Case-Control Study on the Routes of Transmission of SARS-CoV-2 after the Third Pandemic Wave in Tuscany, Central Italy
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data and Design
2.2. Statistical Analyses
2.2.1. Multiple Imputation of Missing Data
2.2.2. Logistic Regression
2.2.3. Ridge Logistic Regression
2.2.4. Combination of Results from Multiple Imputed Data Set
2.2.5. Sensitivity Analyses
2.2.6. Evaluation of the Predictive Performance of the Ridge Regression Model
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Zheng, C.; Shao, W.; Chen, X.; Zhang, B.; Wang, G.; Zhang, W. Real-world effectiveness of COVID-19 vaccines: A literature review and meta-analysis. Int. J. Infect. Dis. 2022, 114, 252–260. [Google Scholar] [CrossRef] [PubMed]
- Chu, D.K.; Akl, E.A.; Duda, S.; Solo, K.; Yaacoub, S.; Schünemann, H.J.; El-Harakeh, A.; Bognanni, A.; Lotfi, T.; Loeb, M.; et al. Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: A systematic review and meta-analysis. Lancet 2020, 395, 1973–1987. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.; Liang, M.; Gao, L.; Ahmed, M.A.; Uy, J.P.; Cheng, C.; Zhou, Q.; Sun, C. Face masks to prevent transmission of COVID-19: A systematic review and meta-analysis. Am. J. Infect. Control 2021, 49, 900–906. [Google Scholar] [CrossRef] [PubMed]
- Alsaqqa, H.H. The Populations’ Resilience Toward the Policymaking Discrepancies in the Pandemic COVID-19 Period. Front. Public Health 2021, 9, 733519. [Google Scholar] [CrossRef]
- Nenna, R.; Zeric, H.; Petrarca, L.; Mancino, E.; Midulla, F. Weighing policymaking: A narrative review of school closures as COVID-19 pandemic-mitigation strategies. Pediatr. Pulmonol. 2021, 57, 1982–1989. [Google Scholar] [CrossRef]
- Auger, K.A.; Shah, S.S.; Richardson, T.; Hartley, D.; Hall, M.; Warniment, A.; Timmons, K.; Bosse, D.; Ferris, S.A.; Brady, P.W.; et al. Association Between Statewide School Closure and COVID-19 Incidence and Mortality in the US. JAMA 2020, 324, 859–870. [Google Scholar] [CrossRef]
- Gandini, S.; Rainisio, M.; Iannuzzo, M.L.; Bellerba, F.; Cecconi, F.; Scorrano, L. A cross-sectional and prospective cohort study of the role of schools in the SARS-CoV-2 second wave in Italy. Lancet Reg. Health-Eur. 2021, 5, 100092. [Google Scholar] [CrossRef]
- Tenforde, M.W.; Fisher, K.A.; Patel, M.M. Identifying COVID-19 Risk Through Observational Studies to Inform Control Measures. JAMA 2021, 325, 1464–1465. [Google Scholar] [CrossRef]
- Hobbs, C.V.; Martin, L.M.; Kim, S.S.; Kirmse, B.M.; Haynie, L.; McGraw, S.; Byers, P.; Taylor, K.G.; Patel, M.M.; Flannery, B.; et al. Factors Associated with Positive SARS-CoV-2 Test Results in Outpatient Health Facilities and Emergency Departments Among Children and Adolescents Aged <18 Years—Mississippi, September–November 2020. MMWR. Morb. Mortal. Wkly. Rep. 2020, 69, 1925–1929. [Google Scholar] [CrossRef]
- Fisher, K.A.; Tenforde, M.W.; Feldstein, L.R.; Lindsell, C.J.; Shapiro, N.I.; Files, D.C.; Gibbs, K.W.; Erickson, H.L.; Prekker, M.E.; Steingrub, J.S.; et al. Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities—United States, July 2020. MMWR. Morb. Mortal. Wkly. Rep. 2020, 69, 1258–1264. [Google Scholar] [CrossRef]
- van Buuren, S. Multiple imputation of discrete and continuous data by fully conditional specification. Stat. Methods Med. Res. 2007, 16, 219–242. [Google Scholar] [CrossRef] [PubMed]
- Burgette, L.F.; Reiter, J.P. Multiple Imputation for Missing Data via Sequential Regression Trees. Am. J. Epidemiol. 2010, 72, 1070–1076. [Google Scholar] [CrossRef] [PubMed]
- Pavlou, M.; Ambler, G.; Seaman, S.; De Iorio, M.; Omar, R.Z. Review and evaluation of penalised regression methods for risk prediction in low-dimensional data with few events. Stat. Med. 2016, 35, 1159–1177. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Krstajic, D.; Buturovic, L.J.; Leahy, D.E.; Thomas, S. Cross-validation pitfalls when selecting and assessing regression and classification models. J. Cheminform. 2014, 6, 10. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rubin, D.B. Multiple Imputation for Nonresponse in Surveys; John Wiley & Sons Inc.: New York, NY, USA, 1987. [Google Scholar] [CrossRef]
- R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2022; Available online: https://www.R-project.org/ (accessed on 16 January 2023).
- van Buuren, S.; Groothuis-Oudshoorn, K. Mice: Multivariate Imputation by Chained Equations in R. J. Stat. Softw. 2011, 45, 1–67. [Google Scholar] [CrossRef] [Green Version]
- Friedman, J.; Hastie, T.; Tibshirani, R. Regularization Paths for Generalized Linear Models via Coordinate Descent. J. Stat. Softw. 2010, 33, 1–22. [Google Scholar] [CrossRef] [Green Version]
- Decree-Law 22 April 2021, n. 52 Urgent Measures for the Gradual Resumption of Economic and Social Activities in Compliance with the Need to Contain the Spread of the COVID-19 Epidemic. 2021. Available online: https://www.gazzettaufficiale.it/eli/gu/2021/04/22/96/sg/pdf (accessed on 16 January 2023).
- Wong, N.S.; Lee, S.S.; Kwan, T.H.; Yeoh, E.K. Settings of virus exposure and their implications in the propagation of transmission networks in a COVID-19 outbreak. Lancet Reg. Health West. Pac. 2020, 4, 100052. [Google Scholar] [CrossRef] [PubMed]
- Lim, C.; Nam, Y.; Oh, W.S.; Ham, S.; Kim, E.; Kim, M.; Kim, S.; Kim, Y.; Jeong, S. Characteristics of transmission routes of COVID-19 cluster infections in Gangwon Province, Korea. Epidemiol. Infect. 2022, 150, e19. [Google Scholar] [CrossRef]
- Liu, T.; Gong, D.; Xiao, J.; Hu, J.; He, G.; Rong, Z.; Ma, W. Cluster infections play important roles in the rapid evolution of COVID-19 transmission: A systematic review. Int. J. Infect. Dis. 2020, 99, 374–380. [Google Scholar] [CrossRef]
- Reicher, S.; Drury, J. Pandemic fatigue? How adherence to covid-19 regulations has been misrepresented and why it matters. BMJ 2021, 372, n137. [Google Scholar] [CrossRef]
- Elliott, M.R.; Valliant, R. Inference for Nonprobability Samples. Stat. Sci. 2017, 32, 249–264. [Google Scholar] [CrossRef]
- Shrank, W.H.; Patrick, A.R.; Alan Brookhart, M. Healthy User and Related Biases in Observational Studies of Preventive Interventions: A Primer for Physicians. J. Gen. Intern. Med. 2011, 26, 546–550. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, Y.; Rocklöv, J. The effective reproductive number of the Omicron variant of SARS-CoV-2 is several times relative to Delta. J. Travel Med. 2022, 29, taac037. [Google Scholar] [CrossRef] [PubMed]
- European Centre for Disease Prevention and Control. Considerations for the Use of Face Masks in the Community in the Context of the SARS-CoV-2 Omicron Variant of Concern Key Messages Target Audience Scientific Evidence on Face Masks for the Prevention of SARS-CoV-2 Infection. Stockholm: 2022. Available online: https://www.ecdc.europa.eu/sites/default/files/documents/Considerations-for-use-of-face-masks-in-the-community-in-the-context-of-the-SARS-CoV-2-Omicron-variant-of-concern.pdf (accessed on 16 January 2023).
Analysis on All Respondents | Index Cases (without Known Contacts with Positives) | Over 20 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Adjusted OR | LB 90% | UB 90% | p-Value | Adjusted OR | LB 90% | UB 90% | p-Value | Adjusted OR | LB 90% | UB 90% | p-Value | |
Public transport (2) | 1.72 | 0.73 | 4.06 | 0.301 | 2.14 | 0.74 | 6.16 | 0.237 | 1.78 | 0.64 | 4.93 | 0.356 |
Public transport (1) | 1.03 | 0.41 | 2.60 | 0.961 | 1.03 | 0.32 | 3.30 | 0.966 | 0.95 | 0.38 | 2.37 | 0.920 |
Family size | 1.05 | 0.88 | 1.25 | 0.650 | 1.03 | 0.82 | 1.29 | 0.841 | 1.06 | 0.89 | 1.27 | 0.588 |
Job exposure (2) | 1.80 | 0.75 | 4.30 | 0.271 | 1.66 | 0.50 | 5.54 | 0.489 | 2.63 | 1.03 | 6.68 | 0.089 |
Job exposure (1) | 0.88 | 0.49 | 1.59 | 0.730 | 0.95 | 0.45 | 1.99 | 0.907 | 0.96 | 0.51 | 1.80 | 0.914 |
Face mask | 0.63 | 0.34 | 1.17 | 0.222 | 0.88 | 0.36 | 2.13 | 0.808 | 0.63 | 0.28 | 1.42 | 0.353 |
Ceremonies | 0.25 | 0.09 | 0.73 | 0.034 | 0.14 | 0.02 | 0.79 | 0.062 | 0.31 | 0.10 | 0.95 | 0.085 |
Hair/Beauty salon | 0.51 | 0.27 | 0.97 | 0.087 | 0.57 | 0.26 | 1.22 | 0.225 | 0.63 | 0.32 | 1.24 | 0.260 |
Religious services | 0.48 | 0.22 | 1.07 | 0.132 | 0.38 | 0.12 | 1.17 | 0.158 | 0.47 | 0.20 | 1.15 | 0.166 |
School/University | 0.48 | 0.20 | 1.12 | 0.156 | 0.50 | 0.15 | 1.62 | 0.333 | 0.61 | 0.19 | 1.91 | 0.477 |
Libraries | 0.35 | 0.05 | 2.30 | 0.363 | 0.00 | 0.00 | Inf | 0.989 | 0.51 | 0.07 | 3.66 | 0.574 |
Hospitals | 0.51 | 0.28 | 0.93 | 0.068 | 0.54 | 0.25 | 1.14 | 0.176 | 0.55 | 0.29 | 1.05 | 0.128 |
Sporting events | 1.16 | 0.41 | 3.32 | 0.816 | 0.53 | 0.08 | 3.46 | 0.579 | 1.40 | 0.46 | 4.25 | 0.618 |
Outdoor performances | 0.17 | 0.05 | 0.61 | 0.023 | 0.24 | 0.06 | 0.99 | 0.098 | 0.19 | 0.05 | 0.74 | 0.045 |
Indoor performances | 0.33 | 0.07 | 1.52 | 0.234 | 0.23 | 0.03 | 1.52 | 0.201 | 0.29 | 0.06 | 1.38 | 0.194 |
Small stores | 0.59 | 0.37 | 0.93 | 0.059 | 0.52 | 0.28 | 0.98 | 0.091 | 0.57 | 0.34 | 0.96 | 0.078 |
Malls/supermarkets | 0.69 | 0.40 | 1.17 | 0.249 | 0.58 | 0.27 | 1.25 | 0.247 | 0.60 | 0.33 | 1.10 | 0.168 |
Hosting friends | 0.35 | 0.22 | 0.58 | 0.001 | 0.19 | 0.09 | 0.39 | <0.001 | 0.35 | 0.20 | 0.62 | 0.002 |
Visiting friends | 0.33 | 0.20 | 0.55 | 0.000 | 0.17 | 0.09 | 0.35 | <0.001 | 0.26 | 0.15 | 0.46 | <0.001 |
Hands-washing | 0.91 | 0.46 | 1.81 | 0.825 | 1.20 | 0.46 | 3.13 | 0.753 | 0.81 | 0.36 | 1.82 | 0.667 |
Courses | 0.57 | 0.26 | 1.28 | 0.258 | 0.46 | 0.15 | 1.38 | 0.245 | 0.55 | 0.22 | 1.33 | 0.265 |
Seaside resort | 0.97 | 0.54 | 1.75 | 0.928 | 0.79 | 0.35 | 1.76 | 0.625 | 0.90 | 0.47 | 1.72 | 0.796 |
Swimming-pool | 0.92 | 0.38 | 2.25 | 0.878 | 0.59 | 0.18 | 1.89 | 0.456 | 0.70 | 0.22 | 2.21 | 0.608 |
Indoor sports | 0.24 | 0.07 | 0.91 | 0.078 | 0.14 | 0.02 | 0.93 | 0.089 | 0.62 | 0.15 | 2.57 | 0.582 |
Outdoor sports | 0.40 | 0.20 | 0.81 | 0.034 | 0.29 | 0.11 | 0.75 | 0.034 | 0.42 | 0.17 | 1.05 | 0.121 |
Night clubs | 4.65 | 1.62 | 13.33 | 0.017 | 3.68 | 0.82 | 16.49 | 0.154 | 6.23 | 1.64 | 23.72 | 0.025 |
Crowded clubs | 1.44 | 0.81 | 2.55 | 0.301 | 1.00 | 0.44 | 2.28 | 0.993 | 1.25 | 0.64 | 2.43 | 0.585 |
Indoor bars | 0.45 | 0.20 | 1.01 | 0.104 | 0.56 | 0.22 | 1.45 | 0.316 | 0.44 | 0.19 | 1.01 | 0.104 |
Open air bars | 1.38 | 0.84 | 2.26 | 0.284 | 0.82 | 0.41 | 1.62 | 0.628 | 1.52 | 0.87 | 2.63 | 0.215 |
Indoor restaurants | 0.59 | 0.31 | 1.13 | 0.181 | 0.57 | 0.26 | 1.24 | 0.235 | 0.69 | 0.34 | 1.37 | 0.373 |
Open-air restaurants | 1.03 | 0.64 | 1.68 | 0.911 | 0.74 | 0.39 | 1.40 | 0.434 | 1.13 | 0.65 | 1.97 | 0.720 |
Outside region | 0.94 | 0.52 | 1.69 | 0.854 | 0.62 | 0.28 | 1.39 | 0.335 | 0.97 | 0.51 | 1.85 | 0.930 |
Where Do You Think You Contracted the Virus? * | Number of Responses (% of all Who Tested Positive) |
---|---|
Household contacts | 10 |
At work | 10 |
At school | 3 |
At the hospital/at the doctor’s cabinet | 3 |
From non-cohabiting family members, friends, acquaintances | 15 |
While carrying out sporting activities | 2 |
While carrying out cultural activities | 1 |
At the bar/restaurant/pub | 10 |
In a shop/at a shopping mall | 6 |
At the cinema/theatre | 0 |
Ceremonies or religious functions | 1 |
Travelling | 11 |
I do not know | 16 |
Other | 7 |
NA | 1 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Levi, M.; Cereda, G.; Cipriani, F.; Voller, F.; Baccini, M. Case-Control Study on the Routes of Transmission of SARS-CoV-2 after the Third Pandemic Wave in Tuscany, Central Italy. Int. J. Environ. Res. Public Health 2023, 20, 1912. https://doi.org/10.3390/ijerph20031912
Levi M, Cereda G, Cipriani F, Voller F, Baccini M. Case-Control Study on the Routes of Transmission of SARS-CoV-2 after the Third Pandemic Wave in Tuscany, Central Italy. International Journal of Environmental Research and Public Health. 2023; 20(3):1912. https://doi.org/10.3390/ijerph20031912
Chicago/Turabian StyleLevi, Miriam, Giulia Cereda, Francesco Cipriani, Fabio Voller, and Michela Baccini. 2023. "Case-Control Study on the Routes of Transmission of SARS-CoV-2 after the Third Pandemic Wave in Tuscany, Central Italy" International Journal of Environmental Research and Public Health 20, no. 3: 1912. https://doi.org/10.3390/ijerph20031912