1
|
Gallego-García P, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Posada D. Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.01.24309632. [PMID: 39006420 PMCID: PMC11245079 DOI: 10.1101/2024.07.01.24309632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Different factors influence the spread of SARS-CoV-2, from the inherent transmission capabilities of the different variants to the control measurements put in place. Here we studied the introduction of the Alpha, Delta, and Omicron-BA.1 variants of concern (VOCs) into Spain. For this, we collected genomic data from the GISAID database and combined it with connectivity data from different countries with Spain to perform a phylodynamic Bayesian analysis of the introductions. Our findings reveal that the introductions of these VOCs predominantly originated from France, especially in the case of Alpha. As travel restrictions were eased during the Delta and Omicron-BA.1 waves, the number of introductions from distinct countries increased, with the United Kingdom and Germany becoming significant sources of the virus. The largest number of introductions detected corresponded to the Delta wave, which was associated with fewer restrictions and the summer period, when Spain receives a considerable number of tourists. This research underscores the importance of monitoring international travel patterns and implementing targeted public health measures to manage the spread of SARS-CoV-2.
Collapse
Affiliation(s)
- Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven – University of Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven – University of Leuven, 3000 Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo 36310, Spain
| |
Collapse
|
2
|
Conesa D, López de Rioja V, Gullón T, Tauste Campo A, Prats C, Alvarez-Lacalle E, Echebarria B. A mixture of mobility and meteorological data provides a high correlation with COVID-19 growth in an infection-naive population: a study for Spanish provinces. Front Public Health 2024; 12:1288531. [PMID: 38528860 PMCID: PMC10962055 DOI: 10.3389/fpubh.2024.1288531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction We use Spanish data from August 2020 to March 2021 as a natural experiment to analyze how a standardized measure of COVID-19 growth correlates with asymmetric meteorological and mobility situations in 48 Spanish provinces. The period of time is selected prior to vaccination so that the level of susceptibility was high, and during geographically asymmetric implementation of non-pharmacological interventions. Methods We develop reliable aggregated mobility data from different public sources and also compute the average meteorological time series of temperature, dew point, and UV radiance in each Spanish province from satellite data. We perform a dimensionality reduction of the data using principal component analysis and investigate univariate and multivariate correlations of mobility and meteorological data with COVID-19 growth. Results We find significant, but generally weak, univariate correlations for weekday aggregated mobility in some, but not all, provinces. On the other hand, principal component analysis shows that the different mobility time series can be properly reduced to three time series. A multivariate time-lagged canonical correlation analysis of the COVID-19 growth rate with these three time series reveals a highly significant correlation, with a median R-squared of 0.65. The univariate correlation between meteorological data and COVID-19 growth is generally not significant, but adding its two main principal components to the mobility multivariate analysis increases correlations significantly, reaching correlation coefficients between 0.6 and 0.98 in all provinces with a median R-squared of 0.85. This result is robust to different approaches in the reduction of dimensionality of the data series. Discussion Our results suggest an important effect of mobility on COVID-19 cases growth rate. This effect is generally not observed for meteorological variables, although in some Spanish provinces it can become relevant. The correlation between mobility and growth rate is maximal at a time delay of 2-3 weeks, which agrees well with the expected 5?10 day delays between infection, development of symptoms, and the detection/report of the case.
Collapse
Affiliation(s)
- David Conesa
- Department of Physics, Universitat Politécnica de Catalunya, Barcelona, Spain
| | | | - Tania Gullón
- Spanish Ministry of Transport, Mobility and Urban Agenda (MITMA), Madrid, Spain
| | - Adriá Tauste Campo
- Department of Physics, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - Clara Prats
- Department of Physics, Universitat Politécnica de Catalunya, Barcelona, Spain
| | | | - Blas Echebarria
- Department of Physics, Universitat Politécnica de Catalunya, Barcelona, Spain
| |
Collapse
|
3
|
Atamer Balkan B, Chang Y, Sparnaaij M, Wouda B, Boschma D, Liu Y, Yuan Y, Daamen W, de Jong MCM, Teberg C, Schachtschneider K, Sikkema RS, van Veen L, Duives D, ten Bosch QA. The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model. PLoS Comput Biol 2024; 20:e1011956. [PMID: 38547311 PMCID: PMC11003685 DOI: 10.1371/journal.pcbi.1011956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/09/2024] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
SARS-CoV-2 transmission in indoor spaces, where most infection events occur, depends on the types and duration of human interactions, among others. Understanding how these human behaviours interface with virus characteristics to drive pathogen transmission and dictate the outcomes of non-pharmaceutical interventions is important for the informed and safe use of indoor spaces. To better understand these complex interactions, we developed the Pedestrian Dynamics-Virus Spread model (PeDViS), an individual-based model that combines pedestrian behaviour models with virus spread models incorporating direct and indirect transmission routes. We explored the relationships between virus exposure and the duration, distance, respiratory behaviour, and environment in which interactions between infected and uninfected individuals took place and compared this to benchmark 'at risk' interactions (1.5 metres for 15 minutes). When considering aerosol transmission, individuals adhering to distancing measures may be at risk due to the buildup of airborne virus in the environment when infected individuals spend prolonged time indoors. In our restaurant case, guests seated at tables near infected individuals were at limited risk of infection but could, particularly in poorly ventilated places, experience risks that surpass that of benchmark interactions. Combining interventions that target different transmission routes can aid in accumulating impact, for instance by combining ventilation with face masks. The impact of such combined interventions depends on the relative importance of transmission routes, which is hard to disentangle and highly context dependent. This uncertainty should be considered when assessing transmission risks upon different types of human interactions in indoor spaces. We illustrated the multi-dimensionality of indoor SARS-CoV-2 transmission that emerges from the interplay of human behaviour and the spread of respiratory viruses. A modelling strategy that incorporates this in risk assessments can help inform policy makers and citizens on the safe use of indoor spaces with varying inter-human interactions.
Collapse
Affiliation(s)
- Büsra Atamer Balkan
- Quantitative Veterinary Epidemiology, Wageningen University & Research, Wageningen, The Netherlands
| | - You Chang
- Quantitative Veterinary Epidemiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn Sparnaaij
- Department of Transport & Planning, Delft University of Technology, Delft, The Netherlands
| | - Berend Wouda
- Gamelab, Delft University of Technology, Delft, The Netherlands
| | - Doris Boschma
- Gamelab, Delft University of Technology, Delft, The Netherlands
| | - Yangfan Liu
- Quantitative Veterinary Epidemiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Yufei Yuan
- Department of Transport & Planning, Delft University of Technology, Delft, The Netherlands
| | - Winnie Daamen
- Department of Transport & Planning, Delft University of Technology, Delft, The Netherlands
| | - Mart C. M. de Jong
- Quantitative Veterinary Epidemiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Colin Teberg
- Steady State Scientific Computing, Chicago, Illinois, United States of America
| | | | | | - Linda van Veen
- Gamelab, Delft University of Technology, Delft, The Netherlands
| | - Dorine Duives
- Department of Transport & Planning, Delft University of Technology, Delft, The Netherlands
| | - Quirine A. ten Bosch
- Quantitative Veterinary Epidemiology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
4
|
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'.
Collapse
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
| |
Collapse
|
5
|
Barbeito I, Precioso D, Sierra MJ, Vegas-Azcárate S, Fernández Balbuena S, Vitoriano B, Goméz-Ullate D, Cao R, Monge S. Effectiveness of non-pharmaceutical interventions in nine fields of activity to decrease SARS-CoV-2 transmission (Spain, September 2020-May 2021). Front Public Health 2023; 11:1061331. [PMID: 37124826 PMCID: PMC10131688 DOI: 10.3389/fpubh.2023.1061331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/15/2023] [Indexed: 05/02/2023] Open
Abstract
Background We estimated the association between the level of restriction in nine different fields of activity and SARS-CoV-2 transmissibility in Spain, from 15 September 2020 to 9 May 2021. Methods A stringency index (0-1) was created for each Spanish province (n = 50) daily. A hierarchical multiplicative model was fitted. The median of coefficients across provinces (95% bootstrap confidence intervals) quantified the effect of increasing one standard deviation in the stringency index over the logarithmic return of the weekly percentage variation of the 7-days SARS-CoV-2 cumulative incidence, lagged 12 days. Results Overall, increasing restrictions reduced SARS-CoV-2 transmission by 22% (RR = 0.78; one-sided 95%CI: 0, 0.82) in 1 week, with highest effects for culture and leisure 14% (0.86; 0, 0.98), social distancing 13% (0.87; 0, 0.95), indoor restaurants 10% (0.90; 0, 0.95) and indoor sports 6% (0.94; 0, 0.98). In a reduced model with seven fields, culture and leisure no longer had a significant effect while ceremonies decreased transmission by 5% (0.95; 0, 0.96). Models R 2 was around 70%. Conclusion Increased restrictions decreased COVID-19 transmission. Limitations include remaining collinearity between fields, and somewhat artificial quantification of qualitative restrictions, so the exact attribution of the effect to specific areas must be done with caution.
Collapse
Affiliation(s)
- Inés Barbeito
- Research Centre for Communication and Information Technology (CITIC), University of A Coruña (UDC), Galicia, Spain
| | - Daniel Precioso
- Department of Informatics Engineering, School of Engineering, University of Cádiz, Andalusia, Spain
| | - María José Sierra
- Centre for the Coordination of Health Alerts and Emergencies, Ministry of Health, Madrid, Spain
- CIBER Infectious Diseases, Madrid, Spain
| | | | | | - Begoña Vitoriano
- Institute of Interdisciplinary Mathematics, Complutense University, Madrid, Spain
| | - David Goméz-Ullate
- Department of Informatics Engineering, School of Engineering, University of Cádiz, Andalusia, Spain
- School of Science and Technology, IE University, Madrid, Spain
| | - Ricardo Cao
- Research Centre for Communication and Information Technology (CITIC), University of A Coruña (UDC), Galicia, Spain
| | - Susana Monge
- CIBER Infectious Diseases, Madrid, Spain
- Department of Communicable Diseases, National Centre of Epidemiology, Institute of Health Carlos III, Madrid, Spain
- *Correspondence: Susana Monge,
| | | |
Collapse
|
6
|
Rees EE, Avery BP, Carabin H, Carson CA, Champredon D, de Montigny S, Dougherty B, Nasri BR, Ogden NH. Effectiveness of non-pharmaceutical interventions to reduce SARS-CoV-2 transmission in Canada and their association with COVID-19 hospitalization rates. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2022; 48:438-448. [PMID: 38162959 PMCID: PMC10756332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Background Non-pharmaceutical interventions (NPIs) aim to reduce the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections mostly by limiting contacts between people where virus transmission can occur. However, NPIs limit social interactions and have negative impacts on economic, physical, mental and social well-being. It is, therefore, important to assess the impact of NPIs on reducing the number of coronavirus disease 2019 (COVID-19) cases and hospitalizations to justify their use. Methods Dynamic regression models accounting for autocorrelation in time series data were used with data from six Canadian provinces (British Columbia, Alberta, Saskatchewan, Manitoba, Ontario, Québec) to assess 1) the effect of NPIs (measured using a stringency index) on SARS-CoV-2 transmission (measured by the effective reproduction number), and 2) the effect of the number of hospitalized COVID-19 patients on the stringency index. Results Increasing stringency index was associated with a statistically significant decrease in the transmission of SARS-CoV-2 in Alberta, Saskatchewan, Manitoba, Ontario and Québec. The effect of stringency on transmission was time-lagged in all of these provinces except for Ontario. In all provinces except for Saskatchewan, increasing hospitalization rates were associated with a statistically significant increase in the stringency index. The effect of hospitalization on stringency was time-lagged. Conclusion These results suggest that NPIs have been effective in Canadian provinces, and that their implementation has been, in part, a response to increasing hospitalization rates of COVID-19 patients.
Collapse
Affiliation(s)
- Erin E Rees
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
| | - Brent P Avery
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - Hélène Carabin
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
- Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC
| | - Carolee A Carson
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
| | - Simon de Montigny
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- School of Public Health, Université de Montréal, Montréal, QC
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, QC
| | - Brendan Dougherty
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - Bouchra R Nasri
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
- School of Public Health, Université de Montréal, Montréal, QC
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
| |
Collapse
|