101
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Affiliation(s)
- Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Li-Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
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102
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Jashari R, Van Esbroeck M, Vanhaebost J, Micalessi I, Kerschen A, Mastrobuoni S. The risk of transmission of the novel coronavirus (SARS-CoV-2) with human heart valve transplantation: evaluation of cardio-vascular tissues from two consecutive heart donors with asymptomatic COVID-19. Cell Tissue Bank 2021; 22:665-674. [PMID: 33687611 PMCID: PMC7941121 DOI: 10.1007/s10561-021-09913-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
We report on two living donors of explanted hearts while receiving heart transplantation that tested positive for SARS-CoV-2 on the day of donation, although clinically asymptomatic. They underwent heart transplantation for ischaemic and hypertrophic obstructive cardiomyopathy, respectively. After evaluation of donor hearts, we cryopreserved and stored two pulmonary valves for clinical application and one aortic valve for research. Light microscopy of myocardium, mitral valve and aortic and pulmonary arterial wall and RT-PCR SARS-CoV-2 test of myocardium, mitral and tricuspid valve and aortic wall for detection of SARS-CoV-2 were performed. Presence of ACE2 in tissues was assessed with immunostaining. Light microscopy revealed a mild eosinophilic myocarditis in the ischemic cardiomyopathy heart, whereas enlarged cardiomyocytes with irregular nucleus and some with cytoplasmic vacuoles in the hypertrophic obstructive cardiomyopathy heart. Aortic and pulmonary wall were histologically normal. Immunostaining revealed diffuse presence of ACE2 in the myocardium of the heart with eosinophilic myocarditis, but only discrete presence in the hypertrophic cardiomyopathy heart. The RT-PCR SARS-CoV-2 test showed no presence of the virus in tested tissues. Despite eosinophilic myocarditis in the ischemic cardiomyopathy heart, no viral traces were found in the myocardium and valve tissues. However, ACE2 was present diffusely in the ischemic cardiomyopathy heart. SARS-CoV-2 could not be detected in the cardiac tissues of these COVID-19 asymptomatic heart donors. In our opinion, clinical application of the valves from these donors presents negligible risk for coronavirus transmission. Nonetheless, considering the uncertainty regarding the risk of virus transmission with the human tissue transplantation, we would not release in any case the pulmonary valve recovered from the eosinophilic myocarditis heart. In contrast, we may consider the release of the pulmonary valve from the dilated cardiomyopathy heart only for a life-threatening situation when no other similar allograft were available.
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Affiliation(s)
- R Jashari
- European Homograft Bank (EHB), UCL St. Luc, Méridien Site, rue du Méridien 100, 1210, Brussels, Belgium.
| | - M Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - J Vanhaebost
- Department of Pathology and Legal Medicine, Belgium and Morphology Research Group, Institute of Experimental and Clinical Research, UCL St. Luc, Brussels, Belgium
| | - I Micalessi
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - A Kerschen
- Department of Pathology and Legal Medicine, Belgium and Morphology Research Group, Institute of Experimental and Clinical Research, UCL St. Luc, Brussels, Belgium
| | - S Mastrobuoni
- European Homograft Bank (EHB), UCL St. Luc, Méridien Site, rue du Méridien 100, 1210, Brussels, Belgium
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103
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Head JR, Andrejko KL, Remais JV. Model-based assessment of SARS-CoV-2 Delta variant transmission dynamics within partially vaccinated K-12 school populations. LANCET REGIONAL HEALTH. AMERICAS 2021; 5:100133. [PMID: 34849504 PMCID: PMC8614621 DOI: 10.1016/j.lana.2021.100133] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND We examined school reopening policies amidst ongoing transmission of the highly transmissible Delta variant, accounting for vaccination among individuals ≥12 years. METHODS We collected data on social contacts among school-aged children in the California Bay Area and developed an individual-based transmission model to simulate transmission of the Delta variant of SARS-CoV-2 in schools. We evaluated the additional infections in students and teachers/staff resulting over a 128-day semester from in-school instruction compared to remote instruction when various NPIs (mask use, cohorts, and weekly testing of students/teachers) were implemented, across various community-wide vaccination coverages (50%, 60%, 70%), and student (≥12 years) and teacher/staff vaccination coverages (50% - 95%). FINDINGS At 70% vaccination coverage, universal masking reduced infections by >57% among students. Masking plus 70% vaccination coverage enabled achievement of <50 excess cases per 1,000 students/teachers, but stricter risk tolerances, such as <25 excess infections per 1,000 students/teachers, required a cohort approach in elementary and middle school populations. In the absence of NPIs, increasing the vaccination coverage of community members from 50% to 70% or elementary teachers from 70% to 95% reduced the excess rate of infection among elementary school students attributable to school transmission by 24% and 37%, respectively. INTERPRETATIONS Amidst Delta variant circulation, we found that schools are not inherently low risk, yet can be made so with high community vaccination coverages and masking. Vaccination of adults protects unvaccinated children. FUNDING National Science Foundation grant no. 2032210; National Institutes of Health grant nos. R01AI125842 and R01AI148336; MIDAS Coordination Center (MIDASSUP2020-4).
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Affiliation(s)
- Jennifer R. Head
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Kristin L. Andrejko
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Justin V. Remais
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, CA, USA,Corresponding author: Justin V. Remais, Ph.D., 2121 Berkeley Way West #5301, Berkeley, CA 94720
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104
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Sanchez-Taltavull D, Castelo-Szekely V, Murugan S, Hamley JID, Rollenske T, Ganal-Vonarburg SC, Büchi I, Keogh A, Li H, Salm L, Spari D, Yilmaz B, Zimmermann J, Gerfin M, Roldan E, Beldi G. Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures. PLoS One 2021; 16:e0258700. [PMID: 34739484 PMCID: PMC8570514 DOI: 10.1371/journal.pone.0258700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/03/2021] [Indexed: 11/18/2022] Open
Abstract
Protecting healthcare professionals is crucial in maintaining a functioning healthcare system. The risk of infection and optimal preventive strategies for healthcare workers during the COVID-19 pandemic remain poorly understood. Here we report the results of a cohort study that included pre- and asymptomatic healthcare workers. A weekly testing regime has been performed in this cohort since the beginning of the COVID-19 pandemic to identify infected healthcare workers. Based on these observations we have developed a mathematical model of SARS-CoV-2 transmission that integrates the sources of infection from inside and outside the hospital. The data were used to study how regular testing and a desynchronisation protocol are effective in preventing transmission of COVID-19 infection at work, and compared both strategies in terms of workforce availability and cost-effectiveness. We showed that case incidence among healthcare workers is higher than would be explained solely by community infection. Furthermore, while testing and desynchronisation protocols are both effective in preventing nosocomial transmission, regular testing maintains work productivity with implementation costs.
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Affiliation(s)
- Daniel Sanchez-Taltavull
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Violeta Castelo-Szekely
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Shaira Murugan
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Jonathan I. D. Hamley
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Tim Rollenske
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Stephanie C. Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Isabel Büchi
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Adrian Keogh
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Hai Li
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Lilian Salm
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Daniel Spari
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Michael Gerfin
- Department of Economics, University of Bern, Bern, Switzerland
| | - Edgar Roldan
- ICTP, The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
| | - Guido Beldi
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
| | - UVCM-COVID researchers
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Bern, Switzerland
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105
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Fierce L, Robey AJ, Hamilton C. Simulating near-field enhancement in transmission of airborne viruses with a quadrature-based model. INDOOR AIR 2021; 31:1843-1859. [PMID: 34297863 PMCID: PMC8447483 DOI: 10.1111/ina.12900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/18/2021] [Indexed: 05/08/2023]
Abstract
Some infectious diseases, such as influenza, tuberculosis, and SARS-CoV-2, may be transmitted when virus-laden particles expelled from an infectious person are inhaled by someone else, which is known as the airborne transmission route. These virus-laden particles are more concentrated in the expiratory jet of an infectious person than elsewhere in a well-mixed room, but this near-field enhancement in virion exposure has not been well quantified. Transmission of airborne viruses depends on factors that are inherently variable and, in many cases, poorly constrained, and quantifying this uncertainty requires large ensembles of model simulations that span the variability in input parameters. However, models that are well-suited to simulate the near-field evolution of respiratory particles are also computationally expensive, which limits the exploration of parametric uncertainty. In order to perform many simulations that span the wide variability in factors governing airborne transmission, we developed the Quadrature-based model of Respiratory Aerosol and Droplets (QuaRAD). QuaRAD is an efficient framework for simulating the evolution of virus-laden particles after they are expelled from an infectious person, their deposition to the nasal cavity of a susceptible person, and the subsequent risk of initial infection. We simulated 10 000 scenarios to quantify the risk of initial infection by a particular virus, SARS-CoV-2. The predicted risk of infection was highly variable among scenarios and, in each scenario, was strongly enhanced near the infectious individual. In more than 50% of scenarios, the physical distancing needed to avoid near-field enhancements in airborne transmission was beyond the recommended safe distance of two meters (six feet) if the infectious person is not wearing a mask, though this distance defining the near-field extent was also highly variable among scenarios; the variability in the near-field extent is explained predominantly by variability in expiration velocity. Our findings suggest that maintaining at least two meters of distance from an infectious person greatly reduces exposure to airborne virions; protections against airborne transmission, such as N95 respirators, should be available when distancing is not possible.
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Affiliation(s)
- Laura Fierce
- Atmospheric Sciences and Global Change DivisionPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Alison J. Robey
- Center for Environmental StudiesWilliams CollegeWilliamstownMassachusettsUSA
| | - Cathrine Hamilton
- Department of ChemistryIndiana University of PennsylvaniaIndianaPennsylvaniaUSA
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106
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Vander Schaaf NA, Fund AJ, Munnich BV, Zastrow AL, Fund EE, Senti TL, Lynn AF, Kane JJ, Love JL, Long GJ, Troendle NJ, Sharda DR. Routine, Cost-Effective SARS-CoV-2 Surveillance Testing Using Pooled Saliva Limits Viral Spread on a Residential College Campus. Microbiol Spectr 2021; 9:e0108921. [PMID: 34643445 PMCID: PMC8515933 DOI: 10.1128/spectrum.01089-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.
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Affiliation(s)
| | - Anthony J. Fund
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Brianna V. Munnich
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Alexi L. Zastrow
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Erin E. Fund
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Tanner L. Senti
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Abigail F. Lynn
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Jonathon J. Kane
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Jennifer L. Love
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Gregory J. Long
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Nicholas J. Troendle
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Daniel R. Sharda
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
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107
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Albani V, Loria J, Massad E, Zubelli J. COVID-19 underreporting and its impact on vaccination strategies. BMC Infect Dis 2021; 21:1111. [PMID: 34711190 PMCID: PMC8552982 DOI: 10.1186/s12879-021-06780-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/05/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Underreporting cases of infectious diseases poses a major challenge in the analysis of their epidemiological characteristics and dynamical aspects. Without accurate numerical estimates it is difficult to precisely quantify the proportions of severe and critical cases, as well as the mortality rate. Such estimates can be provided for instance by testing the presence of the virus. However, during an ongoing epidemic, such tests' implementation is a daunting task. This work addresses this issue by presenting a methodology to estimate underreported infections based on approximations of the stable rates of hospitalization and death. METHODS We present a novel methodology for the stable rate estimation of hospitalization and death related to the Corona Virus Disease 2019 (COVID-19) using publicly available reports from various distinct communities. These rates are then used to estimate underreported infections on the corresponding areas by making use of reported daily hospitalizations and deaths. The impact of underreporting infections on vaccination strategies is estimated under different disease-transmission scenarios using a Susceptible-Exposed-Infective-Removed-like (SEIR) epidemiological model. RESULTS For the considered locations, during the period of study, the estimations suggest that the number of infected individuals could reach 30% of the population of these places, representing, in some cases, more than six times the observed numbers. These results are in close agreement with estimates from independent seroprevalence studies, thus providing a strong validation of the proposed methodology. Moreover, the presence of large numbers of underreported infections can reduce the perceived impact of vaccination strategies in reducing rates of mortality and hospitalization. CONCLUSIONS pBy using the proposed methodology and employing a judiciously chosen data analysis implementation, we estimate COVID-19 underreporting from publicly available data. This leads to a powerful way of quantifying underreporting impact on the efficacy of vaccination strategies. As a byproduct, we evaluate the impact of underreporting in the designing of vaccination strategies.
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Affiliation(s)
- Vinicius Albani
- Department of Mathematics, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Jennifer Loria
- Instituto de Matemática Pura e Aplicada, Rio de Janeiro, Brazil
- Universidad de Costa Rica, San Jose, Costa Rica
| | - Eduardo Massad
- School of Applied Mathematics, Fundação Getúlio Vargas, Rio de Janeiro, Brazil
- School of Medicine, University of São Paulo and LIM01-HCFMUSP, São Paulo, Brazil
| | - Jorge Zubelli
- Mathematics Department, Khalifa University, Abu Dhabi, UAE
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108
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Bok S, Martin DE, Acosta E, Lee M, Shum J. Validation of the COVID-19 Transmission Misinformation Scale and Conditional Indirect Negative Effects on Wearing a Mask in Public. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11319. [PMID: 34769835 PMCID: PMC8583109 DOI: 10.3390/ijerph182111319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/04/2021] [Accepted: 10/19/2021] [Indexed: 12/27/2022]
Abstract
The SARS-CoV-2 (COVID-19) pandemic devastated the world economy. Global infections and deaths altered the behaviors of generations. The Internet acted as an incredible vehicle for communication but was also a source of unfounded rumors. Unfortunately, this freedom of information sharing and fear of COVID-19 fostered unfounded claims about transmission (e.g., 5G networks spread the disease). With negligible enforcement to stop the spread of rumors and government officials spouting unfounded claims, falsities became ubiquitous. Organizations, public health officials, researchers, and businesses spent limited resources addressing rumors instead of implementing policies to overcome challenges (e.g., speaking to defiant mask wearers versus safe reopening actions). The researchers defined COVID-19 transmission misinformation as false beliefs about the spread and prevention of contracting the disease. Design and validation of the 12-item COVID-19 Transmission Misinformation Scale (CTMS) provides a measure to identify transmission misinformation believers. Indirect COVID-19 transmission misinformation beliefs with a fear of COVID-19 decreased wearing a mask in public intentions. Callousness exacerbated COVID-19 transmission misinformation beliefs as a moderator.
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Affiliation(s)
- Stephen Bok
- Marketing Department, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA;
| | - Daniel E. Martin
- Management Department, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA;
| | - Erik Acosta
- Marketing Department, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA;
| | - Maria Lee
- Department of Urban Planning and Public Policy, University of California, Berkeley, CA 92697, USA;
| | - James Shum
- Accounting Department, Loyola Marymount University, Los Angeles, CA 90045, USA;
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109
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Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. WATER RESEARCH 2021. [PMID: 34607084 DOI: 10.1101/2021.01.22.21250320%j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Devin Bowes
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - LaRinda A Holland
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ USA
| | - Rahul Kumar
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Rosa Inchausti
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Wydale K Holmes
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Stephanie Deitrick
- Enterprise GIS & Data Analytics, Information Technology, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Philip Brown
- Municipal Utilities, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Darrell Duty
- Tempe Fire Medical Rescue, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Ray A Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | | | - Elliott Wheeler
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Kevin Dixon
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Tim Constantine
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
| | - Efrem S Lim
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St, Phoenix, AZ 85004, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA.
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Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. WATER RESEARCH 2021; 205:117710. [PMID: 34607084 PMCID: PMC8464352 DOI: 10.1016/j.watres.2021.117710] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Devin Bowes
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - LaRinda A Holland
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ USA
| | - Rahul Kumar
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Rosa Inchausti
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Wydale K Holmes
- Strategic Management and Diversity Office, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Stephanie Deitrick
- Enterprise GIS & Data Analytics, Information Technology, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Philip Brown
- Municipal Utilities, City of Tempe, 31 E Fifth Street, Tempe, AZ 85281, USA
| | - Darrell Duty
- Tempe Fire Medical Rescue, 31 E Fifth Street, City of Tempe, Tempe, AZ 85281, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Ray A Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | | | - Elliott Wheeler
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Kevin Dixon
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Tim Constantine
- Jacobs Engineering Group Inc., 1999 Bryan Street, Dallas, TX 75201, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
| | - Efrem S Lim
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institute of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St, Phoenix, AZ 85004, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA.
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111
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Contreras S, Dehning J, Mohr SB, Bauer S, Spitzner FP, Priesemann V. Low case numbers enable long-term stable pandemic control without lockdowns. SCIENCE ADVANCES 2021; 7:eabg2243. [PMID: 34623913 PMCID: PMC8500516 DOI: 10.1126/sciadv.abg2243] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The traditional long-term solutions for epidemic control involve eradication or population immunity. Here, we analytically derive the existence of a third viable solution: a stable equilibrium at low case numbers, where test-trace-and-isolate policies partially compensate for local spreading events and only moderate restrictions remain necessary. In this equilibrium, daily cases stabilize around ten or fewer new infections per million people. However, stability is endangered if restrictions are relaxed or case numbers grow too high. The latter destabilization marks a tipping point beyond which the spread self-accelerates. We show that a lockdown can reestablish control and that recurring lockdowns are not necessary given sustained, moderate contact reduction. We illustrate how this strategy profits from vaccination and helps mitigate variants of concern. This strategy reduces cumulative cases (and fatalities) four times more than strategies that only avoid hospital collapse. In the long term, immunization, large-scale testing, and international coordination will further facilitate control.
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Affiliation(s)
- Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, 8370456 Santiago, Chile
| | - Jonas Dehning
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Sebastian B. Mohr
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Simon Bauer
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - F. Paul Spitzner
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- Department of Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Corresponding author.
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112
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Patel MS, Jebamani JS, Das Mohapatra S. Value of Including CT Chest in the Management of Acute Abdominal Emergencies: Experience During First Wave of COVID-19 Pandemic at a UK District General Hospital. Cureus 2021; 13:e19073. [PMID: 34849307 PMCID: PMC8619817 DOI: 10.7759/cureus.19073] [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] [Accepted: 10/27/2021] [Indexed: 12/05/2022] Open
Abstract
Aims COVID-19 can present with abdominal pain and affects the management of emergency surgical patients. The aim of this retrospective study was to assess the incidence of positive findings on CT chest in patients presenting with acute abdomen, who underwent CT thorax as part of the Intercollegiate General Surgical Guidance on COVID-19 during the first wave. To correlate CT chest findings with confirmed cases on reverse transcription polymerase chain reaction (RT-PCR), and to determine its influence on surgical management of abdominal emergencies. Methods A retrospective observational study of adult emergency surgical referrals (excluding trauma) for acute abdomen over a 10-week period was performed. COVID-19 changes on CT chest were categorized as per the British Society of Thoracic Imaging (BSTI) CT reporting criteria. Patient demographics, COVID-19 RT-PCR, management and outcome were recorded. Statistical analysis was performed using Microsoft Excel (Microsoft Corporation, Redmond, USA) with p-value significant at ≤0.05. Results Of the 160 patients included, 111 (69.38%) had COVID-19 RT-PCR. Twenty-four patients had CT chest findings suggestive of COVID-19. Amongst these, 45.83% demonstrated classic/probable CT features of COVID-19, of which 36.36% had positive RT-PCR. Most patients who had acute abdominal findings had a normal CT chest (p=0.03). Twenty-five (15.63%) patients presenting with abdominal pain had normal CT abdomen and seven (28%) of these had CT features of COVID-19. Only 43 (34.4%) patients needed a surgical intervention, of which 18.6% had COVID-19 changes on CT, confirmed by positive RT-PCR in 12.5%. Conclusion CT chest is an important investigation during the COVID-19 pandemic in suspected cases to help assess the severity of lung involvement. CT chest as an additional investigation modality in acute abdomen had clinically helped in triaging of patients to appropriate specialties but did not influence emergency surgical management.
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Affiliation(s)
- Maitreyi S Patel
- General Surgery, Barking, Havering and Redbridge University Hospitals NHS Trust, Romford, GBR
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Abd Wahab M, Safaai S, Mohd Saiboon I. Impact of a binary triage system and structural reorganization of emergency department on health care workers exposed to suspected COVID-19 patients-a single-centre analysis. Int J Emerg Med 2021; 14:59. [PMID: 34556031 PMCID: PMC8460200 DOI: 10.1186/s12245-021-00384-3] [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: 04/23/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A binary triage system based on infectivity and facilitated by departmental restructuring was developed to manage suspected COVID-19 patients with an aim to provide effective prevention and control of infection among health care workers (HCWs) in the emergency department. This study analyses the effectiveness of the new triage system and structural reorganization in response to the COVID-19 pandemic. METHODS A cross-sectional observational study was conducted in the Emergency and Trauma Department, Hospital Kuala Lumpur (ETDHKL). The implementation of a binary triage system separates patients with risk of COVID-19 who present with fever and respiratory symptoms from other patients. Data on exposed HCWs to COVID-19 patients were captured pre-restructuring and post-restructuring of the emergency department and analysed using descriptive statistics. RESULTS A total of 846 HCWs were involved in this study. Pre-restructuring reported 542 HCWs exposed to COVID-19 patients while post-restructuring reported 122. Using the four categorical exposure risks for HCWs which are no identifiable risk, low risk, medium risk, and high risk, the number of HCWs exposed during pre-restructuring were 15(1.8%), 504 (59.6%), 15 (1.8%), and 8 (0.9%), respectively, while post-restructuring the numbers were 122 (14.4%), 8 (0.9%), 109 (12.9%), and 5 (0.1%), respectively. There was a 77.5% reduction in the number of exposed HCWs after our implementation of the new system (542 vs 122). CONCLUSION A binary triage system based on severity and infectivity and supported with structural reorganization can be effective in reducing HCWs COVID-19 exposure.
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Affiliation(s)
- Mahathar Abd Wahab
- Emergency and Trauma Department, Kuala Lumpur Hospital, Jalan Pahang, 50586, Kuala Lumpur, Malaysia
| | - Sufian Safaai
- Emergency and Trauma Department, Kuala Lumpur Hospital, Jalan Pahang, 50586, Kuala Lumpur, Malaysia.
| | - Ismail Mohd Saiboon
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latif Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
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114
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Wong CH, Ngan CY, Goldfeder RL, Idol J, Kuhlberg C, Maurya R, Kelly K, Omerza G, Renzette N, De Abreu F, Li L, Browne FA, Liu ET, Wei CL. Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection. COMMUNICATIONS MEDICINE 2021; 1:33. [PMID: 35602196 PMCID: PMC9053197 DOI: 10.1038/s43856-021-00034-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/02/2021] [Indexed: 01/12/2023] Open
Abstract
Background It is estimated that up to 80% of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are asymptomatic and asymptomatic patients can still effectively transmit the virus and cause disease. While much of the effort has been placed on decoding single nucleotide variation in SARS-CoV-2 genomes, considerably less is known about their transcript variation and any correlation with clinical severity in human hosts, as defined here by the presence or absence of symptoms. Methods To assess viral genomic signatures of disease severity, we conducted a systematic characterization of SARS-CoV-2 transcripts and genetic variants in 81 clinical specimens collected from symptomatic and asymptomatic individuals using multi-scale transcriptomic analyses including amplicon-seq, short-read metatranscriptome and long-read Iso-seq. Results Here we show a highly coordinated and consistent pattern of sgRNA expression from individuals with robust SARS-CoV-2 symptomatic infection and their expression is significantly repressed in the asymptomatic infections. We also observe widespread inter- and intra-patient variants in viral RNAs, known as quasispecies frequently found in many RNA viruses. We identify unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Moreover, these frequently occurring structural variants in SARS-CoV-2 genomes serve as a mechanism to further induce SARS-CoV-2 proteome complexity. Conclusions Our results indicate that differential sgRNA expression and structural mutational burden are highly correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development.
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Affiliation(s)
- Chee Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | | | - Jennifer Idol
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Chris Kuhlberg
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Gregory Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Francine De Abreu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Lei Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | | | - Edison T. Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
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Schoeps A, Hoffmann D, Tamm C, Vollmer B, Haag S, Kaffenberger T, Ferguson-Beiser K, Kohlhase-Griebel B, Basenach S, Missal A, Höfling K, Michels H, Schall A, Kappes H, Vogt M, Jahn K, Bärnighausen T, Zanger P. Surveillance of SARS-CoV-2 transmission in educational institutions, August to December 2020, Germany. Epidemiol Infect 2021; 149:e213. [PMID: 34549699 PMCID: PMC8503068 DOI: 10.1017/s0950268821002077] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/05/2021] [Accepted: 09/02/2021] [Indexed: 11/09/2022] Open
Abstract
This study aims at providing estimates on the transmission risk of SARS-CoV-2 in schools and day-care centres. We calculated secondary attack rates (SARs) using individual-level data from state-wide mandatory notification of index cases in educational institutions, followed by contact tracing and PCR-testing of high-risk contacts. From August to December 2020, every sixth of overall 784 independent index cases was associated with secondary cases in educational institutions. Monitoring of 14 594 institutional high-risk contacts (89% PCR-tested) of 441 index cases during quarantine revealed 196 secondary cases (SAR 1.34%, 0.99-1.78). SARS-CoV-2 infection among high-risk contacts was more likely around teacher-indexes compared to student-/child-indexes (incidence rate ratio (IRR) 3.17, 1.79-5.59), and in day-care centres compared to secondary schools (IRR 3.23, 1.76-5.91), mainly due to clusters around teacher-indexes in day-care containing a higher mean number of secondary cases per index case (142/113 = 1.26) than clusters around student-indexes in schools (82/474 = 0.17). In 2020, SARS-CoV-2 transmission risk in educational settings was low overall, but varied strongly between setting and role of the index case, indicating the chance for targeted intervention. Surveillance of SARS-CoV-2 transmission in educational institutions can powerfully inform public health policy and improve educational justice during the pandemic.
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Affiliation(s)
- Anja Schoeps
- Federal State Agency for Consumer & Health Protection Rhineland-Palatinate, Koblenz, Germany
- Heidelberg Institute of Global Heath, University Hospitals, Im Neuenheimer Feld 130.3, 69120Heidelberg, Germany
| | - Dietmar Hoffmann
- District Public Health Authority, Große Langgasse 29, 55116Mainz, Germany
| | - Claudia Tamm
- District Public Health Authority, Peter-Altmaier Platz 1, 56410Montabaur, Germany
| | - Bianca Vollmer
- District Public Health Authority, Peter-Altmaier Platz 1, 56410Montabaur, Germany
| | - Sabine Haag
- District Public Health Authority, Dörrhorststraße 36, 67059Ludwigshafen, Germany
| | - Tina Kaffenberger
- District Public Health Authority, Dörrhorststraße 36, 67059Ludwigshafen, Germany
| | | | | | - Silke Basenach
- District Public Health Authority, Neumayerstraße 10, 67433Neustadt, Germany
| | - Andrea Missal
- District Public Health Authority, Trierer Straße 49-51, 66869Kusel, Germany
| | - Katja Höfling
- District Public Health Authority, In der Malzdürre 7, 57610Altenkirchen, Germany
| | - Harald Michels
- District Public Health Authority, Paulinstraße 60, 54292Trier, Germany
| | - Anett Schall
- District Public Health Authority, Arzheimer Str. 1, 76829Landau in der Pfalz, Germany
| | - Holger Kappes
- District Public Health Authority, Trierer Straße 1, 54634Bitburg, Germany
| | - Manfred Vogt
- Federal State Agency for Consumer & Health Protection Rhineland-Palatinate, Koblenz, Germany
| | - Klaus Jahn
- Ministry of Health, Federal State of Rhineland-Palatinate, Bauhofstraße 9, 55116Mainz, Germany
| | - Till Bärnighausen
- Heidelberg Institute of Global Heath, University Hospitals, Im Neuenheimer Feld 130.3, 69120Heidelberg, Germany
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, USA
- Department of Global Health and Population, Harvard School of Public Health, Boston, USA
| | - Philipp Zanger
- Federal State Agency for Consumer & Health Protection Rhineland-Palatinate, Koblenz, Germany
- Heidelberg Institute of Global Heath, University Hospitals, Im Neuenheimer Feld 130.3, 69120Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospitals, Im Neuenheimer Feld 324, 69120Heidelberg, Germany
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Bellocchio F, Carioni P, Lonati C, Garbelli M, Martínez-Martínez F, Stuard S, Neri L. Enhanced Sentinel Surveillance System for COVID-19 Outbreak Prediction in a Large European Dialysis Clinics Network. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:9739. [PMID: 34574664 PMCID: PMC8472609 DOI: 10.3390/ijerph18189739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/23/2022]
Abstract
Accurate predictions of COVID-19 epidemic dynamics may enable timely organizational interventions in high-risk regions. We exploited the interconnection of the Fresenius Medical Care (FMC) European dialysis clinic network to develop a sentinel surveillance system for outbreak prediction. We developed an artificial intelligence-based model considering the information related to all clinics belonging to the European Nephrocare Network. The prediction tool provides risk scores of the occurrence of a COVID-19 outbreak in each dialysis center within a 2-week forecasting horizon. The model input variables include information related to the epidemic status and trends in clinical practice patterns of the target clinic, regional epidemic metrics, and the distance-weighted risk estimates of adjacent dialysis units. On the validation dates, there were 30 (5.09%), 39 (6.52%), and 218 (36.03%) clinics with two or more patients with COVID-19 infection during the 2-week prediction window. The performance of the model was suitable in all testing windows: AUC = 0.77, 0.80, and 0.81, respectively. The occurrence of new cases in a clinic propagates distance-weighted risk estimates to proximal dialysis units. Our machine learning sentinel surveillance system may allow for a prompt risk assessment and timely response to COVID-19 surges throughout networked European clinics.
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Affiliation(s)
- Francesco Bellocchio
- Fresenius Medical Care Italia SpA, Palazzo Pignano, 26020 Lombardia, Italy; (F.B.); (P.C.); (M.G.)
| | - Paola Carioni
- Fresenius Medical Care Italia SpA, Palazzo Pignano, 26020 Lombardia, Italy; (F.B.); (P.C.); (M.G.)
| | - Caterina Lonati
- Center for Preclinical Research, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Mario Garbelli
- Fresenius Medical Care Italia SpA, Palazzo Pignano, 26020 Lombardia, Italy; (F.B.); (P.C.); (M.G.)
| | - Francisco Martínez-Martínez
- Santa Barbara Smart Health S. L., Parc Cientific Universitat id Valencia, Carrer del Catedràtic Agustín Escardino Benlloch, 9, 46980 Paterna, Spain;
| | - Stefano Stuard
- Fresenius Medical Care Deutschland GmbH, 61352 Bad Homburg, Germany;
| | - Luca Neri
- Fresenius Medical Care Italia SpA, Palazzo Pignano, 26020 Lombardia, Italy; (F.B.); (P.C.); (M.G.)
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Pizarro AB, Persad E, Durao S, Nussbaumer-Streit B, Garritty C, Engela-Volker JS, McElvenny D, Rhodes S, Stocking K, Fletcher T, Van Tongeren M, Martin C, Noertjojo K, Sampson O, Jørgensen KJ, Bruschettini M. Workplace interventions to reduce the risk of SARS-CoV-2 infection outside of healthcare settings. Hippokratia 2021. [DOI: 10.1002/14651858.cd015112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Emma Persad
- Cochrane Austria, Department for Evidence-based Medicine and Evaluation; Danube University Krems; Krems Austria
| | - Solange Durao
- Cochrane South Africa; South African Medical Research Council; Cape Town South Africa
| | - Barbara Nussbaumer-Streit
- Cochrane Austria, Department for Evidence-based Medicine and Evaluation; Danube University Krems; Krems Austria
| | - Chantelle Garritty
- Global Health and Guidelines Division; Public Health Agency of Canada (PHAC); Ottawa Canada
| | - Jean S Engela-Volker
- Division of Population Medicine; Cardiff University School of Medicine; Cardiff UK
| | - Damien McElvenny
- Centre for Occupational and Environmental Health; University of Manchester; Manchester UK
| | - Sarah Rhodes
- Division of Population Health, Health Services Research and Primary Care; University of Manchester; Manchester UK
| | - Katie Stocking
- Centre for Biostatistics, School of Health Sciences, Faculty of Biology, Medicine and Health; University of Manchester; Manchester UK
| | - Tony Fletcher
- Epidemiology Department; Public Health England Centre for Radiation Chemical and Environmental Hazards (CRCE); London UK
| | - Martie Van Tongeren
- Division of Population Health, Health Services Research and Primary Care; University of Manchester; Manchester UK
| | | | | | | | - Karsten Juhl Jørgensen
- Centre for Evidence-Based Medicine Odense (CEBMO) and Cochrane Denmark; Department of Clinical Research, University of Southern Denmark; Odense Denmark
| | - Matteo Bruschettini
- Department of Clinical Sciences Lund, Paediatrics; Lund University, Skåne University Hospital; Lund Sweden
- Cochrane Sweden; Lund University, Skåne University Hospital; Lund Sweden
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Jayakody H, Kiddle G, Perera S, Tisi L, Leese HS. Molecular diagnostics in the era of COVID-19. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3744-3763. [PMID: 34473144 DOI: 10.1039/d1ay00947h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
As the COVID-19 pandemic continues to escalate globally and acquires new mutations, accurate diagnostic technologies continue to play a vital role in controlling and understanding the epidemiology of this disease. A plethora of technologies have enabled the diagnosis of individuals, informed clinical management, aided population-wide screening to determine transmission rates and identified cases within the wider community and high-risk settings. This review explores the application of molecular diagnostics technologies in controlling the spread of COVID-19, and the key factors that affect the sensitivity and specificity of the tests used.
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Affiliation(s)
- Harindi Jayakody
- Materials for Health Lab, Department of Chemical Engineering, University of Bath, Bath, UK.
- Erba Molecular, Ely, Cambridgeshire, UK.
| | - Guy Kiddle
- Erba Molecular, Ely, Cambridgeshire, UK.
| | - Semali Perera
- Materials for Health Lab, Department of Chemical Engineering, University of Bath, Bath, UK.
| | | | - Hannah S Leese
- Materials for Health Lab, Department of Chemical Engineering, University of Bath, Bath, UK.
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119
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Plank MJ, Binny RN, Hendy SC, Lustig A, Ridings K. Vaccination and testing of the border workforce for COVID-19 and risk of community outbreaks: a modelling study. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210686. [PMID: 34631122 PMCID: PMC8479330 DOI: 10.1098/rsos.210686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/17/2021] [Indexed: 05/10/2023]
Abstract
Throughout 2020 and the first part of 2021, Australia and New Zealand have followed a COVID-19 elimination strategy. Both countries require overseas arrivals to quarantine in government-managed facilities at the border. In both countries, community outbreaks of COVID-19 have been started via infection of a border worker. This workforce is rightly being prioritized for vaccination. However, although vaccines are highly effective in preventing disease, their effectiveness in preventing infection with and transmission of SARS-CoV-2 is less certain. There is a danger that vaccination could prevent symptoms of COVID-19 but not prevent transmission. Here, we use a stochastic model of SARS-CoV-2 transmission and testing to investigate the effect that vaccination of border workers has on the risk of an outbreak in an unvaccinated community. We simulate the model starting with a single infected border worker and measure the number of people who are infected before the first case is detected by testing. We show that if a vaccine reduces transmission by 50%, vaccination of border workers increases the risk of a major outbreak from around 7% per seed case to around 9% per seed case. The lower the vaccine effectiveness against transmission, the higher the risk. The increase in risk as a result of vaccination can be mitigated by increasing the frequency of routine testing for high-exposure vaccinated groups.
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Affiliation(s)
- Michael J. Plank
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland, New Zealand
| | - Rachelle N. Binny
- Manaaki Whenua, Lincoln, New Zealand
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland, New Zealand
| | - Shaun C. Hendy
- Department of Physics, University of Auckland, Auckland, New Zealand
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland, New Zealand
| | - Audrey Lustig
- Manaaki Whenua, Lincoln, New Zealand
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland, New Zealand
| | - Kannan Ridings
- Department of Physics, University of Auckland, Auckland, New Zealand
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland, New Zealand
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120
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Port JR, Yinda CK, Owusu IO, Holbrook M, Fischer R, Bushmaker T, Avanzato VA, Schulz JE, Martens C, van Doremalen N, Clancy CS, Munster VJ. SARS-CoV-2 disease severity and transmission efficiency is increased for airborne compared to fomite exposure in Syrian hamsters. Nat Commun 2021; 12:4985. [PMID: 34404778 PMCID: PMC8371001 DOI: 10.1038/s41467-021-25156-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Transmission of SARS-CoV-2 is driven by contact, fomite, and airborne transmission. The relative contribution of different transmission routes remains subject to debate. Here, we show Syrian hamsters are susceptible to SARS-CoV-2 infection through intranasal, aerosol and fomite exposure. Different routes of exposure present with distinct disease manifestations. Intranasal and aerosol inoculation causes severe respiratory pathology, higher virus loads and increased weight loss. In contrast, fomite exposure leads to milder disease manifestation characterized by an anti-inflammatory immune state and delayed shedding pattern. Whereas the overall magnitude of respiratory virus shedding is not linked to disease severity, the onset of shedding is. Early shedding is linked to an increase in disease severity. Airborne transmission is more efficient than fomite transmission and dependent on the direction of the airflow. Carefully characterized SARS-CoV-2 transmission models will be crucial to assess potential changes in transmission and pathogenic potential in the light of the ongoing SARS-CoV-2 evolution.
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Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Irene Offei Owusu
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Myndi Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Robert Fischer
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
- Montana State University, Bozeman, MT, USA
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Rocky Mountain Genomics Core Facility, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institutes of Health, Hamilton, MT, USA.
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121
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Muller K, Muller PA. Mathematical modelling of the spread of COVID-19 on a university campus. Infect Dis Model 2021; 6:1025-1045. [PMID: 34414342 PMCID: PMC8364150 DOI: 10.1016/j.idm.2021.08.004] [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: 04/20/2021] [Revised: 07/29/2021] [Accepted: 08/08/2021] [Indexed: 01/05/2023] Open
Abstract
In this paper we present a deterministic transmission dynamic compartmental model for the spread of the novel coronavirus on a college campus for the purpose of analyzing strategies to mitigate an outbreak. The goal of this project is to determine and compare the utility of certain containment strategies including gateway testing, surveillance testing, and contact tracing as well as individual level control measures such as mask wearing and social distancing. We modify a standard SEIR-type model to reflect what is currently known about COVID-19. We also modify the model to reflect the population present on a college campus, separating it into students and faculty. This is done in order to capture the expected different contact rates between groups as well as the expected difference in outcomes based on age known for COVID-19. We aim to provide insight into which strategies are most effective, rather than predict exact numbers of infections. We analyze effectiveness by looking at relative changes in the total number of cases as well as the effect a measure has on the estimated basic reproductive number. We find that the total number of infections is most sensitive to parameters relating to student behaviors. We also find that contact tracing can be an effective control strategy when surveillance testing is unavailable. Lastly, we validate the model using data from Villanova University's online COVID-19 Dashboard from Fall 2020 and find good agreement between model and data when superspreader events are incorporated in the model as shocks to the number of infected individuals approximately two weeks after each superspreader event.
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Affiliation(s)
- Kaitlyn Muller
- 800 E. Lancaster Avenue, Department of Mathematics and Statistics, Villanova University, Villanova, PA, USA
| | - Peter A. Muller
- 800 E. Lancaster Avenue, Department of Mathematics and Statistics, Villanova University, Villanova, PA, USA
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122
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Shivam S, Bulchandani VB, Sondhi SL. Recursive contact tracing in Reed-Frost epidemic models. Phys Biol 2021; 18. [PMID: 34186523 DOI: 10.1088/1478-3975/ac0fd1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/29/2021] [Indexed: 01/12/2023]
Abstract
We introduce a Reed-Frost epidemic model with recursive contact tracing and asymptomatic transmission. This generalizes the branching-process model introduced by the authors in a previous work (Bulchandani et al 2021Phys. Biol.18045004) to finite populations and general contact networks. We simulate the model numerically for two representative examples, the complete graph and the square lattice. On both networks, we observe clear signatures of a contact-tracing phase transition from an 'epidemic phase' to an 'immune phase' as contact-network coverage is increased. We verify that away from the singular line of perfect tracing, the finite-size scaling of the contact-tracing phase transition on each network lies in the corresponding percolation universality class. Finally, we use the model to quantify the efficacy of recursive contact-tracing in regimes where epidemic spread is not contained.
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Affiliation(s)
- Saumya Shivam
- Department of Physics, Princeton University, Princeton, New Jersey 08544, United States of America
| | - Vir B Bulchandani
- Department of Physics, University of California, Berkeley, Berkeley CA 94720, United States of America.,Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08544, United States of America
| | - S L Sondhi
- Department of Physics, Princeton University, Princeton, New Jersey 08544, United States of America
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123
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Ngo TB, Karkanitsa M, Adusei KM, Graham LA, Ricotta EE, Darrah JR, Blomberg RD, Spathies J, Pauly KJ, Klumpp-Thomas C, Travers J, Mehalko J, Drew M, Hall MD, Memoli MJ, Esposito D, Kozar RA, Griggs C, Cunningham KW, Schulman CI, Crandall M, Neavyn M, Dorfman JD, Lai JT, Whitehill JM, Babu KM, Mohr NM, Van Heukelom J, Fell JC, Rooke W, Kalish H, Thomas FD, Sadtler K. SARS-CoV-2 Seroprevalence and Drug Use in Trauma Patients from Six Sites in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.10.21261849. [PMID: 34401892 PMCID: PMC8366813 DOI: 10.1101/2021.08.10.21261849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In comparison to the general patient population, trauma patients show higher level detections of bloodborne infectious diseases, such as Hepatitis and Human Immunodeficiency Virus. In comparison to bloodborne pathogens, the prevalence of respiratory infections such as SARS-CoV-2 and how that relates with other variables, such as drug usage and trauma type, is currently unknown in trauma populations. Here, we evaluated SARS-CoV-2 seropositivity and antibody isotype profile in 2,542 trauma patients from six Level-1 trauma centers between April and October of 2020 during the first wave of the COVID-19 pandemic. We found that the seroprevalence in trauma victims 18-44 years old (9.79%, 95% confidence interval/CI: 8.33 - 11.47) was much higher in comparison to older patients (45-69 years old: 6.03%, 4.59-5.88; 70+ years old: 4.33%, 2.54 - 7.20). Black/African American (9.54%, 7.77 - 11.65) and Hispanic/Latino patients (14.95%, 11.80 - 18.75) also had higher seroprevalence in comparison, respectively, to White (5.72%, 4.62 - 7.05) and Non-Latino patients (6.55%, 5.57 - 7.69). More than half (55.54%) of those tested for drug toxicology had at least one drug present in their system. Those that tested positive for narcotics or sedatives had a significant negative correlation with seropositivity, while those on anti-depressants trended positive. These findings represent an important consideration for both the patients and first responders that treat trauma patients facing potential risk of respiratory infectious diseases like SARS-CoV-2.
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Affiliation(s)
- Tran B. Ngo
- Section on Immuno-Engineering. National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Maria Karkanitsa
- Section on Immuno-Engineering. National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Kenneth M. Adusei
- Section on Immuno-Engineering. National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | | | - Emily E. Ricotta
- Epidemiology and Population Studies Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD 20894
| | | | | | - Jacquelyn Spathies
- Bioengineering and Physical Sciences Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Kyle J. Pauly
- Bioengineering and Physical Sciences Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20852
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20852
| | - Jennifer Mehalko
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Matthew Drew
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20852
| | - Matthew J Memoli
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD 20894
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Rosemary A. Kozar
- Shock Trauma Center, University of Maryland School of Medicine, Baltimore MD 21201
| | - Christopher Griggs
- Department of Emergency Medicine, Atrium Health’s Carolinas Medical Center, Charlotte NC 28203
| | - Kyle W. Cunningham
- Division of Acute Care Surgery, Atrium Health’s Carolinas Medical Center, Charlotte NC 28203
| | | | - Marie Crandall
- Department of Surgery, University of Florida College of Medicine, Jacksonville FL 33209
| | - Mark Neavyn
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester MA 01655
| | - Jon D. Dorfman
- Maine Medical Center, Department of Emergency Medicine, Tufts University School of Medicine, Portland ME 04102
| | - Jeffrey T. Lai
- Division of Medical Toxicology, Department of Emergency Medicine, University of Massachusetts Medical School, Worcester MA 01655
| | - Jennifer M. Whitehill
- Department of Health Promotion and Policy, University of Massachusetts Amherst, Amherst MA 01003
| | - Kavita M. Babu
- Division of Medical Toxicology, Department of Emergency Medicine, University of Massachusetts Medical School, Worcester MA 01655
| | - Nicholas M. Mohr
- Department of Emergency Medicine, Anesthesia Critical Care, and Epidemiology, University of Iowa Health Care, Iowa City IA 52242
| | - Jon Van Heukelom
- Department of Emergency Medicine, University of Iowa Health Care, Iowa City IA 52242
| | - James C. Fell
- NORC at the University of Chicago, Bethesda, MD 20814
| | | | - Heather Kalish
- Bioengineering and Physical Sciences Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | | | - Kaitlyn Sadtler
- Section on Immuno-Engineering. National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
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Bilinski A, Ciaranello A, Fitzpatrick MC, Giardina J, Shah M, Salomon JA, Kendall EA. SARS-CoV-2 testing strategies to contain school-associated transmission: model-based analysis of impact and cost of diagnostic testing, screening, and surveillance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.12.21257131. [PMID: 34401893 PMCID: PMC8366814 DOI: 10.1101/2021.05.12.21257131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background In March 2021, the Biden administration allocated $10 billion for COVID-19 testing in schools. We evaluate the costs and benefits of testing strategies to reduce the infection risks of full-time in-person K-8 education at different levels of community incidence. Methods We used an agent-based network model to simulate transmission in elementary and middle school communities, parameterized to a US school structure and assuming dominance of the delta COVID-19 variant. We assess the value of different strategies for testing students and faculty/staff, including expanded diagnostic testing ("test to stay" policies that take the place of isolation for symptomatic students or quarantine for exposed classrooms); screening (routinely testing asymptomatic individuals to identify infections and contain transmission); and surveillance (testing a random sample of students to signaling undetected transmission and trigger additional investigation or interventions). Main outcome measures We project 30-day cumulative incidence of SARS-CoV-2 infection; proportion of cases detected; proportion of planned and unplanned days out of school; and the cost of testing programs and of childcare costs associated with different strategies. For screening policies, we further estimate cost per SARS-CoV-2 infection averted in students and staff, and for surveillance, probability of correctly or falsely triggering an outbreak response at different incidence and attack rates. Results Accounting for programmatic and childcare costs, "test to stay" policies achieve similar model-projected transmission to quarantine policies, with reduced overall costs. Weekly universal screening prevents approximately 50% of in-school transmission, with a lower projected societal cost than hybrid or remote schooling. The cost per infection averted in students and staff by weekly screening is lower for older students and schools with higher mitigation and declines as community transmission rises. In settings where local student incidence is unknown or rapidly changing, surveillance may trigger detection of moderate-to-large in-school outbreaks with fewer resources compared to screening. Conclusions "Test to stay" policies and/or screening tests can facilitate consistent in-person school attendance with low transmission risk across a range of community incidence. Surveillance may be a useful reduced-cost option for detecting outbreaks and identifying school environments that may benefit from increased mitigation.
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Abstract
Background: The UK was one of the countries worst affected by the COVID-19 pandemic in Europe. A strict lockdown from early 2021 combined with an aggressive vaccination programme enabled a gradual easing of lockdown measures to be introduced whilst both deaths and reported case numbers reduced to less than 3% of their peak. The emergence of the Delta variant in April 2021 has reversed this trend, and the UK is once again experiencing surging cases, albeit with reduced average severity due to the success of the vaccination rollout. This study presents the results of a modelling exercise which simulates the progression of the pandemic in the UK through projection of daily case numbers as lockdown lifts. Methods: A simulation model based on the Susceptible-Exposed-Infected-Recovered structure was built. A timeline of UK lockdown measures was used to simulate the changing restrictions. The model was tailored for the UK, with some values set based on research and others obtained through calibration against 16 months of historical data. Results: The model projects that if lockdown restrictions are lifted in July 2021, UK COVID-19 cases will peak at hundreds of thousands daily in most viable scenarios, reducing in late 2021 as immunity acquired through both vaccination and infection reduces the susceptible population percentage. Further lockdown measures can be used to reduce daily cases. Other than the ever-present threat of the emergence of new variants, the most significant unknown factors affecting the profile of the pandemic in the UK are the length and strength of immunity, with daily peak cases over 50% higher if immunity lasts 8 months compared to 12 months. Another significant factor is the percentage of unreported cases. The reduced case severity associated with vaccination may lead to a higher proportion of unreported mild or asymptomatic cases, meaning that unmanaged infections resulting from unknown cases will continue to be a major source of infection. Conclusions: Further research into the length and strength of both recovered and vaccinated COVID-19 immunity is critical to delivering more accurate projections from models, thus enabling more finely tuned policy decisions. The model presented in this article, whilst by no means perfect, aims to contribute to greater transparency of the modelling process, which can only increase trust between policy makers, journalists and the general public.
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Sakano T, Urashima M, Takao H, Takeshita K, Kobashi H, Fujiwara T. Differential Kinetics of Cycle Threshold Values during Admission by Symptoms among Patients with Mild COVID-19: A Prospective Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8181. [PMID: 34360473 PMCID: PMC8346104 DOI: 10.3390/ijerph18158181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/12/2023]
Abstract
In the coronavirus disease 2019 (COVID-19) pandemic, more than half of the cases of transmission may occur via asymptomatic individuals, which makes it difficult to contain. However, whether viral load in the throat during admission is different between asymptomatic and symptomatic patients is not well known. By conducting a prospective cohort study of patients with asymptomatic or mild COVID-19, cycle threshold (Ct) values of the polymerase chain reaction test for COVID-19 were examined every other day during admission. The Ct values during admission increased more steadily in symptomatic patients and febrile patients than in asymptomatic patients, with significance (p = 0.01 and p = 0.004, respectively), although the Ct values as a whole were not significantly different between the two groups. Moreover, the Ct values as a whole were higher in patients with dysosmia/dysgeusia than in those without it (p = 0.02), whereas they were lower in patients with a headache than those without (p = 0.01). Patients who were IgG-positive at discharge maintained higher Ct values, e.g., more than 35, during admission than those with IgG-negative (p = 0.03). Assuming that viral load and Ct values are negatively associated, the viral loads as a whole and their changes by time may be different by symptoms and immune reaction, i.e., IgG-positive at discharge.
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Affiliation(s)
- Teppei Sakano
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
- Allm, Inc., Yushin Bldg. Shinkan 2F, 3-27-11 Shibuya, Shibuya-ku, Tokyo 150-0002, Japan
| | - Mitsuyoshi Urashima
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Hiroyuki Takao
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
- Department of Neurosurgery, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Kohei Takeshita
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
| | - Hiroe Kobashi
- Infectious Disease Department, Team Medical Clinic, Tokyo 105-0003, Japan;
| | - Takeo Fujiwara
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
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Leber W, Lammel O, Redlberger-Fritz M, Mustafa-Korninger ME, Glehr RC, Camp J, Agerer B, Lercher A, Popa A, Genger JW, Penz T, Aberle S, Bock C, Bergthaler A, Stiasny K, Hochstrasser EM, Hoellinger C, Siebenhofer A, Griffiths C, Panovska-Griffiths J. Rapid, early and accurate SARS-CoV-2 detection using RT-qPCR in primary care: a prospective cohort study (REAP-1). BMJ Open 2021; 11:e045225. [PMID: 34341034 PMCID: PMC8331320 DOI: 10.1136/bmjopen-2020-045225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/24/2021] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES We explore the importance of SARS-CoV-2 sentinel surveillance testing in primary care during a regional COVID-19 outbreak in Austria. DESIGN Prospective cohort study. SETTING A single sentinel practice serving 22 829 people in the ski-resort of Schladming-Dachstein. PARTICIPANTS All 73 patients presenting with mild-to-moderate flu-like symptoms between 24 February and 03 April, 2020. INTERVENTION Nasopharyngeal sampling to detect SARS-CoV-2 using real-time reverse transcriptase-quantitative PCR (RT-qPCR). OUTCOME MEASURES We compared RT-qPCR at presentation with confirmed antibody status. We split the outbreak in two parts, by halving the period from the first to the last case, to characterise three cohorts of patients with confirmed infection: early acute (RT-qPCR reactive) in the first half; and late acute (reactive) and late convalescent (non-reactive) in the second half. For each cohort, we report the number of cases detected, the accuracy of RT-qPCR, the duration and variety of symptoms, and the number of viral clades present. RESULTS Twenty-two patients were diagnosed with COVID-19 (eight early acute, seven late acute and seven late convalescent), 44 patients tested SARS-CoV-2 negative and 7 were excluded. The sensitivity of RT-qPCR was 100% among all acute cases, dropping to 68.1% when including convalescent. Test specificity was 100%. Mean duration of symptoms for each group were 2 days (range 1-4) among early acute, 4.4 days (1-7) among late acute and 8 days (2-12) among late convalescent. Confirmed infection was associated with loss of taste. Acute infection was associated with loss of taste, nausea/vomiting, breathlessness, sore throat and myalgia; but not anosmia, fever or cough. Transmission clusters of three viral clades (G, GR and L) were identified. CONCLUSIONS RT-qPCR testing in primary care can rapidly and accurately detect SARS-CoV-2 among people with flu-like illness in a heterogeneous viral outbreak. Targeted testing in primary care can support national sentinel surveillance of COVID-19.
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Affiliation(s)
- Werner Leber
- Wolfson Institute of Population Health, Centre for Primary Care, Queen Mary University of London, London, UK
| | | | | | | | - Reingard Christina Glehr
- Institute of General Practice and Evidence-based Health Services Research, Medical University of Graz, Graz, Austria
| | - Jeremy Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stephan Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | | | - Andrea Siebenhofer
- Institute of General Practice and Evidence-based Health Services Research, Medical University of Graz, Graz, Austria
- Goethe University Frankfurt, Institute for General Practice, Frankfurt, Germany
| | - Chris Griffiths
- Wolfson Institute of Population Health, Centre for Primary Care, Queen Mary University of London, London, UK
| | - Jasmina Panovska-Griffiths
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Queen's College, University of Oxford, Oxford, UK
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128
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Shen J, Kong M, Dong B, Birnkrant MJ, Zhang J. A systematic approach to estimating the effectiveness of multi-scale IAQ strategies for reducing the risk of airborne infection of SARS-CoV-2. BUILDING AND ENVIRONMENT 2021; 200:107926. [PMID: 33967376 PMCID: PMC8084626 DOI: 10.1016/j.buildenv.2021.107926] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/04/2021] [Accepted: 04/24/2021] [Indexed: 05/05/2023]
Abstract
The unprecedented coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made more than 125 million people infected and more than 2.7 million people dead globally. Airborne transmission has been recognized as one of the major transmission routes for SARS-CoV-2. This paper presents a systematic approach for evaluating the effectiveness of multi-scale IAQ control strategies in mitigating the infection risk in different scenarios. The IAQ control strategies across multiple scales from a whole building to rooms, and to cubical and personal microenvironments and breathing zone, are introduced, including elevated outdoor airflow rates, high-efficiency filters, advanced air distribution strategies, standalone air cleaning technologies, personal ventilation and face masks. The effectiveness of these strategies for reducing the risk of COVID-19 infection are evaluated for specific indoor spaces, including long-term care facility, school and college, meat plant, retail stores, hospital, office, correctional facility, hotel, restaurant, casino and transportation spaces like airplane, cruise ship, subway, bus and taxi, where airborne transmission are more likely to occur due to high occupancy densities. The baseline cases of these spaces are established according to the existing standards, guidelines or practices. Several integrated mitigation strategies are recommended and classified based on their relative cost and effort of implementation for each indoor space. They can be applied to help meet the current challenge of ongoing COVID-19, and provide better preparation for other possible epidemics and pandemics of airborne infectious diseases in the future.
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Affiliation(s)
- Jialei Shen
- Department of Mechanical and Aerospace Engineering, Syracuse University, 263 Link Hall, Syracuse, NY, 13244, USA
| | - Meng Kong
- Department of Mechanical and Aerospace Engineering, Syracuse University, 263 Link Hall, Syracuse, NY, 13244, USA
| | - Bing Dong
- Department of Mechanical and Aerospace Engineering, Syracuse University, 263 Link Hall, Syracuse, NY, 13244, USA
| | | | - Jianshun Zhang
- Department of Mechanical and Aerospace Engineering, Syracuse University, 263 Link Hall, Syracuse, NY, 13244, USA
- School of Architecture and Urban Planning, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu Province, 210093, China
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Pascual-García A, Klein JD, Villers J, Campillo-Funollet E, Sarkis C. Empowering the crowd: feasible strategies for epidemic management in high-density informal settlements. The case of COVID-19 in Northwest Syria. BMJ Glob Health 2021; 6:e004656. [PMID: 34446431 PMCID: PMC8392737 DOI: 10.1136/bmjgh-2020-004656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
More than 1 billion people live in informal settlements worldwide, where precarious living conditions pose unique challenges to managing a COVID-19 outbreak. Taking Northwest Syria as a case study, we simulated an outbreak in high-density informal Internally Displaced Persons (IDP) camps using a stochastic Susceptible-Exposed-Infectious-Recovered model. Expanding on previous studies, taking social conditions and population health/structure into account, we modelled several interventions feasible in these settings: moderate self-distancing, self-isolation of symptomatic cases and protection of the most vulnerable in 'safety zones'. We considered complementary measures to these interventions that can be implemented autonomously by these communities, such as buffer zones, health checks and carers for isolated individuals, quantifying their impact on the micro-dynamics of disease transmission. All interventions significantly reduce outbreak probability and some of them reduce mortality when an outbreak does occur. Self-distancing reduces mortality by up to 35% if contacts are reduced by 50%. A reduction in mortality by up to 18% can be achieved by providing one self-isolation tent per eight people. Protecting the most vulnerable in a safety zone reduces the outbreak probability in the vulnerable population and has synergistic effects with the other interventions. Our model predicts that a combination of all simulated interventions may reduce mortality by more than 90% and delay an outbreak's peak by almost 2 months. Our results highlight the potential for non-medical interventions to mitigate the effects of the pandemic. Similar measures may be applicable to controlling COVID-19 in other informal settlements, particularly IDP camps in conflict regions, around the world.
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Affiliation(s)
| | - Jordan D Klein
- Office of Population Research, Princeton University, Princeton, New Jersey, USA
| | - Jennifer Villers
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
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130
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Bilinski A, Salomon JA, Giardina J, Ciaranello A, Fitzpatrick MC. Passing the Test: A Model-Based Analysis of Safe School-Reopening Strategies. Ann Intern Med 2021; 174:1090-1100. [PMID: 34097433 PMCID: PMC8252151 DOI: 10.7326/m21-0600] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic has induced historic educational disruptions. In April 2021, about 40% of U.S. public school students were not offered full-time in-person education. OBJECTIVE To assess the risk for SARS-CoV-2 transmission in schools. DESIGN An agent-based network model was developed to simulate transmission in elementary and high school communities, including home, school, and interhousehold interactions. SETTING School structure was parametrized to reflect average U.S. classrooms, with elementary schools of 638 students and high schools of 1451 students. Daily local incidence was varied from 1 to 100 cases per 100 000 persons. PARTICIPANTS Students, faculty, staff, and adult household members. INTERVENTION Isolation of symptomatic individuals, quarantine of an infected individual's contacts, reduced class sizes, alternative schedules, staff vaccination, and weekly asymptomatic screening. MEASUREMENTS Transmission was projected among students, staff, and families after a single infection in school and over an 8-week quarter, contingent on local incidence. RESULTS School transmission varies according to student age and local incidence and is substantially reduced with mitigation measures. Nevertheless, when transmission occurs, it may be difficult to detect without regular testing because of the subclinical nature of most children's infections. Teacher vaccination can reduce transmission to staff, and asymptomatic screening improves understanding of local circumstances and reduces transmission. LIMITATION Uncertainty exists about the susceptibility and infectiousness of children, and precision is low regarding the effectiveness of specific countermeasures, particularly with new variants. CONCLUSION With controlled community transmission and moderate mitigation, elementary schools can open safety, but high schools require more intensive mitigation. Asymptomatic screening can facilitate reopening at higher local incidence while minimizing transmission risk. PRIMARY FUNDING SOURCE Centers for Disease Control and Prevention through the Council of State and Territorial Epidemiologists, National Institute of Allergy and Infectious Diseases, National Institute on Drug Abuse, and Facebook.
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Affiliation(s)
- Alyssa Bilinski
- Interfaculty Initiative in Health Policy, Harvard Graduate School of Arts and Sciences, Cambridge, Massachusetts (A.B.)
| | - Joshua A Salomon
- Center for Health Policy and Center for Primary Care and Outcomes Research, Stanford University School of Medicine, Stanford, California (J.A.S.)
| | - John Giardina
- Interfaculty Initiative in Health Policy, Harvard Graduate School of Arts and Sciences, Cambridge, and Center for Health Decision Science, Harvard T.H. Chan School of Public Health, Boston, Massachusetts (J.G.)
| | - Andrea Ciaranello
- Medical Practice Evaluation Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts (A.C.)
| | - Meagan C Fitzpatrick
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland (M.C.F.)
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131
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Logette E, Lorin C, Favreau C, Oshurko E, Coggan JS, Casalegno F, Sy MF, Monney C, Bertschy M, Delattre E, Fonta PA, Krepl J, Schmidt S, Keller D, Kerrien S, Scantamburlo E, Kaufmann AK, Markram H. A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19. Front Public Health 2021; 9:695139. [PMID: 34395368 PMCID: PMC8356061 DOI: 10.3389/fpubh.2021.695139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/30/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 started spreading toward the end of 2019 causing COVID-19, a disease that reached pandemic proportions among the human population within months. The reasons for the spectrum of differences in the severity of the disease across the population, and in particular why the disease affects more severely the aging population and those with specific preconditions are unclear. We developed machine learning models to mine 240,000 scientific articles openly accessible in the CORD-19 database, and constructed knowledge graphs to synthesize the extracted information and navigate the collective knowledge in an attempt to search for a potential common underlying reason for disease severity. The machine-driven framework we developed repeatedly pointed to elevated blood glucose as a key facilitator in the progression of COVID-19. Indeed, when we systematically retraced the steps of the SARS-CoV-2 infection, we found evidence linking elevated glucose to each major step of the life-cycle of the virus, progression of the disease, and presentation of symptoms. Specifically, elevations of glucose provide ideal conditions for the virus to evade and weaken the first level of the immune defense system in the lungs, gain access to deep alveolar cells, bind to the ACE2 receptor and enter the pulmonary cells, accelerate replication of the virus within cells increasing cell death and inducing an pulmonary inflammatory response, which overwhelms an already weakened innate immune system to trigger an avalanche of systemic infections, inflammation and cell damage, a cytokine storm and thrombotic events. We tested the feasibility of the hypothesis by manually reviewing the literature referenced by the machine-generated synthesis, reconstructing atomistically the virus at the surface of the pulmonary airways, and performing quantitative computational modeling of the effects of glucose levels on the infection process. We conclude that elevation in glucose levels can facilitate the progression of the disease through multiple mechanisms and can explain much of the differences in disease severity seen across the population. The study provides diagnostic considerations, new areas of research and potential treatments, and cautions on treatment strategies and critical care conditions that induce elevations in blood glucose levels.
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Affiliation(s)
- Emmanuelle Logette
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Geneva, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Henry Markram
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Geneva, Switzerland
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Escandón K, Rasmussen AL, Bogoch II, Murray EJ, Escandón K, Popescu SV, Kindrachuk J. COVID-19 false dichotomies and a comprehensive review of the evidence regarding public health, COVID-19 symptomatology, SARS-CoV-2 transmission, mask wearing, and reinfection. BMC Infect Dis 2021; 21:710. [PMID: 34315427 PMCID: PMC8314268 DOI: 10.1186/s12879-021-06357-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Scientists across disciplines, policymakers, and journalists have voiced frustration at the unprecedented polarization and misinformation around coronavirus disease 2019 (COVID-19) pandemic. Several false dichotomies have been used to polarize debates while oversimplifying complex issues. In this comprehensive narrative review, we deconstruct six common COVID-19 false dichotomies, address the evidence on these topics, identify insights relevant to effective pandemic responses, and highlight knowledge gaps and uncertainties. The topics of this review are: 1) Health and lives vs. economy and livelihoods, 2) Indefinite lockdown vs. unlimited reopening, 3) Symptomatic vs. asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 4) Droplet vs. aerosol transmission of SARS-CoV-2, 5) Masks for all vs. no masking, and 6) SARS-CoV-2 reinfection vs. no reinfection. We discuss the importance of multidisciplinary integration (health, social, and physical sciences), multilayered approaches to reducing risk ("Emmentaler cheese model"), harm reduction, smart masking, relaxation of interventions, and context-sensitive policymaking for COVID-19 response plans. We also address the challenges in understanding the broad clinical presentation of COVID-19, SARS-CoV-2 transmission, and SARS-CoV-2 reinfection. These key issues of science and public health policy have been presented as false dichotomies during the pandemic. However, they are hardly binary, simple, or uniform, and therefore should not be framed as polar extremes. We urge a nuanced understanding of the science and caution against black-or-white messaging, all-or-nothing guidance, and one-size-fits-all approaches. There is a need for meaningful public health communication and science-informed policies that recognize shades of gray, uncertainties, local context, and social determinants of health.
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Affiliation(s)
- Kevin Escandón
- School of Medicine, Universidad del Valle, Cali, Colombia.
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
| | - Isaac I Bogoch
- Division of Infectious Diseases, University of Toronto, Toronto General Hospital, Toronto, Canada
| | - Eleanor J Murray
- Department of Epidemiology, Boston University School of Public Health, Boston, USA
| | - Karina Escandón
- Department of Anthropology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Saskia V Popescu
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
- Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
| | - Jason Kindrachuk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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133
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Martínez-Antón JC, Brun A, Vázquez D, Moreno S, Fernández-Balbuena AA, Alda J. Determination of the characteristic inactivation fluence for SARS-CoV-2 under UV-C radiation considering light absorption in culture media. Sci Rep 2021; 11:15293. [PMID: 34315976 PMCID: PMC8316444 DOI: 10.1038/s41598-021-94648-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/14/2021] [Indexed: 01/21/2023] Open
Abstract
The optical absorption coefficient of culture media is critical for the survival analysis of pathogens under optical irradiation. The quality of the results obtained from experiments relies on the optical analysis of the spatial distribution of fluence which also depends on the geometry of the sample. In this contribution, we consider both the geometrical shape and the culture medium's absorption coefficient to evaluate how the spatial distribution of optical radiation affects pathogens/viruses. In this work, we exposed SARS-CoV-2 to UV-C radiation ([Formula: see text] = 254 nm) and we calculated-considering the influence of the optical absorption of the culture medium-a characteristic inactivation fluence of [Formula: see text] = 4.7 J/m2, or an equivalent 10% survival (D90 dose) of 10.8 J/m2. Experimentally, we diluted the virus into sessile drops of Dulbecco's Modified Eagle Medium to evaluate pathogen activity after controlled doses of UV irradiation. To validate the optical absorption mode, we carried out an additional experiment where we varied droplet size. Our model-including optical absorption and geometrical considerations-provides robust results among a variety of experimental situations, and represents our experimental conditions more accurately. These results will help to evaluate the capability of UV disinfecting strategies applied to a variety of everyday situations, including the case of micro-droplets generated by respiratory functions.
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Affiliation(s)
- Juan Carlos Martínez-Antón
- Applied Optics Complutense Group, Faculty of Optics and Optometry, University Complutense of Madrid, Av. Arcos de Jalón, 118, 28037, Madrid, Spain
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Carretera Algete-El Casar de Talamanca, Km 8.1, 28130, Valdeolmos, Madrid, Spain
| | - Daniel Vázquez
- Applied Optics Complutense Group, Faculty of Optics and Optometry, University Complutense of Madrid, Av. Arcos de Jalón, 118, 28037, Madrid, Spain
| | - Sandra Moreno
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Carretera Algete-El Casar de Talamanca, Km 8.1, 28130, Valdeolmos, Madrid, Spain
| | - Antonio A Fernández-Balbuena
- Applied Optics Complutense Group, Faculty of Optics and Optometry, University Complutense of Madrid, Av. Arcos de Jalón, 118, 28037, Madrid, Spain
| | - Javier Alda
- Applied Optics Complutense Group, Faculty of Optics and Optometry, University Complutense of Madrid, Av. Arcos de Jalón, 118, 28037, Madrid, Spain.
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134
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Klaus J, Zini E, Hartmann K, Egberink H, Kipar A, Bergmann M, Palizzotto C, Zhao S, Rossi F, Franco V, Porporato F, Hofmann-Lehmann R, Meli ML. SARS-CoV-2 Infection in Dogs and Cats from Southern Germany and Northern Italy during the First Wave of the COVID-19 Pandemic. Viruses 2021; 13:1453. [PMID: 34452319 PMCID: PMC8402904 DOI: 10.3390/v13081453] [Citation(s) in RCA: 33] [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: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people globally since its first detection in late 2019. Besides humans, cats and, to some extent, dogs were shown to be susceptible to SARS-CoV-2, highlighting the need for surveillance in a One Health context. Seven veterinary clinics from regions with high incidences of coronavirus disease (COVID-19) were recruited during the early pandemic (March to July 2020) for the screening of patients. A total of 2257 oropharyngeal and nasal swab specimen from 877 dogs and 260 cats (including 18 animals from COVID-19-affected households and 92 animals with signs of respiratory disease) were analyzed for the presence of SARS-CoV-2 RNA using reverse transcriptase real-time polymerase chain reaction (RT-qPCR) targeting the viral envelope (E) and RNA dependent RNA polymerase (RdRp) genes. One oropharyngeal swab from an Italian cat, living in a COVID-19-affected household in Piedmont, tested positive in RT-qPCR (1/260; 0.38%, 95% CI: 0.01-2.1%), and SARS-CoV-2 infection of the animal was serologically confirmed six months later. One oropharyngeal swab from a dog was potentially positive (1/877; 0.1%, 95% CI: 0.002-0.63%), but the result was not confirmed in a reference laboratory. Analyses of convenience sera from 118 animals identified one dog (1/94; 1.1%; 95% CI: 0.02-5.7%) from Lombardy, but no cats (0/24), as positive for anti-SARS-CoV-2 receptor binding domain (RBD) antibodies and neutralizing activity. These findings support the hypothesis that the prevalence of SARS-CoV-2 infection in pet cat and dog populations, and hence, the risk of zoonotic transmission to veterinary staff, was low during the first wave of the pandemic, even in hotspot areas.
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Affiliation(s)
- Julia Klaus
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
| | - Eric Zini
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell′Università 16, 35020 Legnaro, Padova, Italy
| | - Katrin Hartmann
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, LMU Munich, 80539 Munich, Germany; (K.H.); (M.B.)
| | - Herman Egberink
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057 Zurich, Switzerland;
| | - Michèle Bergmann
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, LMU Munich, 80539 Munich, Germany; (K.H.); (M.B.)
| | - Carlo Palizzotto
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Shan Zhao
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Francesco Rossi
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Vittoria Franco
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Federico Porporato
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
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135
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Webb G. A COVID-19 Epidemic Model Predicting the Effectiveness of Vaccination in the US. Infect Dis Rep 2021; 13:654-667. [PMID: 34449651 PMCID: PMC8395902 DOI: 10.3390/idr13030062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
A model of a COVID-19 epidemic is used to predict the effectiveness of vaccination in the US. The model incorporates key features of COVID-19 epidemics: asymptomatic and symptomatic infectiousness, reported and unreported cases data, and social measures implemented to decrease infection transmission. The model analyzes the effectiveness of vaccination in terms of vaccination efficiency, vaccination scheduling, and relaxation of social measures that decrease disease transmission. The model demonstrates that the subsiding of the epidemic as vaccination is implemented depends critically on the scale of relaxation of social measures that reduce disease transmission.
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Affiliation(s)
- Glenn Webb
- Department of Mathematics, Vanderbilt University, Nashville, TN 37240, USA
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136
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Irfan O, Li J, Tang K, Wang Z, Bhutta ZA. Risk of infection and transmission of SARS-CoV-2 among children and adolescents in households, communities and educational settings: A systematic review and meta-analysis. J Glob Health 2021; 11:05013. [PMID: 34326997 PMCID: PMC8285769 DOI: 10.7189/jogh.11.05013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND There is uncertainty with respect to SARS-CoV-2 transmission in children (0-19 years) with controversy on effectiveness of school-closures in controlling the pandemic. It is of equal importance to evaluate the risk of transmission in children who are often asymptomatic or mildly symptomatic carriers that may incidentally transmit SARS-CoV-2 in different settings. We conducted this review to assess transmission and risks for SARS-CoV-2 in children (by age-groups or grades) in community and educational-settings compared to adults. METHODS Data for the review were retrieved from PubMed, EMBASE, Cochrane Library, WHO COVID-19 Database, China National Knowledge Infrastructure (CNKI) Database, WanFang Database, Latin American and Caribbean Health Sciences Literature (LILACS), Google Scholar, and preprints from medRixv and bioRixv) covering a timeline from December 1, 2019 to April 1, 2021. Population-screening, contact-tracing and cohort studies reporting prevalence and transmission of SARS-CoV-2 in children were included. Data were extracted according to PRISMA guidelines. Meta-analyses were performed using Review Manager 5.3. RESULTS Ninety studies were included. Compared to adults, children showed comparable national (risk ratio (RR) = 0.87, 95% confidence interval (CI) = 0.71-1.060 and subnational (RR = 0.81, 95% CI = 0.66-1.01) prevalence in population-screening studies, and lower odds of infection in community/household contact-tracing studies (odds ratio (OR) = 0.62, 95% CI = 0.46-0.84). On disaggregation, adolescents observed comparable risk (OR = 1.22, 95% CI = 0.74-2.04) with adults. In educational-settings, children attending daycare/preschools (OR = 0.53, 95% CI = 0.38-0.72) were observed to be at lower-risk when compared to adults, with odds of infection among primary (OR = 0.85, 95% CI = 0.55-1.31) and high-schoolers (OR = 1.30, 95% CI = 0.71-2.38) comparable to adults. Overall, children and adolescents had lower odds of infection in educational-settings compared to community and household clusters. CONCLUSIONS Children (<10 years) showed lower susceptibility to COVID-19 compared to adults, whereas adolescents in communities and high-schoolers had comparable risk. Risks of infection among children in educational-settings was lower than in communities. Evidence from school-based studies demonstrate it is largely safe for children (<10 years) to be at schools, however older children (10-19 years) might facilitate transmission. Despite this evidence, studies focusing on the effectiveness of mitigation measures in educational settings are urgently needed to support both public health and educational policy-making for school reopening.
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Affiliation(s)
- Omar Irfan
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
| | - Jiang Li
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
| | - Kun Tang
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Zhicheng Wang
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Zulfiqar A Bhutta
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
- Institute for Global Health & Development, the Aga Khan University, Karachi, Pakistan
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137
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Walker AS, Pritchard E, House T, Robotham JV, Birrell PJ, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Hay J, Vihta KD, Peto TEA, Stoesser N, Matthews PC, Eyre DW, Pouwels KB. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. eLife 2021; 10:e64683. [PMID: 34250907 PMCID: PMC8282332 DOI: 10.7554/elife.64683] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Methods We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. Results Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. Conclusions Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. Funding Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
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Affiliation(s)
- A Sarah Walker
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- MRC Clinical Trials Unit at UCL, UCLLondonUnited Kingdom
| | - Emma Pritchard
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Thomas House
- Department of Mathematics, University of ManchesterManchesterUnited Kingdom
- IBM Research, Hartree CentreSci-Tech DaresburyUnited Kingdom
| | - Julie V Robotham
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- National Infection Service, Public Health EnglandLondonUnited Kingdom
| | - Paul J Birrell
- National Infection Service, Public Health EnglandLondonUnited Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public HealthCambridgeUnited Kingdom
| | - Iain Bell
- Office for National StatisticsNewportUnited Kingdom
| | - John I Bell
- Office of the Regius Professor of Medicine, University of OxfordOxfordUnited Kingdom
| | - John N Newton
- Health Improvement Directorate, Public Health EnglandLondonUnited Kingdom
| | | | - Ian Diamond
- Office for National StatisticsNewportUnited Kingdom
| | - Ruth Studley
- Office for National StatisticsNewportUnited Kingdom
| | - Jodie Hay
- University of GlasgowGlasgowUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
| | - Karina-Doris Vihta
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Timothy EA Peto
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - David W Eyre
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
- Big Data Institute, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - Koen B Pouwels
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Health Economics Research Centre, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
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Oberste M, Pusch LM, Roth R, Shah-Hosseini K, Dewald F, Müller C, Stach von Goltzheim L, Lehmann C, Buess M, Wolff A, Fätkenheuer G, Wiesmüller G, Klein F, Hellmich M, Neuhann F. Protocol of the Cologne Corona Surveillance (CoCoS) Study- a prospective population-based cohort study. BMC Public Health 2021; 21:1295. [PMID: 34215236 PMCID: PMC8253235 DOI: 10.1186/s12889-021-11206-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Surveillance strategies are critical to cope with the current SARS-CoV-2 pandemic and to evaluate, as well as adjust government-imposed countermeasures. Incidence estimates are widely based on laboratory confirmed cases reported by health authorities. Prevalence and incidence data of SARS-CoV-2 is still scarce, along with demographic and behavioural factors associated with infection risk. METHODS The Cologne Corona Surveillance Study will be conducted in the City of Cologne, which is the fourth-largest city in Germany with a population of approximately 1.1 million. Researchers will apply self-sampling surveillance to a rolling cohort of Cologne residents. Random samples of 6000 Cologne residents 18 years of age and older will be drawn from the registration office. Upon receiving the information and saliva sample kit, participants will be asked to fill out a questionnaire online or via phone, sign written informed consent, and send back written consent, as well as saliva sample. The saliva samples will be tested for SARS-CoV-2 by reverse PCR. The questionnaire will be administered to gather information about personal characteristics such as health status and risks. A second round of testing will take place 6 weeks after the first. DISCUSSION Self-administered saliva sampling proved to be a legitimate and feasible alternative to nasopharyngeal swabs taken by health professionals. However, it is unclear whether the targeted response rate of 40% can be achieved and whether the results are representative of the population. TRIAL REGISTRATION DRKS.de, German Clinical Trials Register (DRKS), Identifier: DRKS00024046 , Registered on 25 February 2021.
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Affiliation(s)
- Max Oberste
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany
| | - Lynn-Marie Pusch
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany
| | - Rebecca Roth
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany
| | - Kija Shah-Hosseini
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany
| | - Felix Dewald
- Institute of Virology, Medical Faculty and University Hospital of Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935, Cologne, Germany
| | - Claudia Müller
- Institute of Virology, Medical Faculty and University Hospital of Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935, Cologne, Germany
| | - Luise Stach von Goltzheim
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany
| | - Clara Lehmann
- Department of Internal Medicine, Medical Faculty and University Hospital of Cologne, University of Cologne, Kerpener Str. 62, 50931, Cologne, Germany
| | | | - Anna Wolff
- Cologne Health Authority, Cologne, Germany
| | - Gerd Fätkenheuer
- Department of Internal Medicine, Medical Faculty and University Hospital of Cologne, University of Cologne, Kerpener Str. 62, 50931, Cologne, Germany
| | | | - Florian Klein
- Institute of Virology, Medical Faculty and University Hospital of Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935, Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics and Computational Biology, Medical Faculty and University Hospital of Cologne, University of Cologne, Robert-Koch-Straße 10, 50931, Cologne, Germany.
| | - Florian Neuhann
- Cologne Health Authority, Cologne, Germany
- Heidelberg Institute of Global Health, University Heidelberg, Heidelberg, Germany
- School of Medicine and Clinical Sciences, Levy Mwanawasa Medical University, Lusaka, Zambia
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139
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Espenhain L, Tribler S, Sværke Jørgensen C, Holm Hansen C, Wolff Sönksen U, Ethelberg S. Prevalence of SARS-CoV-2 antibodies in Denmark: nationwide, population-based seroepidemiological study. Eur J Epidemiol 2021; 36:715-725. [PMID: 34420152 PMCID: PMC8380416 DOI: 10.1007/s10654-021-00796-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/04/2021] [Indexed: 12/23/2022]
Abstract
Seroprevalence studies have proven an important tool to monitor the progression of the coronavirus disease 2019 (COVID-19) pandemic. We present results of consecutive population-based seroprevalence surveys performed in Denmark in 2020. In spring, late summer and autumn/winter of 2020, invitation letters including a questionnaire covering symptoms were sent to representative samples of the population above 12 years and to parents of children below 18 years in the sample. Blood samples were analysed for total Ig and seroprevalence estimates per population segment were calculated and compared to other surveillance parameters. Based on 34 081 participants (participation rate 33%), seroprevalence estimates increased from 1.2% (95%CI: 0.3-1.9%) in May to 4.1% (95%CI: 3.1-4.9%) in December 2020. Seroprevalence estimates were roughly three times higher in those aged 12-29 years compared to 65 + and higher in metropolitan municipalities. By December 2020, 1.5% of the population had tested positive by RT-PCR. Infected individuals in older age groups were hospitalised several fold more often than in younger. Amongst seropositives, loss of taste/smell were the more specific symptoms, 32-56% did not report any symptoms. In more than half of seroconverted families, we did not see evidence of transmission between generations. Seroprevalence increased during 2020; adolescents were primarily infected in the autumn/winter. Denmark has a high per capita test rate; roughly one undiagnosed infection of SARS-CoV-2 were estimated to occur for each diagnosed case. Approximately half were asymptomatically infected. The epidemic appears to have progressed relatively modestly during 2020 in Denmark.
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Affiliation(s)
- Laura Espenhain
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark.
| | - Siri Tribler
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Charlotte Sværke Jørgensen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Christian Holm Hansen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Ute Wolff Sönksen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
- Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014, Copenhagen K, Denmark
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140
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Pană BC, Lopes H, Furtunescu F, Franco D, Rapcea A, Stanca M, Tănase A, Coliţă A. Real-World Evidence: The Low Validity of Temperature Screening for COVID-19 Triage. Front Public Health 2021; 9:672698. [PMID: 34277541 PMCID: PMC8277959 DOI: 10.3389/fpubh.2021.672698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
Background: The COVID-19 pandemic forced health-related organizations to rapidly launch country-wide procedures that were easy to use and inexpensive. Body temperature measurement with non-contact infrared thermometers (NCITs) is among the most common procedures, both in hospital settings and in many other entities. However, practical hospital experiences have raised great doubts about the procedure's validity. Aim: This study aimed to evaluate the validity of the body temperature measured using NCITs among oncological and transplant patients who took the polymerase chain reaction test for SARS-Cov-2 PCR+ and PCR- in a Romanian Hospital. Methods: Body temperature was measured for 5,231 inpatients using NCITs. The cutoff point for fever was equal to or above 37.3°C. Patients then completed a questionnaire about their symptoms, contact, and travel history. Findings: Fever was detected in five of 53 persons with PCR+, resulting in a sensitivity of 9.43% (95% CI, 3.13-20.66%). No fever was verified in 5,131 of 5,171 persons with PCR-, resulting in a specificity of 99.15% (95% CI, 98.86-99.38%). A defensive vision of NCIT procedure (maximum standard error only in favor) had a sensitivity of 15.09% (95% CI, 6.75-27.59%). Conclusions: The use of NCITs in a triage provides little value for detection of COVID-19. Moreover, it provides a false sense of protection against the disease while possibly discriminating individuals that could present fever due to other reasons, such as oncologic treatments, where fever is a common therapeutical consequence. The consumption of qualified human resources should be considered, especially in the context of the shortage of healthcare professionals worldwide.
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Affiliation(s)
- Bogdan C. Pană
- Department of Public Health, University of Medicine and Pharmacy Carol Davila Bucharest, Bucharest, Romania
| | - Henrique Lopes
- Public Health Unit, Institute of Health Sciences, Universidade Católica Portuguesa (Catholic University of Portugal), Lisbon, Portugal
| | - Florentina Furtunescu
- Department of Public Health, University of Medicine and Pharmacy Carol Davila Bucharest, Bucharest, Romania
| | - Diogo Franco
- Public Health Unit, Institute of Health Sciences, Universidade Católica Portuguesa (Catholic University of Portugal), Lisbon, Portugal
| | - Anca Rapcea
- Department of Public Health, University of Medicine and Pharmacy Carol Davila Bucharest, Bucharest, Romania
| | - Mihai Stanca
- Department of Public Health, University of Medicine and Pharmacy Carol Davila Bucharest, Bucharest, Romania
| | - Alina Tănase
- Bone Marrow Transplantation Unit, Fundeni Clinical Institute, Bucharest, Romania
| | - Anca Coliţă
- Department of Pediatrics, University of Medicine and Pharmacy Carol Davila Bucharest, Bucharest, Romania
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141
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Bobrovitz N, Arora RK, Cao C, Boucher E, Liu M, Donnici C, Yanes-Lane M, Whelan M, Perlman-Arrow S, Chen J, Rahim H, Ilincic N, Segal M, Duarte N, Van Wyk J, Yan T, Atmaja A, Rocco S, Joseph A, Penny L, Clifton DA, Williamson T, Yansouni CP, Evans TG, Chevrier J, Papenburg J, Cheng MP. Global seroprevalence of SARS-CoV-2 antibodies: A systematic review and meta-analysis. PLoS One 2021; 16:e0252617. [PMID: 34161316 PMCID: PMC8221784 DOI: 10.1371/journal.pone.0252617] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/18/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Many studies report the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. We aimed to synthesize seroprevalence data to better estimate the level and distribution of SARS-CoV-2 infection, identify high-risk groups, and inform public health decision making. METHODS In this systematic review and meta-analysis, we searched publication databases, preprint servers, and grey literature sources for seroepidemiological study reports, from January 1, 2020 to December 31, 2020. We included studies that reported a sample size, study date, location, and seroprevalence estimate. We corrected estimates for imperfect test accuracy with Bayesian measurement error models, conducted meta-analysis to identify demographic differences in the prevalence of SARS-CoV-2 antibodies, and meta-regression to identify study-level factors associated with seroprevalence. We compared region-specific seroprevalence data to confirmed cumulative incidence. PROSPERO: CRD42020183634. RESULTS We identified 968 seroprevalence studies including 9.3 million participants in 74 countries. There were 472 studies (49%) at low or moderate risk of bias. Seroprevalence was low in the general population (median 4.5%, IQR 2.4-8.4%); however, it varied widely in specific populations from low (0.6% perinatal) to high (59% persons in assisted living and long-term care facilities). Median seroprevalence also varied by Global Burden of Disease region, from 0.6% in Southeast Asia, East Asia and Oceania to 19.5% in Sub-Saharan Africa (p<0.001). National studies had lower seroprevalence estimates than regional and local studies (p<0.001). Compared to Caucasian persons, Black persons (prevalence ratio [RR] 3.37, 95% CI 2.64-4.29), Asian persons (RR 2.47, 95% CI 1.96-3.11), Indigenous persons (RR 5.47, 95% CI 1.01-32.6), and multi-racial persons (RR 1.89, 95% CI 1.60-2.24) were more likely to be seropositive. Seroprevalence was higher among people ages 18-64 compared to 65 and over (RR 1.27, 95% CI 1.11-1.45). Health care workers in contact with infected persons had a 2.10 times (95% CI 1.28-3.44) higher risk compared to health care workers without known contact. There was no difference in seroprevalence between sex groups. Seroprevalence estimates from national studies were a median 18.1 times (IQR 5.9-38.7) higher than the corresponding SARS-CoV-2 cumulative incidence, but there was large variation between Global Burden of Disease regions from 6.7 in South Asia to 602.5 in Sub-Saharan Africa. Notable methodological limitations of serosurveys included absent reporting of test information, no statistical correction for demographics or test sensitivity and specificity, use of non-probability sampling and use of non-representative sample frames. DISCUSSION Most of the population remains susceptible to SARS-CoV-2 infection. Public health measures must be improved to protect disproportionately affected groups, including racial and ethnic minorities, until vaccine-derived herd immunity is achieved. Improvements in serosurvey design and reporting are needed for ongoing monitoring of infection prevalence and the pandemic response.
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Affiliation(s)
- Niklas Bobrovitz
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Critical Care Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Rahul Krishan Arora
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Christian Cao
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Emily Boucher
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael Liu
- Department of Social Policy and Intervention, University of Oxford, Oxford, United Kingdom
| | - Claire Donnici
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Mairead Whelan
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sara Perlman-Arrow
- School of Population and Global Health, McGill University, Montreal, Quebec, Canada
| | - Judy Chen
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Hannah Rahim
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Natasha Ilincic
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mitchell Segal
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nathan Duarte
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Jordan Van Wyk
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Tingting Yan
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Austin Atmaja
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Simona Rocco
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Abel Joseph
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Lucas Penny
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David A. Clifton
- Department of Critical Care Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Cedric P. Yansouni
- JD MacLean Centre for Tropical Diseases, McGill University, Montreal, Quebec, Canada
- Divisions of Infectious Diseases and Medical Microbiology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Timothy Grant Evans
- School of Population and Global Health, McGill University, Montreal, Quebec, Canada
| | - Jonathan Chevrier
- Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Jesse Papenburg
- Division of Pediatric Infectious Diseases, Department of Pediatrics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Matthew P. Cheng
- Divisions of Infectious Diseases and Medical Microbiology, McGill University Health Centre, Montreal, Quebec, Canada
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Kaimann D, Tanneberg I. What containment strategy leads us through the pandemic crisis? An empirical analysis of the measures against the COVID-19 pandemic. PLoS One 2021; 16:e0253237. [PMID: 34153058 PMCID: PMC8216519 DOI: 10.1371/journal.pone.0253237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022] Open
Abstract
Since January 2020, the COVID-19 outbreak has been progressing at a rapid pace. To keep the pandemic at bay, countries have implemented various measures to interrupt the transmission of the virus from person to person and prevent an overload of their health systems. We analyze the impact of these measures implemented against the COVID-19 pandemic by using a sample of 68 countries, Puerto Rico and the 50 federal states of the United States of America, four federal states of Australia, and eight federal states of Canada, involving 6,941 daily observations. We show that measures are essential for containing the spread of the COVID-19 pandemic. After controlling for daily COVID-19 tests, we find evidence to suggest that school closures, shut-downs of non-essential business, mass gathering bans, travel restrictions in and out of risk areas, national border closures and/or complete entry bans, and nationwide curfews decrease the growth rate of the coronavirus and thus the peak of daily confirmed cases. We also find evidence to suggest that combinations of these measures decrease the daily growth rate at a level outweighing that of individual measures. Consequently, and despite extensive vaccinations, we contend that the implemented measures help contain the spread of the COVID-19 pandemic and ease the overstressed capacity of the healthcare systems.
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Affiliation(s)
- Daniel Kaimann
- Department of Management, Paderborn University, Paderborn, Germany
| | - Ilka Tanneberg
- Department of Management, Paderborn University, Paderborn, Germany
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143
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Murad D, Chandrasekaran S, Pillai A, Garner OB, Denny CT. SARS-CoV-2 Infection Detection by PCR and Serologic Testing in Clinical Practice. J Clin Microbiol 2021; 59:e0043121. [PMID: 33903168 PMCID: PMC8218740 DOI: 10.1128/jcm.00431-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/23/2021] [Indexed: 11/20/2022] Open
Abstract
Patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be diagnosed by PCR during acute infection or later in their clinical course by detection of virus-specific antibodies. While in theory complementary, both PCR and serologic tests have practical shortcomings. A retrospective study was performed in order to further define these limitations in a clinical context and to determine how to best utilize these tests in a coherent fashion. A total of 3,075 patients underwent both PCR and serology tests at University of California, Los Angeles (UCLA), in the study period. Among these, 2,731 (89%) had no positive tests at all, 73 (2%) had a positive PCR test and only negative serology tests, 144 (5%) had a positive serology test and only negative PCR tests, and 127 (4%) had positive PCR and serology tests. Approximately half of the patients with discordant results (i.e., PCR positive and serology negative or vice versa) had mistimed tests in reference to the course of their disease. PCR-positive patients who were asymptomatic or pregnant were less likely to generate a detectable humoral immune response to SARS-CoV-2. On a quantitative level, the log number of days between symptom onset and PCR test was positively correlated with cycle threshold (CT) values. However, there was no apparent relationship between PCR CT and serologic (arbitrary units per milliliter) results.
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Affiliation(s)
- Douglas Murad
- Department of Medicine/Department of Information Services and Solutions, David Geffen School of Medicine at UCLA, University of California at Los Angeles Medical Center, Los Angeles, California, USA
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ajaya Pillai
- UCLA Health Information Technology, Los Angeles, California, USA
| | - Omai B. Garner
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Christopher T. Denny
- Division of Hematology/Oncology, Department of Pediatrics, Gwynne Hazen Cherry Memorial Laboratories, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California, Los Angeles, California, USA
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144
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Hurford A, Rahman P, Loredo-Osti JC. Modelling the impact of travel restrictions on COVID-19 cases in Newfoundland and Labrador. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202266. [PMID: 34150314 PMCID: PMC8206704 DOI: 10.1098/rsos.202266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/03/2021] [Indexed: 05/26/2023]
Abstract
In many jurisdictions, public health authorities have implemented travel restrictions to reduce coronavirus disease 2019 (COVID-19) spread. Policies that restrict travel within countries have been implemented, but the impact of these restrictions is not well known. On 4 May 2020, Newfoundland and Labrador (NL) implemented travel restrictions such that non-residents required exemptions to enter the province. We fit a stochastic epidemic model to data describing the number of active COVID-19 cases in NL from 14 March to 26 June. We predicted possible outbreaks over nine weeks, with and without the travel restrictions, and for contact rates 40-70% of pre-pandemic levels. Our results suggest that the travel restrictions reduced the mean number of clinical COVID-19 cases in NL by 92%. Furthermore, without the travel restrictions there is a substantial risk of very large outbreaks. Using epidemic modelling, we show how the NL COVID-19 outbreak could have unfolded had the travel restrictions not been implemented. Both physical distancing and travel restrictions affect the local dynamics of the epidemic. Our modelling shows that the travel restrictions are a plausible reason for the few reported COVID-19 cases in NL after 4 May.
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Affiliation(s)
- Amy Hurford
- Department of Biology, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
- Department of Mathematics and Statistics, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
| | - Proton Rahman
- Faculty of Medicine, Memorial University, St John's, Newfoundland and Labrador, Canada A1C 5B8
| | - J. Concepción Loredo-Osti
- Department of Mathematics and Statistics, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
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145
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Griffin BD, Chan M, Tailor N, Mendoza EJ, Leung A, Warner BM, Duggan AT, Moffat E, He S, Garnett L, Tran KN, Banadyga L, Albietz A, Tierney K, Audet J, Bello A, Vendramelli R, Boese AS, Fernando L, Lindsay LR, Jardine CM, Wood H, Poliquin G, Strong JE, Drebot M, Safronetz D, Embury-Hyatt C, Kobasa D. SARS-CoV-2 infection and transmission in the North American deer mouse. Nat Commun 2021; 12:3612. [PMID: 34127676 PMCID: PMC8203675 DOI: 10.1038/s41467-021-23848-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Widespread circulation of SARS-CoV-2 in humans raises the theoretical risk of reverse zoonosis events with wildlife, reintroductions of SARS-CoV-2 into permissive nondomesticated animals. Here we report that North American deer mice (Peromyscus maniculatus) are susceptible to SARS-CoV-2 infection following intranasal exposure to a human isolate, resulting in viral replication in the upper and lower respiratory tract with little or no signs of disease. Further, shed infectious virus is detectable in nasal washes, oropharyngeal and rectal swabs, and viral RNA is detectable in feces and occasionally urine. We further show that deer mice are capable of transmitting SARS-CoV-2 to naïve deer mice through direct contact. The extent to which these observations may translate to wild deer mouse populations remains unclear, and the risk of reverse zoonosis and/or the potential for the establishment of Peromyscus rodents as a North American reservoir for SARS-CoV-2 remains unknown.
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Affiliation(s)
- Bryan D Griffin
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Mable Chan
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nikesh Tailor
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Emelissa J Mendoza
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Anders Leung
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Bryce M Warner
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ana T Duggan
- Science Technology Cores and Services, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Estella Moffat
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Shihua He
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lauren Garnett
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kaylie N Tran
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Logan Banadyga
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Alixandra Albietz
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kevin Tierney
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jonathan Audet
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Alexander Bello
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Robert Vendramelli
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Amrit S Boese
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lisa Fernando
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - L Robbin Lindsay
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Claire M Jardine
- Department of Pathobiology, Canadian Wildlife Health Cooperative, Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Heidi Wood
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Guillaume Poliquin
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Pediatrics & Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Office of the Scientific Director, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - James E Strong
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Pediatrics & Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Michael Drebot
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - David Safronetz
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Carissa Embury-Hyatt
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Darwyn Kobasa
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
- Department of Medical Microbiology and Infectious Diseases, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.
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146
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Campos EL, Cysne RP, Madureira AL, Mendes GL. Multi-generational SIR modeling: Determination of parameters, epidemiological forecasting and age-dependent vaccination policies. Infect Dis Model 2021; 6:751-765. [PMID: 34127952 PMCID: PMC8189834 DOI: 10.1016/j.idm.2021.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 02/08/2023] Open
Abstract
We use an age-dependent SIR system of equations to model the evolution of the COVID-19. Parameters that measure the amount of interaction in different locations (home, work, school, other) are approximated from in-sample data using a random optimization scheme, and indicate changes in social distancing along the course of the pandemic. That allows the estimation of the time evolution of classical and age-dependent reproduction numbers. With those parameters we predict the disease dynamics, and compare our results with out-of-sample data from the City of Rio de Janeiro. Finally, we provide a numerical investigation regarding age-based vaccination policies, shedding some light on whether is preferable to vaccinate those at most risk (the elderly) or those who spread the disease the most (the youngest). There is no clear upshot, as the results depend on the age of those immunized, contagious parameters, vaccination schedules and efficiency.
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Affiliation(s)
- Eduardo Lima Campos
- EPGE Brazilian School of Economics and Finance (FGV EPGE), Rio de Janeiro, RJ, Brazil
- ENCE - Escola Nacional de Ciências Estatísticas (ENCE/IBGE), Rio de Janeiro, RJ, Brazil
| | - Rubens Penha Cysne
- EPGE Brazilian School of Economics and Finance (FGV EPGE), Rio de Janeiro, RJ, Brazil
| | - Alexandre L. Madureira
- EPGE Brazilian School of Economics and Finance (FGV EPGE), Rio de Janeiro, RJ, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Gélcio L.Q. Mendes
- INCA - Brazilian National Cancer Institute, Coordination of Assistance, Rio de Janeiro, RJ, Brazil
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147
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Dereschuk K, Apostol L, Ranjan I, Chakladar J, Li WT, Rajasekaran M, Chang EY, Ongkeko WM. Identification of Lung and Blood Microbiota Implicated in COVID-19 Prognosis. Cells 2021; 10:1452. [PMID: 34200572 PMCID: PMC8226556 DOI: 10.3390/cells10061452] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/25/2022] Open
Abstract
The implications of the microbiome on Coronavirus disease 2019 (COVID-19) prognosis has not been thoroughly studied. In this study we aimed to characterize the lung and blood microbiome and their implication on COVID-19 prognosis through analysis of peripheral blood mononuclear cell (PBMC) samples, lung biopsy samples, and bronchoalveolar lavage fluid (BALF) samples. In all three tissue types, we found panels of microbes differentially abundant between COVID-19 and normal samples correlated to immune dysregulation and upregulation of inflammatory pathways, including key cytokine pathways such as interleukin (IL)-2, 3, 5-10 and 23 signaling pathways and downregulation of anti-inflammatory pathways including IL-4 signaling. In the PBMC samples, six microbes were correlated with worse COVID-19 severity, and one microbe was correlated with improved COVID-19 severity. Collectively, our findings contribute to the understanding of the human microbiome and suggest interplay between our identified microbes and key inflammatory pathways which may be leveraged in the development of immune therapies for treating COVID-19 patients.
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Affiliation(s)
- Kypros Dereschuk
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Lauren Apostol
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Ishan Ranjan
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Mahadevan Rajasekaran
- Department of Urology, University of California San Diego, La Jolla, CA 92093, USA;
- Urology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Eric Y. Chang
- Department of Radiology, University of California, San Diego, CA 92093, USA;
- Radiology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Weg M. Ongkeko
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, CA 92093, USA; (K.D.); (L.A.); (I.R.); (J.C.); (W.T.L.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
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148
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Koller G, Morrell AP, Galão RP, Pickering S, MacMahon E, Johnson J, Ignatyev K, Neil SJD, Elsharkawy S, Fleck R, Machado PMP, Addison O. More than the Eye Can See: Shedding New Light on SARS-CoV-2 Lateral Flow Device-Based Immunoassays. ACS APPLIED MATERIALS & INTERFACES 2021; 13:25694-25700. [PMID: 34048220 PMCID: PMC8188736 DOI: 10.1021/acsami.1c04283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Containing the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been an unprecedented challenge due to high horizontal transmissivity and asymptomatic carriage rates. Lateral flow device (LFD) immunoassays were introduced in late 2020 to detect SARS-CoV-2 infection in asymptomatic or presymptomatic individuals rapidly. While LFD technologies have been used for over 60 years, their widespread use as a public health tool during a pandemic is unprecedented. By the end of 2020, data from studies into the efficacy of the LFDs emerged and showed these point-of-care devices to have very high specificity (ability to identify true negatives) but inadequate sensitivity with high false-negative rates. The low sensitivity (<50%) shown in several studies is a critical public health concern, as asymptomatic or presymptomatic carriers may wrongly be assumed to be noninfectious, posing a significant risk of further spread in the community. Here, we show that the direct visual readout of SARS-CoV-2 LFDs is an inadequate approach to discriminate a potentially infective viral concentration in a biosample. We quantified significant immobilized antigen-antibody-labeled conjugate complexes within the LFDs visually scored as negative using high-sensitivity synchrotron X-ray fluorescence imaging. Correlating quantitative X-ray fluorescence measurements and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) determined numbers of viral copies, we identified that negatively scored samples could contain up to 100 PFU (equivalent here to ∼10 000 RNA copies/test). The study demonstrates where the shortcomings arise in many of the current direct-readout SARS-CoV-2 LFDs, namely, being a deficiency in the readout as opposed to the potential level of detection of the test, which is orders of magnitude higher. The present findings are of importance both to public health monitoring during the Coronavirus Disease 2019 (COVID-19) pandemic and to the rapid refinement of these tools for immediate and future applications.
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Affiliation(s)
- Garrit Koller
- Centre
for Host Microbiome Interactions, Faculty of Dentistry, Oral &
Craniofacial Sciences, Kingʼs College
London, London, SE1 9RT, United Kingdom
| | - Alexander P. Morrell
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
| | - Rui Pedro Galão
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Suzanne Pickering
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Eithne MacMahon
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
- Guyʼs
and St Thomasʼ NHS Foundation Trust, London SE1 9RT, United Kingdom
| | - Joanna Johnson
- Guyʼs
and St Thomasʼ NHS Foundation Trust, London SE1 9RT, United Kingdom
| | | | - Stuart J. D. Neil
- Department
of Infectious Diseases, School of Immunology & Microbial Sciences, Kingʼs College London, London SE1 9RT, United Kingdom
| | - Sherif Elsharkawy
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
| | - Roland Fleck
- Centre for
Ultrastructural Imaging, Kingʼs College
London, London SE1 9RT, United Kingdom
| | | | - Owen Addison
- Centre
for Oral, Clinical & Translational Sciences, Faculty of Dentistry,
Oral & Craniofacial Sciences, Kingʼs
College London, London SE1 9RT, United Kingdom.
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149
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Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI, Park SK. Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study. Microorganisms 2021; 9:1237. [PMID: 34200249 PMCID: PMC8228238 DOI: 10.3390/microorganisms9061237] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/08/2023] Open
Abstract
Patients with COVID-19 have been reported to experience gastrointestinal symptoms as well as respiratory symptoms, but the effects of COVID-19 on the gut microbiota are poorly understood. We explored gut microbiome profiles associated with the respiratory infection of SARS-CoV-2 during the recovery phase in patients with asymptomatic or mild COVID-19. A longitudinal analysis was performed using the same patients to determine whether the gut microbiota changed after recovery from COVID-19. We applied 16S rRNA amplicon sequencing to analyze two paired fecal samples from 12 patients with asymptomatic or mild COVID-19. Fecal samples were selected at two time points: during SARS-CoV-2 infection (infected state) and after negative conversion of the viral RNA (recovered state). We also compared the microbiome data with those from 36 healthy controls. Microbial evenness of the recovered state was significantly increased compared with the infected state. SARS-CoV-2 infection induced the depletion of Bacteroidetes, while an abundance was observed with a tendency to rapidly reverse in the recovered state. The Firmicutes/Bacteroidetes ratio in the infected state was markedly higher than that in the recovered state. Gut dysbiosis was observed after infection even in patients with asymptomatic or mild COVID-19, while the composition of the gut microbiota was recovered after negative conversion of SARS-CoV-2 RNA. Modifying intestinal microbes in response to COVID-19 might be a useful therapeutic alternative.
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Affiliation(s)
- Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03181, Korea
| | - Eun-Jeong Joo
- Division of Infectious Diseases, Department of Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
| | - Chil-Woo Lee
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystems Inc., Daejeon 34129, Korea;
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07985, Korea;
| | - Dong-Il Park
- Division of Gastroenterology, Department of Medicine, School of Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul 03181, Korea
| | - Soo-Kyung Park
- Division of Gastroenterology, Department of Medicine, School of Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul 03181, Korea
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150
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Andalibi A, Koizumi N, Li MH, Siddique AB. Symptom and Age Homophilies in SARS-CoV-2 Transmission Networks during the Early Phase of the Pandemic in Japan. BIOLOGY 2021; 10:499. [PMID: 34205133 PMCID: PMC8228521 DOI: 10.3390/biology10060499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 01/08/2023]
Abstract
Kanagawa and Hokkaido were affected by COVID-19 in the early stage of the pandemic. Japan's initial response included contact tracing and PCR analysis on anyone who was suspected of having been exposed to SARS-CoV-2. In this retrospective study, we analyzed publicly available COVID-19 registry data from Kanagawa and Hokkaido (n = 4392). Exponential random graph model (ERGM) network analysis was performed to examine demographic and symptomological homophilies. Age, symptomatic, and asymptomatic status homophilies were seen in both prefectures. Symptom homophilies suggest that nuanced genetic differences in the virus may affect its epithelial cell type range and can result in the diversity of symptoms seen in individuals infected by SARS-CoV-2. Environmental variables such as temperature and humidity may also play a role in the overall pathogenesis of the virus. A higher level of asymptomatic transmission was observed in Kanagawa. Moreover, patients who contracted the virus through secondary or tertiary contacts were shown to be asymptomatic more frequently than those who contracted it from primary cases. Additionally, most of the transmissions stopped at the primary and secondary levels. As expected, significant viral transmission was seen in healthcare settings.
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Affiliation(s)
- Ali Andalibi
- College of Science, George Mason University, Fairfax, VA 22030, USA;
| | - Naoru Koizumi
- Schar School of Policy and Government, George Mason University, Arlington, VA 22201, USA; (M.-H.L.); (A.B.S.)
| | - Meng-Hao Li
- Schar School of Policy and Government, George Mason University, Arlington, VA 22201, USA; (M.-H.L.); (A.B.S.)
| | - Abu Bakkar Siddique
- Schar School of Policy and Government, George Mason University, Arlington, VA 22201, USA; (M.-H.L.); (A.B.S.)
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