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Reichmuth ML, Heron L, Beutels P, Hens N, Low N, Althaus CL. Social contacts in Switzerland during the COVID-19 pandemic: Insights from the CoMix study. Epidemics 2024; 47:100771. [PMID: 38821037 DOI: 10.1016/j.epidem.2024.100771] [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: 02/14/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024] Open
Abstract
To mitigate the spread of SARS-CoV-2, the Swiss government enacted restrictions on social contacts from 2020 to 2022. In addition, individuals changed their social contact behavior to limit the risk of COVID-19. In this study, we aimed to investigate the changes in social contact patterns of the Swiss population. As part of the CoMix study, we conducted a survey consisting of 24 survey waves from January 2021 to May 2022. We collected data on social contacts and constructed contact matrices for the age groups 0-4, 5-14, 15-29, 30-64, and 65 years and older. We estimated the change in contact numbers during the COVID-19 pandemic to a synthetic pre-pandemic contact matrix. We also investigated the association of the largest eigenvalue of the social contact and transmission matrices with the stringency of pandemic measures, the effective reproduction number (Re), and vaccination uptake. During the pandemic period, 7084 responders reported an average number of 4.5 contacts (95% confidence interval, CI: 4.5-4.6) per day overall, which varied by age and survey wave. Children aged 5-14 years had the highest number of contacts with 8.5 (95% CI: 8.1-8.9) contacts on average per day and participants that were 65 years and older reported the fewest (3.4, 95% CI: 3.2-3.5) per day. Compared with the pre-pandemic baseline, we found that the 15-29 and 30-64 year olds had the largest reduction in contacts. We did not find statistically significant associations between the largest eigenvalue of the social contact and transmission matrices and the stringency of measures, Re, or vaccination uptake. The number of social contacts in Switzerland fell during the COVID-19 pandemic and remained below pre-pandemic levels after contact restrictions were lifted. The collected social contact data will be critical in informing modeling studies on the transmission of respiratory infections in Switzerland and to guide pandemic preparedness efforts.
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Affiliation(s)
- Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Leonie Heron
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Philippe Beutels
- Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, Antwerp, Belgium
| | - Niel Hens
- Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, Antwerp, Belgium; Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
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Iyengar A, Hanon S, Bruns R, Olsiewski P, Gronvall GK. COVID-19 Mitigation in a K-12 School Setting: A Case Study of Avenues: The World School in New York City. Health Secur 2024; 22:210-222. [PMID: 38624262 DOI: 10.1089/hs.2023.0060] [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] [Indexed: 04/17/2024] Open
Abstract
In this case study, we describe a well-resourced private school in New York City that implemented COVID-19 mitigation measures based on public health expert guidance and the lessons learned from this process. Avenues opened in New York City in 2012 and has since expanded, becoming Avenues: The World School, with campuses in São Paulo, Brazil; Shenzhen, China; the Silicon Valley, California; and online. It offers education at 16 grade levels: 2 early learning years, followed by a prekindergarten through grade 12. We describe the mitigation measures that Avenues implemented on its New York campus. We compare COVID-19 case prevalence at the school with COVID-19 case positivity in New York City, as reported by the New York State Department of Health. We also compare the school's indoor air quality to ambient indoor air quality measures reported in the literature. The school's mitigation measures successfully reduced the prevalence of COVID-19 among its students, staff, and faculty. The school also established a consistently high level of indoor air quality safety through various ventilation mechanisms, designed to reduce common indoor air pollutants. The school received positive parent and community feedback on the policies and procedures it established, with many parents commenting on the high level of trust and quality of communication established by the school. The successful reopening provides useful data for school closure and reopening standards to prepare for future pandemic and epidemic events.
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Affiliation(s)
- Ananya Iyengar
- Ananya Iyengar, MSPH, was a Graduate Research Assistant, at the Johns Hopkins Center for Health Security, Baltimore, MD
| | - Steve Hanon
- Steve Hanon, MBA, is Chief Campus Operations Officer, Avenues: The World School, New York, NY
| | - Richard Bruns
- Richard Bruns, PhD, is a Senior Scholar, at the Johns Hopkins Center for Health Security, Baltimore, MD, Richard Bruns is also an Assistant Scientist, the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Paula Olsiewski
- Paula Olsiewski, PhD, is a Contributing Scholar, at the Johns Hopkins Center for Health Security, Baltimore, MD
| | - Gigi Kwik Gronvall
- Gigi Kwik Gronvall, PhD, is a Senior Scholar, at the Johns Hopkins Center for Health Security, Baltimore, MD, Gigi Kwik Gronvall is also an Associate Professor, in the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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3
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Duval D, Evans B, Sanders A, Hill J, Simbo A, Kavoi T, Lyell I, Simmons Z, Qureshi M, Pearce-Smith N, Arevalo CR, Beck CR, Bindra R, Oliver I. Non-pharmaceutical interventions to reduce COVID-19 transmission in the UK: a rapid mapping review and interactive evidence gap map. J Public Health (Oxf) 2024; 46:e279-e293. [PMID: 38426578 PMCID: PMC11141784 DOI: 10.1093/pubmed/fdae025] [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: 10/16/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Non-pharmaceutical interventions (NPIs) were crucial in the response to the COVID-19 pandemic, although uncertainties about their effectiveness remain. This work aimed to better understand the evidence generated during the pandemic on the effectiveness of NPIs implemented in the UK. METHODS We conducted a rapid mapping review (search date: 1 March 2023) to identify primary studies reporting on the effectiveness of NPIs to reduce COVID-19 transmission. Included studies were displayed in an interactive evidence gap map. RESULTS After removal of duplicates, 11 752 records were screened. Of these, 151 were included, including 100 modelling studies but only 2 randomized controlled trials and 10 longitudinal observational studies.Most studies reported on NPIs to identify and isolate those who are or may become infectious, and on NPIs to reduce the number of contacts. There was an evidence gap for hand and respiratory hygiene, ventilation and cleaning. CONCLUSIONS Our findings show that despite the large number of studies published, there is still a lack of robust evaluations of the NPIs implemented in the UK. There is a need to build evaluation into the design and implementation of public health interventions and policies from the start of any future pandemic or other public health emergency.
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Affiliation(s)
- D Duval
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - B Evans
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - A Sanders
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - J Hill
- Clinical and Public Health Response Division, UKHSA, London E14 5EA, UK
| | - A Simbo
- Evaluation and Epidemiological Science Division, UKHSA, Colindale NW9 5EQ, UK
| | - T Kavoi
- Cheshire and Merseyside Health Protection Team, UKHSA, Liverpool L3 1DS, UK
| | - I Lyell
- Greater Manchester Health Protection Team, UKHSA, Manchester M1 3BN, UK
| | - Z Simmons
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - M Qureshi
- Clinical and Public Health Response Division, UKHSA, London E14 5EA, UK
| | - N Pearce-Smith
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - C R Arevalo
- Research, Evidence and Knowledge Division, UK Health Security Agency (UKHSA), London E14 5EA, UK
| | - C R Beck
- Evaluation and Epidemiological Science Division, UKHSA, Salisbury SP4 0JG, UK
| | - R Bindra
- Clinical and Public Health Response Division, UKHSA, London E14 5EA, UK
| | - I Oliver
- Director General Science and Research and Chief Scientific Officer, UKHSA, London E14 5EA, UK
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Littlecott H, Krishnaratne S, Burns J, Rehfuess E, Sell K, Klinger C, Strahwald B, Movsisyan A, Metzendorf MI, Schoenweger P, Voss S, Coenen M, Müller-Eberstein R, Pfadenhauer LM. Measures implemented in the school setting to contain the COVID-19 pandemic. Cochrane Database Syst Rev 2024; 5:CD015029. [PMID: 38695826 PMCID: PMC11064884 DOI: 10.1002/14651858.cd015029.pub2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
BACKGROUND More than 767 million coronavirus 2019 (COVID-19) cases and 6.9 million deaths with COVID-19 have been recorded as of August 2023. Several public health and social measures were implemented in schools to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent onward transmission. We built upon methods from a previous Cochrane review to capture current empirical evidence relating to the effectiveness of school measures to limit SARS-CoV-2 transmission. OBJECTIVES To provide an updated assessment of the evidence on the effectiveness of measures implemented in the school setting to keep schools open safely during the COVID-19 pandemic. SEARCH METHODS We searched the Cochrane COVID-19 Study Register, Educational Resources Information Center, World Health Organization (WHO) COVID-19 Global literature on coronavirus disease database, and the US Department of Veterans Affairs Evidence Synthesis Program COVID-19 Evidence Reviews on 18 February 2022. SELECTION CRITERIA Eligible studies focused on measures implemented in the school setting to contain the COVID-19 pandemic, among students (aged 4 to 18 years) or individuals relating to the school, or both. We categorized studies that reported quantitative measures of intervention effectiveness, and studies that assessed the performance of surveillance measures as either 'main' or 'supporting' studies based on design and approach to handling key confounders. We were interested in transmission-related outcomes and intended or unintended consequences. DATA COLLECTION AND ANALYSIS Two review authors screened titles, abstracts and full texts. We extracted minimal data for supporting studies. For main studies, one review author extracted comprehensive data and assessed risk of bias, which a second author checked. We narratively synthesized findings for each intervention-comparator-outcome category (body of evidence). Two review authors assessed certainty of evidence. MAIN RESULTS The 15 main studies consisted of measures to reduce contacts (4 studies), make contacts safer (7 studies), surveillance and response measures (6 studies; 1 assessed transmission outcomes, 5 assessed performance of surveillance measures), and multicomponent measures (1 study). These main studies assessed outcomes in the school population (12), general population (2), and adults living with a school-attending child (1). Settings included K-12 (kindergarten to grade 12; 9 studies), secondary (3 studies), and K-8 (kindergarten to grade 8; 1 study) schools. Two studies did not clearly report settings. Studies measured transmission-related outcomes (10), performance of surveillance measures (5), and intended and unintended consequences (4). The 15 main studies were based in the WHO Regions of the Americas (12), and the WHO European Region (3). Comparators were more versus less intense measures, single versus multicomponent measures, and measures versus no measures. We organized results into relevant bodies of evidence, or groups of studies relating to the same 'intervention-comparator-outcome' categories. Across all bodies of evidence, certainty of evidence ratings limit our confidence in findings. Where we describe an effect as 'beneficial', the direction of the point estimate of the effect favours the intervention; a 'harmful' effect does not favour the intervention and 'null' shows no effect either way. Measures to reduce contact (4 studies) We grouped studies into 21 bodies of evidence: moderate- (10 bodies), low- (3 bodies), or very low-certainty evidence (8 bodies). The evidence was very low to moderate certainty for beneficial effects of remote versus in-person or hybrid teaching on transmission in the general population. For students and staff, mostly harmful effects were observed when more students participated in remote teaching. Moderate-certainty evidence showed that in the general population there was probably no effect on deaths and a beneficial effect on hospitalizations for remote versus in-person teaching, but no effect for remote versus hybrid teaching. The effects of hybrid teaching, a combination of in-person and remote teaching, were mixed. Very low-certainty evidence showed that there may have been a harmful effect on risk of infection among adults living with a school student for closing playgrounds and cafeterias, a null effect for keeping the same teacher, and a beneficial effect for cancelling extracurricular activities, keeping the same students together and restricting entry for parents and caregivers. Measures to make contact safer (7 studies) We grouped studies into eight bodies of evidence: moderate- (5 bodies), and low-certainty evidence (3 bodies). Low-certainty evidence showed that there may have been a beneficial effect of mask mandates on transmission-related outcomes. Moderate-certainty evidence showed full mandates were probably more beneficial than partial or no mandates. Evidence of a beneficial effect of physical distancing on risk of infection among staff and students was mixed. Moderate-certainty evidence showed that ventilation measures probably reduce cases among staff and students. One study (very low-certainty evidence) found that there may be a beneficial effect of not sharing supplies and increasing desk space on risk of infection for adults living with a school student, but showed there may be a harmful effect of desk shields. Surveillance and response measures (6 studies) We grouped studies into seven bodies of evidence: moderate- (3 bodies), low- (1 body), and very low-certainty evidence (3 bodies). Daily testing strategies to replace or reduce quarantine probably helped to reduce missed school days and decrease the proportion of asymptomatic school contacts testing positive (moderate-certainty evidence). For studies that assessed the performance of surveillance measures, the proportion of cases detected by rapid antigen detection testing ranged from 28.6% to 95.8%, positive predictive value ranged from 24.0% to 100.0% (very low-certainty evidence). There was probably no onward transmission from contacts of a positive case (moderate-certainty evidence) and replacing or shortening quarantine with testing may have reduced missed school days (low-certainty evidence). Multicomponent measures (1 study) Combining multiple measures may have led to a reduction in risk of infection among adults living with a student (very low-certainty evidence). AUTHORS' CONCLUSIONS A range of measures can have a beneficial effect on transmission-related outcomes, healthcare utilization and school attendance. We rated the current findings at a higher level of certainty than the original review. Further high-quality research into school measures to control SARS-CoV-2 in a wider variety of contexts is needed to develop a more evidence-based understanding of how to keep schools open safely during COVID-19 or a similar public health emergency.
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Affiliation(s)
- Hannah Littlecott
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Shari Krishnaratne
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jacob Burns
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Eva Rehfuess
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Kerstin Sell
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Carmen Klinger
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Brigitte Strahwald
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Ani Movsisyan
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Maria-Inti Metzendorf
- Institute of General Practice, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Petra Schoenweger
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Stephan Voss
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Michaela Coenen
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Roxana Müller-Eberstein
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Lisa M Pfadenhauer
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Chair of Public Health and Health Services Research, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
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Bokányi E, Vizi Z, Koltai J, Röst G, Karsai M. Real-time estimation of the effective reproduction number of COVID-19 from behavioral data. Sci Rep 2023; 13:21452. [PMID: 38052841 PMCID: PMC10698193 DOI: 10.1038/s41598-023-46418-z] [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: 01/27/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
Monitoring the effective reproduction number [Formula: see text] of a rapidly unfolding pandemic in real-time is key to successful mitigation and prevention strategies. However, existing methods based on case numbers, hospital admissions or fatalities suffer from multiple measurement biases and temporal lags due to high test positivity rates or delays in symptom development or administrative reporting. Alternative methods such as web search and social media tracking are less directly indicating epidemic prevalence over time. We instead record age-stratified anonymous contact matrices at a daily resolution using a longitudinal online-offline survey in Hungary during the first two waves of the COVID-19 pandemic. This approach is innovative, cheap, and provides information in near real-time for estimating [Formula: see text] at a daily resolution. Moreover, it allows to complement traditional surveillance systems by signaling periods when official monitoring infrastructures are unreliable due to observational biases.
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Affiliation(s)
- Eszter Bokányi
- Institute of Logic, Language and Computation, University of Amsterdam, 1090GE, Amsterdam, The Netherlands
| | - Zsolt Vizi
- National Laboratory for Health Security, University of Szeged, Szeged, 6720, Hungary
| | - Júlia Koltai
- National Laboratory for Health Security, Centre for Social Sciences, Budapest, 1097, Hungary
- Faculty of Social Sciences, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Gergely Röst
- National Laboratory for Health Security, University of Szeged, Szeged, 6720, Hungary
| | - Márton Karsai
- Department of Network and Data Science, Central European University, 1100, Vienna, Austria.
- National Laboratory for Health Security, Alfréd Rényi Institute of Mathematics, Budapest, 1053, Hungary.
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Murphy C, Lim WW, Mills C, Wong JY, Chen D, Xie Y, Li M, Gould S, Xin H, Cheung JK, Bhatt S, Cowling BJ, Donnelly CA. Effectiveness of social distancing measures and lockdowns for reducing transmission of COVID-19 in non-healthcare, community-based settings. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20230132. [PMID: 37611629 PMCID: PMC10446910 DOI: 10.1098/rsta.2023.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 08/25/2023]
Abstract
Social distancing measures (SDMs) are community-level interventions that aim to reduce person-to-person contacts in the community. SDMs were a major part of the responses first to contain, then to mitigate, the spread of SARS-CoV-2 in the community. Common SDMs included limiting the size of gatherings, closing schools and/or workplaces, implementing work-from-home arrangements, or more stringent restrictions such as lockdowns. This systematic review summarized the evidence for the effectiveness of nine SDMs. Almost all of the studies included were observational in nature, which meant that there were intrinsic risks of bias that could have been avoided were conditions randomly assigned to study participants. There were no instances where only one form of SDM had been in place in a particular setting during the study period, making it challenging to estimate the separate effect of each intervention. The more stringent SDMs such as stay-at-home orders, restrictions on mass gatherings and closures were estimated to be most effective at reducing SARS-CoV-2 transmission. Most studies included in this review suggested that combinations of SDMs successfully slowed or even stopped SARS-CoV-2 transmission in the community. However, individual effects and optimal combinations of interventions, as well as the optimal timing for particular measures, require further investigation. This article is part of the theme issue 'The effectiveness of non-pharmaceutical interventions on the COVID-19 pandemic: the evidence'.
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Affiliation(s)
- Caitriona Murphy
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Wey Wen Lim
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Cathal Mills
- Department of Statistics, University of Oxford, Oxford, UK
| | - Jessica Y. Wong
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Dongxuan Chen
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong, People's Republic of China
| | - Yanmy Xie
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Mingwei Li
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong, People's Republic of China
| | - Susan Gould
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Hualei Xin
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Justin K. Cheung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Kobenhavn, Denmark
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Benjamin J. Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong, People's Republic of China
| | - Christl A. Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
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7
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Munday JD, Abbott S, Meakin S, Funk S. Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England. PLoS Comput Biol 2023; 19:e1011453. [PMID: 37699018 PMCID: PMC10516435 DOI: 10.1371/journal.pcbi.1011453] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 09/22/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Mathematical and statistical models can be used to make predictions of how epidemics may progress in the near future and form a central part of outbreak mitigation and control. Renewal equation based models allow inference of epidemiological parameters from historical data and forecast future epidemic dynamics without requiring complex mechanistic assumptions. However, these models typically ignore interaction between age groups, partly due to challenges in parameterising a time varying interaction matrix. Social contact data collected regularly during the COVID-19 epidemic provide a means to inform interaction between age groups in real-time. We developed an age-specific forecasting framework and applied it to two age-stratified time-series: incidence of SARS-CoV-2 infection, estimated from a national infection and antibody prevalence survey; and, reported cases according to the UK national COVID-19 dashboard. Jointly fitting our model to social contact data from the CoMix study, we inferred a time-varying next generation matrix which we used to project infections and cases in the four weeks following each of 29 forecast dates between October 2020 and November 2021. We evaluated the forecasts using proper scoring rules and compared performance with three other models with alternative data and specifications alongside two naive baseline models. Overall, incorporating age interaction improved forecasts of infections and the CoMix-data-informed model was the best performing model at time horizons between two and four weeks. However, this was not true when forecasting cases. We found that age group interaction was most important for predicting cases in children and older adults. The contact-data-informed models performed best during the winter months of 2020-2021, but performed comparatively poorly in other periods. We highlight challenges regarding the incorporation of contact data in forecasting and offer proposals as to how to extend and adapt our approach, which may lead to more successful forecasts in future.
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Affiliation(s)
- James D. Munday
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sophie Meakin
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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8
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Backer JA, Bogaardt L, Beutels P, Coletti P, Edmunds WJ, Gimma A, van Hagen CCE, Hens N, Jarvis CI, Vos ERA, Wambua J, Wong D, van Zandvoort K, Wallinga J. Dynamics of non-household contacts during the COVID-19 pandemic in 2020 and 2021 in the Netherlands. Sci Rep 2023; 13:5166. [PMID: 36997550 PMCID: PMC10060924 DOI: 10.1038/s41598-023-32031-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
The COVID-19 pandemic was in 2020 and 2021 for a large part mitigated by reducing contacts in the general population. To monitor how these contacts changed over the course of the pandemic in the Netherlands, a longitudinal survey was conducted where participants reported on their at-risk contacts every two weeks, as part of the European CoMix survey. The survey included 1659 participants from April to August 2020 and 2514 participants from December 2020 to September 2021. We categorized the number of unique contacted persons excluding household members, reported per participant per day into six activity levels, defined as 0, 1, 2, 3-4, 5-9 and 10 or more reported contacts. After correcting for age, vaccination status, risk status for severe outcome of infection, and frequency of participation, activity levels increased over time, coinciding with relaxation of COVID-19 control measures.
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Affiliation(s)
- Jantien A Backer
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
| | - Laurens Bogaardt
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Pietro Coletti
- UHasselt, Data Science Institute and I-BioStat, Hasselt, Belgium
| | - W John Edmunds
- London School of Hygiene and Tropical Medicine, London, UK
| | - Amy Gimma
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Niel Hens
- University of Antwerp, Antwerp, Belgium
- UHasselt, Data Science Institute and I-BioStat, Hasselt, Belgium
| | | | - Eric R A Vos
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - James Wambua
- UHasselt, Data Science Institute and I-BioStat, Hasselt, Belgium
| | - Denise Wong
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Jacco Wallinga
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Leiden University Medical Center, Leiden, The Netherlands
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9
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Ganem F, Bordas A, Folch C, Alonso L, Montoro-Fernandez M, Colom-Cadena A, Mas A, Mendioroz J, Asso L, Anton A, Pumarola T, González MV, Blanco I, Soler-Palacín P, Soriano-Arandes A, Casabona J. The COVID-19 Sentinel Schools Network of Catalonia (CSSNC) project: Associated factors to prevalence and incidence of SARS-CoV-2 infection in educational settings during the 2020-2021 academic year. PLoS One 2022; 17:e0277764. [PMID: 36395191 PMCID: PMC9671345 DOI: 10.1371/journal.pone.0277764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
The Sentinel Schools project was designed to monitor and evaluate the epidemiology of COVID-19 in Catalonia, gathering evidence for health and education policies to inform the development of health protocols and public health interventions to control of SARS-CoV-2 infection in schools. The aim of this study was to estimate the prevalence and incidence of SARS-CoV-2 infections and to identify their determinants among students and staff during February to June in the academic year 2020-2021. We performed two complementary studies, a cross-sectional and a longitudinal component, using a questionnaire to collect nominal data and testing for SARS-CoV-2 detection. We describe the results and perform a univariate and multivariate analysis. The initial crude seroprevalence was 14.8% (95% CI: 13.1-16.5) and 22% (95% CI: 18.3-25.8) for students and staff respectively, and the active infection prevalence was 0.7% (95% CI: 0.3-1) and 1.1% (95% CI: 0.1-2). The overall incidence for persons at risk was 2.73 per 100 person-month and 2.89 and 2.34 per 100 person-month for students and staff, respectively. Socioeconomic, self-reported knowledge, risk perceptions and contact pattern variables were positively associated with the outcome while sanitary measure compliance was negatively associated, the same significance trend was observed in multivariate analysis. In the longitudinal component, epidemiological close contact with SARS-CoV-2 infection was a risk factor for SARS-CoV-2 infection while the highest socioeconomic status level was protective as was compliance with sanitary measures. The small number of active cases detected in these schools suggests a low transmission among children in school and the efficacy of public health measures implemented, at least in the epidemiological scenario of the study period. The major contribution of this study was to provide results and evidence that help analyze the transmission dynamic of SARS-CoV-2 and evaluate the associations between sanitary protocols implemented, and measures to avoid SARS-CoV-2 spread in schools.
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Affiliation(s)
- Fabiana Ganem
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Departament de Pediatria, d’Obstetrícia i Ginecologia i de Medicina Preventiva i de Salut Publica, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Anna Bordas
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Cinta Folch
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- * E-mail:
| | - Lucia Alonso
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Marcos Montoro-Fernandez
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
| | - Andreu Colom-Cadena
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Ariadna Mas
- Direcció Assistencial d’Atenció Primària i Comunitària, Institut Català de la Salut, Barcelona, Catalonia, Spain
| | - Jacobo Mendioroz
- Subdirecció general de Vigilància i Resposta a Emergències de l’Agència de Salut Pública de Catalunya, Departament de Salut, Catalonia, Spain
| | - Laia Asso
- Agència de Salut Pública de Catalunya (ASPCAT), Departament de Salut, Generalitat de Catalunya, Catalonia, Spain
| | - Andres Anton
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Maria Victoria González
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut Català de la Salut, Institut D’Investigació en Ciències de La Salut Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
| | - Ignacio Blanco
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut Català de la Salut, Institut D’Investigació en Ciències de La Salut Germans Trias i Pujol (IGTP), Badalona, Catalonia, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Antoni Soriano-Arandes
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Casabona
- Centre of Epidemiological Studies on Sexually Transmitted Infections and AIDS of Catalonia (CEEISCAT), Health Department, Government of Catalonia, Badalona, Spain
- Departament de Pediatria, d’Obstetrícia i Ginecologia i de Medicina Preventiva i de Salut Publica, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), Badalona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
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10
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Eales O, Wang H, Haw D, Ainslie KEC, Walters CE, Atchison C, Cooke G, Barclay W, Ward H, Darzi A, Ashby D, Donnelly CA, Elliott P, Riley S. Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021. PLoS Comput Biol 2022; 18:e1010724. [PMID: 36417468 PMCID: PMC9728904 DOI: 10.1371/journal.pcbi.1010724] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/07/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards. AIM We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence. METHODS On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions. RESULTS Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. CONCLUSION High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Haowei Wang
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - David Haw
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Kylie E. C. Ainslie
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Caroline E. Walters
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Christina Atchison
- School of Public Health, Imperial College London, London, United Kingdom
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- National Institute for Health Research Imperial Biomedical Research Centre, London
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Helen Ward
- School of Public Health, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- National Institute for Health Research Imperial Biomedical Research Centre, London
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, United Kingdom
- National Institute for Health Research Imperial Biomedical Research Centre, London
- Institute of Global Health Innovation at Imperial College London, London, United Kingdom
| | - Deborah Ashby
- School of Public Health, Imperial College London, London, United Kingdom
| | - Christl A. Donnelly
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Paul Elliott
- School of Public Health, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- National Institute for Health Research Imperial Biomedical Research Centre, London
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Health Data Research (HDR) UK London at Imperial College, London, United Kingdom
- UK Dementia Research Institute at Imperial College, London, United Kingdom
| | - Steven Riley
- School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
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11
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Inferring age-specific differences in susceptibility to and infectiousness upon SARS-CoV-2 infection based on Belgian social contact data. PLoS Comput Biol 2022; 18:e1009965. [PMID: 35353810 PMCID: PMC9000131 DOI: 10.1371/journal.pcbi.1009965] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/11/2022] [Accepted: 02/24/2022] [Indexed: 11/19/2022] Open
Abstract
Several important aspects related to SARS-CoV-2 transmission are not well known due to a lack of appropriate data. However, mathematical and computational tools can be used to extract part of this information from the available data, like some hidden age-related characteristics. In this paper, we present a method to investigate age-specific differences in transmission parameters related to susceptibility to and infectiousness upon contracting SARS-CoV-2 infection. More specifically, we use panel-based social contact data from diary-based surveys conducted in Belgium combined with the next generation principle to infer the relative incidence and we compare this to real-life incidence data. Comparing these two allows for the estimation of age-specific transmission parameters. Our analysis implies the susceptibility in children to be around half of the susceptibility in adults, and even lower for very young children (preschooler). However, the probability of adults and the elderly to contract the infection is decreasing throughout the vaccination campaign, thereby modifying the picture over time.
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12
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Gimma A, Munday JD, Wong KLM, Coletti P, van Zandvoort K, Prem K, Klepac P, Rubin GJ, Funk S, Edmunds WJ, Jarvis CI. Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study. PLoS Med 2022; 19:e1003907. [PMID: 35231023 PMCID: PMC8887739 DOI: 10.1371/journal.pmed.1003907] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/06/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND During the Coronavirus Disease 2019 (COVID-19) pandemic, the United Kingdom government imposed public health policies in England to reduce social contacts in hopes of curbing virus transmission. We conducted a repeated cross-sectional study to measure contact patterns weekly from March 2020 to March 2021 to estimate the impact of these policies, covering 3 national lockdowns interspersed by periods of less restrictive policies. METHODS AND FINDINGS The repeated cross-sectional survey data were collected using online surveys of representative samples of the UK population by age and gender. Survey participants were recruited by the online market research company Ipsos MORI through internet-based banner and social media ads and email campaigns. The participant data used for this analysis are restricted to those who reported living in England. We calculated the mean daily contacts reported using a (clustered) bootstrap and fitted a censored negative binomial model to estimate age-stratified contact matrices and estimate proportional changes to the basic reproduction number under controlled conditions using the change in contacts as a scaling factor. To put the findings in perspective, we discuss contact rates recorded throughout the year in terms of previously recorded rates from the POLYMOD study social contact study. The survey recorded 101,350 observations from 19,914 participants who reported 466,710 contacts over 53 weeks. We observed changes in social contact patterns in England over time and by participants' age, personal risk factors, and perception of risk. The mean reported contacts for adults 18 to 59 years old ranged between 2.39 (95% confidence interval [CI] 2.20 to 2.60) contacts and 4.93 (95% CI 4.65 to 5.19) contacts during the study period. The mean contacts for school-age children (5 to 17 years old) ranged from 3.07 (95% CI 2.89 to 3.27) to 15.11 (95% CI 13.87 to 16.41). This demonstrates a sustained decrease in social contacts compared to a mean of 11.08 (95% CI 10.54 to 11.57) contacts per participant in all age groups combined as measured by the POLYMOD social contact study in 2005 to 2006. Contacts measured during periods of lockdowns were lower than in periods of eased social restrictions. The use of face coverings outside the home has remained high since the government mandated use in some settings in July 2020. The main limitations of this analysis are the potential for selection bias, as participants are recruited through internet-based campaigns, and recall bias, in which participants may under- or overreport the number of contacts they have made. CONCLUSIONS In this study, we observed that recorded contacts reduced dramatically compared to prepandemic levels (as measured in the POLYMOD study), with changes in reported contacts correlated with government interventions throughout the pandemic. Despite easing of restrictions in the summer of 2020, the mean number of reported contacts only returned to about half of that observed prepandemic at its highest recorded level. The CoMix survey provides a unique repeated cross-sectional data set for a full year in England, from the first day of the first lockdown, for use in statistical analyses and mathematical modelling of COVID-19 and other diseases.
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Affiliation(s)
- Amy Gimma
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - James D. Munday
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kerry L. M. Wong
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Pietro Coletti
- UHasselt, Data Science Institute and I-BioStat, Hasselt, Belgium
| | - Kevin van Zandvoort
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kiesha Prem
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Petra Klepac
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - G. James Rubin
- Department of Psychological Medicine, King’s College London, Denmark Hill, London, United Kingdom
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - W. John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Christopher I. Jarvis
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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13
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Quantifying pupil-to-pupil SARS-CoV-2 transmission and the impact of lateral flow testing in English secondary schools. Nat Commun 2022; 13:1106. [PMID: 35232987 PMCID: PMC8888696 DOI: 10.1038/s41467-022-28731-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/04/2022] [Indexed: 12/24/2022] Open
Abstract
A range of measures have been implemented to control within-school SARS-CoV-2 transmission in England, including the self-isolation of close contacts and twice weekly mass testing of secondary school pupils using lateral flow device tests (LFTs). Despite reducing transmission, isolating close contacts can lead to high levels of absences, negatively impacting pupils. To quantify pupil-to-pupil SARS-CoV-2 transmission and the impact of implemented control measures, we fit a stochastic individual-based model of secondary school infection to both swab testing data and secondary school absences data from England, and then simulate outbreaks from 31st August 2020 until 23rd May 2021. We find that the pupil-to-pupil reproduction number, Rschool, has remained below 1 on average across the study period, and that twice weekly mass testing using LFTs has helped to control pupil-to-pupil transmission. We also explore the potential benefits of alternative containment strategies, finding that a strategy of repeat testing of close contacts rather than isolation, alongside mass testing, substantially reduces absences with only a marginal increase in pupil-to-pupil transmission. Twice weekly mass testing using lateral flow tests has helped to control pupil-to-pupil transmission in English secondary schools. Here, the authors show that repeat testing of contacts alongside mass testing could greatly reduce absences with only a marginal increase in transmission, compared to isolating contacts.
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14
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Liu QH, Zhang J, Peng C, Litvinova M, Huang S, Poletti P, Trentini F, Guzzetta G, Marziano V, Zhou T, Viboud C, Bento AI, Lv J, Vespignani A, Merler S, Yu H, Ajelli M. Model-based evaluation of alternative reactive class closure strategies against COVID-19. Nat Commun 2022; 13:322. [PMID: 35031600 PMCID: PMC8760266 DOI: 10.1038/s41467-021-27939-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0-26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.
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Affiliation(s)
- Quan-Hui Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Shudong Huang
- College of Computer Science, Sichuan University, Chengdu, China
| | - Piero Poletti
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Filippo Trentini
- Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy
| | - Giorgio Guzzetta
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | | | - Tao Zhou
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Jiancheng Lv
- College of Computer Science, Sichuan University, Chengdu, China
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Stefano Merler
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
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15
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Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. Proc Natl Acad Sci U S A 2021; 118:2112605118. [PMID: 34753823 PMCID: PMC8609560 DOI: 10.1073/pnas.2112605118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Schools play a central role in the transmission of many respiratory infections. Heterogeneous social contact patterns associated with the social structures of schools (i.e., classes/grades) are likely to influence the within-school transmission dynamics, but data-driven evidence on fine-scale transmission patterns between students has been limited. Using a mathematical model, we analyzed a large-scale dataset of seasonal influenza outbreaks in Matsumoto city, Japan, to infer social interactions within and between classes/grades from observed transmission patterns. While the relative contribution of within-class and within-grade transmissions to the reproduction number varied with the number of classes per grade, the overall within-school reproduction number, which determines the initial growth of cases and the risk of sustained transmission, was only minimally associated with class sizes and the number of classes per grade. This finding suggests that interventions that change the size and number of classes, e.g., splitting classes and staggered attendance, may have a limited effect on the control of school outbreaks. We also found that vaccination and mask-wearing of students were associated with reduced susceptibility (vaccination and mask-wearing) and infectiousness (mask-wearing), and hand washing was associated with increased susceptibility. Our results show how analysis of fine-grained transmission patterns between students can improve understanding of within-school disease dynamics and provide insights into the relative impact of different approaches to outbreak control.
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Sharma M, Mindermann S, Rogers-Smith C, Leech G, Snodin B, Ahuja J, Sandbrink JB, Monrad JT, Altman G, Dhaliwal G, Finnveden L, Norman AJ, Oehm SB, Sandkühler JF, Aitchison L, Gavenčiak T, Mellan T, Kulveit J, Chindelevitch L, Flaxman S, Gal Y, Mishra S, Bhatt S, Brauner JM. Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe. Nat Commun 2021; 12:5820. [PMID: 34611158 PMCID: PMC8492703 DOI: 10.1038/s41467-021-26013-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 12/24/2022] Open
Abstract
European governments use non-pharmaceutical interventions (NPIs) to control resurging waves of COVID-19. However, they only have outdated estimates for how effective individual NPIs were in the first wave. We estimate the effectiveness of 17 NPIs in Europe's second wave from subnational case and death data by introducing a flexible hierarchical Bayesian transmission model and collecting the largest dataset of NPI implementation dates across Europe. Business closures, educational institution closures, and gathering bans reduced transmission, but reduced it less than they did in the first wave. This difference is likely due to organisational safety measures and individual protective behaviours-such as distancing-which made various areas of public life safer and thereby reduced the effect of closing them. Specifically, we find smaller effects for closing educational institutions, suggesting that stringent safety measures made schools safer compared to the first wave. Second-wave estimates outperform previous estimates at predicting transmission in Europe's third wave.
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Affiliation(s)
- Mrinank Sharma
- Department of Statistics, University of Oxford, Oxford, UK.
- Department of Engineering Science, University of Oxford, Oxford, UK.
- Future of Humanity Institute, University of Oxford, Oxford, UK.
| | - Sören Mindermann
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, Oxford, UK.
| | - Charlie Rogers-Smith
- OATML Group (work done while at OATML as an external collaborator), Department of Computer Science, University of Oxford, Oxford, UK
| | - Gavin Leech
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Benedict Snodin
- Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Janvi Ahuja
- Future of Humanity Institute, University of Oxford, Oxford, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Jonas B Sandbrink
- Future of Humanity Institute, University of Oxford, Oxford, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Joshua Teperowski Monrad
- Future of Humanity Institute, University of Oxford, Oxford, UK
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
- Department of Health Policy, London School of Economics and Political Science, London, UK
| | - George Altman
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Gurpreet Dhaliwal
- The Francis Crick Institute, London, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Lukas Finnveden
- Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Alexander John Norman
- Mathematical, Physical and Life Sciences (MPLS) Doctoral Training Centre, University of Oxford, Oxford, UK
| | - Sebastian B Oehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- University of Cambridge, Cambridge, UK
| | | | | | | | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Jan Kulveit
- Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Leonid Chindelevitch
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Yarin Gal
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, Oxford, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jan Markus Brauner
- Future of Humanity Institute, University of Oxford, Oxford, UK.
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, Oxford, UK.
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Verelst F, Hermans L, Vercruysse S, Gimma A, Coletti P, Backer JA, Wong KLM, Wambua J, van Zandvoort K, Willem L, Bogaardt L, Faes C, Jarvis CI, Wallinga J, Edmunds WJ, Beutels P, Hens N. SOCRATES-CoMix: a platform for timely and open-source contact mixing data during and in between COVID-19 surges and interventions in over 20 European countries. BMC Med 2021; 19:254. [PMID: 34583683 PMCID: PMC8478607 DOI: 10.1186/s12916-021-02133-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/16/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND SARS-CoV-2 dynamics are driven by human behaviour. Social contact data are of utmost importance in the context of transmission models of close-contact infections. METHODS Using online representative panels of adults reporting on their own behaviour as well as parents reporting on the behaviour of one of their children, we collect contact mixing (CoMix) behaviour in various phases of the COVID-19 pandemic in over 20 European countries. We provide these timely, repeated observations using an online platform: SOCRATES-CoMix. In addition to providing cleaned datasets to researchers, the platform allows users to extract contact matrices that can be stratified by age, type of day, intensity of the contact and gender. These observations provide insights on the relative impact of recommended or imposed social distance measures on contacts and can inform mathematical models on epidemic spread. CONCLUSION These data provide essential information for policymakers to balance non-pharmaceutical interventions, economic activity, mental health and wellbeing, during vaccine rollout.
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Affiliation(s)
- Frederik Verelst
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Lisa Hermans
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium.
| | - Sarah Vercruysse
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium
| | - Amy Gimma
- London School of Hygiene and Tropical Medicine, London, UK
| | - Pietro Coletti
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium
| | - Jantien A Backer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kerry L M Wong
- London School of Hygiene and Tropical Medicine, London, UK
| | - James Wambua
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium
| | | | - Lander Willem
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Laurens Bogaardt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Christel Faes
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium
| | | | - Jacco Wallinga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Dept Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - W John Edmunds
- London School of Hygiene and Tropical Medicine, London, UK
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- School of Public Health and Community Medicine, The University of New South Wales, Sydney, Australia
| | - Niel Hens
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Data Science Institute and I-BioStat, Hasselt University, Hasselt, Belgium
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