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Shim K, Hwang EH, Kim G, Woo YM, An YJ, Baek SH, Oh T, Kim Y, Jang K, Hong JJ, Koo BS. Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors. Heliyon 2024; 10:e30222. [PMID: 38737246 PMCID: PMC11088249 DOI: 10.1016/j.heliyon.2024.e30222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
After the first outbreak, SARS-CoV-2 infection continues to occur due to the emergence of new variants. There is limited information available on the comparative evaluation of evolutionary characteristics of SARS-CoV-2 among different countries over time, and its relatedness to epidemiological and socio-environmental factors within those countries. We assessed comparative Bayesian evolutionary characteristics for SARS-CoV-2 in eight countries from 2020 to 2022 using BEAST version 2.6.7. Additionally, the relatedness between virus evolution factors and both epidemiological and socio-environmental factors was analyzed using Pearson's correlation coefficient. The estimated substitution rates in the gene encoding S protein of SARS-CoV-2 exhibited a continuous increase from 2020 to 2022 and were divided into two distinct groups in 2022 (p value < 0.05). Effective population size (Ne) generally showed decreased patterns by time. Notably, the change rates of the substitution rates were negatively correlated with the cumulative vaccination rates in 2021. A strict and rapid vaccination policy in the United Arab Emirates dramatically reduced the evolution of the virus, compared to other countries. Also, the average yearly temperature in countries were negatively correlated with the substitution rates. The changes of six epitopes in SARS-CoV-2 were related to various socio-environmental factors. We figured out comparative virus evolutionary traits and the association of epidemiological and socio-environmental factors especially cumulative vaccination rates and average temperature.
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Affiliation(s)
- Kyuyoung Shim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Young Min Woo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - You Jung An
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Taehwan Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Yujin Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Kiwon Jang
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
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Zhu W, Yuan S, Mao S, Chen J, Zheng Y, Jiang X, Yu X, Jiang C, Fang Q, Wang W, Yuan Z, Yao Y. Relationship of close contact settings with transmission and infection during the SARS-CoV-2 Omicron BA.2 epidemic in Shanghai. BMJ Glob Health 2023; 8:e012289. [PMID: 38135296 DOI: 10.1136/bmjgh-2023-012289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/07/2023] [Indexed: 12/24/2023] Open
Abstract
INTRODUCTION We analysed case-contact clusters during the Omicron BA.2 epidemic in Shanghai to assess the risk of infection of contacts in different settings and to evaluate the effect of demographic factors on the association of infectivity and susceptibility to the Omicron variant. METHODS Data on the settings and frequency of contact, demographic characteristics and comorbidities of index cases, contacts and secondary cases were analysed. Independent effect of multiple variables on the risk for transmission and infection was evaluated using generalised estimating equations. RESULTS From 1 March to 1 June 2022, we identified 450 770 close contacts of 90 885 index cases. The risk for infection was greater for contacts in farmers' markets (fixed locations where farmers gather to sell products, adjusted OR (aOR): 3.62; 95% CI 2.87 to 4.55) and households (aOR: 2.68; 95% CI 2.15 to 3.35). Children (0-4 years) and elderly adults (60 years and above) had higher risk for infection and transmission. During the course of the epidemic, the risk for infection and transmission in different age groups initially increased, and then decreased on about 21 April (17th day of citywide home quarantine). Compared with medical workers (reference, aOR: 1.00), unemployed contacts (aOR: 1.77; 95% CI 1.53 to 2.04) and preschoolers (aOR: 1.61; 95% CI 1.26 to 2.05) had the highest risk for infection; delivery workers (aOR: 1.90, 95% CI 1.51 to 2.40) and public service workers (aOR: 1.85; 95% CI 1.64 to 2.10) had the highest risk for transmission. Contacts who had comorbidities (aOR: 1.10; 95% CI 1.09 to 1.12) had a higher risk for infection, particularly those with lung diseases or immune deficiency. CONCLUSION Farmers' markets and households were the main setting for transmission of Omicron. Children, the elderly, delivery workers and public service workers had the highest risk for transmission and infection. These findings should be considered when implementing targeted interventions.
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Affiliation(s)
- Wenlong Zhu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shiying Yuan
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Shenghua Mao
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jian Chen
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yaxu Zheng
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xianjin Jiang
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiao Yu
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chenyan Jiang
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qiwen Fang
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Weibing Wang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Zheng'an Yuan
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Ye Yao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
- Department of Biostatics, School of Public Health, Fudan University, Shanghai, China
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Madhusudanan A, Iddon C, Cevik M, Naismith JH, Fitzgerald S. Non-pharmaceutical interventions for COVID-19: a systematic review on environmental control measures. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20230130. [PMID: 37611631 PMCID: PMC10446906 DOI: 10.1098/rsta.2023.0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 08/25/2023]
Abstract
The purpose of this review was to identify the effectiveness of environmental control (EC) non-pharmaceutical interventions (NPIs) in reducing transmission of SARS-CoV-2 through conducting a systematic review. EC NPIs considered in this review are room ventilation, air filtration/cleaning, room occupancy, surface disinfection, barrier devices, [Formula: see text] monitoring and one-way-systems. Systematic searches of databases from Web of Science, Medline, EMBASE, preprint servers MedRxiv and BioRxiv were conducted in order to identify studies reported between 1 January 2020 and 1 December 2022. All articles reporting on the effectiveness of ventilation, air filtration/cleaning, room occupancy, surface disinfection, barrier devices, [Formula: see text] monitoring and one-way systems in reducing transmission of SARS-CoV-2 were retrieved and screened. In total, 13 971 articles were identified for screening. The initial title and abstract screening identified 1328 articles for full text review. Overall, 19 references provided evidence for the effectiveness of NPIs: 12 reported on ventilation, 4 on air cleaning devices, 5 on surface disinfection, 6 on room occupancy and 1 on screens/barriers. No studies were found that considered the effectiveness of [Formula: see text] monitoring or the implementation of one-way systems. Many of these studies were assessed to have critical risk of bias in at least one domain, largely due to confounding factors that could have affected the measured outcomes. As a result, there is low confidence in the findings. Evidence suggests that EC NPIs of ventilation, air cleaning devices and reduction in room-occupancy may have a role in reducing transmission in certain settings. However, the evidence was usually of low or very low quality and certainty, and hence the level of confidence ascribed to this conclusion is low. Based on the evidence found, it was not possible to draw any specific conclusions regarding the effectiveness of surface disinfection and the use of barrier devices. From these results, we further conclude that community agreed standards for well-designed epidemiological studies with low risk of bias are needed. Implementation of such standards would enable more confident assessment in the future of the effectiveness of EC NPIs in reducing transmission of SARS-CoV-2 and other pathogens in real-world settings. 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)
| | - Christopher Iddon
- Department of Civil, Environmental and Geomatic Engineering, University College London, WC1E 6BT, London, UK
| | - Muge Cevik
- Department of Infection and Global Health, School of Medicine, University of St Andrews, KY16 9TF, St Andrews, UK
| | | | - Shaun Fitzgerald
- Department of Engineering, University of Cambridge, CB2 1PZ, Cambridge, UK
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He Y, Martinez L, Ge Y, Feng Y, Chen Y, Tan J, Westbrook A, Li C, Cheng W, Ling F, Cheng H, Wu S, Zhong W, Handel A, Huang H, Sun J, Shen Y. Social Mixing and Network Characteristics of COVID-19 Patients Before and After Widespread Interventions: A Population-based Study. Epidemiol Infect 2023; 151:1-38. [PMID: 37577939 PMCID: PMC10540215 DOI: 10.1017/s0950268823001292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/28/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
SARS-CoV-2 rapidly spreads among humans via social networks, with social mixing and network characteristics potentially facilitating transmission. However, limited data on topological structural features has hindered in-depth studies. Existing research is based on snapshot analyses, preventing temporal investigations of network changes. Comparing network characteristics over time offers additional insights into transmission dynamics. We examined confirmed COVID-19 patients from an eastern Chinese province, analyzing social mixing and network characteristics using transmission network topology before and after widespread interventions. Between the two time periods, the percentage of singleton networks increased from 38.9 to 62.8 ; the average shortest path length decreased from 1.53 to 1.14 ; the average betweenness reduced from 0.65 to 0.11 ; the average cluster size dropped from 4.05 to 2.72 ; and the out-degree had a slight but nonsignificant decline from 0.75 to 0.63 Results show that nonpharmaceutical interventions effectively disrupted transmission networks, preventing further disease spread. Additionally, we found that the networks’ dynamic structure provided more information than solely examining infection curves after applying descriptive and agent-based modeling approaches. In summary, we investigated social mixing and network characteristics of COVID-19 patients during different pandemic stages, revealing transmission network heterogeneities.
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Affiliation(s)
- Yuncong He
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, USA
| | - Yang Ge
- School of Health Professions, University of Southern Mississippi, Hattiesburg, USA
| | - Yan Feng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yewen Chen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Jianbin Tan
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Adrianna Westbrook
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, USA
| | - Wei Cheng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Feng Ling
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Huimin Cheng
- Department of Statistics, University of Georgia, Athens, USA
| | - Shushan Wu
- Department of Statistics, University of Georgia, Athens, USA
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, Athens, USA
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Hui Huang
- Center for Applied Statistics and School of Statistics, Renmin University of China, Beijing, China
| | - Jimin Sun
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ye Shen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
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Larsen SL, Shin I, Joseph J, West H, Anorga R, Mena GE, Mahmud AS, Martinez PP. Quantifying the impact of SARS-CoV-2 temporal vaccination trends and disparities on disease control. SCIENCE ADVANCES 2023; 9:eadh9920. [PMID: 37531439 PMCID: PMC10396293 DOI: 10.1126/sciadv.adh9920] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 vaccines have been distributed at unprecedented speed. Still, little is known about temporal vaccination trends, their association with socioeconomic inequality, and their consequences for disease control. Using data from 161 countries/territories and 58 states, we examined vaccination rates across high and low socioeconomic status (SES), showing that disparities in coverage exist at national and subnational levels. We also identified two distinct vaccination trends: a rapid initial rollout, quickly reaching a plateau, or sigmoidal and slow to begin. Informed by these patterns, we implemented an SES-stratified mechanistic model, finding profound differences in mortality and incidence across these two vaccination types. Timing of initial rollout affects disease outcomes more substantially than final coverage or degree of SES disparity. Unexpectedly, timing is not associated with wealth inequality or GDP per capita. While socioeconomic disparity should be addressed, accelerating initial rollout for all over focusing on increasing coverage is an accessible intervention that could minimize the burden of disease across socioeconomic groups.
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Affiliation(s)
- Sophie L. Larsen
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ikgyu Shin
- Department of Statistics, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jefrin Joseph
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Haylee West
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Rafael Anorga
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL, USA
| | | | - Ayesha S. Mahmud
- Department of Demography, University of California, Berkeley, CA, USA
| | - Pamela P. Martinez
- Department of Statistics, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Wang H, Yuan Y, Wu B, Xiao M, Wang Z, Diao T, Zeng R, Chen L, Lei Y, Long P, Guo Y, Lai X, Wen Y, Li W, Cai H, Song L, Ni W, Zhao Y, Ouyang K, Wang J, Wang Q, Liu L, Wang C, Pan A, Li X, Gong R, Wu T. Neutralization against SARS-CoV-2 Delta/Omicron variants and B cell response after inactivated vaccination among COVID-19 convalescents. Front Med 2023; 17:747-757. [PMID: 36738428 PMCID: PMC9898702 DOI: 10.1007/s11684-022-0954-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023]
Abstract
Emerging SARS-CoV-2 variants have made COVID-19 convalescents susceptible to re-infection and have raised concern about the efficacy of inactivated vaccination in neutralization against emerging variants and antigen-specific B cell response. To this end, a study on a long-term cohort of 208 participants who have recovered from COVID-19 was conducted, and the participants were followed up at 3.3 (Visit 1), 9.2 (Visit 2), and 18.5 (Visit 3) months after SARS-CoV-2 infection. They were classified into three groups (no-vaccination (n = 54), one-dose (n = 62), and two-dose (n = 92) groups) on the basis of the administration of inactivated vaccination. The neutralizing antibody (NAb) titers against the wild-type virus continued to decrease in the no-vaccination group, but they rose significantly in the one-dose and two-dose groups, with the highest NAb titers being observed in the two-dose group at Visit 3. The NAb titers against the Delta variant for the no-vaccination, one-dose, and two-dose groups decreased by 3.3, 1.9, and 2.3 folds relative to the wild-type virus, respectively, and those against the Omicron variant decreased by 7.0, 4.0, and 3.8 folds, respectively. Similarly, the responses of SARS-CoV-2 RBD-specific B cells and memory B cells were boosted by the second vaccine dose. Results showed that the convalescents benefited from the administration of the inactivated vaccine (one or two doses), which enhanced neutralization against highly mutated SARS-CoV-2 variants and memory B cell responses. Two doses of inactivated vaccine among COVID-19 convalescents are therefore recommended for the prevention of the COVID-19 pandemic, and vaccination guidelines and policies need to be updated.
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Affiliation(s)
- Hao Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Yuan
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bihao Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingzhong Xiao
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Zhen Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tingyue Diao
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Zeng
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanshou Lei
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Pinpin Long
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi Guo
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xuefeng Lai
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuying Wen
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenhui Li
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hao Cai
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lulu Song
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Ni
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Youyun Zhao
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Kani Ouyang
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Jingzhi Wang
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China
| | - Qi Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Liu
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chaolong Wang
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - An Pan
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaodong Li
- Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, 430061, China.
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China.
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Tangchun Wu
- Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Mishra S, Walker JD, Wilhelm L, Larivière V, Bubela T, Straus SE. Use and misuse of research: Canada's response to covid-19 and its health inequalities. BMJ 2023; 382:e075666. [PMID: 37487605 DOI: 10.1136/bmj-2023-075666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Affiliation(s)
- Sharmistha Mishra
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital-Unity Health Toronto, Toronto, Ontario, Canada
| | - Jennifer D Walker
- ICES, Ontario, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Linda Wilhelm
- Canadian Arthritis Patient Alliance, Bloomfield, Kings County, New Brunswick, Canada (patient author)
| | | | - Tania Bubela
- Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sharon E Straus
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital-Unity Health Toronto, Toronto, Ontario, Canada
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Beale S, Hoskins S, Byrne T, Fong WLE, Fragaszy E, Geismar C, Kovar J, Navaratnam AMD, Nguyen V, Patel P, Yavlinsky A, Johnson AM, Van Tongeren M, Aldridge RW, Hayward A. Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales. J Occup Med Toxicol 2023; 18:5. [PMID: 37013634 PMCID: PMC10068189 DOI: 10.1186/s12995-023-00371-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Workers across different occupations vary in their risk of SARS-CoV-2 infection, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase. METHODS Data from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR). RESULTS Increased risk was seen in nurses (aRR = 1.44, 1.25-1.65; AF = 30%, 20-39%), doctors (aRR = 1.33, 1.08-1.65; AF = 25%, 7-39%), carers (1.45, 1.19-1.76; AF = 31%, 16-43%), primary school teachers (aRR = 1.67, 1.42- 1.96; AF = 40%, 30-49%), secondary school teachers (aRR = 1.48, 1.26-1.72; AF = 32%, 21-42%), and teaching support occupations (aRR = 1.42, 1.23-1.64; AF = 29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020-May 2021) and attenuated later (June-October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves. CONCLUSIONS Occupational differences in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.
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Affiliation(s)
- Sarah Beale
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK.
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK.
| | - Susan Hoskins
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
| | - Thomas Byrne
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Wing Lam Erica Fong
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Ellen Fragaszy
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
- Department of Infectious Disease Epidemiology, London, School of Hygiene and Tropical Medicine , Keppel Street, London, WC1E 7HT, UK
| | - Cyril Geismar
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
| | - Jana Kovar
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
| | - Annalan M D Navaratnam
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
| | - Vincent Nguyen
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
| | - Parth Patel
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Alexei Yavlinsky
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Anne M Johnson
- Institute for Global Health, University College London, London, WC1N 1EH, UK
| | - Martie Van Tongeren
- Division of Population Health, Health Services Research & Primary Care, University of Manchester, Manchester, M13 9NT, UK
| | - Robert W Aldridge
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK
| | - Andrew Hayward
- Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK
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9
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Dekker MM, Coffeng LE, Pijpers FP, Panja D, de Vlas SJ. Reducing societal impacts of SARS-CoV-2 interventions through subnational implementation. eLife 2023; 12:80819. [PMID: 36880190 PMCID: PMC10023153 DOI: 10.7554/elife.80819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
To curb the initial spread of SARS-CoV-2, many countries relied on nation-wide implementation of non-pharmaceutical intervention measures, resulting in substantial socio-economic impacts. Potentially, subnational implementations might have had less of a societal impact, but comparable epidemiological impact. Here, using the first COVID-19 wave in the Netherlands as a case in point, we address this issue by developing a high-resolution analysis framework that uses a demographically stratified population and a spatially explicit, dynamic, individual contact-pattern based epidemiology, calibrated to hospital admissions data and mobility trends extracted from mobile phone signals and Google. We demonstrate how a subnational approach could achieve similar level of epidemiological control in terms of hospital admissions, while some parts of the country could stay open for a longer period. Our framework is exportable to other countries and settings, and may be used to develop policies on subnational approach as a better strategic choice for controlling future epidemics.
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Affiliation(s)
- Mark M Dekker
- Department of Information and Computing Sciences, Utrecht UniversityUtrechtNetherlands
- Centre for Complex Systems Studies, Utrecht UniversityUtrechtNetherlands
- PBL Netherlands Environmental Assessment AgencyThe HagueNetherlands
| | - Luc E Coffeng
- Department of Public Health, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
| | - Frank P Pijpers
- Statistics NetherlandsThe HagueNetherlands
- Korteweg-de Vries Institute for Mathematics, University of AmsterdamAmsterdamNetherlands
| | - Debabrata Panja
- Department of Information and Computing Sciences, Utrecht UniversityUtrechtNetherlands
- Centre for Complex Systems Studies, Utrecht UniversityUtrechtNetherlands
| | - Sake J de Vlas
- Department of Public Health, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
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10
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Mazzonna F, Gatti N. Cultural differences, intergenerational contacts, and the spread of Covid-19: Evidence from Swiss language regions. POPULATION STUDIES 2023; 77:111-121. [PMID: 36692393 DOI: 10.1080/00324728.2022.2155691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Covid-19 pandemic displayed large variations between and within countries in the speed of contagion and in observed fatality rates. This work sheds light on the role of social ties in old age, exploiting the high cultural variation between German-speaking and Latin- (French- and Italian-) speaking regions in Switzerland. We show that older adults in Latin-speaking regions exhibit a larger social network and more intergenerational contacts than their German-speaking counterparts. These differences are consistent with the heterogeneous incidence of the disease across language regions. Even controlling for several determinants of the contagion, we find large differences in the incidence of Covid-19 among older adults, in both the first and second waves of the pandemic. These findings also hold when exploiting language variations within the three Swiss bilingual cantons. We rule out the possibility that our results are driven by differences in canton-specific policies or in citizens' compliance with containment measures.
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Affiliation(s)
- Fabrizio Mazzonna
- Università della Svizzera italiana.,IZA Institute of Labor Economics
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11
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Tian X, Zhang Y, Wang W, Fang F, Zhang W, Zhu Z, Wan Y. The impacts of vaccination status and host factors during early infection on SARS-CoV-2 persistence:a retrospective single-center cohort study. Int Immunopharmacol 2023; 114:109534. [PMID: 36476489 PMCID: PMC9708622 DOI: 10.1016/j.intimp.2022.109534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Viral persistence is a crucial factor that influences the transmissibility of SARS-CoV-2. However, the impacts of vaccination and physiological variables on viral persistence have not been adequately clarified. METHODS We collected the clinical records of 377 COVID-19 patients, which contained unvaccinated patients and patients received two doses of an inactivated vaccine or an mRNA vaccine. The impacts of vaccination on disease severity and viral persistence and the correlations between 49 laboratory variables and viral persistence were analyzed separately. Finally, we established a multivariate regression model to predict the persistence of viral RNA. RESULTS Both inactivated and mRNA vaccines significantly reduced the rate of moderate cases, while the vaccine related shortening of viral RNA persistence was only observed in moderate patients. Correlation analysis showed that 10 significant laboratory variables were shared by the unvaccinated mild patients and mild patients inoculated with an inactivated vaccine, but not by the mild patients inoculated with an mRNA vaccine. A multivariate regression model established based on the variables correlating with viral persistence in unvaccinated mild patients could predict the persistence of viral RNA for all patients except three moderate patients inoculated with an mRNA vaccine. CONCLUSION Vaccination contributed limitedly to the clearance of viral RNA in COVID-19 patients. While, laboratory variables in early infection could predict the persistence of viral RNA.
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Affiliation(s)
- Xiangxiang Tian
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China; Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, China; Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China; Department of Clinical Laboratory, The First People's Hospital of Shangqiu, Shangqiu 476000, China
| | - Yifan Zhang
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China; Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, China; Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wanhai Wang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, China
| | - Fang Fang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China; State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Yanmin Wan
- Department of Radiology, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China; Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China; State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China.
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12
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Schulenburg A, Cota W, Costa GS, Ferreira SC. Effects of infection fatality ratio and social contact matrices on vaccine prioritization strategies. CHAOS (WOODBURY, N.Y.) 2022; 32:093102. [PMID: 36182373 DOI: 10.1063/5.0096532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
Effective strategies of vaccine prioritization are essential to mitigate the impacts of severe infectious diseases. We investigate the role of infection fatality ratio (IFR) and social contact matrices on vaccination prioritization using a compartmental epidemic model fueled by real-world data of different diseases and countries. Our study confirms that massive and early vaccination is extremely effective to reduce the disease fatality if the contagion is mitigated, but the effectiveness is increasingly reduced as vaccination beginning delays in an uncontrolled epidemiological scenario. The optimal and least effective prioritization strategies depend non-linearly on epidemiological variables. Regions of the epidemiological parameter space, in which prioritizing the most vulnerable population is more effective than the most contagious individuals, depend strongly on the IFR age profile being, for example, substantially broader for COVID-19 in comparison with seasonal influenza. Demographics and social contact matrices deform the phase diagrams but do not alter their qualitative shapes.
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Affiliation(s)
- Arthur Schulenburg
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Wesley Cota
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Guilherme S Costa
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Silvio C Ferreira
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
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13
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Iddon C, Jones B, Sharpe P, Cevik M, Fitzgerald S. A population framework for predicting the proportion of people infected by the far-field airborne transmission of SARS-CoV-2 indoors. BUILDING AND ENVIRONMENT 2022; 221:109309. [PMID: 35757305 PMCID: PMC9212805 DOI: 10.1016/j.buildenv.2022.109309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The number of occupants in a space influences the risk of far-field airborne transmission of SARS-CoV-2 because the likelihood of having infectious and susceptible people both correlate with the number of occupants. This paper explores the relationship between occupancy and the probability of infection, and how this affects an individual person and a population of people. Mass-balance and dose-response models determine far-field transmission risks for an individual person and a population of people after sub-dividing a large reference space into 10 identical comparator spaces. For a single infected person, the dose received by an individual person in the comparator space is 10 times higher because the equivalent ventilation rate per infected person is lower when the per capita ventilation rate is preserved. However, accounting for population dispersion, such as the community prevalence of the virus, the probability of an infected person being present and uncertainty in their viral load, shows the transmission probability increases with occupancy and the reference space has a higher transmission risk. Also, far-field transmission is likely to be a rare event that requires a high emission rate, and there are a set of Goldilocks conditions that are just right when equivalent ventilation is effective at mitigating against transmission. These conditions depend on the viral load, because when they are very high or low, equivalent ventilation has little effect on transmission risk. Nevertheless, resilient buildings should deliver the equivalent ventilation rate required by standards as minimum.
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Affiliation(s)
- Christopher Iddon
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Benjamin Jones
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Patrick Sharpe
- Department of Architecture and Built Environment, University of Nottingham, Nottingham, UK
| | - Muge Cevik
- Department of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
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14
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Myall A, Price JR, Peach RL, Abbas M, Mookerjee S, Zhu N, Ahmad I, Ming D, Ramzan F, Teixeira D, Graf C, Weiße AY, Harbarth S, Holmes A, Barahona M. Prediction of hospital-onset COVID-19 infections using dynamic networks of patient contact: an international retrospective cohort study. Lancet Digit Health 2022; 4:e573-e583. [PMID: 35868812 PMCID: PMC9296105 DOI: 10.1016/s2589-7500(22)00093-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/19/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Real-time prediction is key to prevention and control of infections associated with health-care settings. Contacts enable spread of many infections, yet most risk prediction frameworks fail to account for their dynamics. We developed, tested, and internationally validated a real-time machine-learning framework, incorporating dynamic patient-contact networks to predict hospital-onset COVID-19 infections (HOCIs) at the individual level. METHODS We report an international retrospective cohort study of our framework, which extracted patient-contact networks from routine hospital data and combined network-derived variables with clinical and contextual information to predict individual infection risk. We trained and tested the framework on HOCIs using the data from 51 157 hospital inpatients admitted to a UK National Health Service hospital group (Imperial College Healthcare NHS Trust) between April 1, 2020, and April 1, 2021, intersecting the first two COVID-19 surges. We validated the framework using data from a Swiss hospital group (Department of Rehabilitation, Geneva University Hospitals) during a COVID-19 surge (from March 1 to May 31, 2020; 40 057 inpatients) and from the same UK group after COVID-19 surges (from April 2 to Aug 13, 2021; 43 375 inpatients). All inpatients with a bed allocation during the study periods were included in the computation of network-derived and contextual variables. In predicting patient-level HOCI risk, only inpatients spending 3 or more days in hospital during the study period were examined for HOCI acquisition risk. FINDINGS The framework was highly predictive across test data with all variable types (area under the curve [AUC]-receiver operating characteristic curve [ROC] 0·89 [95% CI 0·88-0·90]) and similarly predictive using only contact-network variables (0·88 [0·86-0·90]). Prediction was reduced when using only hospital contextual (AUC-ROC 0·82 [95% CI 0·80-0·84]) or patient clinical (0·64 [0·62-0·66]) variables. A model with only three variables (ie, network closeness, direct contacts with infectious patients [network derived], and hospital COVID-19 prevalence [hospital contextual]) achieved AUC-ROC 0·85 (95% CI 0·82-0·88). Incorporating contact-network variables improved performance across both validation datasets (AUC-ROC in the Geneva dataset increased from 0·84 [95% CI 0·82-0·86] to 0·88 [0·86-0·90]; AUC-ROC in the UK post-surge dataset increased from 0·49 [0·46-0·52] to 0·68 [0·64-0·70]). INTERPRETATION Dynamic contact networks are robust predictors of individual patient risk of HOCIs. Their integration in clinical care could enhance individualised infection prevention and early diagnosis of COVID-19 and other nosocomial infections. FUNDING Medical Research Foundation, WHO, Engineering and Physical Sciences Research Council, National Institute for Health Research (NIHR), Swiss National Science Foundation, and German Research Foundation.
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Affiliation(s)
- Ashleigh Myall
- Department of Infectious Disease, Imperial College London, London, UK; Department of Mathematics, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK.
| | - James R Price
- National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Robert L Peach
- Department of Mathematics, Imperial College London, London, UK; Department of Brain Sciences, Imperial College London, London, UK; Department of Neurology, University Hospital of Würzburg, Würzburg, Germany
| | - Mohamed Abbas
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK; Infection Control Programme, Geneva University Hospitals, Geneva, Switzerland
| | - Sid Mookerjee
- National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Nina Zhu
- Department of Infectious Disease, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK
| | - Isa Ahmad
- Department of Infectious Disease, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK
| | - Damien Ming
- Department of Infectious Disease, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK
| | - Farzan Ramzan
- Department of Infectious Disease, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK
| | - Daniel Teixeira
- Infection Control Programme, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Graf
- Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Geneva, Switzerland
| | - Andrea Y Weiße
- School of Biological Sciences and School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Stephan Harbarth
- Infection Control Programme, Geneva University Hospitals, Geneva, Switzerland
| | - Alison Holmes
- Department of Infectious Disease, Imperial College London, London, UK; National Institute for Health Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK
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15
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant transmits much more rapidly than prior SARS-CoV-2 viruses. The primary mode of transmission is via short range aerosols that are emitted from the respiratory tract of an index case. There is marked heterogeneity in the spread of this virus, with 10% to 20% of index cases contributing to 80% of secondary cases, while most index cases have no subsequent transmissions. Vaccination, ventilation, masking, eye protection, and rapid case identification with contact tracing and isolation can all decrease the transmission of this virus.
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Affiliation(s)
- Eric A Meyerowitz
- Montefiore Medical Center, 111 East 210th Street, Bronx, NY 10467, USA.
| | - Aaron Richterman
- Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
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16
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Gomes MGM, Ferreira MU, Corder RM, King JG, Souto-Maior C, Penha-Gonçalves C, Gonçalves G, Chikina M, Pegden W, Aguas R. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. J Theor Biol 2022; 540:111063. [PMID: 35189135 PMCID: PMC8855661 DOI: 10.1016/j.jtbi.2022.111063] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022]
Abstract
Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as "frailty variation". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being crucial to protect vulnerable individuals from severe outcomes as the virus becomes endemic.
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Affiliation(s)
- M Gabriela M Gomes
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK; Centro de Matemática e Aplicações, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marcelo U Ferreira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Rodrigo M Corder
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jessica G King
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Caetano Souto-Maior
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Guilherme Gonçalves
- Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittburgh, PA, USA
| | - Wesley Pegden
- Department of Mathematical Sciences, Carnegie Mellon University, Pittburgh, PA, USA
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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17
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Vickers DM, Baral S, Mishra S, Kwong JC, Sundaram M, Katz A, Calzavara A, Maheu-Giroux M, Buckeridge DL, Williamson T. Stringency of containment and closures on the growth of SARS-CoV-2 in Canada prior to accelerated vaccine roll-out. Int J Infect Dis 2022; 118:73-82. [PMID: 35202783 PMCID: PMC8863413 DOI: 10.1016/j.ijid.2022.02.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Many studies have examined the effectiveness of non-pharmaceutical interventions (NPIs) on SARS-CoV-2 transmission worldwide. However, less attention has been devoted to understanding the limits of NPIs across the course of the pandemic and along a continuum of their stringency. In this study, we explore the relationship between the growth of SARS-CoV-2 cases and an NPI stringency index across Canada before the accelerated vaccine roll-out. METHODS We conducted an ecological time-series study of daily SARS-CoV-2 case growth in Canada from February 2020 to February 2021. Our outcome was a back-projected version of the daily growth ratio in a stringency period (i.e., a 10-point range of the stringency index) relative to the last day of the previous period. We examined the trends in case growth using a linear mixed-effects model accounting for stringency period, province, and mobility in public domains. RESULTS Case growth declined rapidly by 20-60% and plateaued within the first month of the first wave, irrespective of the starting values of the stringency index. When stringency periods increased, changes in case growth were not immediate and were faster in the first wave than in the second. In the first wave, the largest decreasing trends from our mixed effects model occurred in both early and late stringency periods, depending on the province, at a geometric mean index value of 30⋅1 out of 100. When compared with the first wave, the stringency periods in the second wave possessed little association with case growth. CONCLUSIONS The minimal association in the first wave, and the lack thereof in the second, is compatible with the hypothesis that NPIs do not, per se, lead to a decline in case growth. Instead, the correlations we observed might be better explained by a combination of underlying behaviors of the populations in each province and the natural dynamics of SARS-CoV-2. Although there exist alternative explanations for the equivocal relationship between NPIs and case growth, the onus of providing evidence shifts to demonstrating how NPIs can consistently have flat association, despite incrementally high stringency.
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Affiliation(s)
- David M. Vickers
- Centre for Health Informatics and Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada,Corresponding author: David M. Vickers, PhD, Centre for Health Informatics, 5th Floor, TRW Building, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada, Phone: +001 403 771 6893
| | - Stefan Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, United States
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada,Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Jeffrey C. Kwong
- ICES, Toronto, ON, Canada,Public Health Ontario, ON, Canada,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada,Centre for Vaccine Preventable Diseases, University of Toronto, Toronto, ON, Canada,Department of Family and Community Medicine, University of Toronto, ON, Canada
| | - Maria Sundaram
- ICES, Toronto, ON, Canada,Centre for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Alan Katz
- Departments of Community Health Sciences and Family Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Mathieu Maheu-Giroux
- Department of Epidemiology, Biostatistics, and Occupational Health, School of Population and Global Health, McGill University, Montréal, QC, Canada
| | - David L. Buckeridge
- Department of Epidemiology, Biostatistics, and Occupational Health, School of Population and Global Health, McGill University, Montréal, QC, Canada
| | - Tyler Williamson
- Centre for Health Informatics and Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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18
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Lee A, Morling J. Beyond the pandemic: building forward better? Public Health 2022; 204:12-13. [PMID: 35114605 PMCID: PMC8802212 DOI: 10.1016/j.puhe.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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19
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Gomes MGM, Ferreira MU, Corder RM, King JG, Souto-Maior C, Penha-Gonçalves C, Gonçalves G, Chikina M, Pegden W, Aguas R. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2020.04.27.20081893. [PMID: 32511451 PMCID: PMC7239079 DOI: 10.1101/2020.04.27.20081893] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as "frailty variation". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being critical to protect vulnerable individuals from severe outcomes as the virus becomes endemic.
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Affiliation(s)
- M Gabriela M Gomes
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
- Centro de Matemática e Aplicações, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marcelo U Ferreira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Rodrigo M Corder
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jessica G King
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Caetano Souto-Maior
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Guilherme Gonçalves
- Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittburgh, PA, USA
| | - Wesley Pegden
- Department of Mathematical Sciences, Carnegie Mellon University, , Pittburgh" , PA, USA
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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20
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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21
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Gao J, Wang C, Chu Y, Han Y, Gao Y, Wang Y, Wang C, Liu H, Han L, Zhang Y. Graphene oxide-graphene Van der Waals heterostructure transistor biosensor for SARS-CoV-2 protein detection. Talanta 2021; 240:123197. [PMID: 34996016 PMCID: PMC8719368 DOI: 10.1016/j.talanta.2021.123197] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
The current outbreaking of the coronavirus SARS-CoV-2 pandemic threatens global health and has caused serious concern. Currently there is no specific drug against SARS-CoV-2, therefore, a fast and accurate diagnosis method is an urgent need for the diagnosis, timely treatment and infection control of COVID-19 pandemic. In this work, we developed a field effect transistor (FET) biosensor based on graphene oxide-graphene (GO/Gr) van der Waals heterostructure for selective and ultrasensitive SARS-CoV-2 proteins detection. The GO/Gr van der Waals heterostructure was in-situ formed in the microfluidic channel through π-π stacking. The developed biosensor is capable of SARS-CoV-2 proteins detection within 20 min in the large dynamic range from 10 fg/mL to 100 pg/mL with the limit of detection of as low as ∼8 fg/mL, which shows ∼3 × sensitivity enhancement compared with Gr-FET biosensor. The performance enhancement mechanism was studied based on the transistor-based biosensing theory and experimental results, which is mainly attributed to the enhanced SARS-CoV-2 capture antibody immobilization density due to the introduction of the GO layer on the graphene surface. The spiked SARS-CoV-2 protein samples in throat swab buffer solution were tested to confirm the practical application of the biosensor for SARS-CoV-2 proteins detection. The results indicated that the developed GO/Gr van der Waals heterostructure FET biosensor has strong selectivity and high sensitivity, providing a potential method for SARS-CoV-2 fast and accurate detection.
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Affiliation(s)
- Jianwei Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Chunhua Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yujin Chu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yingkuan Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yakun Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yanhao Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Chao Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Hong Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong, 250100, China.
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yu Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
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22
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Do DP, Frank R. U.S. frontline workers and COVID-19 inequities. Prev Med 2021; 153:106833. [PMID: 34624386 PMCID: PMC8492358 DOI: 10.1016/j.ypmed.2021.106833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/15/2021] [Accepted: 10/03/2021] [Indexed: 11/27/2022]
Abstract
We overcome a lack of frontline worker status information in most COVID-19 data repositories to document the extent to which occupation has contributed to COVID-19 disparities in the United States. Using national data from over a million U.S. respondents to a Facebook-Carnegie Mellon University survey administered from September 2020 to March 2021, we estimated the likelihoods of frontline workers, compared to non-frontline workers, 1) to ever test positive for SARs-Cov-2 and 2) to test positive for SARs-Cov-2 within the past two weeks. Net of other covariates including education level, county-level political environment, and rural residence, both healthcare and non-healthcare frontline workers had higher odds of having ever tested positive for SARs-Cov-2 across the study time period. Similarly, non-healthcare frontline workers were more likely to test positive in the previous 14 days. Conversely, healthcare frontline workers were less likely to have recently tested positive. Our findings suggest that occupational exposure has played an independent role in the uneven spread of the virus. In particular, non-healthcare frontline workers have experienced sustained higher risk of testing positive for SARs-Cov-2 compared to non-frontline workers. Alongside more worker protections, future COVID-19 and other highly infectious disease response strategies must be augmented by a more robust recognition of the role that structural factors, such as the highly stratified U.S. occupational landscape, have played in the uneven toll of the COVID-19 pandemic.
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Affiliation(s)
- D Phuong Do
- Public Health Policy & Administration, University of Wisconsin Zilber School of Public Health, USA.
| | - Reanne Frank
- Sociology and Faculty Affiliate of the Institute for Population Research, Ohio State University, USA.
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23
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Joffe AR, Redman D. The SARS-CoV-2 Pandemic in High Income Countries Such as Canada: A Better Way Forward Without Lockdowns. Front Public Health 2021; 9:715904. [PMID: 34926364 PMCID: PMC8672418 DOI: 10.3389/fpubh.2021.715904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/29/2021] [Indexed: 12/18/2022] Open
Abstract
The SARS-CoV-2 pandemic has caused tragic morbidity and mortality. In attempt to reduce this morbidity and mortality, most countries implemented population-wide lockdowns. Here we show that the lockdowns were based on several flawed assumptions, including "no one is protected until everyone is protected," "lockdowns are highly effective to reduce transmission," "lockdowns have a favorable cost-benefit balance," and "lockdowns are the only effective option." Focusing on the latter, we discuss that Emergency Management principles provide a better way forward to manage the public emergency of the pandemic. Specifically, there are three priorities including the following: first, protect those most at risk by separating them from the threat (mitigation); second, ensure critical infrastructure is ready for people who get sick (preparation and response); and third, shift the response from fear to confidence (recovery). We argue that, based on Emergency Management principles, the age-dependent risk from SARS-CoV-2, the minimal (at best) efficacy of lockdowns, and the terrible cost-benefit trade-offs of lockdowns, we need to reset the pandemic response. We can manage risk and save more lives from both COVID-19 and lockdowns, thus achieving far better outcomes in both the short- and long-term.
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Affiliation(s)
- Ari R. Joffe
- Department of Pediatrics and John Dossetor Health Ethics Center, Faculty of Medicine, University of Alberta, Edmonton, AB, Canada
| | - David Redman
- Retired LCol, Alberta Emergency Management Agency, St. Paul, AB, Canada
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24
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Aguilar-Gaxiola SA, Ramirez SM, Kissam E. A Reality Check From the Fields-What's Next? JAMA Netw Open 2021; 4:e2125128. [PMID: 34524443 DOI: 10.1001/jamanetworkopen.2021.25128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergio A Aguilar-Gaxiola
- Clinical Internal Medicine, Center for Reducing Health Disparities, Department of Internal Medicine, University of California, Davis Health, Sacramento
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25
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Susswein Z, Valdano E, Brett T, Rohani P, Colizza V, Bansal S. Ignoring spatial heterogeneity in drivers of SARS-CoV-2 transmission in the US will impede sustained elimination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.09.21261807. [PMID: 34401885 PMCID: PMC8366803 DOI: 10.1101/2021.08.09.21261807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To dissect the transmission dynamics of SARS-CoV-2 in the United States, we integrate parallel streams of high-resolution data on contact, mobility, seasonality, vaccination and seroprevalence within a metapopulation network. We find the COVID-19 pandemic in the US is characterized by a geographically localized mosaic of transmission along an urban-rural gradient, with many outbreaks sustained by between-county transmission. We detect a dynamic tension between the spatial scale of public health interventions and population susceptibility as pre-pandemic contact is resumed. Further, we identify regions rendered particularly at risk from invasion by variants of concern due to spatial connectivity. These findings emphasize the public health importance of accounting for the hierarchy of spatial scales in transmission and the heterogeneous impacts of mobility on the landscape of contagion risk.
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26
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Mishra S, Ma H, Moloney G, Yiu KC, Darvin D, Landsman D, Kwong JC, Calzavara A, Straus S, Chan AK, Gournis E, Rilkoff H, Xia Y, Katz A, Williamson T, Malikov K, Kustra R, Maheu-Giroux M, Sander B, Baral SD. Increasing concentration of COVID-19 by socioeconomic determinants and geography in Toronto, Canada: an observational study. Ann Epidemiol 2021; 65:84-92. [PMID: 34320380 PMCID: PMC8730782 DOI: 10.1016/j.annepidem.2021.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Inequities in the burden of COVID-19 were observed early in Canada and around the world suggesting economically marginalized communities faced disproportionate risks. However, there has been limited systematic assessment of how heterogeneity in risks has evolved in large urban centers over time. PURPOSE To address this gap, we quantified the magnitude of risk heterogeneity in Toronto, Ontario from January-November, 2020 using a retrospective, population-based observational study using surveillance data. METHODS We generated epidemic curves by social determinants of health (SDOH) and crude Lorenz curves by neighbourhoods to visualize inequities in the distribution of COVID-19 and estimated Gini coefficients. We examined the correlation between SDOH using Pearson-correlation coefficients. RESULTS Gini coefficient of cumulative cases by population size was 0.41 (95% confidence interval [CI]:0.36-0.47) and estimated for: household income (0.20, 95%CI: 0.14-0.28); visible minority (0.21, 95%CI:0.16-0.28); recent immigration (0.12, 95%CI:0.09-0.16); suitable housing (0.21, 95%CI:0.14-0.30); multi-generational households (0.19, 95%CI:0.15-0.23); and essential workers (0.28, 95%CI:0.23-0.34). CONCLUSIONS There was rapid epidemiologic transition from higher to lower income neighbourhoods with Lorenz curve transitioning from below to above the line of equality across SDOH. Moving forward necessitates integrating programs and policies addressing socioeconomic inequities and structural racism into COVID-19 prevention and vaccination programs.
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Affiliation(s)
- Sharmistha Mishra
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada.
| | - Huiting Ma
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
| | - Gary Moloney
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
| | - Kristy Cy Yiu
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
| | - Dariya Darvin
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
| | - David Landsman
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
| | - Jeffrey C Kwong
- ICES, Toronto, Canada; Public Health Ontario, Toronto, Canada; Department of Family and Community Medicine, Faculty of Medicine, University of Toronto, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
| | | | - Sharon Straus
- Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, Canada.
| | - Adrienne K Chan
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Division of Infectious Diseases, Sunnybrook Health Sciences, University of Toronto, Toronto, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Effie Gournis
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Toronto Public Health, City of Toronto, Toronto, Canada.
| | | | - Yiqing Xia
- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada; Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Canada.
| | - Alan Katz
- Departments of Community Health Sciences and Family Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada.
| | - Kamil Malikov
- Capacity Planning and Analytics Division, Ontario Ministry of Health, Toronto, Canada.
| | - Rafal Kustra
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
| | - Mathieu Maheu-Giroux
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Canada.
| | - Beate Sander
- ICES, Toronto, Canada; Public Health Ontario, Toronto, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Stefan D Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, United States.
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- St. Michael's Hospital, Unity Health Toronto, Toronto, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada; ICES, Toronto, Canada; Public Health Ontario, Toronto, Canada; Department of Family and Community Medicine, Faculty of Medicine, University of Toronto, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada; Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, Canada; Division of Infectious Diseases, Sunnybrook Health Sciences, University of Toronto, Toronto, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada; Toronto Public Health, City of Toronto, Toronto, Canada; Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Canada; Departments of Community Health Sciences and Family Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada; Capacity Planning and Analytics Division, Ontario Ministry of Health, Toronto, Canada; Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, United States
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