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Waseel F, Streftaris G, Rudrusamy B, Dass SC. Assessing the dynamics and impact of COVID-19 vaccination on disease spread: A data-driven approach. Infect Dis Model 2024; 9:527-556. [PMID: 38525308 PMCID: PMC10958481 DOI: 10.1016/j.idm.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
The COVID-19 pandemic has significantly impacted global health, social, and economic situations since its emergence in December 2019. The primary focus of this study is to propose a distinct vaccination policy and assess its impact on controlling COVID-19 transmission in Malaysia using a Bayesian data-driven approach, concentrating on the year 2021. We employ a compartmental Susceptible-Exposed-Infected-Recovered-Vaccinated (SEIRV) model, incorporating a time-varying transmission rate and a data-driven method for its estimation through an Exploratory Data Analysis (EDA) approach. While no vaccine guarantees total immunity against the disease, and vaccine immunity wanes over time, it is critical to include and accurately estimate vaccine efficacy, as well as a constant vaccine immunity decay or wane factor, to better simulate the dynamics of vaccine-induced protection over time. Based on the distribution and effectiveness of vaccines, we integrated a data-driven estimation of vaccine efficacy, calculated at 75% for Malaysia, underscoring the model's realism and relevance to the specific context of the country. The Bayesian inference framework is used to assimilate various data sources and account for underlying uncertainties in model parameters. The model is fitted to real-world data from Malaysia to analyze disease spread trends and evaluate the effectiveness of our proposed vaccination policy. Our findings reveal that this distinct vaccination policy, which emphasizes an accelerated vaccination rate during the initial stages of the program, is highly effective in mitigating the spread of COVID-19 and substantially reducing the pandemic peak and new infections. The study found that vaccinating 57-66% of the population (as opposed to 76% in the real data) with a better vaccination policy such as proposed here is able to significantly reduce the number of new infections and ultimately reduce the costs associated with new infections. The study contributes to the development of a robust and informative representation of COVID-19 transmission and vaccination, offering valuable insights for policymakers on the potential benefits and limitations of different vaccination policies, particularly highlighting the importance of a well-planned and efficient vaccination rollout strategy. While the methodology used in this study is specifically applied to national data from Malaysia, its successful application to local regions within Malaysia, such as Selangor and Johor, indicates its adaptability and potential for broader application. This demonstrates the model's adaptability for policy assessment and improvement across various demographic and epidemiological landscapes, implying its usefulness for similar datasets from various geographical regions.
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Affiliation(s)
- Farhad Waseel
- School of Mathematical and Computer Sciences, Heriot-Watt University Malaysia, Putrajaya, Malaysia
- Faculty of Mathematics, Kabul University, Kabul, Afghanistan
| | - George Streftaris
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, United Kingdom
- Maxwell Institute for Mathematical Sciences, United Kingdom
| | - Bhuvendhraa Rudrusamy
- School of Engineering and Physical Sciences, Heriot-Watt University Malaysia, Putrajaya, Malaysia
| | - Sarat C. Dass
- School of Mathematical and Computer Sciences, Heriot-Watt University Malaysia, Putrajaya, Malaysia
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Owusu-Boaitey N, Russell TW, Meyerowitz-Katz G, Levin AT, Herrera-Esposito D. Dynamics of SARS-CoV-2 seroassay sensitivity: a systematic review and modelling study. Euro Surveill 2023; 28:2200809. [PMID: 37227301 PMCID: PMC10283460 DOI: 10.2807/1560-7917.es.2023.28.21.2200809] [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: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 05/26/2023] Open
Abstract
BackgroundSerological surveys have been the gold standard to estimate numbers of SARS-CoV-2 infections, the dynamics of the epidemic, and disease severity. Serological assays have decaying sensitivity with time that can bias their results, but there is a lack of guidelines to account for this phenomenon for SARS-CoV-2.AimOur goal was to assess the sensitivity decay of seroassays for detecting SARS-CoV-2 infections, the dependence of this decay on assay characteristics, and to provide a simple method to correct for this phenomenon.MethodsWe performed a systematic review and meta-analysis of SARS-CoV-2 serology studies. We included studies testing previously diagnosed, unvaccinated individuals, and excluded studies of cohorts highly unrepresentative of the general population (e.g. hospitalised patients).ResultsOf the 488 screened studies, 76 studies reporting on 50 different seroassays were included in the analysis. Sensitivity decay depended strongly on the antigen and the analytic technique used by the assay, with average sensitivities ranging between 26% and 98% at 6 months after infection, depending on assay characteristics. We found that a third of the included assays departed considerably from manufacturer specifications after 6 months.ConclusionsSeroassay sensitivity decay depends on assay characteristics, and for some types of assays, it can make manufacturer specifications highly unreliable. We provide a tool to correct for this phenomenon and to assess the risk of decay for a given assay. Our analysis can guide the design and interpretation of serosurveys for SARS-CoV-2 and other pathogens and quantify systematic biases in the existing serology literature.
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Affiliation(s)
- Nana Owusu-Boaitey
- Case Western Reserve University School of Medicine, Cleveland, United States
- These authors contributed equally to this work
| | - Timothy W Russell
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Andrew T Levin
- Dartmouth College, Hanover, United States
- National Bureau for Economic Research, Cambridge, United States
- Centre for Economic Policy Research, London, United Kingdom
| | - Daniel Herrera-Esposito
- These authors contributed equally to this work
- Department of Psychology, University of Pennsylvania, Philadelphia, United States
- Laboratorio de Neurociencias, Universidad de la República, Montevideo, Uruguay
- Centro Interdisciplinario en Ciencia de Datos y Aprendizaje Automático, Universidad de la República, Montevideo, Uruguay
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Triambak S, Mahapatra D, Barik N, Chutjian A. Plausible explanation for the third COVID-19 wave in India and its implications. Infect Dis Model 2023; 8:183-191. [PMID: 36643865 PMCID: PMC9824946 DOI: 10.1016/j.idm.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023] Open
Abstract
Recently some of us used a random-walk Monte Carlo simulation approach to study the spread of COVID-19. The calculations were reasonably successful in describing secondary and tertiary waves of infection, in countries such as the USA, India, South Africa and Serbia. However, they failed to predict the observed third wave for India. In this work we present a more complete set of simulations for India, that take into consideration two aspects that were not incorporated previously. These include the stochastic movement of an erstwhile protected fraction of the population, and the reinfection of some recovered individuals because of their exposure to a new variant of the SARS-CoV-2 virus. The extended simulations now show the third COVID-19 wave for India that was missing in the earlier calculations. They also suggest an additional fourth wave, which was indeed observed during approximately the same time period as the model prediction.
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Affiliation(s)
- S. Triambak
- Department of Physics and Astronomy, University of the Western Cape, P/B X17, Bellville, 7535, South Africa,Corresponding author
| | - D.P. Mahapatra
- Department of Physics, Utkal University, Vani Vihar, Bhubaneshwar, 751004, India
| | - N. Barik
- Department of Physics, Utkal University, Vani Vihar, Bhubaneshwar, 751004, India
| | - A. Chutjian
- Armenian Engineers and Scientists of America, 326 Mira Loma Ave., Glendale, CA, 91204, USA
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Amati R, Piumatti G, Franscella G, Buttaroni P, Camerini AL, Corna L, Levati S, Fadda M, Fiordelli M, Annoni AM, Bezani K, Amendola A, Fragoso Corti C, Sabatini S, Kaufmann M, Frei A, Puhan MA, Crivelli L, Albanese E. Trajectories of Seroprevalence and Neutralizing Activity of Antibodies against SARS-CoV-2 in Southern Switzerland between July 2020 and July 2021: An Ongoing, Prospective Population-Based Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3703. [PMID: 36834397 PMCID: PMC9964112 DOI: 10.3390/ijerph20043703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVES The COVID-19 pandemic continues, and evidence on infection- and vaccine-induced immunity is key. We assessed COVID-19 immunity and the neutralizing antibody response to virus variants across age groups in the Swiss population. STUDY DESIGN We conducted a cohort study in representative community-dwelling residents aged five years or older in southern Switzerland (total population 353,343), and we collected blood samples in July 2020 (in adults only, N = 646), November-December 2020 (N = 1457), and June-July 2021 (N = 885). METHODS We used a previously validated Luminex assay to measure antibodies targeting the spike (S) and the nucleocapsid (N) proteins of the virus and a high-throughput cell-free neutralization assay optimized for multiple spike protein variants. We calculated seroprevalence with a Bayesian logistic regression model accounting for the population's sociodemographic structure and the test performance, and we compared the neutralizing activity between vaccinated and convalescent participants across virus variants. RESULTS The overall seroprevalence was 7.8% (95% CI: 5.4-10.4) by July 2020 and 20.2% (16.4-24.4) by December 2020. By July 2021, the overall seroprevalence increased substantially to 72.5% (69.1-76.4), with the highest estimates of 95.6% (92.8-97.8) among older adults, who developed up to 10.3 more antibodies via vaccination than after infection compared to 3.7 times more in adults. The neutralizing activity was significantly higher for vaccine-induced than infection-induced antibodies for all virus variants (all p values < 0.037). CONCLUSIONS Vaccination chiefly contributed to the reduction in immunonaive individuals, particularly those in older age groups. Our findings on the greater neutralizing activity of vaccine-induced antibodies than infection-induced antibodies are greatly informative for future vaccination campaigns.
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Affiliation(s)
- Rebecca Amati
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | | | - Giovanni Franscella
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Peter Buttaroni
- Faculty of Informatics, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Anne-Linda Camerini
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Laurie Corna
- Department of Business Economics, Health and Social Care, University of Applied Sciences and Arts of Southern Switzerland, 6928 Manno, Switzerland
| | - Sara Levati
- Department of Business Economics, Health and Social Care, University of Applied Sciences and Arts of Southern Switzerland, 6928 Manno, Switzerland
| | - Marta Fadda
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Maddalena Fiordelli
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Health Sciences, University of Lucerne, 6002 Lucerne, Switzerland
| | - Anna Maria Annoni
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Kleona Bezani
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Antonio Amendola
- Department of Business Economics, Health and Social Care, University of Applied Sciences and Arts of Southern Switzerland, 6928 Manno, Switzerland
| | - Cristina Fragoso Corti
- Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland, 6501 Bellinzona, Switzerland
| | - Serena Sabatini
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Marco Kaufmann
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Anja Frei
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Milo Alan Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Luca Crivelli
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Business Economics, Health and Social Care, University of Applied Sciences and Arts of Southern Switzerland, 6928 Manno, Switzerland
| | - Emiliano Albanese
- Institute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
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Seroprevalence of SARS-CoV-2 among Children Visiting a Tertiary Hospital during the Prevaccination Period, Southwest Region, Saudi Arabia. Vaccines (Basel) 2022; 10:vaccines10081344. [PMID: 36016232 PMCID: PMC9415489 DOI: 10.3390/vaccines10081344] [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: 07/30/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background: In the early days of the COVID-19 pandemic, tests to ascertain whether individuals were infected with SARS-CoV-2 were often unavailable. One method to deal with this issue is to test for SARS-CoV-2 antibodies. This study sought to determine the seroprevalence of SARS-CoV-2 in children in Saudi Arabia before vaccines were available to them. Methods: This study was conducted among children who visited the tertiary Maternity and Children Hospital in Abha city, Saudi Arabia. Serum samples were screened for SARS-CoV-2-specific IgG, IgM, and IgA antibodies using ELISA. The crude and adjusted seroprevalence values among the studied children were calculated. Results: Among the 413 children studied, the ages of enrolled patients ranged from newborn to 12 years, with a median age of three years. We identified 127 (30.7%) seropositive children. IgG was exclusively positive in 43 (10.4%); IgM was exclusively positive in 8 (1.9%), and IgA was exclusively positive in 15 (3.6%) children. Conclusions: This study is the first to estimate the seroprevalence of SARS-CoV-2 among the pediatric population seeking medical care in southwestern Saudi Arabia. The findings shed light on the dynamics of virus transmission in the community and provide a good reference for future studies. Future research should examine factors related to SARS-CoV-2 infection and seroprevalence among pediatric populations.
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