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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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Wang J, Xie Q, Song H, Chen X, Zhang X, Zhao X, Hao Y, Zhang Y, Li H, Li N, Fan K, Wang X. Utilizing nanozymes for combating COVID-19: advancements in diagnostics, treatments, and preventative measures. J Nanobiotechnology 2023; 21:200. [PMID: 37344839 DOI: 10.1186/s12951-023-01945-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/29/2023] [Indexed: 06/23/2023] Open
Abstract
The emergence of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses significant challenges to global public health. Despite the extensive efforts of researchers worldwide, there remains considerable opportunities for improvement in timely diagnosis, specific treatment, and effective vaccines for SARS-CoV-2. This is due, in part, to the large number of asymptomatic carriers, rapid virus mutations, inconsistent confinement policies, untimely diagnosis and limited clear treatment plans. The emerging of nanozymes offers a promising approach for combating SARS-CoV-2 due to their stable physicochemical properties and high surface areas, which enable easier and multiple nano-bio interactions in vivo. Nanozymes inspire the development of sensitive and economic nanosensors for rapid detection, facilitate the development of specific medicines with minimal side effects for targeted therapy, trigger defensive mechanisms in the form of vaccines, and eliminate SARS-CoV-2 in the environment for prevention. In this review, we briefly present the limitations of existing countermeasures against coronavirus disease 2019 (COVID-19). We then reviewed the applications of nanozyme-based platforms in the fields of diagnostics, therapeutics and the prevention in COVID-19. Finally, we propose opportunities and challenges for the further development of nanozyme-based platforms for COVID-19. We expect that our review will provide valuable insights into the new emerging and re-emerging infectious pandemic from the perspective of nanozymes.
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Affiliation(s)
- Jia Wang
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Qingpeng Xie
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Haoyue Song
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Xiaohang Chen
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Xiaoxuan Zhang
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Xiangyu Zhao
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Yujia Hao
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Yuan Zhang
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Huifei Li
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Na Li
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xing Wang
- Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030001, China.
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Taiyuan, 030001, China.
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Li T, Xiao Y. Optimal strategies for coordinating infection control and socio-economic activities. MATHEMATICS AND COMPUTERS IN SIMULATION 2023; 207:533-555. [PMID: 36694593 PMCID: PMC9854248 DOI: 10.1016/j.matcom.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
It becomes challenging to identify feasible control strategies for simultaneously relaxing the countermeasures and containing the Covid-19 pandemic, given China's huge population size, high susceptibility, persist vaccination waning, and relatively weak strength of health systems. We propose a novel mathematical model with waning of immunity and solve the optimal control problem, in order to provide an insight on how much detecting and social distancing are required to coordinate socio-economic activities and epidemic control. We obtain the optimal intensity of countermeasures, i.e., the dynamic nucleic acid screening and social distancing, under which the health system is functioning normally and people can engage in a certain level of socio-economic activities. We find that it is the isolation capacity or the restriction of the case fatality rate (CFR) rather than the hospital capacity that mainly determines the optimal strategies. And the solved optimal controls under quarterly CFR restrictions exhibit oscillations. It is worth noticing that, if without considering booster or very low booster rate, the optimal strategy is a "on-off" mode, alternating between lock down and opening with certain social distancing, which reflects the importance and necessity of China's static management on a certain area during Covid-19 outbreak. The findings suggest some feasible paths to smoothly transit from the Covid-19 pandemic to an endemic phase.
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Affiliation(s)
- Tangjuan Li
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, PR China
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Kodera S, Hikita K, Rashed EA, Hirata A. The Effects of Time Window-Averaged Mobility on Effective Reproduction Number of COVID-19 Viral Variants in Urban Cities. J Urban Health 2023; 100:29-39. [PMID: 36445638 PMCID: PMC9707419 DOI: 10.1007/s11524-022-00697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/28/2022] [Indexed: 12/03/2022]
Abstract
During epidemics, the estimation of the effective reproduction number (ERN) associated with infectious disease is a challenging topic for policy development and medical resource management. The emergence of new viral variants is common in widespread pandemics including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A simple approach is required toward an appropriate and timely policy decision for understanding the potential ERN of new variants is required for policy revision. We investigated time-averaged mobility at transit stations as a surrogate to correlate with the ERN using the data from three urban prefectures in Japan. The optimal time windows, i.e., latency and duration, for the mobility to relate with the ERN were investigated. The optimal latency and duration were 5-6 and 8 days, respectively (the Spearman's ρ was 0.109-0.512 in Tokyo, 0.365-0.607 in Osaka, and 0.317-0.631 in Aichi). The same linear correlation was confirmed in Singapore and London. The mobility-adjusted ERN of the Alpha variant was 15-30%, which was 20-40% higher than the original Wuhan strain in Osaka, Aichi, and London. Similarly, the mobility-adjusted ERN of the Delta variant was 20%-40% higher than that of the Wuhan strain in Osaka and Aichi. The proposed metric would be useful for the proper evaluation of the infectivity of different SARS-CoV-2 variants in terms of ERN as well as the design of the forecasting system.
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Affiliation(s)
- Sachiko Kodera
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, Nagoya, 466-8555, Japan.
| | - Keigo Hikita
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Essam A Rashed
- Graduate School of Information Science, University of Hyogo, Kobe, 650-0047, Japan
| | - Akimasa Hirata
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, Nagoya, 466-8555, Japan.,Center of Biomedical Physics and Information Technology, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
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Nassiri H, Mohammadpour SI, Dahaghin M. How do the smart travel ban policy and intercity travel pattern affect COVID-19 trends? Lessons learned from Iran. PLoS One 2022; 17:e0276276. [PMID: 36256674 PMCID: PMC9578609 DOI: 10.1371/journal.pone.0276276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
COVID-19, as the most significant epidemic of the century, infected 467 million people and took the lives of more than 6 million individuals as of March 19, 2022. Due to the rapid transmission of the disease and the lack of definitive treatment, countries have employed nonpharmaceutical interventions. This study aimed to investigate the effectiveness of the smart travel ban policy, which has been implemented for non-commercial vehicles in the intercity highways of Iran since November 21, 2020. The other goal was to suggest efficient COVID-19 forecasting tools and to examine the association of intercity travel patterns and COVID-19 trends in Iran. To this end, weekly confirmed cases and deaths due to COVID-19 and the intercity traffic flow reported by loop detectors were aggregated at the country's level. The Box-Jenkins methodology was employed to evaluate the policy's effectiveness, using the interrupted time series analysis. The results indicated that the autoregressive integrated moving average with explanatory variable (ARIMAX) model outperformed the univariate ARIMA model in predicting the disease trends based on the MAPE criterion. The weekly intercity traffic and its lagged variables were entered as covariates in both models of the disease cases and deaths. The results indicated that the weekly intercity traffic increases the new weekly COVID-19 cases and deaths with a time lag of two and five weeks, respectively. Besides, the interrupted time series analysis indicated that the smart travel ban policy had decreased intercity travel by around 29%. Nonetheless, it had no significant direct effect on COVID-19 trends. This study suggests that the travel ban policy would not be efficient lonely unless it is coupled with active measures and adherence to health protocols by the people.
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Affiliation(s)
- Habibollah Nassiri
- Civil Engineering Department, Sharif University of Technology, Tehran, Iran
- * E-mail:
| | | | - Mohammad Dahaghin
- Civil Engineering Department, Sharif University of Technology, Tehran, Iran
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Arovah NI. The correlates of physical activity during COVID-19 pandemic among Indonesian young adults: A longitudinal study. JOURNAL OF EDUCATION AND HEALTH PROMOTION 2022; 11:179. [PMID: 35847142 PMCID: PMC9277751 DOI: 10.4103/jehp.jehp_720_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/03/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND Social distancing policy during the COVID-19 pandemic may affect physical activity levels. This study aimed to compare physical activity levels before and during the pandemic and to explore physical activity correlates among Indonesian young adults. MATERIALS AND METHODS This longitudinal study was conducted before the pandemic (n = 141) in September 2019 and was followed by an online follow-up survey during the pandemic (79% response rate) in September 2020. Physical activity was measured using the global physical activity questionnaire and was classified into "sufficient" and "insufficient." The potential correlates of physical activity were constructs from social-cognitive theory and health belief model. Those were measured using a validated questionnaire in the follow-up survey. Physical activity levels before and during pandemics were compared using the Wilcoxon signed-rank test. Simple logistic regressions were used to assess the relationships between each potential correlate and physical activity status during the pandemic. RESULTS Physical activity levels decreased significantly during the pandemic, mostly in the work-related domain. Participants with favorable physical activity-related constructs were more likely to be physically active. The odds ratio ranged from 3.41 (95% confidence interval [CI] = 1.15-10.11) in participants with higher self-efficacy to 4.50 (95% CI = 1.44-14.06) in those with higher outcome expectations of physical activity. CONCLUSION A significant decline in physical activity during the COVID-19 pandemic among Indonesian young adults was confirmed. The application of behavioral change theories for explaining physical activity status during the pandemic in this population is also supported. It is recommended to incorporate these constructs to develop physical activity interventions in this target population.
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Affiliation(s)
- Novita Intan Arovah
- Department of Sports Science, Faculty of Sports Science, Yogyakarta State University, Yogyakarta, Indonesia
- Address for correspondence: Dr. Novita Intan Arovah, Faculty of Sports Science, Yogyakarta State University, Colombo Street No 1, Karang Malang, Yogyakarta 55281, Indonesia. E-mail:
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Righolt CH, Zhang G, Sever E, Wilkinson K, Mahmud SM. Patterns and descriptors of COVID-19 testing and lab-confirmed COVID-19 incidence in Manitoba, Canada, March 2020-May 2021: A population-based study. ACTA ACUST UNITED AC 2021; 2:100038. [PMID: 34409400 PMCID: PMC8360706 DOI: 10.1016/j.lana.2021.100038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 11/20/2022]
Abstract
Background We studied lab-confirmed COVID-19 infection (LCCI) testing, incidence, and severity. Methods We included all Manitoba residents and limited our severity analysis to LCCI patients. We calculated testing, incidence and vaccination rates between March 8, 2020 and June 1, 2021. We estimated the association between patient characteristics and testing (rate ratio [RR]; Poisson regression), including the reason for testing (screening, symptomatic, contact/outbreak asymptomatic), incidence (hazard ratio [HR]; Cox regression), and severity (prevalence ratio [PR], Cox regression). Findings The overall testing rate during the second/third wave was 570/1,000 person-years, with an LCCI rate of 50/1,000 person-years. The secondary attack rate during the second/third wave was 16%. Across regions, young children (<10) had the lowest positivity for symptomatic testing, the highest positivity for asymptomatic testing, and the highest risk of LCCI as asymptomatic contact. People in the lowest income quintile had the highest risk of LCCI, 1.3-6x the hazard of those in the highest income quintile. Long-term care (LTC) residents were particularly affected in the second wave with HRs>10 for asymptomatic residents. Interpretation Although the severity of LCCI in children was low, they have a high risk of asymptomatic positivity. The groups most vulnerable to LCCI, who should remain a focus of public health, were residents of Manitoba's North, LTC facilities, and low-income neighbourhoods. Funding Canada Research Chair Program
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Affiliation(s)
| | | | | | | | - Salaheddin M. Mahmud
- Correspondence Author: Dr. Salaheddin Mahmud, MD PhD FRCPC, Professor and Director, Vaccine and Drug Evaluation Centre, Department of Community Health Sciences, University of Manitoba, 337 - 750 McDermot Avenue, Winnipeg, Manitoba, R3E 0T5 Canada
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Inter-provincial disparity of COVID-19 transmission and control in Nepal. Sci Rep 2021; 11:13363. [PMID: 34172764 PMCID: PMC8233407 DOI: 10.1038/s41598-021-92253-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Despite the global efforts to mitigate the ongoing COVID-19 pandemic, the disease transmission and the effective controls still remain uncertain as the outcome of the epidemic varies from place to place. In this regard, the province-wise data from Nepal provides a unique opportunity to study the effective control strategies. This is because (a) some provinces of Nepal share an open-border with India, resulting in a significantly high inflow of COVID-19 cases from India; (b) despite the inflow of a considerable number of cases, the local spread was quite controlled until mid-June of 2020, presumably due to control policies implemented; and (c) the relaxation of policies caused a rapid surge of the COVID-19 cases, providing a multi-phasic trend of disease dynamics. In this study, we used this unique data set to explore the inter-provincial disparities of the important indicators, such as epidemic trend, epidemic growth rate, and reproduction numbers. Furthermore, we extended our analysis to identify prevention and control policies that are effective in altering these indicators. Our analysis identified a noticeable inter-province variation in the epidemic trend (3 per day to 104 per day linear increase during third surge period), the median daily growth rate (1 to 4% per day exponential growth), the basic reproduction number (0.71 to 1.21), and the effective reproduction number (maximum values ranging from 1.20 to 2.86). Importantly, results from our modeling show that the type and number of control strategies that are effective in altering the indicators vary among provinces, underscoring the need for province-focused strategies along with the national-level strategy in order to ensure the control of a local spread.
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Jiao J, Fefferman N. The dynamics of evolutionary rescue from a novel pathogen threat in a host metapopulation. Sci Rep 2021; 11:10932. [PMID: 34035424 PMCID: PMC8149858 DOI: 10.1038/s41598-021-90407-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
When a novel disease strikes a naïve host population, there is evidence that the most immediate response can involve host evolution while the pathogen remains relatively unchanged. When hosts also live in metapopulations, there may be critical differences in the dynamics that emerge from the synergy among evolutionary, ecological, and epidemiological factors. Here we used a Susceptible-Infected-Recovery model to explore how spatial and temporal ecological factors may drive the epidemiological and rapid-evolutionary dynamics of host metapopulations. For simplicity, we assumed two host genotypes: wild type, which has a positive intrinsic growth rate in the absence of disease, and robust type, which is less likely to catch the infection given exposure but has a lower intrinsic growth rate in the absence of infection. We found that the robust-type host would be strongly selected for in the presence of disease when transmission differences between the two types is large. The growth rate of the wild type had dual but opposite effects on host composition: a smaller increase in wild-type growth increased wild-type competition and lead to periodical disease outbreaks over the first generations after pathogen introduction, while larger growth increased disease by providing more susceptibles, which increased robust host density but decreased periodical outbreaks. Increased migration had a similar impact as the increased differential susceptibility, both of which led to an increase in robust hosts and a decrease in periodical outbreaks. Our study provided a comprehensive understanding of the combined effects among migration, disease epidemiology, and host demography on host evolution with an unchanging pathogen. The findings have important implications for wildlife conservation and zoonotic disease control.
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Affiliation(s)
- Jing Jiao
- National Institute for Mathematical and Biological Synthesis, The University of Tennessee, 1122 Volunteer Blvd., Suite 106, Knoxville, TN, 37996, USA.
- Department of Biological Science, Florida State University, 319 Stadium Dr, Tallahassee, FL, 32304, USA.
| | - Nina Fefferman
- National Institute for Mathematical and Biological Synthesis, The University of Tennessee, 1122 Volunteer Blvd., Suite 106, Knoxville, TN, 37996, USA
- Ecology & Evolutionary Biology, The University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996, USA
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Adhikari K, Gautam R, Pokharel A, Uprety KN, Vaidya NK. Transmission dynamics of COVID-19 in Nepal: Mathematical model uncovering effective controls. J Theor Biol 2021; 521:110680. [PMID: 33771611 PMCID: PMC7987500 DOI: 10.1016/j.jtbi.2021.110680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 01/24/2023]
Abstract
While most of the countries around the globe are combating the pandemic of COVID-19, the level of its impact is quite variable among different countries. In particular, the data from Nepal, a developing country having an open border provision with highly COVID-19 affected country India, has shown a biphasic pattern of epidemic, a controlled phase (until July 21, 2020) followed by an outgrown phase (after July 21, 2020). To uncover the effective strategies implemented during the controlled phase, we develop a mathematical model that is able to describe the data from both phases of COVID-19 dynamics in Nepal. Using our best parameter estimates with 95% confidence interval, we found that during the controlled phase most of the recorded cases were imported from outside the country with a small number generated from the local transmission, consistent with the data. Our model predicts that these successful strategies were able to maintain the reproduction number at around 0.21 during the controlled phase, preventing 442,640 cases of COVID-19 and saving more than 1,200 lives in Nepal. However, during the outgrown phase, when the strategies such as border screening and quarantine, lockdown, and detection and isolation, were altered, the reproduction number raised to 1.8, resulting in exponentially growing cases of COVID-19. We further used our model to predict the long-term dynamics of COVID-19 in Nepal and found that without any interventions the current trend may result in about 18.76 million cases (10.70 million detected and 8.06 million undetected) and 89 thousand deaths in Nepal by the end of 2021. Finally, using our predictive model, we evaluated the effects of various control strategies on the long-term outcome of this epidemics and identified ideal strategies to curb the epidemic in Nepal.
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Affiliation(s)
| | - Ramesh Gautam
- Ratna Rajya Laxmi Campus, Tribhuvan University, Kathmandu, Nepal
| | - Anjana Pokharel
- Padma Kanya Multiple Campus, Tribhuvan University, Kathmandu, Nepal
| | - Kedar Nath Uprety
- Central Department of Mathematics, Tribhuvan University, Kathmandu, Nepal
| | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA; Computational Science Research Center, San Diego State University, San Diego, CA, USA; Viral Information Institute, San Diego State University, San Diego, CA, USA.
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11
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Kristjanpoller W, Michell K, Minutolo MC. A causal framework to determine the effectiveness of dynamic quarantine policy to mitigate COVID-19. Appl Soft Comput 2021; 104:107241. [PMID: 33679272 PMCID: PMC7920818 DOI: 10.1016/j.asoc.2021.107241] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 12/19/2022]
Abstract
Since the start of the pandemic caused by the novel coronavirus, COVID-19, more than 106 million people have been infected and global deaths have surpassed 2.4 million. In Chile, the government restricted the activities and movement of people, organizations, and companies, under the concept of dynamic quarantine across municipalities for a predefined period of time. Chile is an interesting context to study because reports to have a higher quantity of infections per million people as well as a higher number of polymerize chain reaction (PCR) tests per million people. The higher testing rate means that Chile has good measurement of the contagious compared to other countries. Further, the heterogeneity of the social, economic, and demographic variables collected of each Chilean municipality provides a robust set of control data to better explain the contagious rate for each city. In this paper, we propose a framework to determine the effectiveness of the dynamic quarantine policy by analyzing different causal models (meta-learners and causal forest) including a time series pattern related to effective reproductive number. Additionally, we test the ability of the proposed framework to understand and explain the spread over benchmark traditional models and to interpret the Shapley Additive Explanations (SHAP) plots. The conclusions derived from the proposed framework provide important scientific information for government policymakers in disease control strategies, not only to analyze COVID-19 but to have a better model to determine social interventions for future outbreaks.
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Affiliation(s)
- Werner Kristjanpoller
- Departamento de Industrias, Universidad Técnica Federico Santa María, Av. España 1680, Valparaíso, Chile
| | - Kevin Michell
- Departamento de Industrias, Universidad Técnica Federico Santa María, Av. España 1680, Valparaíso, Chile
| | - Marcel C Minutolo
- Robert Morris University, 6001 University Blvd Moon Township, PA 15108, United States of America
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Shao W, Xie J, Zhu Y. Mediation by human mobility of the association between temperature and COVID-19 transmission rate. ENVIRONMENTAL RESEARCH 2021; 194:110608. [PMID: 33338486 PMCID: PMC7832246 DOI: 10.1016/j.envres.2020.110608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/14/2020] [Accepted: 12/07/2020] [Indexed: 05/04/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a major threat to global health. Relevant studies have shown that ambient temperature may influence the spread of novel coronavirus. However, the effect of ambient temperature on COVID-19 remains controversial. Human mobility is also closely related to the pandemic of COVID-19, which could be affected by temperature at the same time. The purpose of this study is to explore the underlying mechanism of the association of temperature with COVID-19 transmission rate by linking human mobility. The effective reproductive number, meteorological conditions and human mobility data in 47 countries are collected. Panel data models with fixed effects are used to analyze the association of ambient temperature with COVID-19 transmission rate, and the mediation by human mobility. Our results show that there is a negative relationship between temperature and COVID-19 transmission rate. We also observe that temperature is positively associated with human mobility and human mobility is positively related to COVID-19 transmission rate. Thus, the suppression effect (also known as the inconsistent mediation effect) of human mobility is confirmed, which remains robust when different lag structures are used. These findings provide evidence that temperature can influence the spread of COVID-19 by affecting human mobility. Therefore, although temperature is negatively related to COVID-19 transmission rate, governments and the public should pay more attention to control measures since people are more likely to go out when temperature rising. Our results could partially explain the reason why COVID-19 is not prevented by warm weather in some countries.
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Affiliation(s)
- Wenjing Shao
- School of Management, University of Science and Technology of China, Hefei, China.
| | - Jingui Xie
- School of Management, Technical University of Munich, Heilbronn, Germany.
| | - Yongjian Zhu
- School of Management, University of Science and Technology of China, Hefei, China.
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13
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Cindrich SL, Lansing JE, Brower CS, McDowell CP, Herring MP, Meyer JD. Associations Between Change in Outside Time Pre- and Post-COVID-19 Public Health Restrictions and Mental Health: Brief Research Report. Front Public Health 2021; 9:619129. [PMID: 33585393 PMCID: PMC7874172 DOI: 10.3389/fpubh.2021.619129] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) and associated pandemic has resulted in systemic changes to much of life, affecting both physical and mental health. Time spent outside is associated with positive mental health; however, opportunities to be outside were likely affected by the COVID-19 public health restrictions that encouraged people not to leave their homes unless it was required. This study investigated the impact of acute COVID-19 public health restrictions on outside time in April 2020, and quantified the association between outside time and both stress and positive mental health, using secondary analyses of cross-sectional data from the COVID and Well-being Study. Participants (n = 3,291) reported demographics, health behaviors, amount of time they spent outside pre/post COVID-19 public health restrictions (categorized as increased, maintained, or decreased), current stress (Perceived Stress Scale-4), and positive mental health (Short Warwick-Edinburgh Mental Well-being Scale). Outside time was lower following COVID-19 restrictions (p < 0.001; Cohen's d = −0.19). Participants who increased or maintained outside time following COVID-19 restrictions reported lower stress (p < 0.001, 5.93 [5.74–6.12], Hedges' g = −0.18; p < 0.001, mean = 5.85 [5.67–6.02], Hedges' g = −0.21; respectively) and higher positive mental health (p < 0.001, 24.49 [24.20–24.77], Hedges' g = 0.21; p < 0.001, 24.78 [24.52–25.03], Hedges' g = 0.28) compared to those who decreased outside time. These findings indicate that there are likely to be negative stress and mental health implications if strategies are not implemented to encourage and maintain safe time outside during large-scale workplace and societal changes (e.g., during a pandemic).
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Affiliation(s)
- Sydney L Cindrich
- Department of Kinesiology, Iowa State University, Ames, IA, United States
| | - Jeni E Lansing
- Department of Kinesiology, Iowa State University, Ames, IA, United States
| | - Cassandra S Brower
- Department of Kinesiology, Iowa State University, Ames, IA, United States
| | - Cillian P McDowell
- The Irish Longitudinal Study of Ageing, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Matthew P Herring
- The Irish Longitudinal Study of Ageing, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Physical Activity for Health Research Cluster, Health Research Institute, University of Limerick, Limerick, Ireland.,Department of Physical Education and Sport Sciences, University of Limerick, Limerick, Ireland
| | - Jacob D Meyer
- Department of Kinesiology, Iowa State University, Ames, IA, United States
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14
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Gnanvi JE, Salako KV, Kotanmi GB, Glèlè Kakaï R. On the reliability of predictions on Covid-19 dynamics: A systematic and critical review of modelling techniques. Infect Dis Model 2021; 6:258-272. [PMID: 33458453 PMCID: PMC7802527 DOI: 10.1016/j.idm.2020.12.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 12/18/2022] Open
Abstract
Since the emergence of the novel 2019 coronavirus pandemic in December 2019 (COVID-19), numerous modellers have used diverse techniques to assess the dynamics of transmission of the disease, predict its future course and determine the impact of different control measures. In this study, we conducted a global systematic literature review to summarize trends in the modelling techniques used for Covid-19 from January 1st, 2020 to November 30th, 2020. We further examined the accuracy and precision of predictions by comparing predicted and observed values for cumulative cases and deaths as well as uncertainties of these predictions. From an initial 4311 peer-reviewed articles and preprints found with our defined keywords, 242 were fully analysed. Most studies were done on Asian (78.93%) and European (59.09%) countries. Most of them used compartmental models (namely SIR and SEIR) (46.1%) and statistical models (growth models and time series) (31.8%) while few used artificial intelligence (6.7%), Bayesian approach (4.7%), Network models (2.3%) and Agent-based models (1.3%). For the number of cumulative cases, the ratio of the predicted over the observed values and the ratio of the amplitude of confidence interval (CI) or credibility interval (CrI) of predictions and the central value were on average larger than 1 indicating cases of inaccurate and imprecise predictions, and large variation across predictions. There was no clear difference among models used for these two ratios. In 75% of predictions that provided CI or CrI, observed values fall within the 95% CI or CrI of the cumulative cases predicted. Only 3.7% of the studies predicted the cumulative number of deaths. For 70% of the predictions, the ratio of predicted over observed cumulative deaths was less or close to 1. Also, the Bayesian model made predictions closer to reality than classical statistical models, although these differences are only suggestive due to the small number of predictions within our dataset (9 in total). In addition, we found a significant negative correlation (rho = - 0.56, p = 0.021) between this ratio and the length (in days) of the period covered by the modelling, suggesting that the longer the period covered by the model the likely more accurate the estimates tend to be. Our findings suggest that while predictions made by the different models are useful to understand the pandemic course and guide policy-making, some were relatively accurate and precise while other not.
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Affiliation(s)
- Janyce Eunice Gnanvi
- Laboratoire de Biomathématiques et d’Estimations Forestières, Université d’Abomey-Calavi, 04 BP 1525, Cotonou, Benin
| | - Kolawolé Valère Salako
- Laboratoire de Biomathématiques et d’Estimations Forestières, Université d’Abomey-Calavi, 04 BP 1525, Cotonou, Benin
| | - Gaëtan Brezesky Kotanmi
- Laboratoire de Biomathématiques et d’Estimations Forestières, Université d’Abomey-Calavi, 04 BP 1525, Cotonou, Benin
| | - Romain Glèlè Kakaï
- Laboratoire de Biomathématiques et d’Estimations Forestières, Université d’Abomey-Calavi, 04 BP 1525, Cotonou, Benin
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15
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Renardy M, Eisenberg M, Kirschner D. Predicting the second wave of COVID-19 in Washtenaw County, MI. J Theor Biol 2020; 507:110461. [PMID: 32866493 PMCID: PMC7455546 DOI: 10.1016/j.jtbi.2020.110461] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/24/2020] [Indexed: 01/11/2023]
Abstract
The COVID-19 pandemic has highlighted the patchwork nature of disease epidemics, with infection spread dynamics varying wildly across countries and across states within the US. To explore this issue, we study and predict the spread of COVID-19 in Washtenaw County, MI, which is home to University of Michigan and Eastern Michigan University, and in close proximity to Detroit, MI, a major epicenter of the epidemic in Michigan. We apply a discrete and stochastic network-based modeling framework allowing us to track every individual in the county. In this framework, we construct contact networks based on synthetic population datasets specific for Washtenaw County that are derived from US Census datasets. We assign individuals to households, workplaces, schools, and group quarters (such as prisons or long term care facilities). In addition, we assign casual contacts to each individual at random. Using this framework, we explicitly simulate Michigan-specific government-mandated workplace and school closures as well as social distancing measures. We perform sensitivity analyses to identify key model parameters and mechanisms contributing to the observed disease burden in the three months following the first observed cases of COVID-19 in Michigan. We then consider several scenarios for relaxing restrictions and reopening workplaces to predict what actions would be most prudent. In particular, we consider the effects of 1) different timings for reopening, and 2) different levels of workplace vs. casual contact re-engagement. We find that delaying reopening does not reduce the magnitude of the second peak of cases, but only delays it. Reducing levels of casual contact, on the other hand, both delays and lowers the second peak. Through simulations and sensitivity analyses, we explore mechanisms driving the magnitude and timing of a second wave of infections upon re-opening. We find that the most significant factors are workplace and casual contacts and protective measures taken by infected individuals who have sought care. This model can be adapted to other US counties using synthetic population databases and data specific to those regions.
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Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC. Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. JAMA 2020; 324:782-793. [PMID: 32648899 DOI: 10.1001/jama.2020.12839] [Citation(s) in RCA: 2905] [Impact Index Per Article: 726.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
IMPORTANCE The coronavirus disease 2019 (COVID-19) pandemic, due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide sudden and substantial increase in hospitalizations for pneumonia with multiorgan disease. This review discusses current evidence regarding the pathophysiology, transmission, diagnosis, and management of COVID-19. OBSERVATIONS SARS-CoV-2 is spread primarily via respiratory droplets during close face-to-face contact. Infection can be spread by asymptomatic, presymptomatic, and symptomatic carriers. The average time from exposure to symptom onset is 5 days, and 97.5% of people who develop symptoms do so within 11.5 days. The most common symptoms are fever, dry cough, and shortness of breath. Radiographic and laboratory abnormalities, such as lymphopenia and elevated lactate dehydrogenase, are common, but nonspecific. Diagnosis is made by detection of SARS-CoV-2 via reverse transcription polymerase chain reaction testing, although false-negative test results may occur in up to 20% to 67% of patients; however, this is dependent on the quality and timing of testing. Manifestations of COVID-19 include asymptomatic carriers and fulminant disease characterized by sepsis and acute respiratory failure. Approximately 5% of patients with COVID-19, and 20% of those hospitalized, experience severe symptoms necessitating intensive care. More than 75% of patients hospitalized with COVID-19 require supplemental oxygen. Treatment for individuals with COVID-19 includes best practices for supportive management of acute hypoxic respiratory failure. Emerging data indicate that dexamethasone therapy reduces 28-day mortality in patients requiring supplemental oxygen compared with usual care (21.6% vs 24.6%; age-adjusted rate ratio, 0.83 [95% CI, 0.74-0.92]) and that remdesivir improves time to recovery (hospital discharge or no supplemental oxygen requirement) from 15 to 11 days. In a randomized trial of 103 patients with COVID-19, convalescent plasma did not shorten time to recovery. Ongoing trials are testing antiviral therapies, immune modulators, and anticoagulants. The case-fatality rate for COVID-19 varies markedly by age, ranging from 0.3 deaths per 1000 cases among patients aged 5 to 17 years to 304.9 deaths per 1000 cases among patients aged 85 years or older in the US. Among patients hospitalized in the intensive care unit, the case fatality is up to 40%. At least 120 SARS-CoV-2 vaccines are under development. Until an effective vaccine is available, the primary methods to reduce spread are face masks, social distancing, and contact tracing. Monoclonal antibodies and hyperimmune globulin may provide additional preventive strategies. CONCLUSIONS AND RELEVANCE As of July 1, 2020, more than 10 million people worldwide had been infected with SARS-CoV-2. Many aspects of transmission, infection, and treatment remain unclear. Advances in prevention and effective management of COVID-19 will require basic and clinical investigation and public health and clinical interventions.
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Affiliation(s)
- W Joost Wiersinga
- Division of Infectious Diseases, Department of Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew Rhodes
- Department of Intensive Care Medicine, St George's University Hospitals Foundation Trust, London, United Kingdom
| | - Allen C Cheng
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Australia
- School of Public Health and Preventive Medicine, Monash University, Monash University, Melbourne, Australia
| | - Sharon J Peacock
- National Infection Service, Public Health England, London, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Hallie C Prescott
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor
- VA Center for Clinical Management Research, Ann Arbor, Michigan
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Renardy M, Kirschner D. Predicting the second wave of COVID-19 in Washtenaw County, MI. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.06.20147223. [PMID: 32676613 PMCID: PMC7359538 DOI: 10.1101/2020.07.06.20147223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Marissa Renardy and Denise Kirschner University of Michigan Medical School The COVID-19 pandemic has highlighted the patchwork nature of disease epidemics, with infection spread dynamics varying wildly across countries and across states within the US. These heteroge- neous patterns are also observed within individual states, with patches of concentrated outbreaks. Data is being generated daily at all of these spatial scales, and answers to questions regarded re- opening strategies are desperately needed. Mathematical modeling is useful in exactly these cases, and using modeling at a county scale may be valuable to further predict disease dynamics for the purposes of public health interventions. To explore this issue, we study and predict the spread of COVID-19 in Washtenaw County, MI, the home to University of Michigan, Eastern Michigan University, and Google, as well as serving as a sister city to Detroit, MI where there has been a serious outbreak. Here, we apply a discrete and stochastic network-based modeling framework allowing us to track every individual in the county. In this framework, we construct contact net- works based on synthetic population datasets specific for Washtenaw County that are derived from US Census datasets. We assign individuals to households, workplaces, schools, and group quarters (such as prisons). In addition, we assign casual contacts to each individual at random. Using this framework, we explicitly simulate Michigan-specific government-mandated workplace and school closures as well as social distancing measures. We also perform sensitivity analyses to identify key model parameters and mechanisms contributing to the observed disease burden in the three months following the first observed cases on COVID-19 in Michigan. We then consider several scenarios for relaxing restrictions and reopening workplaces to predict what actions would be most prudent. In particular, we consider the effects of 1) different timings for reopening, and 2) different levels of workplace vs. casual contact re-engagement. Through simulations and sensitivity analyses, we explore mechanisms driving magnitude and timing of a second wave of infections upon re-opening. This model can be adapted to other US counties using synthetic population databases and data specific to those regions.
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