinfection with XBB. However, for 54% of the individuals, the interval between their XBB infection and the last vaccine dose exceeded one year, potentially leading to a decline in antibody levels. In addition, we identified 90 mutations in RS circulating XBB, spread throughout the genome, notably in the Spike protein region associated with immune resistance. This study provides insights into the dynamics and impact of a recombinant variant becoming predominant for the first time in the state. Continued surveillance of SARS-CoV-2 genomic evolution is crucial for effective public health management.
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Affiliation(s)
- Bruna Candia Piccoli
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Thais Regina Y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Luíza Funck Tessele
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Bruna Campestrini Casarin
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Ana Paula Seerig
- Vigilância em SaúdeSecretaria Municipal da Saúde de Santa Maria, Rio Grande do Sul, Brazil
| | - Andressa de Almeida Vieira
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Vitor Teles Santos
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | | | - Priscila Arruda Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica (LABIOMIC), Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
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Mak WA, Visser W, Koeleman JGM, Ong DSY. SARS-CoV-2-specific T cell responses: a comparative analysis between QuantiFERON SARS-CoV-2, T-SPOT.COVID, and an in-house Omicron ELISpot. J Virol Methods 2024; 327:114949. [PMID: 38710307 DOI: 10.1016/j.jviromet.2024.114949] [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: 11/07/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND T cell immunity plays a pivotal role in mitigating the severity of coronavirus disease 2019 (COVID-19). Therefore, reliable functional T cell assays are required to evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell immunity in specific patient populations. METHODS We recruited a cohort of 23 healthcare workers who received their bivalent Omicron BA.1 / ancestral mRNA booster vaccination or were infected with the Omicron variant at a median of 144 days and 227 days before blood collection, respectively. In this cohort, we compared the performances of two widely utilized commercial SARS-CoV-2 interferon-gamma release assays (IGRAs), i.e., QuantiFERON SARS-CoV-2 and T-SPOT.COVID, and an in-house designed Omicron enzyme-linked immunospot (ELISpot). RESULTS The QuantiFERON SARS-CoV-2 and T-SPOT.COVID assays detected SARS-CoV-2 spike-specific T cells in 34.8 % and 21.7 % of participants, respectively. Moreover, our in-house designed ELISpot that included Omicron BA.4 and BA.5 full-spike peptides detected T cell responses in 47.8 % of participants and was strongly associated with the T-SPOT.COVID. CONCLUSION The evaluation of SARS-CoV-2 T cell immunity using commercially accessible assays may yield disparate outcomes as results from different assays are not directly comparable. A specific Omicron ELISpot should be considered to assess Omicron-specific T cell immunity.
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Affiliation(s)
- Willem A Mak
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands; Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands.
| | - Wendy Visser
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - Johannes G M Koeleman
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - David S Y Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
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Torres-Flores A, Ontiveros-Padilla LA, Madera-Sandoval RL, Tepale-Segura A, Gajón-Martínez J, Rivera-Hernández T, Ferat-Osorio EA, Cérbulo-Vázquez A, Arriaga-Pizano LA, Bonifaz L, Paz-De la Rosa G, Rojas-Martínez O, Suárez-Martínez A, Peralta-Sánchez G, Sarfati-Mizrahi D, Sun W, Chagoya-Cortés HE, Palese P, Krammer F, García-Sastre A, Lozano-Dubernard B, López-Macías C. Newcastle disease virus vector-based SARS-CoV-2 vaccine candidate AVX/COVID-12 activates T cells and is recognized by antibodies from COVID-19 patients and vaccinated individuals. Front Immunol 2024; 15:1394114. [PMID: 38873610 PMCID: PMC11169921 DOI: 10.3389/fimmu.2024.1394114] [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: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Several effective vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and implemented in the population. However, the current production capacity falls short of meeting global demand. Therefore, it is crucial to further develop novel vaccine platforms that can bridge the distribution gap. AVX/COVID-12 is a vector-based vaccine that utilizes the Newcastle Disease virus (NDV) to present the SARS-CoV-2 spike protein to the immune system. Methods This study aims to analyze the antigenicity of the vaccine candidate by examining antibody binding and T-cell activation in individuals infected with SARS-CoV-2 or variants of concern (VOCs), as well as in healthy volunteers who received coronavirus disease 2019 (COVID-19) vaccinations. Results Our findings indicate that the vaccine effectively binds antibodies and activates T-cells in individuals who received 2 or 3 doses of BNT162b2 or AZ/ChAdOx-1-S vaccines. Furthermore, the stimulation of T-cells from patients and vaccine recipients with AVX/COVID-12 resulted in their proliferation and secretion of interferon-gamma (IFN-γ) in both CD4+ and CD8+ T-cells. Discussion The AVX/COVID-12 vectored vaccine candidate demonstrates the ability to stimulate robust cellular responses and is recognized by antibodies primed by the spike protein present in SARS-CoV-2 viruses that infected patients, as well as in the mRNA BNT162b2 and AZ/ChAdOx-1-S vaccines. These results support the inclusion of the AVX/COVID-12 vaccine as a booster in vaccination programs aimed at addressing COVID-19 caused by SARS-CoV-2 and its VOCs.
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Affiliation(s)
- Alejandro Torres-Flores
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
- Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Luis Alberto Ontiveros-Padilla
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ruth Lizzeth Madera-Sandoval
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) “Dr, Manuel Martínez Báez”, Secretaría de Salud, Ciudad de México, Mexico
| | - Araceli Tepale-Segura
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
| | - Julián Gajón-Martínez
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
| | - Tania Rivera-Hernández
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
- Investigadores por México, Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Ciudad de México, Mexico
| | - Eduardo Antonio Ferat-Osorio
- División de Investigación en Salud, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Cuauhtémoc, Ciudad de México, Mexico
| | - Arturo Cérbulo-Vázquez
- Servicio de Medicina Genómica. Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de México, Mexico
| | - Lourdes Andrea Arriaga-Pizano
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
| | - Laura Bonifaz
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
- Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, IMSS, Ciudad de México, Mexico
| | | | | | | | | | | | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Constantino López-Macías
- UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Unidad de Investigación Médica en Inmunoquímica, Ciudad de México, Mexico
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4
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Hyun H, Nham E, Seong H, Yoon JG, Noh JY, Cheong HJ, Kim WJ, Yoon SK, Park SJ, Gwak W, Lee JW, Kim B, Song JY. Long-term humoral and cellular immunity against vaccine strains and Omicron subvariants (BQ.1.1, BN.1, XBB.1, and EG.5) after bivalent COVID-19 vaccination. Front Immunol 2024; 15:1385135. [PMID: 38756783 PMCID: PMC11096540 DOI: 10.3389/fimmu.2024.1385135] [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: 02/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Background The assessment of long-term humoral and cellular immunity post-vaccination is crucial for establishing an optimal vaccination strategy. Methods This prospective cohort study evaluated adults (≥18 years) who received a BA.4/5 bivalent vaccine. We measured the anti-receptor binding domain immunoglobulin G antibody and neutralizing antibodies (NAb) against wild-type and Omicron subvariants (BA.5, BQ.1.1, BN.1, XBB.1 and EG.5) up to 9 months post-vaccination. T-cell immune responses were measured before and 4 weeks after vaccination. Results A total of 108 (28 SARS-CoV-2-naïve and 80 previously infected) participants were enrolled. Anti-receptor binding domain immunoglobulin G (U/mL) levels were higher at 9 months post-vaccination than baseline in SAR-CoV-2-naïve individuals (8,339 vs. 1,834, p<0.001). NAb titers against BQ.1.1, BN.1, and XBB.1 were significantly higher at 9 months post-vaccination than baseline in both groups, whereas NAb against EG.5 was negligible at all time points. The T-cell immune response (median spot forming unit/106 cells) was highly cross-reactive at both baseline (wild-type/BA.5/XBB.1.5, 38.3/52.5/45.0 in SARS-CoV-2-naïve individuals; 51.6/54.9/54.9 in SARS-CoV-2-infected individuals) and 4 weeks post-vaccination, with insignificant boosting post-vaccination. Conclusion Remarkable cross-reactive neutralization was observed against BQ.1.1, BN.1, and XBB.1 up to 9 months after BA.4/5 bivalent vaccination, but not against EG.5. The T-cell immune response was highly cross-reactive.
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Affiliation(s)
- Hakjun Hyun
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Eliel Nham
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hye Seong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Gu Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sun Kyung Yoon
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Se-Jin Park
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - WonSeok Gwak
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - June-Woo Lee
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Byoungguk Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
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van den Dijssel J, Duurland MC, Konijn VA, Kummer LY, Hagen RR, Kuijper LH, Wieske L, van Dam KP, Stalman EW, Steenhuis M, Geerdes DM, Mok JY, Kragten AH, Menage C, Koets L, Veldhuisen B, Verstegen NJ, van der Schoot CE, van Esch WJ, D'Haens GR, Löwenberg M, Volkers AG, Rispens T, Kuijpers TW, Eftimov F, van Gisbergen KP, van Ham SM, Ten Brinke A, van de Sandt CE. mRNA-1273 vaccinated inflammatory bowel disease patients receiving TNF inhibitors develop broad and robust SARS-CoV-2-specific CD8 + T cell responses. J Autoimmun 2024; 144:103175. [PMID: 38387105 DOI: 10.1016/j.jaut.2024.103175] [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: 11/10/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
SARS-CoV-2-specific CD8+ T cells recognize conserved viral peptides and in the absence of cross-reactive antibodies form an important line of protection against emerging viral variants as they ameliorate disease severity. SARS-CoV-2 mRNA vaccines induce robust spike-specific antibody and T cell responses in healthy individuals, but their effectiveness in patients with chronic immune-mediated inflammatory disorders (IMIDs) is less well defined. These patients are often treated with systemic immunosuppressants, which may negatively affect vaccine-induced immunity. Indeed, TNF inhibitor (TNFi)-treated inflammatory bowel disease (IBD) patients display reduced ability to maintain SARS-CoV-2 antibody responses post-vaccination, yet the effects on CD8+ T cells remain unclear. Here, we analyzed the impact of IBD and TNFi treatment on mRNA-1273 vaccine-induced CD8+ T cell responses compared to healthy controls in SARS-CoV-2 experienced and inexperienced patients. CD8+ T cells were analyzed for their ability to recognize 32 SARS-CoV-2-specific epitopes, restricted by 10 common HLA class I allotypes using heterotetramer combinatorial coding. This strategy allowed in-depth ex vivo profiling of the vaccine-induced CD8+ T cell responses using phenotypic and activation markers. mRNA vaccination of TNFi-treated and untreated IBD patients induced robust spike-specific CD8+ T cell responses with a predominant central memory and activated phenotype, comparable to those in healthy controls. Prominent non-spike-specific CD8+ T cell responses were observed in SARS-CoV-2 experienced donors prior to vaccination. Non-spike-specific CD8+ T cells persisted and spike-specific CD8+ T cells notably expanded after vaccination in these patient cohorts. Our data demonstrate that regardless of TNFi treatment or prior SARS-CoV-2 infection, IBD patients benefit from vaccination by inducing a robust spike-specific CD8+ T cell response.
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Affiliation(s)
- Jet van den Dijssel
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Mariël C Duurland
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Veronique Al Konijn
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Laura Yl Kummer
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ruth R Hagen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Lisan H Kuijper
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Neurophysiology, St Antonius Hospital, Nieuwegein, Netherlands
| | - Koos Pj van Dam
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eileen W Stalman
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Juk Yee Mok
- Sanquin Reagents B.V., Amsterdam, Netherlands
| | | | - Charlotte Menage
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lianne Koets
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; National Screening Laboratory of Sanquin, Research and Laboratory Services, Amsterdam, Netherlands
| | - Barbera Veldhuisen
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Immunohematology Diagnostics, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Niels Jm Verstegen
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Geert Ram D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Adriaan G Volkers
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Theo Rispens
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, University of Amsterdam, Amsterdam, Netherlands
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Klaas Pjm van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - S Marieke van Ham
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Anja Ten Brinke
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carolien E van de Sandt
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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Underwood AP, Sølund C, Jacobsen K, Binderup A, Fernandez-Antunez C, Mikkelsen LS, Inekci D, Villadsen SL, Castruita JAS, Pinholt M, Fahnøe U, Ramirez S, Brix L, Weis N, Bukh J. Neutralizing antibody and CD8 + T cell responses following BA.4/5 bivalent COVID-19 booster vaccination in adults with and without prior exposure to SARS-CoV-2. Front Immunol 2024; 15:1353353. [PMID: 38571939 PMCID: PMC10987722 DOI: 10.3389/fimmu.2024.1353353] [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: 12/10/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
As severe acute respiratory coronavirus 2 (SARS-CoV-2) variants continue to emerge, it is important to characterize immune responses against variants which can inform on protection efficacies following booster vaccination. In this study, neutralizing breadth and antigen-specific CD8+ T cell responses were analyzed in both infection-naïve and infection-experienced individuals following administration of a booster bivalent Wuhan-Hu-1+BA.4/5 Comirnaty® mRNA vaccine. Significantly higher neutralizing titers were found after this vaccination compared to the pre-third booster vaccination time point. Further, neutralizing breadth to omicron variants, including BA.1, BA.2, BA.5, BQ.1 and XBB.1, was found to be boosted following bivalent vaccination. SARS-CoV-2-specific CD8+ T cells were identified, but with no evidence that frequencies were increased following booster vaccinations. Spike protein-specific CD8+ T cells were the only responses detected after vaccination and non-spike-specific CD8+ T cells were only detected after infection. Both spike-specific and non-spike-specific CD8+ T cells were found at much lower frequencies than CD8+ T cells specific to cytomegalovirus (CMV), Epstein-Barr virus (EBV) and influenza (Flu). Taken together, these results show that the bivalent Wuhan-Hu-1+BA.4/5 Comirnaty® mRNA vaccine boosted the breadth of neutralization to newer SARS-CoV-2 variants and that vaccination is able to induce spike protein-specific CD8+ T cell responses, which are maintained longitudinally.
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Affiliation(s)
- Alexander P. Underwood
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Christina Sølund
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Lotte S. Mikkelsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Signe Lysemose Villadsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Jose A. S. Castruita
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
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7
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Zhao J, Zhang H, Jiang L, Cheng F, Li W, Wang Z, Liu H, Li S, Jiang Y, Li M, Li Y, Liu S, Fang M, Zhou X, Ye X, Zhao S, Zheng Y, Meng S. Increased antibody titers but induced T cell AICD and apoptosis response in COVID-19 convalescents by inactivated vaccine booster. Microbiol Spectr 2024; 12:e0243523. [PMID: 38319108 PMCID: PMC10913726 DOI: 10.1128/spectrum.02435-23] [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: 06/10/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
It is urgently needed to evaluate the necessity and benefits of booster vaccination against the coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2) Omicron to facilitate clinical decision-making for 2019 coronavirus disease (COVID-19) convalescents. We conducted a multicenter, prospective clinical trial (registration number: ChiCTR2100045810) in the first patients with COVID-19 from 28 January 2020 to 20 February 2020 to assess the long-term durability of neutralizing antibodies against live Omicron BA.5 and further assess the efficiency and safety of CoronaVac in the convalescent group. A total of 96 COVID-19 convalescents were enrolled in this study. Neutralizing antibody titers in convalescents were significantly reduced in 9-10 months. A dose-refreshing vaccination in 28 convalescents with an antibody titer below 96 significantly induced neutralizing antibodies against live Omicron by 4.84-fold. Meanwhile, the abundance of naive T cells increased dramatically, and TEMRA and TEM cells gradually decreased after vaccination. Activation-induced cell death and apoptosis-related genes were significantly elevated after vaccination in all T-cell subtypes. One-dose booster vaccination was effective in inducing a robust antibody response against SARS-CoV-2 Omicron in COVID-19 convalescents with low antibody titers. However, vaccine-mediated T-cell consumption and regeneration patterns may be detrimental to the antiviral response.IMPORTANCEThe globally dominant coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2) Omicron variant raises the possibility of repeat infections among 2019 coronavirus disease (COVID-19) convalescents with low neutralizing antibody titers. The importance of this multicenter study lies in its evaluation of the long-term durability of neutralizing antibodies in COVID-19 convalescents and the efficacy of a booster vaccination against the live Omicron. The findings suggest that a one-dose booster vaccination is effective in inducing a robust antibody response against SARS-CoV-2 Omicron in convalescents with low antibody titers. However, the study also highlights the potential detrimental effects on the antiviral response due to vaccine-mediated T-cell consumption and regeneration patterns. These results are crucial for facilitating clinical decision-making for COVID-19 convalescents and informing public health policies regarding booster vaccinations.
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Affiliation(s)
- Jingmin Zhao
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Han Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lina Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Fang Cheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Department of Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zihao Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongyang Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shaohua Li
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yiyun Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Meiling Li
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yan Li
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Shuhong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Min Fang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Ye
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shousong Zhao
- Department of Infectious Diseases, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yuxuan Zheng
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Songdong Meng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Nesamari R, Omondi MA, Baguma R, Höft MA, Ngomti A, Nkayi AA, Besethi AS, Magugu SFJ, Mosala P, Walters A, Clark GM, Mennen M, Skelem S, Adriaanse M, Grifoni A, Sette A, Keeton RS, Ntusi NAB, Riou C, Burgers WA. Post-pandemic memory T cell response to SARS-CoV-2 is durable, broadly targeted, and cross-reactive to the hypermutated BA.2.86 variant. Cell Host Microbe 2024; 32:162-169.e3. [PMID: 38211583 PMCID: PMC10901529 DOI: 10.1016/j.chom.2023.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has given rise to recombinant Omicron lineages that dominate globally (XBB.1), as well as the emergence of hypermutated variants (BA.2.86). In this context, durable and cross-reactive T cell immune memory is critical for continued protection against severe COVID-19. We examined T cell responses to SARS-CoV-2 approximately 1.5 years since Omicron first emerged. We describe sustained CD4+ and CD8+ spike-specific T cell memory responses in healthcare workers in South Africa (n = 39) who were vaccinated and experienced at least one SARS-CoV-2 infection. Spike-specific T cells are highly cross-reactive with all Omicron variants tested, including BA.2.86. Abundant nucleocapsid and membrane-specific T cells are detectable in most participants. The bulk of SARS-CoV-2-specific T cell responses have an early-differentiated phenotype, explaining their persistent nature. Overall, hybrid immunity leads to the accumulation of spike and non-spike T cells evident 3.5 years after the start of the pandemic, with preserved recognition of highly mutated SARS-CoV-2 variants.
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Affiliation(s)
- Rofhiwa Nesamari
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Millicent A Omondi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Anathi A Nkayi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Asiphe S Besethi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Siyabulela F J Magugu
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Paballo Mosala
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gesina M Clark
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Alba Grifoni
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A B Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa; Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; South African Medical Research Council Extramural Unit on Intersection of Non-communicable Disease and Infectious Diseases, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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9
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Lineburg KE, Crooks P, Raju J, Le Texier L, Khaledi P, Berry K, Swaminathan S, Panikkar A, Rehan S, Guppy-Coles K, Neller MA, Khanna R, Smith C. Breakthrough SARS-COV-2 infection induces broad anti-viral T cell immunity. iScience 2023; 26:108474. [PMID: 38077128 PMCID: PMC10698266 DOI: 10.1016/j.isci.2023.108474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 05/18/2024] Open
Abstract
Vaccines have curtailed the devastation wrought by COVID-19. Nevertheless, emerging variants result in a high incidence of breakthrough infections. Here we assess the impact of vaccination and breakthrough infection on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) T cell immunity. We demonstrate that COVID-19 vaccination induces robust spike-specific T cell responses that, within the CD4+ compartment, display comparable IFN-γ responses to SARS-CoV-2 infection without vaccination. Vaccine-induced CD8+ IFN-γ responses however, were significantly greater than those primed by SARS-CoV-2 infection alone. This increased responsiveness is associated with induction of novel HLA-restricted CD8+ T cell epitopes not primed by infection alone (without vaccination). Despite these augmented responses, breakthrough infection still induced de novo T cell responses against additional SARS-CoV-2 CD8+ epitopes that display HLA-associated immunodominance hierarchies consistent with those in unvaccinated COVID-19 convalescent individuals. This study demonstrates the unique modulation of anti-viral T cell responses against multiple viral antigens following consecutive yet distinct priming events in COVID-19 vaccination and breakthrough infection.
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Affiliation(s)
- Katie Eireann Lineburg
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Pauline Crooks
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Jyothy Raju
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Laetitia Le Texier
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Panteha Khaledi
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kiana Berry
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Srividhya Swaminathan
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Archana Panikkar
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Sweera Rehan
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kristyan Guppy-Coles
- Cardiology, Royal Brisbane and Women’s Hospital, Metro North Hospital and Health Services, Queensland Health, QLD 4006, Australia
| | - Michelle Anne Neller
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
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10
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Ssali I, Mugaba S, Watelo AK, Bemanzi J, Katende JS, Oluka GK, Ankunda V, Baine C, Kato L, Onyachi N, Muwanga M, Jjuuko M, Kayiwa J, Nsereko C, Auma BO, Weiskopf D, Sette A, Lutalo T, Musenero M, Kaleebu P, Serwanga J. Spike protein is a key target for stronger and more persistent T-cell responses-a study of mild and asymptomatic SARS-CoV-2 infection. Int J Infect Dis 2023; 136:49-56. [PMID: 37683720 DOI: 10.1016/j.ijid.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVES Understanding the immune response in very mild and asymptomatic COVID-19 is crucial for developing effective vaccines and immunotherapies, yet remains poorly characterized. This longitudinal study examined the evolution of interferon (IFN)-γ responses to SARS-CoV-2 peptides in 109 asymptomatic or mildly symptomatic Ugandan COVID-19 patients across 365 days and explored their association with antibody generation. METHODS T-cell responses to spike-containing clusters of differentiation (CD4)-S and CD8 nCoV-A (CD8-A) megapools, and the non-spike CD4-R and CD8 nCoV-B (CD8-B) megapools, were assessed and correlated with demographic and temporal variables. RESULTS SARS-CoV-2-specific IFN-γ responses were consistently detected in all peptide pools and time points, with the spike-targeted response exhibiting higher potency and durability than the non-spike responses. Throughout the entire 365-day infection timeline, a robust positive correlation was observed between CD4 T-cell responses to the spike-derived peptides and anti-spike immunoglobulin G antibody levels, underscoring their interdependent dynamics in the immune response against SARS-CoV-2; in contrast, CD8 T-cell responses exhibited no such correlation, highlighting their distinctive, autonomous role in defense. No meaningful variations in complete blood count parameters were observed between individuals with COVID-19 infection and those without, indicating clinical insignificance. CONCLUSIONS This study highlights the dominant role of spike-directed T-cell responses in mild and asymptomatic disease and provides crucial longitudinal data from Sub-Saharan African settings. The findings provide valuable insights into the dynamics of T-cell responses and their potential significance in developing effective strategies for combating COVID-19.
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Affiliation(s)
- Ivan Ssali
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | | | - Juliana Bemanzi
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Ssebwana Katende
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Gerald Kevin Oluka
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Violet Ankunda
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Nathan Onyachi
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Moses Muwanga
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Mark Jjuuko
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - John Kayiwa
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Christopher Nsereko
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Betty Oliver Auma
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, USA
| | - Tom Lutalo
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Monica Musenero
- Science, Technology, and Innovation Secretariat, Office of the President, Government of Uganda, Kampala, Uganda
| | - Pontiano Kaleebu
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jennifer Serwanga
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda.
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11
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Scarpa F, Locci C, Azzena I, Casu M, Fiori PL, Ciccozzi A, Giovanetti M, Quaranta M, Ceccarelli G, Pascarella S, Ciccozzi M, Sanna D. SARS-CoV-2 Recombinants: Genomic Comparison between XBF and Its Parental Lineages. Microorganisms 2023; 11:1824. [PMID: 37512996 PMCID: PMC10383834 DOI: 10.3390/microorganisms11071824] [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: 05/31/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Recombination events are very common and represent one of the primary drivers of RNA virus evolution. The XBF SARS-CoV-2 lineage is one of the most recently generated recombinants during the COVID-19 pandemic. It is a recombinant of BA.5.2.3 and BA.2.75.3, both descendants of lineages that caused many concerns (BA.5 and BA.2.75, respectively). Here, we performed a genomic survey focused on comparing the recombinant XBF with its parental lineages to provide a comprehensive assessment of the evolutionary potential, epidemiological trajectory, and potential risks. Genetic analyses indicated that although XBF initially showed the typical expansion depicted by a steep curve, causing several concerns, currently there is no indication of significant expansion potential or a contagion rate surpassing that of other currently active or previously prevalent lineages. BSP indicated that the peak has been reached around 19 October 2022 and then the genetic variability suffered slight oscillations until early 5 March 2023 when the population size reduced for the last time starting its last plateau that is still lasting. Structural analyses confirmed its reduced potential, also indicating that properties of NTDs and RBDs of XBF and its parental lineages present no significant difference. Of course, cautionary measures must still be taken and genome-based monitoring remains the best tool for detecting any important changes in viral genome composition.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
- Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
| | - Miriana Quaranta
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Campus Bio-Medico, Fondazione Policlinico Universitario, 00128 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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12
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Perdiguero B, Marcos-Villar L, López-Bravo M, Sánchez-Cordón PJ, Zamora C, Valverde JR, Sorzano CÓS, Sin L, Álvarez E, Ramos M, Del Val M, Esteban M, Gómez CE. Immunogenicity and efficacy of a novel multi-patch SARS-CoV-2/COVID-19 vaccine candidate. Front Immunol 2023; 14:1160065. [PMID: 37404819 PMCID: PMC10316789 DOI: 10.3389/fimmu.2023.1160065] [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: 02/06/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction While there has been considerable progress in the development of vaccines against SARS-CoV-2, largely based on the S (spike) protein of the virus, less progress has been made with vaccines delivering different viral antigens with cross-reactive potential. Methods In an effort to develop an immunogen with the capacity to induce broad antigen presentation, we have designed a multi-patch synthetic candidate containing dominant and persistent B cell epitopes from conserved regions of SARS-CoV-2 structural proteins associated with long-term immunity, termed CoV2-BMEP. Here we describe the characterization, immunogenicity and efficacy of CoV2-BMEP using two delivery platforms: nucleic acid DNA and attenuated modified vaccinia virus Ankara (MVA). Results In cultured cells, both vectors produced a main protein of about 37 kDa as well as heterogeneous proteins with size ranging between 25-37 kDa. In C57BL/6 mice, both homologous and heterologous prime/boost combination of vectors induced the activation of SARS-CoV-2-specific CD4 and CD8 T cell responses, with a more balanced CD8+ T cell response detected in lungs. The homologous MVA/MVA immunization regimen elicited the highest specific CD8+ T cell responses in spleen and detectable binding antibodies (bAbs) to S and N antigens of SARS-CoV-2. In SARS-CoV-2 susceptible k18-hACE2 Tg mice, two doses of MVA-CoV2-BMEP elicited S- and N-specific bAbs as well as cross-neutralizing antibodies against different variants of concern (VoC). After SARS-CoV-2 challenge, all animals in the control unvaccinated group succumbed to the infection while vaccinated animals with high titers of neutralizing antibodies were fully protected against mortality, correlating with a reduction of virus infection in the lungs and inhibition of the cytokine storm. Discussion These findings revealed a novel immunogen with the capacity to control SARS-CoV-2 infection, using a broader antigen presentation mechanism than the approved vaccines based solely on the S antigen.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - María López-Bravo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pedro J. Sánchez-Cordón
- Veterinary Pathology Department, Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carmen Zamora
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Ramón Valverde
- Scientific Computing, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carlos Óscar S. Sorzano
- Biocomputing Unit and Computational Genomics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Laura Sin
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Enrique Álvarez
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Manuel Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Margarita Del Val
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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13
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Scarpa F, Azzena I, Locci C, Casu M, Fiori PL, Ciccozzi A, Angeletti S, Imperia E, Giovanetti M, Maruotti A, Borsetti A, Cauda R, Cassone A, Via A, Pascarella S, Sanna D, Ciccozzi M. Molecular In-Depth on the Epidemiological Expansion of SARS-CoV-2 XBB.1.5. Microorganisms 2023; 11:microorganisms11040912. [PMID: 37110335 PMCID: PMC10142263 DOI: 10.3390/microorganisms11040912] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Since the beginning of the pandemic, the generation of new variants periodically recurs. The XBB.1.5 SARS-CoV-2 variant is one of the most recent. This research was aimed at verifying the potential hazard of this new subvariant. To achieve this objective, we performed a genome-based integrative approach, integrating results from genetic variability/phylodynamics with structural and immunoinformatic analyses to obtain as comprehensive a viewpoint as possible. The Bayesian Skyline Plot (BSP) shows that the viral population size reached the plateau phase on 24 November 2022, and the number of lineages peaked at the same time. The evolutionary rate is relatively low, amounting to 6.9 × 10−4 subs/sites/years. The NTD domain is identical for XBB.1 and XBB.1.5 whereas their RBDs only differ for the mutations at position 486, where the Phe (in the original Wuhan) is replaced by a Ser in XBB and XBB.1, and by a Pro in XBB.1.5. The variant XBB.1.5 seems to spread more slowly than sub-variants that have caused concerns in 2022. The multidisciplinary molecular in-depth analyses on XBB.1.5 performed here does not provide evidence for a particularly high risk of viral expansion. Results indicate that XBB.1.5 does not possess features to become a new, global, public health threat. As of now, in its current molecular make-up, XBB.1.5 does not represent the most dangerous variant.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (F.S.); (M.C.)
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, Department of Medicine and Surgery, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Research Unit of Laboratory, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
- Science and Technology for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
| | | | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Correspondence: (F.S.); (M.C.)
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