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Galmiche S, Charmet T, Rakover A, Chény O, Omar F, David C, Mailles A, Carrat F, Fontanet A. Risk of SARS-CoV-2 infection in professional settings, shops, shared transport, and leisure activities in France, 2020-2022. BMC Public Health 2024; 24:2411. [PMID: 39232732 PMCID: PMC11376041 DOI: 10.1186/s12889-024-19651-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/30/2024] [Indexed: 09/06/2024] Open
Abstract
PURPOSE The aim of the study was to identify settings associated with SARS-CoV-2 transmission throughout the COVID-19 pandemic in France. METHODS Cases with recent SARS-CoV-2 infection were matched with controls (4:1 ratio) on age, sex, region, population size, and calendar week. Odds ratios for SARS-CoV-2 infection were estimated for nine periods in models adjusting for socio-demographic characteristics, health status, COVID-19 vaccine, and past infection. RESULTS Between October 27, 2020 and October 2, 2022, 175,688 cases were matched with 43,922 controls. An increased risk of infection was documented throughout the study for open-space offices compared to offices without open space (OR range across the nine periods: 1.12 to 1.57) and long-distance trains (1.25 to 1.88), and during most of the study for convenience stores (OR range in the periods with increased risk: 1.15 to 1.44), take-away delivery (1.07 to 1.28), car-pooling with relatives (1.09 to 1.68), taxis (1.08 to 1.89), airplanes (1.20 to 1.78), concerts (1.31 to 2.09) and night-clubs (1.45 to 2.95). No increase in transmission was associated with short-distance shared transport, car-pooling booked over platforms, markets, supermarkets and malls, hairdressers, museums, movie theatres, outdoor sports, and swimming pools. The increased risk of infection in bars and restaurants was no longer present in restaurants after reopening in June 2021. It persisted in bars only among those aged under 40 years. CONCLUSION Closed settings in which people are less likely to wear masks were most affected by SARS-CoV-2 transmission and should be the focus of air quality improvement. CLINICALTRIALS GOV (03/09/2022): NCT04607941.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France.
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, 75006, France.
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Olivia Chény
- Clinical Research Coordination Office, Institut Pasteur, Université Paris Cité, Paris, 75015, France
| | - Faïza Omar
- Department of Public Affairs - Public Statistics, Institut Ipsos, Paris, 75013, France
| | - Christophe David
- Department of Public Affairs - Public Statistics, Institut Ipsos, Paris, 75013, France
| | | | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, Hôpital Saint-Antoine, AP-HP, Paris, 75012, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
- Unité PACRI, Conservatoire National des Arts et Métiers, Paris, 75003, France
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Nunes MC, Thommes E, Fröhlich H, Flahault A, Arino J, Baguelin M, Biggerstaff M, Bizel-Bizellot G, Borchering R, Cacciapaglia G, Cauchemez S, Barbier--Chebbah A, Claussen C, Choirat C, Cojocaru M, Commaille-Chapus C, Hon C, Kong J, Lambert N, Lauer KB, Lehr T, Mahe C, Marechal V, Mebarki A, Moghadas S, Niehus R, Opatowski L, Parino F, Pruvost G, Schuppert A, Thiébaut R, Thomas-Bachli A, Viboud C, Wu J, Crépey P, Coudeville L. Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report. Infect Dis Model 2024; 9:501-518. [PMID: 38445252 PMCID: PMC10912817 DOI: 10.1016/j.idm.2024.02.008] [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: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
In July 2023, the Center of Excellence in Respiratory Pathogens organized a two-day workshop on infectious diseases modelling and the lessons learnt from the Covid-19 pandemic. This report summarizes the rich discussions that occurred during the workshop. The workshop participants discussed multisource data integration and highlighted the benefits of combining traditional surveillance with more novel data sources like mobility data, social media, and wastewater monitoring. Significant advancements were noted in the development of predictive models, with examples from various countries showcasing the use of machine learning and artificial intelligence in detecting and monitoring disease trends. The role of open collaboration between various stakeholders in modelling was stressed, advocating for the continuation of such partnerships beyond the pandemic. A major gap identified was the absence of a common international framework for data sharing, which is crucial for global pandemic preparedness. Overall, the workshop underscored the need for robust, adaptable modelling frameworks and the integration of different data sources and collaboration across sectors, as key elements in enhancing future pandemic response and preparedness.
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Affiliation(s)
- Marta C. Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL) and Centre International de Recherche en Infectiologie (CIRI), Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Edward Thommes
- New Products and Innovation (NPI), Sanofi Vaccines (Global), Toronto, Ontario, Canada
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department of Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT (b-it), Bonn, Germany
| | - Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland and Swiss School of Public Health, Zürich, Switzerland
| | - Julien Arino
- Department of Mathematics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Matthew Biggerstaff
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Gaston Bizel-Bizellot
- Departement of Computational Biology, Departement of Global Health, Institut Pasteur, Paris, France
| | - Rebecca Borchering
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Giacomo Cacciapaglia
- Institut de Physique des Deux Infinis de Lyon (IP2I), UMR5822, IN2P3/CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000 CNRS, Paris, France
| | - Alex Barbier--Chebbah
- Decision and Bayesian Computation, Institut Pasteur, Université Paris Cité, CNRS UMR 3571, France
| | - Carsten Claussen
- Fraunhofer-Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Christine Choirat
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Monica Cojocaru
- Mathematics & Statistics Department, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Chitin Hon
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China
| | - Jude Kong
- Africa-Canada Artificial Intelligence and Data Innovation Consortium (ACADIC), Global South Artificial Intelligence for Pandemic and Epidemic Preparedness and Response Network (AI4PEP), Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
| | | | | | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | | | - Vincent Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, Paris, France
| | | | - Seyed Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Rene Niehus
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Lulla Opatowski
- UMR 1018, Team “Anti-infective Evasion and Pharmacoepidemiology”, Université Paris-Saclay, UVSQ, INSERM, France
- Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Université Paris Cité, Paris, France
| | - Francesco Parino
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | | | - Andreas Schuppert
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Rodolphe Thiébaut
- Bordeaux University, Department of Public Health, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France
| | | | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jianhong Wu
- York Emergency Mitigation, Engagement, Response, and Governance Institute, Laboratory for Industrial and Applied Mathematics, York University, Toronto, Ontario, Canada
| | - Pascal Crépey
- EHESP, Université de Rennes, CNRS, IEP Rennes, Arènes - UMR 6051, RSMS – Inserm U 1309, Rennes, France
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Lièvre G, Sicsic J, Galmiche S, Charmet T, Fontanet A, Mueller JE. Are the 7C psychological antecedents associated with COVID-19 vaccine behaviours beyond intentions? A cross-sectional study on at-least-one-dose and up-to-date vaccination status, and uptake speed among adults in France. Vaccine 2024; 42:3288-3299. [PMID: 38643038 DOI: 10.1016/j.vaccine.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Widely documented psychological antecedents of vaccination are confidence in vaccines, complacency, convenience, calculation, collective responsibility (5C model) with the recent addition of confidence in the wider system and social conformism. While the capacity of these seven antecedents (7C) to explain variance in COVID-19 vaccine intentions has been previously documented, we study whether these factors also are associated with vaccine behaviours, beyond intentions. METHODS From February to June 2022, we recruited a sample of adults in France, including persons with notified recent SARS-CoV-2 infection, along with relatives and randomly selected non-infected persons. Participants completed self-administered questionnaires assessing COVID-19 vaccination history and the 7C antecedents. We defined vaccination behaviours as three outcomes: at-least-one-dose vaccine status by 2022 (N = 49,019), up-to-date vaccination status (N = 46,566), and uptake speed of first dose (N = 25,998). We conducted multivariable logistic regressions and Cox models. RESULTS Among the 49,019 participants, 95.0% reported receipt of at least one dose and 89.8% were up to date with recommendations. All 7C antecedents were significantly associated with the outcomes, although effects were weaker for up-to-date vaccination status and uptake speed. The strongest effects (most vs. least vaccine-favourable attitude level, at-least-one-dose vaccination status) were observed for collective responsibility (OR: 14.44; 95%CI: 10.72-19.45), calculation (OR: 10.29; 95%CI: 7.53-14.05), and confidence in the wider system (OR: 8.94; 95%CI: 6.51-12.27). CONCLUSION This study demonstrates that the 7C not only explain vaccine intention, but also vaccine behaviours, and underpins the importance of developing vaccine promotion strategies considering the 7C antecedents.
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Affiliation(s)
- Gaëlle Lièvre
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | | | - Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Judith E Mueller
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Univ. Rennes, EHESP, CNRS, Inserm, Arènes - UMR 6051, RSMS (Recherche sur les Services et Management en Santé) - U 1309 - F-35000 Rennes, France.
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Rakover A, Galmiche S, Charmet T, Chény O, Omar F, David C, Martin S, Mailles A, Fontanet A. Source of SARS-CoV-2 infection: results from a series of 584,846 cases in France from October 2020 to August 2022. BMC Public Health 2024; 24:325. [PMID: 38287286 PMCID: PMC10826227 DOI: 10.1186/s12889-024-17772-y] [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: 10/03/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND We aimed to study the source of infection for recently SARS-CoV-2-infected individuals from October 2020 to August 2022 in France. METHODS Participants from the nationwide ComCor case-control study who reported recent SARS-CoV-2 infection were asked to document the source and circumstances of their infection through an online questionnaire. Multivariable logistic regression was used to identify the factors associated with not identifying any source of infection. RESULTS Among 584,846 adults with a recent SARS-CoV-2 infection in France, 46.9% identified the source of infection and an additional 22.6% suspected an event during which they might have become infected. Known and suspected sources of infection were household members (30.8%), extended family (15.6%), work colleagues (15.0%), friends (11.0%), and possibly multiple/other sources (27.6%). When the source of infection was known, was not a household member, and involved a unique contact (n = 69,788), characteristics associated with transmission events were indoors settings (91.6%), prolonged (> 15 min) encounters (50.5%), symptomatic source case (64.9%), and neither the source of infection nor the participant wearing a mask (82.2%). Male gender, older age, lower education, living alone, using public transportation, attending places of public recreation (bars, restaurants, nightclubs), public gatherings, and cultural events, and practicing indoor sports were all independently associated with not knowing the source of infection. CONCLUSION Two-thirds of infections were attributed to interactions with close relatives, friends, or work colleagues. Extra-household indoor encounters without masks were commonly reported and represented avoidable circumstances of infection. TRIAL REGISTRATION ClinicalTrials.gov registration number: NCT04607941.
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Affiliation(s)
- Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France.
| | - Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Centre for Translational Research, Paris, France
| | | | | | - Sophie Martin
- Caisse Nationale de L'Assurance Maladie, Paris, France
| | | | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
- Conservatoire National Des Arts Et Métiers, Unité PACRI, Paris, France
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Xu K, Li J, Lu X, Ge X, Wang K, Wang J, Qiao Z, Quan Y, Li C. The Immunogenicity of CpG, MF59-like, and Alum Adjuvant Delta Strain Inactivated SARS-CoV-2 Vaccines in Mice. Vaccines (Basel) 2024; 12:60. [PMID: 38250873 PMCID: PMC10819607 DOI: 10.3390/vaccines12010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
The continuous evolution and mutation of SARS-CoV-2 have highlighted the need for more effective vaccines. In this study, CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines were prepared, and the immunogenicity of these vaccines in mice was evaluated. The Delta + MF59-like vaccine group produced the highest levels of S- and RBD-binding antibodies and live Delta virus neutralization levels after one shot of immunization, while mice in the Delta + Alum vaccine group had the highest levels of these antibodies after two doses, and the Delta + MF59-like and Delta + Alum vaccine groups produced high levels of cross-neutralization antibodies against prototype, Beta, and Gamma strain SARS-CoV-2 viruses. There was no significant decrease in neutralizing antibody levels in any vaccine group during the observation period. CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines excited different antibody subtypes compared with unadjuvanted vaccines; the Delta + CpG vaccine group had a higher proportion of IgG2b antibodies, indicating bias towards Th1 immunity. The proportions of IgG1 and IgG2b in the Delta + MF59-like vaccine group were similar to those of the unadjuvanted vaccine. However, the Delta + Alum vaccine group had a higher proportion of IgG1 antibodies, indicating bias towards Th2 immunity. Antigen-specific cytokine secretion CD4/8+ T cells were analyzed. In conclusion, the results of this study show differences in the immune efficacy of CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines in mice, which have significant implications for the selection strategy for vaccine adjuvants.
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Affiliation(s)
- Kangwei Xu
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Jing Li
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Xu Lu
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Xiaoqin Ge
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Kaiqin Wang
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Jiahao Wang
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Zhizhong Qiao
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Yaru Quan
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Changgui Li
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
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Zhang S, Agyeman AA, Hadjichrysanthou C, Standing JF. SARS-CoV-2 viral dynamic modeling to inform model selection and timing and efficacy of antiviral therapy. CPT Pharmacometrics Syst Pharmacol 2023; 12:1450-1460. [PMID: 37534815 PMCID: PMC10583246 DOI: 10.1002/psp4.13022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
Mathematical models of viral dynamics have been reported to describe adequately the dynamic changes of severe acute respiratory syndrome-coronavirus 2 viral load within an individual host. In this study, eight published viral dynamic models were assessed, and model selection was performed. Viral load data were collected from a community surveillance study, including 2155 measurements from 162 patients (124 household and 38 non-household contacts). An extended version of the target-cell limited model that includes an eclipse phase and an immune response component that enhances viral clearance described best the data. In general, the parameter estimates showed good precision (relative standard error <10), apart from the death rate of infected cells. The parameter estimates were used to simulate the outcomes of a clinical trial of the antiviral tixagevimab-cilgavimab, a monoclonal antibody combination which blocks infection of the target cells by neutralizing the virus. The simulated outcome of the effectiveness of the antiviral therapy in controlling viral replication was in a good agreement with the clinical trial data. Early treatment with high antiviral efficacy is important for desired therapeutic outcome.
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Affiliation(s)
- Shengyuan Zhang
- Department of Pharmaceutics, School of PharmacyUniversity College LondonLondonUK
| | - Akosua A. Agyeman
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Christoforos Hadjichrysanthou
- Department of MathematicsUniversity of SussexBrightonUK
- Department of Infectious Disease Epidemiology, School of Public HealthImperial College LondonLondonUK
| | - Joseph F. Standing
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
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Galmiche S, Charmet T, Madec Y, Rakover A, Schaeffer L, Chény O, Omar F, Martin S, Mailles A, Carrat F, Fontanet A. Reduction of SARS-CoV-2 intra-household child-to-parent transmission associated with ventilation: results from a case-control study. BMC Public Health 2023; 23:1240. [PMID: 37365557 DOI: 10.1186/s12889-023-16144-2] [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: 02/23/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023] Open
Abstract
PURPOSE Our objective was to describe circumstances of SARS-CoV-2 household transmission and to identify factors associated with a lower risk of transmission in a nationwide case-control study in France. METHODS In a descriptive analysis, we analysed cases reporting transmission from someone in the household (source case). Index cases could invite a non-infected household member to participate as a related control. In such situations, we compared the exposures of the index case and related control to the source case by conditional logistic regression matched for household, restricted to households in which the source case was a child, and the index case and related control were the infected child's parents. RESULTS From October 27, 2020 to May 16, 2022, we included 104 373 cases for the descriptive analysis with a documented infection from another household member. The source case was mostly the index case's child (46.9%) or partner (45.7%). In total, 1026 index cases invited a related control to participate in the study. In the case-control analysis, we included 611 parental pairs of cases and controls exposed to the same infected child. COVID-19 vaccination with 3 + doses versus no vaccination (OR 0.1, 95%CI: 0.04-0.4), isolation from the source case (OR 0.6, 95%CI: 0.4-0.97) and the ventilation of indoor areas (OR 0.6, 95%CI: 0.4-0.9) were associated with lower risk of infection. CONCLUSION Household transmission was common during the SARS-CoV-2 pandemic in France. Mitigation strategies, including isolation and ventilation, decreased the risk of secondary transmission within the household. TRIAL REGISTRATION ClinicalTrials.gov registration number: NCT04607941.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Yoann Madec
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Laura Schaeffer
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Centre for Translational Research, Paris, France
| | | | - Sophie Martin
- Caisse Nationale de L'Assurance Maladie, Paris, France
| | | | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France.
- Conservatoire National Des Arts Et Métiers, Unité PACRI, Paris, France.
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8
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Han W, Chen N, Xu X, Sahil A, Zhou J, Li Z, Zhong H, Gao E, Zhang R, Wang Y, Sun S, Cheung PPH, Gao X. Predicting the antigenic evolution of SARS-COV-2 with deep learning. Nat Commun 2023; 14:3478. [PMID: 37311849 PMCID: PMC10261845 DOI: 10.1038/s41467-023-39199-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.
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Affiliation(s)
- Wenkai Han
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ningning Chen
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xinzhou Xu
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Adil Sahil
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juexiao Zhou
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Huawen Zhong
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elva Gao
- The KAUST School, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Yu Wang
- Syneron Technology, Guangzhou, 510000, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China.
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China.
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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9
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Supplisson O, Charmet T, Galmiche S, Schaeffer L, Chény O, Lévy A, Jeandet N, Omar F, David C, Mailles A, Fontanet A. SARS-CoV-2 self-test uptake and factors associated with self-testing during Omicron BA.1 and BA.2 waves in France, January to May 2022. Euro Surveill 2023; 28:2200781. [PMID: 37140451 PMCID: PMC10161682 DOI: 10.2807/1560-7917.es.2023.28.18.2200781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/03/2023] [Indexed: 05/05/2023] Open
Abstract
BackgroundFollowing the SARS-CoV-2 Omicron variant spread, the use of unsupervised antigenic rapid diagnostic tests (self-tests) increased.AimThis study aimed to measure self-test uptake and factors associated with self-testing.MethodsIn this cross-sectional study from 20 January to 2 May 2022, the case series from a case-control study on factors associated with SARS-CoV-2 infection were used to analyse self-testing habits in France. A multivariable quasi-Poisson regression was used to explore the variables associated with self-testing among symptomatic cases who were not contacts of another infected individual. The control series from the same study was used as a proxy for the self-test background rate in the non-infected population of France.ResultsDuring the study period, 179,165 cases who tested positive through supervised tests were recruited. Of these, 64.7% had performed a self-test in the 3 days preceding this supervised test, of which 79,038 (68.2%) were positive. The most frequently reported reason for self-testing was the presence of symptoms (64.6%). Among symptomatic cases who were not aware of being contacts of another case, self-testing was positively associated with being female, higher education, household size, being a teacher and negatively associated with older age, not French by birth, healthcare-related work and immunosuppression. Among the control series, 12% self-tested during the 8 days preceding questionnaire filling, with temporal heterogeneity.ConclusionThe analysis showed high self-test uptake in France with some inequalities which must be addressed through education and facilitated access (cost and availability) for making it a more efficient epidemic control tool.
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Affiliation(s)
- Olivier Supplisson
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Center for Interdisciplinary Research in Biology, Ecology and Evolution of Health team (Collège de France, CNRS/UMR 7241, Inserm U1050), Paris, France
- Sorbonne Université, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Simon Galmiche
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Sorbonne Université, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Clinical Operation Coordination Office, Paris, France
| | - Anne Lévy
- Caisse Nationale d'Assurance Maladie, Paris, France
| | | | | | | | | | - Arnaud Fontanet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Conservatoire National des Arts et Métiers, unité PACRI, Paris, France
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10
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Durojaye OA, Okoro NO, Odiba AS, Nwanguma BC. MasitinibL shows promise as a drug-like analog of masitinib that elicits comparable SARS-Cov-2 3CLpro inhibition with low kinase preference. Sci Rep 2023; 13:6972. [PMID: 37117213 PMCID: PMC10141821 DOI: 10.1038/s41598-023-33024-2] [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: 02/03/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023] Open
Abstract
SARS-CoV-2 infection has led to several million deaths worldwide and ravaged the economies of many countries. Hence, developing therapeutics against SARS-CoV-2 remains a core priority in the fight against COVID-19. Most of the drugs that have received emergency use authorization for treating SARS-CoV-2 infection exhibit a number of limitations, including side effects and questionable efficacy. This challenge is further compounded by reinfection after vaccination and the high likelihood of mutations, as well as the emergence of viral escape mutants that render SARS-CoV-2 spike glycoprotein-targeting vaccines ineffective. Employing de novo drug synthesis or repurposing to discover broad-spectrum antivirals that target highly conserved pathways within the viral machinery is a focus of current research. In a recent drug repurposing study, masitinib, a clinically safe drug against the human coronavirus OC43 (HCoV-OC43), was identified as an antiviral agent with effective inhibitory activity against the SARS-CoV-2 3CLpro. Masitinib is currently under clinical trial in combination with isoquercetin in hospitalized patients (NCT04622865). Nevertheless, masitinib has kinase-related side effects; hence, the development of masitinib analogs with lower anti-tyrosine kinase activity becomes necessary. In this study, in an attempt to address this limitation, we executed a comprehensive virtual workflow in silico to discover drug-like compounds matching selected pharmacophore features in the SARS-CoV-2 3CLpro-bound state of masitinib. We identified a novel lead compound, "masitinibL", a drug-like analog of masitinib that demonstrated strong inhibitory properties against the SARS-CoV-2 3CLpro. In addition, masitinibL further displayed low selectivity for tyrosine kinases, which strongly suggests that masitinibL is a highly promising therapeutic that is preferable to masitinib.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Department of Chemical Sciences, Coal City University, Emene, Enugu State, Nigeria
| | - Nkwachukwu Oziamara Okoro
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Arome Solomon Odiba
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
| | - Bennett Chima Nwanguma
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
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11
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Tamandjou Tchuem CR, Auvigne V, Vaux S, Montagnat C, Paireau J, Monnier Besnard S, Gabet A, Benhajkassen N, Le Strat Y, Parent Du Chatelet I, Levy-Bruhl D. Vaccine effectiveness and duration of protection of COVID-19 mRNA vaccines against Delta and Omicron BA.1 symptomatic and severe COVID-19 outcomes in adults aged 50 years and over in France. Vaccine 2023; 41:2280-2288. [PMID: 36870880 PMCID: PMC9968619 DOI: 10.1016/j.vaccine.2023.02.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
The emergence of SARS-CoV-2 variants calls for continuous monitoring of vaccine effectiveness (VE). We estimated the absolute effectiveness of complete 2-dose primary vaccination and booster vaccination with COVID-19 mRNA vaccines, and the duration of protection against Delta and Omicron BA.1 symptomatic infection and severe outcomes. French residents aged ≥50 years, who presented with SARS-CoV-2-like symptoms and tested for SARS-CoV-2 between June 6, 2021 and February 10, 2022 were included. A test-negative study was conducted to estimate VE against symptomatic infection, using conditional logistic regression models. Cox proportional hazard regressions were performed to assess additional protection against severe COVID-19 outcomes (any hospitalization, and intensive care units [ICU] admission or in-hospital death). In total, 273732 cases and 735 919 controls were included. VE against symptomatic infection after 2-doses vaccination was 86% (95% CI: 75-92%) for Delta and 70% (58-79%) for Omicron, 7-30 days post vaccination. Protection waned over time, reaching 60% (57-63%) against Delta and 20% (16.-24%) for Omicron BA.1 > 120 days after vaccination. The booster dose fully restored protection against symtpomatic Delta infection (95% [81-99%]) but only partially against symptomatic Omicron BA.1 infection (63% [59-67%]). VE against Delta-related severe outcomes was above 95% with 2 doses, and persisted for at least four months. Protection against any Omicron BA.1-hospitalization was 92% (65%-99%) at 8-30 days, and 82% (67%-91%) > 120 days from the second dose. Against BA.1 ICU admission or in-patient death, VE stood at 98% (0-100%) at 8-30 days, and was 90% (40-99%) > 120 days from the second dose. Protection confered by mRNA vaccines against severe disease caused by either Delta or Omicron BA.1 appeared high and sustained over time. Protection against symptomatic diseases after 2 doses decreased rapidly, especially against Omicron BA.1. A booster dose restored high protection against Delta but only a partial one against Omicron BA.1.
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Affiliation(s)
- Cynthia Raissa Tamandjou Tchuem
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Vincent Auvigne
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Sophie Vaux
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | | | - Juliette Paireau
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France; Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 2000, Paris, France.
| | - Stéphanie Monnier Besnard
- Direction des maladies non transmissibles et traumatismes, Unité traumatismes et Avancée en âge, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Amélie Gabet
- Direction des maladies non transmissibles et traumatismes, Unité Cardio-métabolique et respiratoire, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Nabil Benhajkassen
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Yann Le Strat
- Direction Appui, Traitements et Analyses de données, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Isabelle Parent Du Chatelet
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
| | - Daniel Levy-Bruhl
- Direction des maladies infectieuses - Unité infections respiratoires et vaccination, Santé publique France, 12 rue du Val d'Osne, Saint-Maurice 94415, France.
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12
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Peebles K, Arciuolo RJ, Romano AS, Sell J, Greene SK, Lim S, Mulready-Ward C, Ternier A, Badenhop B, Blaney K, Real JE, Spencer M, McPherson TD, Ahuja SD, Sullivan Meissner J, Zucker JR, Rosen JB. Pfizer-BioNTech Coronavirus Disease 2019 Vaccine Effectiveness Against Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Long-term Care Facility Staff With and Without Prior Infection in New York City, January-June 2021. J Infect Dis 2023; 227:533-542. [PMID: 36626187 PMCID: PMC9927076 DOI: 10.1093/infdis/jiac448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Evidence is accumulating of coronavirus disease 2019 (COVID-19) vaccine effectiveness among persons with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. METHODS We evaluated the effect against incident SARS-CoV-2 infection of (1) prior infection without vaccination, (2) vaccination (2 doses of Pfizer-BioNTech COVID-19 vaccine) without prior infection, and (3) vaccination after prior infection, all compared with unvaccinated persons without prior infection. We included long-term care facility staff in New York City aged <65 years with weekly SARS-CoV-2 testing from 21 January to 5 June 2021. Test results were obtained from state-mandated laboratory reporting. Vaccination status was obtained from the Citywide Immunization Registry. Cox proportional hazards models adjusted for confounding with inverse probability of treatment weights. RESULTS Compared with unvaccinated persons without prior infection, incident SARS-CoV-2 infection risk was lower in all groups: 54.6% (95% confidence interval, 38.0%-66.8%) lower among unvaccinated, previously infected persons; 80.0% (67.6%-87.7%) lower among fully vaccinated persons without prior infection; and 82.4% (70.8%-89.3%) lower among persons fully vaccinated after prior infection. CONCLUSIONS Two doses of Pfizer-BioNTech COVID-19 vaccine reduced SARS-CoV-2 infection risk by ≥80% and, for those with prior infection, increased protection from prior infection alone. These findings support recommendations that all eligible persons, regardless of prior infection, be vaccinated against COVID-19.
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Affiliation(s)
- Kathryn Peebles
- Correspondence: Kathryn Peebles, Division of Epidemiology, New York City Department of Health and Mental Hygiene, 42-09 28th St, Queens, NY 11101 ()
| | - Robert J Arciuolo
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Anthony S Romano
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Jessica Sell
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Sharon K Greene
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Sungwoo Lim
- Division of Epidemiology, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Candace Mulready-Ward
- Division of Family and Child Health, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Alexandra Ternier
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Brittan Badenhop
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Kathleen Blaney
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Joseph E Real
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Magdalene Spencer
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Tristan D McPherson
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Shama Desai Ahuja
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Jeanne Sullivan Meissner
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
| | - Jane R Zucker
- Division of Disease Control, New York City Department of Health and Mental Hygiene, Queens, New York, USA
- Immunization Services Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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13
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Wolf JM, Wolf LM, Bello GL, Maccari JG, Nasi LA. Molecular evolution of SARS-CoV-2 from December 2019 to August 2022. J Med Virol 2023; 95:e28366. [PMID: 36458547 PMCID: PMC9877913 DOI: 10.1002/jmv.28366] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/24/2022] [Accepted: 11/20/2022] [Indexed: 12/04/2022]
Abstract
Severe acute respiratorysyndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6.4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic. The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARSCoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history. A total of 2897 SARS-CoV-2 whole-genome sequences with available information from the country and sampling date (December 2019 to August 2022), were obtained and were evaluated by Bayesian approach. The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 (highest posterior density 95% [HPD95%]: 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18), and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between December 2019 and June 2020, 11 clades were detected (20I [Alpha] and 19A, 19B, 20B, 20C, 20A, 20D, 20E [EU1], 20F, 20H [Beta]). From July to December 2020, 4 clades were identified (20J [Gamma, V3], 21 C [Epsilon], 21D [Eta], and 21G [Lambda]). Between January and June 2021, 3 clades of the Delta variant were detected (21A, 21I, and 21J). Between July and December 2021, two variants were detected, Delta (21A, 21I, and 21J) and Omicron (21K, 21L, 22B, and 22C). Between January and June 2022, the Delta (21I and 21J) and Omicron (21K, 21L, and 22A) variants were detected. Finally, between July and August 2022, 3 clades of Omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the Omicron variant predominates worldwide, with the 21L clade branching into 3 (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the United Kingdom, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the United States of America, and Lambda in Peru. The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the Omicron).
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Affiliation(s)
| | - Lucas Michel Wolf
- Veterinary MedicineUFRGS (Universidade Federal do Rio Grande do Sul)Porto AlegreRio Grande do SulBrasil
| | - Graziele Lima Bello
- Programa Institutos Nacionais de Ciência e TecnologiaInstituto Nacional de Ciência e Tecnologia em Tuberculose (INCT‐TB)Porto AlegreRio Grande do SulBrasil
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14
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Gim H, Oh S, Lee H, Lee S, Seo H, Park Y, Park JH. Reduction in COVID-19 Vaccine Effectiveness against SARS-CoV-2 Variants in Seoul according to Age, Sex, and Symptoms: A Test-Negative Case-Control Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16958. [PMID: 36554839 PMCID: PMC9779328 DOI: 10.3390/ijerph192416958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND We evaluated vaccine effectiveness (VE) against infections with SARS-CoV-2 variants of concern in Seoul, the capital of the Republic of Korea, having the highest population density in the country, under real-world conditions. METHODS We evaluated the reduction in the effectiveness of mRNA and viral-vector COVID-19 vaccines against infection by the SARS-CoV-2 delta variant in a subpopulation from April 2021 to July 2021 who visited screening clinics in Seoul using a test-negative case-control study design. Moreover, we conducted a case-control study matching the ten-year-old age group, sex, healthcare workers, and five districts of Seoul, which are considered confounding factors. RESULTS The full VE in the pre-delta-dominant period was 95.0% (95% confidence interval [CI]: 91.2-97.2); however, it decreased to 61.1% (95% CI: 53.2-67.6) during the delta-dominant period. Notably, we found that COVID-19 VE was significantly decreased in individuals aged ≥80 years (52.9%, 95% CI: -9.9-79.8), men (50.6 %, 95% CI: 39.4-59.8), and asymptomatic individuals (49.8%, 95% CI: 36.5-60.3) during the widespread SARS-CoV-2 delta variant circulation. CONCLUSIONS Vaccine-mediated protection drastically declined during the delta-dominant period and in vulnerable groups. This study suggests the requirement for additional countermeasures, such as the administration of a booster vaccine, in vulnerable groups based on age, sex, and symptomatic manifestation.
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Affiliation(s)
- Hyerin Gim
- Infectious Disease Research Center, Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Soyoung Oh
- Infectious Disease Research Center, Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Heeda Lee
- Infectious Disease Research Center, Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Seul Lee
- Infectious Disease Research Center, Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Haesook Seo
- Infectious Disease Research Center, Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Yumi Park
- Citizen’s Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul 04524, Republic of Korea
| | - Jae-Hyun Park
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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15
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Bartsch YC, Chen JW, Kang J, Burns MD, St Denis KJ, Sheehan ML, Davis JP, Edlow AG, Balazs AB, Yonker LM, Alter G. BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children. NPJ Vaccines 2022; 7:158. [DOI: 10.1038/s41541-022-00575-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/03/2022] [Indexed: 12/04/2022] Open
Abstract
AbstractCurrently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of variants of concerns (VOCs) has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine-induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of VOCs that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine-induced antibody titers in children 5-11 years receiving two doses of the age-recommended 10 μg dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12–15 years) or adults receiving the 30 μg dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-VOC responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to VOCs in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2-induced antibody response in children, vaccine-induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to the attenuation of disease.
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16
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Chi WY, Li YD, Huang HC, Chan TEH, Chow SY, Su JH, Ferrall L, Hung CF, Wu TC. COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection. J Biomed Sci 2022; 29:82. [PMID: 36243868 PMCID: PMC9569411 DOI: 10.1186/s12929-022-00853-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/01/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) has been the most severe public health challenge in this century. Two years after its emergence, the rapid development and deployment of effective COVID-19 vaccines have successfully controlled this pandemic and greatly reduced the risk of severe illness and death associated with COVID-19. However, due to its ability to rapidly evolve, the SARS-CoV-2 virus may never be eradicated, and there are many important new topics to work on if we need to live with this virus for a long time. To this end, we hope to provide essential knowledge for researchers who work on the improvement of future COVID-19 vaccines. In this review, we provided an up-to-date summary for current COVID-19 vaccines, discussed the biological basis and clinical impact of SARS-CoV-2 variants and subvariants, and analyzed the effectiveness of various vaccine booster regimens against different SARS-CoV-2 strains. Additionally, we reviewed potential mechanisms of vaccine-induced severe adverse events, summarized current studies regarding immune correlates of protection, and finally, discussed the development of next-generation vaccines.
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Affiliation(s)
- Wei-Yu Chi
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Hsin-Che Huang
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy En Haw Chan
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Urology, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sih-Yao Chow
- Downstream Process Science, EirGenix Inc., Zhubei, Hsinchu, Taiwan R.O.C
| | - Jun-Han Su
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Louise Ferrall
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA
| | - T-C Wu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA.
- The Johns Hopkins Medical Institutions, CRB II Room 309, 1550 Orleans St, MD, 21231, Baltimore, USA.
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17
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Feng XL, Yu D, Zhang M, Li X, Zou QC, Ma W, Han JB, Xu L, Yang C, Qu W, Deng ZH, Long J, Long Y, Li M, Yao YG, Dong XQ, Zeng J, Li MH. Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates. Virol Sin 2022; 37:804-812. [PMID: 36167254 PMCID: PMC9507998 DOI: 10.1016/j.virs.2022.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 01/19/2023] Open
Abstract
The continuously arising of SARS-CoV-2 variants has been posting a great threat to public health safety globally, from B.1.17 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) to B.1.1.529 (Omicron). The emerging or re-emerging of the SARS-CoV-2 variants of concern is calling for the constant monitoring of their epidemics, pathogenicity and immune escape. In this study, we aimed to characterize replication and pathogenicity of the Alpha and Delta variant strains isolated from patients infected in Laos. The amino acid mutations within the spike fragment of the isolates were determined via sequencing. The more efficient replication of the Alpha and Delta isolates was documented than the prototyped SARS-CoV-2 in Calu-3 and Caco-2 cells, while such features were not observed in Huh-7, Vero E6 and HPA-3 cells. We utilized both animal models of human ACE2 (hACE2) transgenic mice and hamsters to evaluate the pathogenesis of the isolates. The Alpha and Delta can replicate well in multiple organs and cause moderate to severe lung pathology in these animals. In conclusion, the spike protein of the isolated Alpha and Delta variant strains was characterized, and the replication and pathogenicity of the strains in the cells and animal models were also evaluated.
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Affiliation(s)
- Xiao-Li Feng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Dandan Yu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mi Zhang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Xiaohong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Wentai Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Bao Han
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Ling Xu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Cuixian Yang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Wang Qu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Junyi Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Gang Yao
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing-Qi Dong
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China,Corresponding authors.
| | - Jianxiong Zeng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China,Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,Corresponding authors.
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Corresponding authors.
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18
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Ahmad A, Fawaz MAM, Aisha A. A comparative overview of SARS-CoV-2 and its variants of concern. LE INFEZIONI IN MEDICINA 2022; 30:328-343. [PMID: 36148164 PMCID: PMC9448317 DOI: 10.53854/liim-3003-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/05/2022] [Indexed: 06/16/2023]
Abstract
In December 2019, the severe acute respiratory syndrome 2 (SARS-CoV-2) coronavirus outbreak began in Wuhan, China, and quickly spread to practically every corner of the globe, killing millions of people. SARS-CoV-2 produced numerous variants, five of which have been identified as variants of concern (VOC) by the World Health Organization (WHO) (Alpha, Beta, Gamma, Delta, and Omicron). We conducted a comparative epidemiological analysis of SARS-CoV-2 and its VOC in this paper. We compared the effects of various spike (S) protein mutations in SARS-CoV-2 and its VOC on transmissibility, illness severity, hospitalization risk, fatality rate, immunological evasion, and vaccine efficacy in this review. We also looked into the clinical characteristics of patients infected with SARS-CoV-2 and its VOC.
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Affiliation(s)
- Aqeel Ahmad
- Department of Medical Biochemistry, College of Medicine, Shaqra University, Shaqra, Saudi Arabia
| | - Mohammed Ali Mullah Fawaz
- Department of Microbiology, Aware Medical Education and Research Institute (Aware Group), Shantivanam, Hyderabad, India
| | - Arafeen Aisha
- Department of Pathology, College of Medicine, Majmaah University, Majmaah, Saudi Arabia
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19
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Lee KS, Wong TY, Russ BP, Horspool AM, Miller OA, Rader NA, Givi JP, Winters MT, Wong ZYA, Cyphert HA, Denvir J, Stoilov P, Barbier M, Roan NR, Amin MS, Martinez I, Bevere JR, Damron FH. SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice. PLoS One 2022; 17:e0273430. [PMID: 36037222 PMCID: PMC9423646 DOI: 10.1371/journal.pone.0273430] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/08/2022] [Indexed: 01/27/2023] Open
Abstract
The COVID-19 pandemic has been fueled by SARS-CoV-2 novel variants of concern (VOC) that have increased transmissibility, receptor binding affinity, and other properties that enhance disease. The goal of this study is to characterize unique pathogenesis of the Delta VOC strain in the K18-hACE2-mouse challenge model. Challenge studies suggested that the lethal dose of Delta was higher than Alpha or Beta strains. To characterize the differences in the Delta strain's pathogenesis, a time-course experiment was performed to evaluate the overall host response to Alpha or Delta variant challenge. qRT-PCR analysis of Alpha- or Delta-challenged mice revealed no significant difference between viral RNA burden in the lung, nasal wash or brain. However, histopathological analysis revealed high lung tissue inflammation and cell infiltration following Delta- but not Alpha-challenge at day 6. Additionally, pro-inflammatory cytokines were highest at day 6 in Delta-challenged mice suggesting enhanced pneumonia. Total RNA-sequencing analysis of lungs comparing challenged to no challenge mice revealed that Alpha-challenged mice have more total genes differentially activated. Conversely, Delta-challenged mice have a higher magnitude of differential gene expression. Delta-challenged mice have increased interferon-dependent gene expression and IFN-γ production compared to Alpha. Analysis of TCR clonotypes suggested that Delta challenged mice have increased T-cell infiltration compared to Alpha challenged. Our data suggest that Delta has evolved to engage interferon responses in a manner that may enhance pathogenesis. The in vivo and in silico observations of this study underscore the need to conduct experiments with VOC strains to best model COVID-19 when evaluating therapeutics and vaccines.
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Affiliation(s)
- Katherine S. Lee
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Ting Y. Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Brynnan P. Russ
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Alexander M. Horspool
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Olivia A. Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Nathaniel A. Rader
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Jerome P. Givi
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, WV, United States of America
| | - Michael T. Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
| | - Zeriel Y. A. Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Holly A. Cyphert
- Department of Biological Sciences, Marshall University, Huntington, WV, United States of America
| | - James Denvir
- Department of Biomedical Sciences, Marshall University, Huntington, WV, United States of America
| | - Peter Stoilov
- Department of Biochemistry, School of Medicine, West Virginia University Morgantown, Morgantown, WV, United States of America
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Nadia R. Roan
- Department or Urology, University of California, San Francisco, San Francisco, CA, United States of America
- Gladstone Institute of Virology, San Francisco, CA, United States of America
| | - Md. Shahrier Amin
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, WV, United States of America
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- West Virginia University Cancer Institute, School of Medicine, Morgantown, WV, United States of America
| | - Justin R. Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
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20
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Cao L, Lou J, Chan SY, Zheng H, Liu C, Zhao S, Li Q, Mok CKP, Chan RWY, Chong MKC, Wu WKK, Chen Z, Wong ELY, Chan PKS, Zee BCY, Yeoh EK, Wang MH. Rapid evaluation of COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 variants by analysis of genetic distance. Nat Med 2022; 28:1715-1722. [PMID: 35710987 PMCID: PMC9388371 DOI: 10.1038/s41591-022-01877-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 05/20/2022] [Indexed: 11/20/2022]
Abstract
Timely evaluation of the protective effects of Coronavirus Disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is urgently needed to inform pandemic control planning. Based on 78 vaccine efficacy or effectiveness (VE) data from 49 studies and 1,984,241 SARS-CoV-2 sequences collected from 31 regions, we analyzed the relationship between genetic distance (GD) of circulating viruses against the vaccine strain and VE against symptomatic infection. We found that the GD of the receptor-binding domain of the SARS-CoV-2 spike protein is highly predictive of vaccine protection and accounted for 86.3% (P = 0.038) of the VE change in a vaccine platform-based mixed-effects model and 87.9% (P = 0.006) in a manufacturer-based model. We applied the VE-GD model to predict protection mediated by existing vaccines against new genetic variants and validated the results by published real-world and clinical trial data, finding high concordance of predicted VE with observed VE. We estimated the VE against the Delta variant to be 82.8% (95% prediction interval: 68.7-96.0) using the mRNA vaccine platform, closely matching the reported VE of 83.0% from an observational study. Among the four sublineages of Omicron, the predicted VE varied between 11.9% and 33.3%, with the highest VE predicted against BA.1 and the lowest against BA.2, using the mRNA vaccine platform. The VE-GD framework enables predictions of vaccine protection in real time and offers a rapid evaluation method against novel variants that may inform vaccine deployment and public health responses.
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Affiliation(s)
- Lirong Cao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Jingzhi Lou
- Beth Bioinformatics Co. Ltd., Hong Kong SAR, China
| | - See Yeung Chan
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Beth Bioinformatics Co. Ltd., Hong Kong SAR, China
| | - Hong Zheng
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Caiqi Liu
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shi Zhao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Qi Li
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Chris Ka Pun Mok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Renee Wan Yi Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Marc Ka Chun Chong
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - William Ka Kei Wu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eliza Lai Yi Wong
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Health Systems and Policy Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul Kay Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Benny Chung Ying Zee
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Eng Kiong Yeoh
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Health Systems and Policy Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Maggie Haitian Wang
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.
- CUHK Shenzhen Research Institute, Shenzhen, China.
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21
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Alexandre M, Marlin R, Prague M, Coleon S, Kahlaoui N, Cardinaud S, Naninck T, Delache B, Surenaud M, Galhaut M, Dereuddre-Bosquet N, Cavarelli M, Maisonnasse P, Centlivre M, Lacabaratz C, Wiedemann A, Zurawski S, Zurawski G, Schwartz O, Sanders RW, Le Grand R, Levy Y, Thiébaut R. Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection. eLife 2022; 11:75427. [PMID: 35801637 PMCID: PMC9282856 DOI: 10.7554/elife.75427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
The definition of correlates of protection is critical for the development of next-generation SARS-CoV-2 vaccine platforms. Here, we propose a model-based approach for identifying mechanistic correlates of protection based on mathematical modelling of viral dynamics and data mining of immunological markers. The application to three different studies in non-human primates evaluating SARS-CoV-2 vaccines based on CD40-targeting, two-component spike nanoparticle and mRNA 1273 identifies and quantifies two main mechanisms that are a decrease of rate of cell infection and an increase in clearance of infected cells. Inhibition of RBD binding to ACE2 appears to be a robust mechanistic correlate of protection across the three vaccine platforms although not capturing the whole biological vaccine effect. The model shows that RBD/ACE2 binding inhibition represents a strong mechanism of protection which required significant reduction in blocking potency to effectively compromise the control of viral replication.
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Affiliation(s)
- Marie Alexandre
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mélanie Prague
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Severin Coleon
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Benoit Delache
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Mathilde Galhaut
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | | | | | - Sandra Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | - Gerard Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | | | - Rogier W Sanders
- Department of Medical Microbiology, University of Amsterdam, Amsterdam, Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Yves Levy
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Rodolphe Thiébaut
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
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22
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Manipulation of Spray-Drying Conditions to Develop an Inhalable Ivermectin Dry Powder. Pharmaceutics 2022; 14:pharmaceutics14071432. [PMID: 35890327 PMCID: PMC9325229 DOI: 10.3390/pharmaceutics14071432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, predominantly affects the respiratory tract. As a consequence, it seems intuitive to develop antiviral agents capable of targeting the virus right on its main anatomical site of replication. Ivermectin, a U.S. FDA-approved anti-parasitic drug, was originally shown to inhibit SARS-CoV-2 replication in vitro, albeit at relatively high concentrations, which is difficult to achieve in the lung. In this study, we tested the spray-drying conditions to develop an inhalable dry powder formulation that could ensure sufficient antiviral drug concentrations, which are difficult to achieve in the lungs based on the oral dosage used in clinical trials. Here, by using ivermectin as a proof-of-concept, we evaluated spray-drying conditions that could lead to the development of antivirals in an inhalable dry powder formulation, which could then be used to ensure sufficient drug concentrations in the lung. Thus, we used ivermectin in proof-of-principle experiments to evaluate our system, including physical characterization and in vitro aerosolization of prepared dry powder. The ivermectin dry powder was prepared with a mini spray-dryer (Buchi B-290), using a 23 factorial design and manipulating spray-drying conditions such as feed concentration (0.2% w/v and 0.8% w/v), inlet temperature (80 °C and 100 °C) and presence/absence of L-leucine (0% and 10%). The prepared dry powder was in the size range of 1−5 μm and amorphous in nature with wrinkle morphology. We observed a higher fine particle fraction (82.5 ± 1.4%) in high feed concentration (0.8% w/v), high inlet temperature (100 °C) and the presence of L-leucine (10% w/w). The stability study conducted for 28 days confirmed that the spray-dried powder was stable at 25 ± 2 °C/<15% RH and 25 ± 2 °C/ 53% RH. Interestingly, the ivermectin dry powder formulation inhibited SARS-CoV-2 replication in vitro with a potency similar to ivermectin solution (EC50 values of 15.8 µM and 14.1 µM, respectively), with a comparable cell toxicity profile in Calu-3 cells. In summary, we were able to manipulate the spray-drying conditions to develop an effective ivermectin inhalable dry powder. Ongoing studies based on this system will allow the development of novel formulations based on single or combinations of drugs that could be used to inhibit SARS-CoV-2 replication in the respiratory tract.
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Silverman RA, Ceci A, Cohen A, Helmick M, Short E, Bordwine P, Friedlander MJ, Finkielstein CV. Vaccine Effectiveness during Outbreak of COVID-19 Alpha (B.1.1.7) Variant in Men's Correctional Facility, United States. Emerg Infect Dis 2022; 28:1313-1320. [PMID: 35731137 PMCID: PMC9239860 DOI: 10.3201/eid2807.220091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In April 2021, a COVID-19 outbreak occurred at a correctional facility in rural Virginia, USA. Eighty-four infections were identified among 854 incarcerated persons by facilitywide testing with reverse transcription quantitative PCR (qRT-PCR). We used whole-genome sequencing to link all infections to 2 employees infected with the B.1.1.7α (UK) variant. The relative risk comparing unvaccinated to fully vaccinated persons (mRNA-1273 [Moderna, https://www.modernatx.com]) was 7.8 (95% CI 4.8–12.7), corresponding to a vaccine effectiveness of 87.1% (95% CI 79.0%–92.1%). Average qRT-PCR cycle threshold values were lower, suggesting higher viral loads, among unvaccinated infected than vaccinated cases for the nucleocapsid, envelope, and spike genes. Vaccination was highly effective at preventing SARS-CoV-2 infection in this high-risk setting. This approach can be applied to similar settings to estimate vaccine effectiveness as variants emerge to guide public health strategies during the ongoing pandemic.
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SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study. Clin Microbiol Infect 2022; 28:1471-1476. [PMID: 35777605 PMCID: PMC9239704 DOI: 10.1016/j.cmi.2022.05.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/31/2022]
Abstract
OBJECTIVES This study assessed the roles of various exposures and personal protective equipment (PPE) use on healthcare workers'risk (HCWs) of COVID-19 working in primary care, long-term-care facilities or hospitals. METHODS We conducted a matched case-control (1:1) study (10 April-9 July 2021). Cases (HCWs with confirmed COVID-19) and controls (HCWs without any COVID-19-positive test or symptoms) were invited by email to complete an online questionnaire on their exposures and PPE use over the 10-day period preceding inclusion. Risk factors were analyzed using multivariable conditional logistic regression. RESULTS A total of 2076 cases and 2076 matched controls were included. The analysis retained exposure to an infected person outside work (adjusted odd ratio, 19.9 [95% confidence intervaI, 12.4-31.9]), an infected colleague (2.26 [1.53-3.33]) or COVID-19 patients (2.37 [1.66-3.40]), as independent predictors of COVID-19 in HCWs, while partial (0.30 [0.22-0.40]) or complete (0.19 [0.14-0.27]) immunization was protective. Eye protection (0.57 [0.37-0.87]) and wearing a gown (0.58 [0.34-0.97]) for COVID-19 patient care were protective, while wearing an apron slightly increased the risk of infection (1.47 [1.00-2.18]). Protection of N95 respirators and surgical facemasks did not differ. Compared to medical professions, being a nurse (3.79 [2.50-5.76]) or a nurse's aide (9.08 [5.30-15.5]) was associated with COVID-19. Results were consistent across all healthcare settings. CONCLUSIONS HCWs were more likely to get COVID-19 in their personal sphere than during occupational activities. Our results suggest that eye protection for HCWs during patient care should be actively promoted.
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Saberiyan M, Karimi E, Khademi Z, Movahhed P, Safi A, Mehri-Ghahfarrokhi A. SARS-CoV-2: phenotype, genotype, and characterization of different variants. Cell Mol Biol Lett 2022; 27:50. [PMID: 35715738 PMCID: PMC9204680 DOI: 10.1186/s11658-022-00352-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), a major international public health concern. Because of very similar amino acid sequences of the seven domain names, SARS-CoV-2 belongs to the Coronavirinae subfamily of the family Coronaviridae, order Nidovirales, and realm Riboviria, placed in exceptional clusters, but categorized as a SARS-like species. As the RNA virus family with the longest genome, the Coronaviridae genome consists of a single strand of positive RNA (25-32 kb in length). Four major structural proteins of this genome include the spike (S), membrane (M), envelope (E), and the nucleocapsid (N) protein, all of which are encoded within the 3' end of the genome. By engaging with its receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 infects host cells. According to the most recent epidemiological data, as the illness spread globally, several genetic variations of SARS-CoV-2 appeared quickly, with the World Health Organization (WHO) naming 11 of them. Among these, seven SARS-CoV-2 subtypes have received the most attention. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.617.2) are now designated as variations of concern (VOC) (B.1.1.529). Lambda (C.37) and Mu are variations of interest (VOI) (B.1.621). The remaining six are either being monitored or are no longer considered a threat. On the basis of studies done so far, antiviral drugs, antibiotics, glucocorticoids, recombinant intravenous immunoglobulin, plasma therapy, and IFN-α2b have been used to treat patients. Moreover, full vaccination is associated with lower infection and helps prevent transmission, but the risk of infection cannot be eliminated completely in vaccinated people.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Elham Karimi
- Department of Medical Genetics, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Khademi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Parvaneh Movahhed
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Safi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ameneh Mehri-Ghahfarrokhi
- Clinical Research Development Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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Cortés-Sarabia K, Gutiérrez-Torres M, Mendoza-Renteria EM, Leyva-Vázquez MA, Vences-Velázquez A, Hernández-Sotelo D, Beltrán-Anaya FO, Del Moral-Hernández O, Illades-Aguiar B. Variation in the Humoral Immune Response Induced by the Administration of the BNT162b2 Pfizer/BioNTech Vaccine: A Systematic Review. Vaccines (Basel) 2022; 10:vaccines10060909. [PMID: 35746517 PMCID: PMC9229764 DOI: 10.3390/vaccines10060909] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
The BNT162b2 Pfizer/BioNTech vaccine was the first emergency approved vaccine during the COVID-19 pandemic. The aim of this systematic review was to examine the variations in the humoral immune response induced by the administration of the BNT162b2 vaccine in patients with previous SARS-CoV-2 infection, the elderly, and those with comorbidities and immunosuppression states. Additionally, we analyzed the effect of generated neutralizing antibodies against the new variants of concern of SARS-CoV-2. Pubmed, Science Direct, Mendeley, and WorldWide Science were searched between 1 January 2020 and October 2021 using the keywords “BNT162b2”, “serology”, “comorbidity”, “immunosuppression”, and “variants of concern”dA total of 20 peer-reviewed publications were selected. The analysis showed that those individuals with previous infections have a considerably higher antibody response after the administration of BNT162b2 vaccine in contrast with seronegative individuals. With regard to variation in immune responses, elderly individuals, patients with cancer, or patients who had undergone a kidney transplant, dialysis, or who were pregnant had a lower antibody response in comparison to healthy individuals. Finally, antibodies developed against the S protein produced by the BNT162b2 vaccine, possessed lower neutralizing activity against the alpha, beta, gamma, and delta variants of SARS-CoV-2. In conclusion, patients with immunodeficiencies and comorbidities have a lesser antibody response, about which further studies need to be performed in order to analyze the effectiveness and duration of the humoral immunity associated with vaccination in these specific populations.
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Affiliation(s)
- Karen Cortés-Sarabia
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico; (K.C.-S.); (M.G.-T.); (E.M.M.-R.); (A.V.-V.)
| | - Mayralina Gutiérrez-Torres
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico; (K.C.-S.); (M.G.-T.); (E.M.M.-R.); (A.V.-V.)
| | - Escarlet Maleny Mendoza-Renteria
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico; (K.C.-S.); (M.G.-T.); (E.M.M.-R.); (A.V.-V.)
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
| | - Amalia Vences-Velázquez
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico; (K.C.-S.); (M.G.-T.); (E.M.M.-R.); (A.V.-V.)
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigénetica del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
| | - Oscar Del Moral-Hernández
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
- Correspondence: (O.D.M.-H.); (B.I.-A.)
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
- Correspondence: (O.D.M.-H.); (B.I.-A.)
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Gong W, Parkkila S, Wu X, Aspatwar A. SARS-CoV-2 variants and COVID-19 vaccines: Current challenges and future strategies. Int Rev Immunol 2022; 42:393-414. [PMID: 35635216 DOI: 10.1080/08830185.2022.2079642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022]
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite strict control measures implemented worldwide and immunization using novel vaccines, the pandemic continues to rage due to emergence of several variants of SARS-CoV-2 with increased transmission and immune escape. The rapid spread of variants of concern (VOC) in the recent past has created a massive challenge for the control of COVID-19 pandemic via the currently used vaccines. Vaccines that are safe and effective against the current and future variants of SARS-CoV-2 are essential in controlling the COVID-19 pandemic. Rapid production and massive rollout of next-generation vaccines against the variants are key steps to control the COVID-19 pandemic and to help us return to normality. Coordinated surveillance of SARS-CoV-2, rapid redesign of new vaccines and extensive vaccination are needed to counter the current SARS-CoV-2 variants and prevent the emergence of new variants. In this article, we review the latest information on the VOCs and variants of interest (VOIs) and present the information on the clinical trials that are underway on evaluating the effectiveness of COVID-19 vaccines on VOCs. We also discuss the current challenges posed by the VOCs in controlling the COVID-19 pandemic and future strategies to overcome the threat posed by the highly virulent and rapidly transmissible variants of SARS-CoV2.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Bignon E, Marazzi M, Grandemange S, Monari A. Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer. Chem Sci 2022; 13:6098-6105. [PMID: 35685814 PMCID: PMC9132136 DOI: 10.1039/d2sc00108j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms. Among the complex pathways induced by the viral infection, autophagy is particularly crucial and is strongly influenced by the action of the non-structural protein 6 (Nsp6) interacting with the endoplasmic reticulum membrane. Importantly, differently from other non-structural proteins, Nsp6 is mutated in the recently emerged Omicron variant, suggesting a possible different role of autophagy. In this contribution we explore, for the first time, the structural properties of Nsp6 thanks to long-timescale molecular dynamics simulations and machine learning analysis, identifying the interaction patterns with the lipid membrane. We also show how the mutation brought by the Omicron variant may indeed modify some of the specific interactions, and more particularly help anchor the viral protein to the lipid bilayer interface. The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms.![]()
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Affiliation(s)
| | - Marco Marazzi
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering and Chemical Research Institute "Andres M. del Rio" (IQAR), Universidad de Alcalá 28805 Alcalá de Hénares Spain
| | | | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS F-75006 Paris France
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29
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Zeng B, Gao L, Zhou Q, Yu K, Sun F. Effectiveness of COVID-19 vaccines against SARS-CoV-2 variants of concern: a systematic review and meta-analysis. BMC Med 2022; 20:200. [PMID: 35606843 PMCID: PMC9126103 DOI: 10.1186/s12916-022-02397-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND It was urgent and necessary to synthesize the evidence for vaccine effectiveness (VE) against SARS-CoV-2 variants of concern (VOC). We conducted a systematic review and meta-analysis to provide a comprehensive overview of the effectiveness profile of COVID-19 vaccines against VOC. METHODS Published randomized controlled trials (RCTs), cohort studies, and case-control studies that evaluated the VE against VOC (Alpha, Beta, Gamma, Delta, or Omicron) were searched until 4 March 2022. Pooled estimates and 95% confidence intervals (CIs) were calculated using random-effects meta-analysis. VE was defined as (1-estimate). RESULTS Eleven RCTs (161,388 participants), 20 cohort studies (52,782,321 participants), and 26 case-control studies (2,584,732 cases) were included. Eleven COVID-19 vaccines (mRNA-1273, BNT162b2, ChAdOx1, Ad26.COV2.S, NVX-CoV2373, BBV152, CoronaVac, BBIBP-CorV, SCB-2019, CVnCoV, and HB02) were included in this analysis. Full vaccination was effective against Alpha, Beta, Gamma, Delta, and Omicron variants, with VE of 88.0% (95% CI, 83.0-91.5), 73.0% (95% CI, 64.3-79.5), 63.0% (95% CI, 47.9-73.7), 77.8% (95% CI, 72.7-82.0), and 55.9% (95% CI, 40.9-67.0), respectively. Booster vaccination was more effective against Delta and Omicron variants, with VE of 95.5% (95% CI, 94.2-96.5) and 80.8% (95% CI, 58.6-91.1), respectively. mRNA vaccines (mRNA-1273/BNT162b2) seemed to have higher VE against VOC over others; significant interactions (pinteraction < 0.10) were observed between VE and vaccine type (mRNA vaccines vs. not mRNA vaccines). CONCLUSIONS Full vaccination of COVID-19 vaccines is highly effective against Alpha variant, and moderate effective against Beta, Gamma, and Delta variants. Booster vaccination is more effective against Delta and Omicron variants. mRNA vaccines seem to have higher VE against Alpha, Beta, Gamma, and Delta variants over others.
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Affiliation(s)
- Baoqi Zeng
- Department of Science and Education, Peking University Binhai Hospital, Tianjin, China
| | - Le Gao
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Qingxin Zhou
- Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Kai Yu
- Department of Science and Education, Peking University Binhai Hospital, Tianjin, China.
| | - Feng Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Centre, Beijing, China.
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30
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Peng L, Renauer PA, Ökten A, Fang Z, Park JJ, Zhou X, Lin Q, Dong MB, Filler R, Xiong Q, Clark P, Lin C, Wilen CB, Chen S. Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2. Cell Rep Med 2022; 3:100634. [PMID: 35561673 PMCID: PMC9040489 DOI: 10.1016/j.xcrm.2022.100634] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/06/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
Lipid nanoparticle (LNP)-mRNA vaccines offer protection against COVID-19; however, multiple variant lineages caused widespread breakthrough infections. Here, we generate LNP-mRNAs specifically encoding wild-type (WT), B.1.351, and B.1.617 SARS-CoV-2 spikes, and systematically study their immune responses. All three LNP-mRNAs induced potent antibody and T cell responses in animal models; however, differences in neutralization activity have been observed between variants. All three vaccines offer potent protection against in vivo challenges of authentic viruses of WA-1, Beta, and Delta variants. Single-cell transcriptomics of WT- and variant-specific LNP-mRNA-vaccinated animals reveal a systematic landscape of immune cell populations and global gene expression. Variant-specific vaccination induces a systemic increase of reactive CD8 T cells and altered gene expression programs in B and T lymphocytes. BCR-seq and TCR-seq unveil repertoire diversity and clonal expansions in vaccinated animals. These data provide assessment of efficacy and direct systems immune profiling of variant-specific LNP-mRNA vaccination in vivo.
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Affiliation(s)
- Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Arya Ökten
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Zhenhao Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Qianqian Lin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Department of Immunobiology, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA
| | - Renata Filler
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA
| | - Paul Clark
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA.
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA; Department of Cell Biology, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
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31
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Charonis SA, James LM, Georgopoulos AP. SARS-CoV-2 in silico binding affinity to human leukocyte antigen (HLA) Class II molecules predicts vaccine effectiveness across variants of concern (VOC). Sci Rep 2022; 12:8074. [PMID: 35577837 PMCID: PMC9109665 DOI: 10.1038/s41598-022-11956-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/26/2022] [Indexed: 11/08/2022] Open
Abstract
There is widespread concern about the clinical effectiveness of current vaccines in preventing Covid-19 caused by SARS-CoV-2 Variants of Concern (Williams in Lancet Respir Med 29:333-335, 2021; Hayawi in Vaccines 9:1305, 2021), including those identified at present (Alpha, Beta, Gamma, Delta, Omicron) and possibly new ones arising in the future. It would be valuable to be able to predict vaccine effectiveness for any variant. Here we offer such an estimate of predicted vaccine effectiveness for any SARS-CoV-2 variant based on the amount of overlap of in silico high binding affinity of the variant and Wildtype spike glycoproteins to a pool of frequent Human Leukocyte Antigen Class II molecules which are necessary for initiating antibody production (Blum et al. in Annu Rev Immunol 31:443-473, 2013). The predictive model was strong (r = 0.910) and statistically significant (P = 0.013).
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Affiliation(s)
- Spyros A Charonis
- The HLA SARS-CoV-2 Research Group, Department of Veterans Affairs Health Care System, Brain Sciences Center (11B), Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Lisa M James
- The HLA SARS-CoV-2 Research Group, Department of Veterans Affairs Health Care System, Brain Sciences Center (11B), Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Apostolos P Georgopoulos
- The HLA SARS-CoV-2 Research Group, Department of Veterans Affairs Health Care System, Brain Sciences Center (11B), Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA.
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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Lopera TJ, Chvatal-Medina M, Flórez-Álvarez L, Zapata-Cardona MI, Taborda NA, Rugeles MT, Hernandez JC. Humoral Response to BNT162b2 Vaccine Against SARS-CoV-2 Variants Decays After Six Months. Front Immunol 2022; 13:879036. [PMID: 35585980 PMCID: PMC9108166 DOI: 10.3389/fimmu.2022.879036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 vaccines have shown very high effectiveness in real-world scenarios. However, there is compelling evidence for a fast-paced waning of immunity. The increasing number of new variants that could alter the severity, transmissibility, and potential to evade the immune response raised significant concern. Therefore, elucidating changes in the humoral immune response against viral variants induced by vaccines over time is crucial for improving immunization protocols. We carried out a 6-month longitudinal prospective study in which 60 individuals between 21 and 71 years of age who have received the complete scheme of the BNT162b2 vaccine were followed to determine titers of serum neutralizing activity. The neutralizing capacity was measured at one, three, and six-months post-vaccination by plaque reduction neutralization assay using SARS-CoV-2 B.1 (D614G) and the Gamma, Alpha, Delta, and Mu variants. Data were analyzed using GraphPad 5.0. Neutralizing activity against five different SARS-CoV-2 variants was detected in the serum samples of all vaccinated participants to a different extent after one month, with a progressive decrease according to age and gender. Overall, after one month of vaccination, the neutralizing titer was lower for all evaluated variants when compared to B.1, most remarkable against Delta and Mu, with a reduction of 83.1% and 92.3%, respectively. In addition, the Titer at 3- or 6-months follow-up decreased dramatically for all variants. Our results support the decaying of serum neutralizing activity, both over time and across SARS-CoV-2 variants, being more significant in older men. Since Delta and Mu appear to evade the neutralizing activity, these and further new variants of immune escape mutations should be considered for novel vaccine formulations.
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Affiliation(s)
- Tulio J. Lopera
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | | | - Natalia A. Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan C. Hernandez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- *Correspondence: Juan C. Hernandez,
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Effectiveness of COVID-19 Vaccines in the General Population of an Italian Region before and during the Omicron Wave. Vaccines (Basel) 2022; 10:vaccines10050662. [PMID: 35632418 PMCID: PMC9146679 DOI: 10.3390/vaccines10050662] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 01/27/2023] Open
Abstract
We performed a cohort analysis of the entire population of Abruzzo, Italy, to evaluate the real-world effectiveness of SARS-CoV-2 vaccines against infection, COVID-19 hospitalization or death, over time and during the Omicron wave. All resident or domiciled subjects were included, and official vaccination, COVID-19, demographic, hospital and co-pay exemption datasets were extracted up to 18 February 2022. Multivariable analyses were adjusted for age, gender, hypertension, diabetes, major cardio- and cerebrovascular events, COPD, kidney diseases, and cancer. During the follow-up (average 244 days), 252,365 subjects received three vaccine doses (of BNT162b2, ChAdOx1 nCoV-19, mRNA-1273 or JNJ-78436735), 684,860 two doses, 29,401 one dose, and 313,068 no dose. Overall, 13.4% of the individuals were infected with SARS-CoV-2 (n = 170,761); 1.1% of them had severe COVID-19, and 0.6% died. Compared with the unvaccinated, those receiving two or three vaccine doses showed an 80% to 90% lower risk of COVID-19 hospitalization or death. Protection decreased during the Omicron wave and six months after the last dose, but it remained substantial. Lethal disease was uncommon during the Omicron wave and in the young population, even among the unvaccinated. Some of the current policies may need a re-evaluation in light of these findings. The results from the Omicron wave will inevitably require confirmation.
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Golec M, Fronczek M, Zembala-John J, Chrapiec M, Konka A, Wystyrk K, Botor H, Brzoza Z, Kasperczyk S, Bułdak RJ. Early and Longitudinal Humoral Response to the SARS-CoV-2 mRNA BNT162b2 Vaccine in Healthcare Workers: Significance of BMI, Adipose Tissue and Muscle Mass on Long-Lasting Post-Vaccinal Immunity. Viruses 2022; 14:868. [PMID: 35632610 PMCID: PMC9143881 DOI: 10.3390/v14050868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND This study aimed to investigate the early and longitudinal humoral response in Healthcare Workers (HCWs) after two doses of the BNT162b2 vaccine and to assess the association between metabolic and anthropometric parameters and the humoral response after vaccination. METHODS The study included 243 fully vaccinated HCWs: 25.50% previously infected with SARS-CoV-2 (with prior history of COVID-19-PH) and 74.40%-uninfected, seronegative before the first vaccination (with no prior history of COVID-19-NPH). IgG antibodies were measured, and sera were collected: prior to the vaccination, 21 days after the first dose, and 14 days and 8 months after the second dose. RESULTS 21 days after the first dose, 90.95% of individuals were seropositive; 14 days after the second dose, persistent immunity was observed in 99.18% HCWs, 8 months after complete vaccination-in 61.73%. Statistical analysis revealed that HCWs with PH had a greater chance of maintaining a humoral response beyond eight months after vaccination. Increased muscle mass, decreased fat mass, and younger age may positively affect long-term immunity. Smokers have a reduced chance of developing immunity compared to non-smokers. CONCLUSIONS Fully vaccinated HCWs with PH are more likely to be seropositive than fully inoculated volunteers with NPH.
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Affiliation(s)
- Marlena Golec
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
| | - Martyna Fronczek
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, H. Jordana 38, 41-808 Zabrze, Poland
| | - Joanna Zembala-John
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
- Department of Medicine and Environmental Epidemiology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, H. Jordana 19, 41-808 Zabrze, Poland
- Silesian Center for Heart Diseases in Zabrze, M. Curie-Skłodowskiej 9, 41-800 Zabrze, Poland
| | - Martyna Chrapiec
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
| | - Adam Konka
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
| | - Karolina Wystyrk
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
| | - Hanna Botor
- Acellmed Ltd., M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland;
| | - Zenon Brzoza
- Department of Internal Diseases, Allergology, Endocrinology and Gastroenterology, Institute of Medical Sciences, University of Opole, Al. W. Witosa 26, 40-451 Opole, Poland;
| | - Sławomir Kasperczyk
- Department of Biochemistry, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, H. Jordana 19, 41-808 Zabrze, Poland;
| | - Rafał Jakub Bułdak
- Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C, 41-800 Zabrze, Poland; (M.F.); (J.Z.-J.); (M.C.); (A.K.); (K.W.)
- Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, 45-052 Opole, Poland
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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Machado BAS, Hodel KVS, Fonseca LMDS, Pires VC, Mascarenhas LAB, da Silva Andrade LPC, Moret MA, Badaró R. The Importance of Vaccination in the Context of the COVID-19 Pandemic: A Brief Update Regarding the Use of Vaccines. Vaccines (Basel) 2022; 10:591. [PMID: 35455340 PMCID: PMC9027942 DOI: 10.3390/vaccines10040591] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic has led the world to undertake the largest vaccination campaign in human history. In record time, unprecedented scientific and governmental efforts have resulted in the acquisition of immunizers utilizing different technologies (nucleotide acids, viral vectors, inactivated and protein-based vaccines). Currently, 33 vaccines have already been approved by regulatory agencies in different countries, and more than 10 billion doses have been administered worldwide. Despite the undeniable impact of vaccination on the control of the pandemic, the recurrent emergence of new variants of interest has raised new challenges. The recent viral mutations precede new outbreaks that rapidly spread at global proportions. In addition, reducing protective efficacy rates have been observed among the main authorized vaccines. Besides these issues, several other crucial issues for the appropriate combatting of the pandemic remain uncertain or under investigation. Particularly noteworthy issues include the use of vaccine-boosting strategies to increase protection; concerns related to the long-term safety of vaccines, child immunization reliability and uncommon adverse events; the persistence of the virus in society; and the transition from a pandemic to an endemic state. In this review, we describe the updated scenario regarding SARS-CoV-2 variants and COVID-19 vaccines. In addition, we outline current discussions covering COVID-19 vaccine safety and efficacy, and the future pandemic perspectives.
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Affiliation(s)
- Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Larissa Moraes dos Santos Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Vinícius Couto Pires
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Luis Alberto Brêda Mascarenhas
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Leone Peter Correia da Silva Andrade
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
| | - Marcelo Albano Moret
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
- UNEB, Universidade do Estado da Bahia, Salvador 41150-000, Brazil
| | - Roberto Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (V.C.P.); (L.A.B.M.); (L.P.C.d.S.A.); (M.A.M.); (R.B.)
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To A, Wong TAS, Lieberman MM, Thompson K, Ball AH, Pessaint L, Greenhouse J, Daham N, Cook A, Narvaez B, Flinchbaugh Z, Van Ry A, Yalley-Ogunro J, Elyard HA, Lai CY, Donini O, Lehrer AT. A Recombinant Subunit Vaccine Induces a Potent, Broadly Neutralizing, and Durable Antibody Response in Macaques against the SARS-CoV-2 P.1 (Gamma) Variant. ACS Infect Dis 2022; 8:825-840. [PMID: 35263081 PMCID: PMC8938837 DOI: 10.1021/acsinfecdis.1c00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 12/12/2022]
Abstract
FDA-approved and emergency use-authorized vaccines using new mRNA and viral-vector technology are highly effective in preventing moderate to severe disease; however, information on their long-term efficacy and protective breadth against severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) is currently scarce. Here, we describe the durability and broad-spectrum VOC immunity of a prefusion-stabilized spike (S) protein adjuvanted with liquid or lyophilized CoVaccine HT in cynomolgus macaques. This recombinant subunit vaccine is highly immunogenic and induces robust spike-specific and broadly neutralizing antibody responses effective against circulating VOCs (B.1.351 [Beta], P.1 [Gamma], and B.1.617 [Delta]) for at least three months after the final boost. Protective efficacy and postexposure immunity were evaluated using a heterologous P.1 challenge nearly three months after the last immunization. Our results indicate that while immunization with both high and low S doses shorten and reduce viral loads in the upper and lower respiratory tract, a higher antigen dose is required to provide durable protection against disease as vaccine immunity wanes. Histologically, P.1 infection causes similar COVID-19-like lung pathology as seen with early pandemic isolates. Postchallenge IgG concentrations were restored to peak immunity levels, and vaccine-matched and cross-variant neutralizing antibodies were significantly elevated in immunized macaques indicating an efficient anamnestic response. Only low levels of P.1-specific neutralizing antibodies with limited breadth were observed in control (nonvaccinated but challenged) macaques, suggesting that natural infection may not prevent reinfection by other VOCs. Overall, these results demonstrate that a properly dosed and adjuvanted recombinant subunit vaccine can provide protective immunity against circulating VOCs for at least three months.
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Affiliation(s)
- Albert To
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Teri Ann S. Wong
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Michael M. Lieberman
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Karen Thompson
- Department of Pathology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Aquena H. Ball
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | | | - Jack Greenhouse
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | | | - Anthony Cook
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Brandon Narvaez
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Zack Flinchbaugh
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Alex Van Ry
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Jake Yalley-Ogunro
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Hanne Andersen Elyard
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | - Chih-Yun Lai
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
| | | | - Axel T. Lehrer
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawai‘i at Mānoa, Honolulu, HI, 96813, USA
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Rodríguez-Espinosa D, Montagud-Marrahi E, Cacho J, Arana C, Taurizano N, Hermida E, Del Risco-Zevallos J, Casals J, Rosario A, Cuadrado-Payán E, Molina-Andújar A, Rodríguez N, Vilella A, Bodro M, Ventura-Aguiar P, Revuelta I, Cofàn F, Poch E, Oppenheimer F, Vera M, Rodas LM, Cases A, Bayés B, Diekmann F, Maduell F, Broseta JJ, Cucchiari D. Incidence of severe breakthrough SARS-CoV-2 infections in vaccinated kidney transplant and haemodialysis patients. J Nephrol 2022; 35:769-778. [PMID: 35191008 PMCID: PMC8860282 DOI: 10.1007/s40620-022-01257-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/11/2022] [Indexed: 12/28/2022]
Abstract
Introduction Given the increased COVID-19 observed in kidney transplant recipients (KTRs) and haemodialysis patients, several studies have tried to establish the efficacy of mRNA vaccines in these populations by evaluating their humoral and cellular responses. However, there is currently no information on clinical protection (deaths and hospitalizations), a gap that this study aims to fill. Methods Observational prospective study involving 1,336 KTRs and haemodialysis patients from three dialysis units affiliated to Hospital Clínic of Barcelona, Spain, vaccinated with two doses of mRNA-1273 (Moderna) or BNT162b2 (Pfizer-BioNTech) SARS-CoV-2 mRNA vaccines. The outcomes measured were SARS-CoV-2 infection diagnosed by a positive RT-PCR fourteen days after the second vaccine dose, hospital admissions derived from infection, and a severe COVID-19 composite outcome, defined as either ICU admission, invasive and non-invasive mechanical ventilation, or death. Results Six per cent (18/302) of patients on haemodialysis were infected, of whom four required hospital admission (1.3%), only one (0.3%) had severe COVID-19, and none of them died. In contrast, 4.3% (44/1034) of KTRs were infected, and presented more hospital admissions (26 patients, 2.5%), severe COVID-19 (11 patients, 1.1%) or death (4 patients, 0.4%). KTRs had a significantly higher risk of hospital admission than HD patients, and this risk increased with age and male sex (HR 3.37 and 4.74, respectively). Conclusions The study highlights the need for booster doses in KTRs. In contrast, the haemodialysis population appears to have an adequate clinical response to vaccination, at least up to four months from its administration. Graphical abstract ![]()
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Affiliation(s)
- Diana Rodríguez-Espinosa
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Enrique Montagud-Marrahi
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Judit Cacho
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Carolt Arana
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Natalia Taurizano
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Evelyn Hermida
- Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,Fresenius Medical Care, Barcelona, Spain
| | - Jimena Del Risco-Zevallos
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Joaquim Casals
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Anney Rosario
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Elena Cuadrado-Payán
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Alicia Molina-Andújar
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | | | - Anna Vilella
- Department of Preventive Medicine and Epidemiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - Marta Bodro
- Department of Infectious Diseases, Hospital Clínic, Barcelona, Spain
| | - Pedro Ventura-Aguiar
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ignacio Revuelta
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,University of Barcelona, Barcelona, Spain.,Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Frederic Cofàn
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Esteban Poch
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Frederic Oppenheimer
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Manel Vera
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Lida M Rodas
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Aleix Cases
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Beatriu Bayés
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Fritz Diekmann
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,University of Barcelona, Barcelona, Spain.,Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Francisco Maduell
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - José Jesús Broseta
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain.
| | - David Cucchiari
- Department of Nephrology and Kidney, Renal Transplantation, Hospital Clínic of Barcelona, Villarroel 170, 08036, Barcelona, Spain. .,Laboratori Experimental de Nefrologia I Trasplantament (LENIT), Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.
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Grant R, Charmet T, Schaeffer L, Galmiche S, Madec Y, Von Platen C, Chény O, Omar F, David C, Rogoff A, Paireau J, Cauchemez S, Carrat F, Septfons A, Levy-Bruhl D, Mailles A, Fontanet A. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France. THE LANCET REGIONAL HEALTH. EUROPE 2022; 13:100278. [PMID: 34849500 PMCID: PMC8616730 DOI: 10.1016/j.lanepe.2021.100278] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND We aimed to assess the settings and activities associated with SARS-CoV-2 infection in the context of B.1.617.2 (Delta) variant circulation in France, as well as the protection against symptomatic Delta infection. METHODS In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 23 May and 13 August 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire and multivariable logistic regression analysis was used to determine the association between acute SARS-CoV-2 infection and recent activity-related exposures, past history of SARS-CoV-2 infection, and COVID-19 vaccination. FINDINGS We did not find any differences in the settings and activities associated with Delta versus non-Delta infections and grouped them for subsequent analyses. In multivariable analysis involving 12634 cases (8644 Delta and 3990 non-Delta) and 5560 controls, we found individuals under 40 years and attending bars (aOR:1.9; 95%CI:1.6-2.2) or parties (aOR:3.4; 95%CI:2.8-4.2) to be at increased risk of infection. In those aged 40 years and older, having children attend daycare (aOR:1.9; 95%CI:1.1-3.3), kindergarten (aOR:1.6; 95%CI:1.2-2.1), primary school (aOR:1.4; 95%CI:1.2-1.6) or middle school (aOR:1.3; 95%CI:1.2-1.6) were associated with increased risk of infection. We found strong protection against symptomatic Delta infection for those with prior infection whether it was recent (2-6 months) (95%; 95%CI:90-97) or associated with one dose (85%; 95%CI:78-90) or two doses of mRNA vaccine (96%; 95%CI:87-99). For those without past infection, protection was lower with two doses of mRNA vaccine (67%; 95%CI:63-71). INTERPRETATION In line with other observational studies, we find reduced vaccine effectiveness against symptomatic Delta infections. The settings and activities at increased risk of infection indicate where efforts to reinforce individual and public health measures need to be concentrated.
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Affiliation(s)
- Rebecca Grant
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
- Sorbonne University, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Simon Galmiche
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Yoann Madec
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Cassandre Von Platen
- Institut Pasteur, Université de Paris, Centre for Translational Research, F-75015 Paris, France
| | - Olivia Chény
- Institut Pasteur, Université de Paris, Centre for Translational Research, F-75015 Paris, France
| | | | | | | | - Juliette Paireau
- Institut Pasteur, Université de Paris, CNRS UMR2000, Mathematical Modelling of Infectious Diseases Unit, F-75015 Paris, France
| | - Simon Cauchemez
- Institut Pasteur, Université de Paris, CNRS UMR2000, Mathematical Modelling of Infectious Diseases Unit, F-75015 Paris, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, hôpital Saint-Antoine, APHP, 27 rue Chaligny, Paris F75571
| | | | | | | | - Arnaud Fontanet
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
- Conservatoire National des Arts et Métiers, Unité PACRI, Paris, France
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Fiolet T, Kherabi Y, MacDonald CJ, Ghosn J, Peiffer-Smadja N. Comparing COVID-19 vaccines for their characteristics, efficacy and effectiveness against SARS-CoV-2 and variants of concern: a narrative review. Clin Microbiol Infect 2022; 28:202-221. [PMID: 34715347 PMCID: PMC8548286 DOI: 10.1016/j.cmi.2021.10.005] [Citation(s) in RCA: 526] [Impact Index Per Article: 263.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Vaccines are critical cost-effective tools to control the coronavirus disease 2019 (COVID-19) pandemic. However, the emergence of variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may threaten the global impact of mass vaccination campaigns. AIMS The objective of this study was to provide an up-to-date comparative analysis of the characteristics, adverse events, efficacy, effectiveness and impact of the variants of concern for 19 COVID-19 vaccines. SOURCES References for this review were identified through searches of PubMed, Google Scholar, BioRxiv, MedRxiv, regulatory drug agencies and pharmaceutical companies' websites up to 22nd September 2021. CONTENT Overall, all COVID-19 vaccines had a high efficacy against the original strain and the variants of concern, and were well tolerated. BNT162b2, mRNA-1273 and Sputnik V after two doses had the highest efficacy (>90%) in preventing symptomatic cases in phase III trials. mRNA vaccines, AZD1222, and CoronaVac were effective in preventing symptomatic COVID-19 and severe infections against Alpha, Beta, Gamma or Delta variants. Regarding observational real-life data, full immunization with mRNA vaccines and AZD1222 seems to effectively prevent SARS-CoV-2 infection against the original strain and Alpha and Beta variants but with reduced effectiveness against the Delta strain. A decline in infection protection was observed at 6 months for BNT162b2 and AZD1222. Serious adverse event rates were rare for mRNA vaccines-anaphylaxis 2.5-4.7 cases per million doses, myocarditis 3.5 cases per million doses-and were similarly rare for all other vaccines. Prices for the different vaccines varied from $2.15 to $29.75 per dose. IMPLICATIONS All vaccines appear to be safe and effective tools to prevent severe COVID-19, hospitalization, and death against all variants of concern, but the quality of evidence greatly varies depending on the vaccines considered. Questions remain regarding a booster dose and waning immunity, the duration of immunity, and heterologous vaccination. The benefits of COVID-19 vaccination outweigh the risks, despite rare serious adverse effects.
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Affiliation(s)
- Thibault Fiolet
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussy, 'Exposome and Heredity' team, CESP UMR1018, Villejuif, France.
| | - Yousra Kherabi
- Université de Paris, IAME, INSERM, Paris, France; Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Conor-James MacDonald
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussy, 'Exposome and Heredity' team, CESP UMR1018, Villejuif, France
| | - Jade Ghosn
- Université de Paris, IAME, INSERM, Paris, France; Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Nathan Peiffer-Smadja
- Université de Paris, IAME, INSERM, Paris, France; Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, France; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College, London, UK
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da Silva SJR, de Lima SC, da Silva RC, Kohl A, Pena L. Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants. Front Med (Lausanne) 2022; 8:836826. [PMID: 35174189 PMCID: PMC8841511 DOI: 10.3389/fmed.2021.836826] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
The worldwide spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented public health crisis in the 21st century. As the pandemic evolves, the emergence of SARS-CoV-2 has been characterized by the emergence of new variants of concern (VOCs), which resulted in a catastrophic impact on SARS-CoV-2 infection. In light of this, research groups around the world are unraveling key aspects of the associated illness, coronavirus disease 2019 (COVID-19). A cumulative body of data has indicated that the SARS-CoV-2 viral load may be a determinant of the COVID-19 severity. Here we summarize the main characteristics of the emerging variants of SARS-CoV-2, discussing their impact on viral transmissibility, viral load, disease severity, vaccine breakthrough, and lethality among COVID-19 patients. We also provide a rundown of the rapidly expanding scientific evidence from clinical studies and animal models that indicate how viral load could be linked to COVID-19 prognosis and vaccine efficacy among vaccinated individuals, highlighting the differences compared to unvaccinated individuals.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Suelen Cristina de Lima
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Ronaldo Celerino da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
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Parra-Lucares A, Segura P, Rojas V, Pumarino C, Saint-Pierre G, Toro L. Emergence of SARS-CoV-2 Variants in the World: How Could This Happen? Life (Basel) 2022; 12:194. [PMID: 35207482 PMCID: PMC8879166 DOI: 10.3390/life12020194] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions.
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Affiliation(s)
- Alfredo Parra-Lucares
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
| | - Paula Segura
- Department of Anatomic Pathology, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Verónica Rojas
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
| | - Catalina Pumarino
- School of Medicine, Faculty of Medicine, Universidad de Chile, 8380456 Santiago, Chile;
| | - Gustavo Saint-Pierre
- Microbiology Unit, Clinical Laboratory, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Luis Toro
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Division of Nephrology, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Critical Care Unit, Clínica Las Condes, 7591047 Santiago, Chile
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Bahnan W, Wrighton S, Sundwall M, Bläckberg A, Larsson O, Höglund U, Khakzad H, Godzwon M, Walle M, Elder E, Strand AS, Happonen L, André O, Ahnlide JK, Hellmark T, Wendel-Hansen V, Wallin RPA, Malmstöm J, Malmström L, Ohlin M, Rasmussen M, Nordenfelt P. Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2. Front Immunol 2022; 12:808932. [PMID: 35095897 PMCID: PMC8796240 DOI: 10.3389/fimmu.2021.808932] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Spike-specific antibodies are central to effective COVID19 immunity. Research efforts have focused on antibodies that neutralize the ACE2-Spike interaction but not on non-neutralizing antibodies. Antibody-dependent phagocytosis is an immune mechanism enhanced by opsonization, where typically, more bound antibodies trigger a stronger phagocyte response. Here, we show that Spike-specific antibodies, dependent on concentration, can either enhance or reduce Spike-bead phagocytosis by monocytes independently of the antibody neutralization potential. Surprisingly, we find that both convalescent patient plasma and patient-derived monoclonal antibodies lead to maximum opsonization already at low levels of bound antibodies and is reduced as antibody binding to Spike protein increases. Moreover, we show that this Spike-dependent modulation of opsonization correlate with the outcome in an experimental SARS-CoV-2 infection model. These results suggest that the levels of anti-Spike antibodies could influence monocyte-mediated immune functions and propose that non-neutralizing antibodies could confer protection to SARS-CoV-2 infection by mediating phagocytosis.
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Affiliation(s)
- Wael Bahnan
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sebastian Wrighton
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Martin Sundwall
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Anna Bläckberg
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
- Infectious Disease Clinic, Skåne University Hospital, Lund, Sweden
| | | | | | - Hamed Khakzad
- Equipe Signalisation Calcique et Infections Microbiennes, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1282, Gif-sur-Yvette, France
| | | | - Maria Walle
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Anna Söderlund Strand
- Department of Laboratory Medicine, Clinical Microbiology, Skane University Hospital Lund, Lund University, Lund, Sweden
| | - Lotta Happonen
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Oscar André
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johannes Kumra Ahnlide
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Thomas Hellmark
- Department of Clinical Sciences Lund, Nephrology, Skane University Hospital Lund, Lund University, Lund, Sweden
| | | | | | - Johan Malmstöm
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Lars Malmström
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
- Institute for Computational Science, Zurich, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
- SciLifeLab Drug Discovery and Development, Lund University, Lund, Sweden
| | - Magnus Rasmussen
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
- Infectious Disease Clinic, Skåne University Hospital, Lund, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
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Syahniar R, Kharisma DS. SARS-CoV-2 vaccine challenge based on spike glycoprotein against several new variants. Clin Exp Vaccine Res 2022; 11:173-183. [PMID: 35799876 PMCID: PMC9200648 DOI: 10.7774/cevr.2022.11.2.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/30/2022] [Indexed: 11/15/2022] Open
Abstract
The coronavirus disease 2019 pandemic has not ended, and several variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continue to emerge. The emergence of new variants is worrying because higher transmission leads to spikes in infections, vaccine efforts, and other therapeutic developments. Existing literature reports that with new variants affecting vaccine efficacy, hospitalization and risk of a recurrent infection increase. In this review article, we describe the latest variants of SARS-CoV-2, and the impact of each new variant on the efficacy of the developed vaccines reported in the literature and findings. The report concludes that the emergence of a variant that completely evades the immune response and reduces neutralizing antibodies.
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Affiliation(s)
- Rike Syahniar
- Department of Microbiology, Faculty of Medicine and Health, Universitas Muhammadiyah Jakarta, South Jakarta, Indonesia
| | - Dayu Swasti Kharisma
- Department of Microbiology, Faculty of Medicine and Health, Universitas Muhammadiyah Jakarta, South Jakarta, Indonesia
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45
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Luong Ngyen LB, Bauer R, Lesieur Z, Galtier F, Duval X, Vanhems P, Lainé F, Tattevin P, Durier C, Launay O. Vaccine effectiveness against COVID-19 hospitalization in adults in France: A test negative case control study. Infect Dis Now 2021; 52:40-43. [PMID: 34920180 PMCID: PMC8673927 DOI: 10.1016/j.idnow.2021.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Background Measuring vaccine effectiveness (VE) using real-life data is critical to confirm the effectiveness of licensed vaccine, which could strengthen vaccination adherence. Methods We measured VE against adult COVID-19 hospitalization in five hospitals in France using a test negative design. We compared the odds of vaccinated patients hospitalized with COVID-19 with the odds of vaccinated patients hospitalized for the same symptoms with a negative test. Results A total of 853 patients (463 cases and 390 controls) were included, with a total of 170 patients vaccinated (104 with one dose, 65 with two doses, and one with three doses). There were four cases of breakthrough infections, all in immunocompromised patients. The VE was 84.0% (CI0.95 = [72.6; 90.6]) for one dose and 96.2% (CI0.95 = [86.8; 98.9]) for two doses. Conclusion Our results confirm the high VE of COVID-19 vaccine in France to prevent hospitalizations due to the alpha variant.
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Affiliation(s)
| | | | | | - Florence Galtier
- Inserm, CIC 1411, CHU de Montpellier, Saint-Éloi Hospital, Montpellier, France
| | - Xavier Duval
- Inserm, CIC 1425, AP-HP, Hôpital Bichat, Paris, France
| | - Philippe Vanhems
- Service d'hygiène, épidémiologie, infectiovigilance et prévention, hospices civils de Lyon, Lyon, France
| | | | - Pierre Tattevin
- Services de maladies infectieuses et réanimation médicale, hôpital Pontchaillou, CHU de Rennes, Rennes, France
| | | | - Odile Launay
- Inserm, CIC 1417, Hôpital Cochin, AP-HP, Paris, France; Inserm, F-CRIN I-REIVAC, Paris, France
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46
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Hayawi K, Shahriar S, Serhani MA, Alashwal H, Masud MM. Vaccine versus Variants (3Vs): Are the COVID-19 Vaccines Effective against the Variants? A Systematic Review. Vaccines (Basel) 2021; 9:1305. [PMID: 34835238 PMCID: PMC8622454 DOI: 10.3390/vaccines9111305] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the emergence and spread of new SARS-CoV-2 variants, concerns are raised about the effectiveness of the existing vaccines to protect against these new variants. Although many vaccines were found to be highly effective against the reference COVID-19 strain, the same level of protection may not be found against mutation strains. The objective of this study is to systematically review relevant studies in the literature and compare the efficacy of COVID-19 vaccines against new variants. METHODS We conducted a systematic review of research published in Scopus, PubMed, and Google Scholar until 30 August 2021. Studies including clinical trials, prospective cohorts, retrospective cohorts, and test negative case-controls that reported vaccine effectiveness against any COVID-19 variants were considered. PRISMA recommendations were adopted for screening, eligibility, and inclusion. RESULTS 129 unique studies were reviewed by the search criteria, of which 35 met the inclusion criteria. These comprised of 13 test negative case-control studies, 6 Phase 1-3 clinical trials, and 16 observational studies. The study location, type, vaccines used, variants considered, and reported efficacies were highlighted. CONCLUSION Full vaccination (two doses) offers strong protection against Alpha (B.1.1.7) with 13 out of 15 studies reporting more than 84% efficacy. The results are not conclusive against the Beta (B.1.351) variant for fully vaccinated individuals with 4 out of 7 studies reporting efficacies between 22 and 60% and 3 out of 7 studies reporting efficacies between 75 and 100%. Protection against Gamma (P.1) variant was lower than 50% according to two studies in fully vaccinated individuals. The data on Delta (B.1.617.2) variant is limited but indicates lower protection compared to other variants.
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Affiliation(s)
- Kadhim Hayawi
- College of Technological Innovation, Zayed University, Abu Dhabi 51133, United Arab Emirates; (K.H.); (S.S.)
| | - Sakib Shahriar
- College of Technological Innovation, Zayed University, Abu Dhabi 51133, United Arab Emirates; (K.H.); (S.S.)
| | - Mohamed Adel Serhani
- College of Information Technology, UAE University, Abu Dhabi 15551, United Arab Emirates; (H.A.); (M.M.M.)
| | - Hany Alashwal
- College of Information Technology, UAE University, Abu Dhabi 15551, United Arab Emirates; (H.A.); (M.M.M.)
| | - Mohammad M. Masud
- College of Information Technology, UAE University, Abu Dhabi 15551, United Arab Emirates; (H.A.); (M.M.M.)
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Telford E, Ortega-Perez I, Mellon G, Lacarra B, Adjadj E, Madelaine C, D'Ortenzio E, Yazdanpanah Y. Chronicles of a pandemic: How France coordinated the scientific research response to COVID-19. Infect Dis Now 2021; 51:641-646. [PMID: 34464755 PMCID: PMC8401018 DOI: 10.1016/j.idnow.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/25/2021] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Guillaume Mellon
- AP-HP, Assistance Publique-Hôpitaux de Paris, COREB, Hôpital Bichat, 75018 Paris, France
| | - Boris Lacarra
- AP-HP, Assistance Publique-Hôpitaux de Paris, Médecine intensive-Reanimation pédiatrique, Hôpital Robert-Debré and Université de Paris, 75019 Paris, France
| | | | - Claire Madelaine
- Inserm, 75013 Paris, France; ANRS | Emerging Infectious Diseases, 75013 Paris, France
| | - Eric D'Ortenzio
- Inserm, 75013 Paris, France; ANRS | Emerging Infectious Diseases, 75013 Paris, France; Université de Paris, Infection, Antimicrobien, Modélisation, Evolution (IAME), Inserm, 75018 Paris, France; AP-HP, Hôpital Bichat, Service de maladies infectieuses et tropicales, 75018 Paris, France
| | - Yazdan Yazdanpanah
- Inserm, 75013 Paris, France; ANRS | Emerging Infectious Diseases, 75013 Paris, France; AP-HP, Hôpital Bichat, Service de maladies infectieuses et tropicales, 75018 Paris, France; University Medical School, Paris, France
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48
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Abstract
Since the COVID-19 pandemic first began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has continuously evolved with many variants emerging across the world. These variants are categorized as the variant of interest (VOI), variant of concern (VOC), and variant under monitoring (VUM). As of September 15, 2021, there are four SARS-CoV-2 lineages designated as the VOC (alpha, beta, gamma, and delta variants). VOCs have increased transmissibility compared to the original virus, and have the potential for increasing disease severity. In addition, VOCs exhibit decreased susceptibility to vaccine-induced and infection-induced immune responses, and thus possess the ability to reinfect previously infected and recovered individuals. Given their ability to evade immune responses, VOC are less susceptible to monoclonal antibody treatments. VOCs can also impact the effectiveness of mRNA and adenovirus vector vaccines, although the currently authorized COVID-19 vaccines are still effective in preventing infection and severe disease. Current measures to reduce transmission as well as efforts to monitor and understand the impact of variants should be continued. Here, we review the molecular features, epidemiology, impact on transmissibility, disease severity, and vaccine effectiveness of VOCs.
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Affiliation(s)
- Jun Yong Choi
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea.
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
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49
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Lefèvre B, Tondeur L, Madec Y, Grant R, Lina B, van der Werf S, Rabaud C, Fontanet A. Beta SARS-CoV-2 variant and BNT162b2 vaccine effectiveness in long-term care facilities in France. LANCET HEALTHY LONGEVITY 2021; 2:e685-e687. [PMID: 34580665 PMCID: PMC8457759 DOI: 10.1016/s2666-7568(21)00230-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Benjamin Lefèvre
- Infectious and Tropical Diseases, CHRU-Nancy, Université de Lorraine, Nancy, France.,APEMAC, Université de Lorraine, Nancy, France
| | - Laura Tondeur
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris 75015, France
| | - Yoann Madec
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris 75015, France
| | - Rebecca Grant
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris 75015, France.,Sorbonne University, Paris, France
| | - Bruno Lina
- CNR des Virus des Infections Respiratoires, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France.,VirPath, Centre International de Recherche En Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon, France
| | - Sylvie van der Werf
- Department of Virology, CNRS UMR 3569, Institut Pasteur, Paris 75015, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris 75015, France
| | - Christian Rabaud
- Infectious and Tropical Diseases, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris 75015, France.,Conservatoire national des arts et métiers, Unité PACRI, Paris, France
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50
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Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2021; 9:1052. [PMID: 34696160 PMCID: PMC8540924 DOI: 10.3390/vaccines9101052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since late 2019 the newly emerged pandemic SARS-CoV-2, the causative agent of COVID-19, has hit the world with recurring waves of infections necessitating the global implementation of non-pharmaceutical interventions, including strict social distancing rules, the wearing of masks and the isolation of infected individuals in order to restrict virus transmissions and prevent the breakdown of our healthcare systems. These measures are not only challenging on an economic level but also have a strong impact on social lifestyles. Using traditional and novel technologies, highly efficient vaccines against SARS-CoV-2 were developed and underwent rapid clinical evaluation and approval to accelerate the immunization of the world population, aiming to end the pandemic and return to normality. However, the emergence of virus variants with improved transmission, enhanced fitness and partial immune escape from the first generation of vaccines poses new challenges, which are currently being addressed by scientists and pharmaceutical companies all over the world. In this ongoing pandemic, the evaluation of SARS-CoV-2 vaccines underlies diverse unpredictable dynamics, posed by the first broad application of the mRNA vaccine technology and their compliance, the occurrence of unexpected side effects and the rapid emergence of variations in the viral antigen. However, despite these hurdles, we conclude that the available SARS-CoV-2 vaccines are very safe and efficiently protect from severe COVID-19 and are thereby the most powerful tools to prevent further harm to our healthcare systems, economics and individual lives. This review summarizes the unprecedented pathways of vaccine development and approval during the ongoing SARS-CoV-2 pandemic. We focus on the real-world effectiveness and unexpected positive and negative side effects of the available vaccines and summarize the timeline of the applied adaptations to the recommended vaccination strategies in the light of emerging virus variants. Finally, we highlight upcoming strategies to improve the next generations of SARS-CoV-2 vaccines.
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Affiliation(s)
- Franziska Günl
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Angeles Mecate-Zambrano
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Selina Rehländer
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Saskia Hinse
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Linda Brunotte
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
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