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Viloria Winnett A, Stenzel T, Ismagilov RF. Validating combination throat-nasal swabs for COVID-19 tests would improve early detection, especially for the most vulnerable. Clin Infect Dis 2024:ciae381. [PMID: 39041943 DOI: 10.1093/cid/ciae381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/09/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Abstract
Early detection of severe acute respiratory syndrome coronavirus 2 infection by diagnostic tests can prompt actions to reduce transmission and improve treatment efficacy, especially for vulnerable groups such as immunocompromised individuals. Recent evidence suggests that sampling the throat in addition to the nose improves clinical sensitivity during early infection for both antigen and molecular coronavirus disease 2019 tests. We urge test manufacturers to validate tests for use with throat swab, in combination with nasal swabs.
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Affiliation(s)
- Alexander Viloria Winnett
- California Institute of Technology, Division of Chemistry and Chemical Engineering; Division of Biology & Biological Engineering; Pasadena, CA, USA
- University of California Los Angeles - California Institute of Technology Medical Scientist Training Program, Los Angeles, CA, USA
| | - Timothy Stenzel
- Former Director, Office of In Vitro Diagnostics, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Rustem F Ismagilov
- California Institute of Technology, Division of Chemistry and Chemical Engineering; Division of Biology & Biological Engineering; Pasadena, CA, USA
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2
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Collin A, Hejblum BP, Vignals C, Lehot L, Thiébaut R, Moireau P, Prague M. Using a population-based Kalman estimator to model the COVID-19 epidemic in France: estimating associations between disease transmission and non-pharmaceutical interventions. Int J Biostat 2024; 20:13-41. [PMID: 36607837 DOI: 10.1515/ijb-2022-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/08/2022] [Indexed: 01/07/2023]
Abstract
In response to the COVID-19 pandemic caused by SARS-CoV-2, governments have adopted a wide range of non-pharmaceutical interventions (NPI). These include stringent measures such as strict lockdowns, closing schools, bars and restaurants, curfews, and barrier gestures such as mask-wearing and social distancing. Deciphering the effectiveness of each NPI is critical to responding to future waves and outbreaks. To this end, we first develop a dynamic model of the French COVID-19 epidemics over a one-year period. We rely on a global extended Susceptible-Infectious-Recovered (SIR) mechanistic model of infection that includes a dynamic transmission rate over time. Multilevel data across French regions are integrated using random effects on the parameters of the mechanistic model, boosting statistical power by multiplying integrated observation series. We estimate the parameters using a new population-based statistical approach based on a Kalman filter, used for the first time in analysing real-world data. We then fit the estimated time-varying transmission rate using a regression model that depends on the NPIs while accounting for vaccination coverage, the occurrence of variants of concern (VoC), and seasonal weather conditions. We show that all NPIs considered have an independent significant association with transmission rates. In addition, we show a strong association between weather conditions that reduces transmission in summer, and we also estimate increased transmissibility of VoC.
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Affiliation(s)
- Annabelle Collin
- Inria, Inria Bordeaux - Sud-Ouest, Bordeaux INP, IMB UMR 5251, Université Bordeaux, Talence, France
| | - Boris P Hejblum
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
| | - Carole Vignals
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
- CHU Pellegrin, F-33000 Bordeaux, France
| | - Laurent Lehot
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
| | - Rodolphe Thiébaut
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
- CHU Pellegrin, F-33000 Bordeaux, France
| | - Philippe Moireau
- ISPED Inserm U1219 Bordeaux Population Health Bureau 23 146 rue Leo Saignat CS 61292 33076 Bordeaux Cedex, France
| | - Mélanie Prague
- Inria, Inria Saclay-Ile de France, France and LMS, CNRS UMR 7649, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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3
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Cuevas-Maraver J, Kevrekidis PG, Chen QY, Kevrekidis GA, Drossinos Y. Vaccination compartmental epidemiological models for the delta and omicron SARS-CoV-2 variants. Math Biosci 2024; 367:109109. [PMID: 37981262 DOI: 10.1016/j.mbs.2023.109109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/14/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
We explore the inclusion of vaccination in compartmental epidemiological models concerning the delta and omicron variants of the SARS-CoV-2 virus that caused the COVID-19 pandemic. We expand on our earlier compartmental-model work by incorporating vaccinated populations. We present two classes of models that differ depending on the immunological properties of the variant. The first one is for the delta variant, where we do not follow the dynamics of the vaccinated individuals since infections of vaccinated individuals were rare. The second one for the far more contagious omicron variant incorporates the evolution of the infections within the vaccinated cohort. We explore comparisons with available data involving two possible classes of counts, fatalities and hospitalizations. We present our results for two regions, Andalusia and Switzerland (including the Principality of Liechtenstein), where the necessary data are available. In the majority of the considered cases, the models are found to yield good agreement with the data and have a reasonable predictive capability beyond their training window, rendering them potentially useful tools for the interpretation of the COVID-19 and further pandemic waves, and for the design of intervention strategies during these waves.
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Affiliation(s)
- J Cuevas-Maraver
- Grupo de Física No Lineal, Departamento de Física Aplicada I, Universidad de Sevilla. Escuela Politécnica Superior, C/ Virgen de África, 7, 41011 Sevilla, Spain; Instituto de Matemáticas de la Universidad de Sevilla (IMUS), Edificio Celestino Mutis. Avda. Reina Mercedes s/n, 41012 Sevilla, Spain.
| | - P G Kevrekidis
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Q Y Chen
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - G A Kevrekidis
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA; Los Alamos National Laboratory, Los Alamos, NM, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore MD, USA
| | - Y Drossinos
- Thermal Hydraulics & Multiphase Flow Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, N.C.S.R. "Demokritos", GR 15341, Agia Paraskevi, Greece
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4
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Carazo S, Denis G, Padet L, Deshaies P, Villeneuve J, Paquet-Bolduc B, Laliberté D, Talbot D, De Serres G. SARS-CoV-2 infection among healthcare workers: the role of occupational and household exposures during the first three pandemic waves in Quebec, Canada. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e180. [PMID: 38028905 PMCID: PMC10654992 DOI: 10.1017/ash.2023.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023]
Abstract
Objective We described the evolution of SARS-CoV-2 source of infection in a cohort of healthcare workers (HCWs) of Quebec, Canada, during the first three pandemic waves. We also estimated their household secondary attack rate (SAR) and its risk factors. Design Cross-sectional surveys. Participants HCWs with a SARS-CoV-2 infection confirmed by polymerasa chain reaction and diagnosed between March 2020 and May 2021. Methods We collected demographic, clinical, vaccination, and employment information, self-reported perceived source of infection, and transmission to household members during the first three pandemic waves. SAR was calculated for households with ≥2 members where the HCW was the index case. A Poisson regression model estimated the association between risk factors and SAR. Results Among the 11,670 HCWs completing the survey, 91%, perceived their workplace as the source of infection during the first wave (March-July 2020), 71% during the second wave (July 2020-March 2021), and 40% during the third wave (March-May 2021). Conversely, HCWs reported an increasing proportion of household-acquired infections with each wave from 4% to 14% and 33%, respectively. The overall household SAR of 7,990 HCWs living with ≥1 person was 30% (95%CI: 29-30). SAR increased with the presence of symptoms, older age, and during Alpha-variant predominant period. Conclusions HCWs and their household members were largely affected during the first pandemic waves of COVID-19, but the relative importance of occupational exposure changed overtime. Pandemic preparedness in healthcare settings is essential to protect HCWs from emerging biological hazard exposures.
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Affiliation(s)
- Sara Carazo
- Biological and Occupational Risks Unit, Institut national de santé publique du Québec, Quebec City, QC, Canada
- Social and Preventive Medicine Department, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Geoffroy Denis
- School of Population and Global Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Public Health Department, CIUSSS Centre Sud de Montréal, Montreal, QC, Canada
- General Directorate of Public Health, Quebec Ministry of Health and Social Services, Quebec City, QC, Canada
| | - Lauriane Padet
- Biological and Occupational Risks Unit, Institut national de santé publique du Québec, Quebec City, QC, Canada
| | - Pierre Deshaies
- Public Health Department, CISSS de Chaudière-Appalaches, Levis, QC, Canada
| | - Jasmin Villeneuve
- Biological and Occupational Risks Unit, Institut national de santé publique du Québec, Quebec City, QC, Canada
| | - Bianka Paquet-Bolduc
- Infection Prevention and Control Unit, Institut Universitaire en cardiologie et pneumologie de Québec, Quebec City, QC, Canada
| | - Denis Laliberté
- Public Health Department, CIUSSS de la Capitale-Nationale, Quebec City, QC, Canada
| | - Denis Talbot
- Social and Preventive Medicine Department, Faculty of Medicine, Laval University, Quebec City, QC, Canada
- CHU de Québec-Laval University Research Center, Quebec City, QC, Canada
| | - Gaston De Serres
- Biological and Occupational Risks Unit, Institut national de santé publique du Québec, Quebec City, QC, Canada
- Social and Preventive Medicine Department, Faculty of Medicine, Laval University, Quebec City, QC, Canada
- CHU de Québec-Laval University Research Center, Quebec City, QC, Canada
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5
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Marinov TT, Marinova RS, Marinov RT, Shelby N. Novel Approach for Identification of Basic and Effective Reproduction Numbers Illustrated with COVID-19. Viruses 2023; 15:1352. [PMID: 37376651 DOI: 10.3390/v15061352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
This paper presents a novel numerical technique for the identification of effective and basic reproduction numbers, Re and R0, for long-term epidemics, using an inverse problem approach. The method is based on the direct integration of the SIR (Susceptible-Infectious-Removed) system of ordinary differential equations and the least-squares method. Simulations were conducted using official COVID-19 data for the United States and Canada, and for the states of Georgia, Texas, and Louisiana, for a period of two years and ten months. The results demonstrate the applicability of the method in simulating the dynamics of the epidemic and reveal an interesting relationship between the number of currently infectious individuals and the effective reproduction number, which is a useful tool for predicting the epidemic dynamics. For all conducted experiments, the results show that the local maximum (and minimum) values of the time-dependent effective reproduction number occur approximately three weeks before the local maximum (and minimum) values of the number of currently infectious individuals. This work provides a novel and efficient approach for the identification of time-dependent epidemics parameters.
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Affiliation(s)
- Tchavdar T Marinov
- Department of Natural Sciences, Southern University at New Orleans, 6801 Press Drive, New Orleans, LA 70126, USA
| | - Rossitza S Marinova
- Department of Mathematical & Physical Sciences, Concordia University of Edmonton, 7128 Ada Boulevard, Edmonton, AB T5B 4E4, Canada
- Department Computer Science, Varna Free University, 9007 Varna, Bulgaria
| | - Radoslav T Marinov
- Rescale, 33 New Montgomery Street, Suite 950, San Francisco, CA 94105, USA
| | - Nicci Shelby
- Department of Natural Sciences, Southern University at New Orleans, 6801 Press Drive, New Orleans, LA 70126, USA
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6
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Wanelik KM, Begon M, Fenton A, Norman RA, Beldomenico PM. Positive feedback loops exacerbate the influence of superspreaders in disease transmission. iScience 2023; 26:106618. [PMID: 37250299 PMCID: PMC10214397 DOI: 10.1016/j.isci.2023.106618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/13/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Superspreaders are recognized as being important drivers of disease spread. However, models to date have assumed random occurrence of superspreaders, irrespective of whom they were infected by. Evidence suggests though that those individuals infected by superspreaders may be more likely to become superspreaders themselves. Here, we begin to explore, theoretically, the effects of such a positive feedback loop on (1) the final epidemic size, (2) the herd immunity threshold, (3) the basic reproduction number, R0, and (4) the peak prevalence of superspreaders, using a generic model for a hypothetical acute viral infection and illustrative parameter values. We show that positive feedback loops can have a profound effect on our chosen epidemic outcomes, even when the transmission advantage of superspreaders is moderate, and despite peak prevalence of superspreaders remaining low. We argue that positive superspreader feedback loops in different infectious diseases, including SARS-CoV-2, should be investigated further, both theoretically and empirically.
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Affiliation(s)
- Klara M. Wanelik
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Mike Begon
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andy Fenton
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rachel A. Norman
- Department of Computing Science and Mathematics, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Pablo M. Beldomenico
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (Consejo de Investigaciones Científicas y Técnicas - Universidad Nacional del Litoral), Esperanza, Argentina
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7
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Palmore TN, Henderson DK. For Patient Safety, It Is Not Time to Take Off Masks in Health Care Settings. Ann Intern Med 2023. [PMID: 37186917 DOI: 10.7326/m23-1190] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Affiliation(s)
- Tara N Palmore
- George Washington University School of Medicine and Health Sciences, Washington, DC (T.N.P.)
| | - David K Henderson
- Clinical Center, National Institutes of Health, Bethesda, Maryland (D.K.H.)
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8
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Tjaden AH, Edelstein SL, Ahmed N, Calamari L, Dantuluri KL, Gibbs M, Hinkelman A, Mongraw‐Chaffin M, Sanders JW, Saydah S, Plumb ID. Association between COVID-19 and consistent mask wearing during contact with others outside the household-A nested case-control analysis, November 2020-October 2021. Influenza Other Respir Viruses 2023; 17:e13080. [PMID: 36606308 PMCID: PMC9835433 DOI: 10.1111/irv.13080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Face masks have been recommended to reduce SARS-CoV-2 transmission. However, evidence of the individual benefit of face masks remains limited, including by vaccination status. METHODS As part of the COVID-19 Community Research Partnership cohort study, we performed a nested case-control analysis to assess the association between self-reported consistent mask use during contact with others outside the household and subsequent odds of symptomatic SARS-CoV-2 infection (COVID-19) during November 2020-October 2021. Using conditional logistic regression, we compared 359 case-participants to 3544 control-participants who were matched by date, adjusting for enrollment site, age group, sex, race/ethnicity, urban/rural county classification, and healthcare worker occupation. RESULTS COVID-19 was associated with not consistently wearing a mask (adjusted odds ratio [aOR] 1.49; 95% confidence interval [CI] [1.14, 1.95]). Compared with persons ≥14 days after mRNA vaccination who also reported always wearing a mask, COVID-19 was associated with being unvaccinated (aOR 5.94; 95% CI [3.04, 11.62]), not wearing a mask (aOR 1.62; 95% CI [1.07, 2.47]), or both unvaccinated and not wearing a mask (aOR 9.07; 95% CI [4.81, 17.09]). CONCLUSIONS Our findings indicate that consistent mask wearing can complement vaccination to reduce the risk of COVID-19.
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Affiliation(s)
- Ashley H. Tjaden
- Milken Institute School of Public Health, Biostatistics CenterGeorge Washington UniversityRockvilleMarylandUSA
| | - Sharon L. Edelstein
- Milken Institute School of Public Health, Biostatistics CenterGeorge Washington UniversityRockvilleMarylandUSA
| | - Naheed Ahmed
- Department of Population HealthNYU Grossman School of MedicineNew York CityNew YorkUSA
| | - Lydia Calamari
- Carolinas Medical CenterAtrium HealthCharlotteNorth CarolinaUSA
| | - Keerti L. Dantuluri
- Department of Pediatrics (Infectious Diseases)Levine Children's Hospital, Atrium HealthCharlotteNorth CarolinaUSA
| | - Michael Gibbs
- Carolinas Medical CenterAtrium HealthCharlotteNorth CarolinaUSA
| | - Amy Hinkelman
- Campbell University School of Osteopathic MedicineLillingtonNorth CarolinaUSA
| | - Morgana Mongraw‐Chaffin
- Department of Epidemiology and PreventionWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - John W. Sanders
- Section on Cardiovascular Medicine, Department of MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Sharon Saydah
- U.S. Centers for Disease Control and Prevention COVID‐19 ResponseAtlantaGeorgiaUSA
| | - Ian D. Plumb
- U.S. Centers for Disease Control and Prevention COVID‐19 ResponseAtlantaGeorgiaUSA
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9
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Truszkowska A, Zino L, Butail S, Caroppo E, Jiang Z, Rizzo A, Porfiri M. Exploring a COVID-19 Endemic Scenario: High-Resolution Agent-Based Modeling of Multiple Variants. ADVANCED THEORY AND SIMULATIONS 2023; 6:2200481. [PMID: 36718198 PMCID: PMC9878004 DOI: 10.1002/adts.202200481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Indexed: 11/13/2022]
Abstract
Our efforts as a society to combat the ongoing COVID-19 pandemic are continuously challenged by the emergence of new variants. These variants can be more infectious than existing strains and many of them are also more resistant to available vaccines. The appearance of these new variants cause new surges of infections, exacerbated by infrastructural difficulties, such as shortages of medical personnel or test kits. In this work, a high-resolution computational framework for modeling the simultaneous spread of two COVID-19 variants: a widely spread base variant and a new one, is established. The computational framework consists of a detailed database of a representative U.S. town and a high-resolution agent-based model that uses the Omicron variant as the base variant and offers flexibility in the incorporation of new variants. The results suggest that the spread of new variants can be contained with highly efficacious tests and mild loss of vaccine protection. However, the aggressiveness of the ongoing Omicron variant and the current waning vaccine immunity point to an endemic phase of COVID-19, in which multiple variants will coexist and residents continue to suffer from infections.
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Affiliation(s)
- Agnieszka Truszkowska
- Center for Urban Science and ProgressTandon School of EngineeringNew York University370 Jay StreetBrooklynNY11201USA,Department of Mechanical and Aerospace EngineeringTandon School of EngineeringNew York UniversitySix MetroTech CenterBrooklynNY11201USA,Department of Chemical and Materials EngineeringUniversity of Alabama in Huntsville301 Sparkman DriveHuntsvilleAL35899USA
| | - Lorenzo Zino
- Engineering and Technology Institute GroningenUniversity of GroningenNijenborgh 4GroningenAG9747The Netherlands,Department of Electronics and TelecommunicationsPolitecnico di TorinoCorso Duca degli Abruzzi 24Turin10129Italy
| | - Sachit Butail
- Department of Mechanical EngineeringNorthern Illinois UniversityDeKalbIL60115USA
| | - Emanuele Caroppo
- Department of Mental HealthLocal Health Unit ROMA 2Rome00159Italy,University Research Center He.R.A.Université Cattolica del Sacro CuoreRome00168Italy
| | - Zhong‐Ping Jiang
- Department of Electrical and Computer EngineeringTandon School of EngineeringNew York University370 Jay StreetBrooklynNY11201USA
| | - Alessandro Rizzo
- Department of Electronics and TelecommunicationsPolitecnico di TorinoCorso Duca degli Abruzzi 24Turin10129Italy,Institute for InventionInnovation and EntrepreneurshipTandon School of EngineeringNew York UniversitySix MetroTech CenterBrooklynNY11201USA
| | - Maurizio Porfiri
- Center for Urban Science and ProgressTandon School of EngineeringNew York University370 Jay StreetBrooklynNY11201USA,Department of Mechanical and Aerospace EngineeringTandon School of EngineeringNew York UniversitySix MetroTech CenterBrooklynNY11201USA,Department of Biomedical EngineeringTandon School of EngineeringNew York UniversitySix MetroTech CenterBrooklynNY11201USA
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10
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Wang C, Huang X, Lau EHY, Cowling BJ, Tsang TK. Association Between Population-Level Factors and Household Secondary Attack Rate of SARS-CoV-2: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2022; 10:ofac676. [PMID: 36655186 PMCID: PMC9835764 DOI: 10.1093/ofid/ofac676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Background Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of population-level factors, such as transmission intensity in the community, on SAR estimates is rarely explored. Methods In this study, we included articles with original data to compute the household SAR. To determine the impact of transmission intensity in the community on household SAR estimates, we explored the association between SAR estimates and the incidence rate of cases by country during the study period. Results We identified 163 studies to extract data on SARs from 326 031 cases and 2 009 859 household contacts. The correlation between the incidence rate of cases during the study period and SAR estimates was 0.37 (95% CI, 0.24-0.49). We found that doubling the incidence rate of cases during the study period was associated with a 1.2% (95% CI, 0.5%-1.8%) higher household SAR. Conclusions Our findings suggest that the incidence rate of cases during the study period is associated with higher SAR. Ignoring this factor may overestimate SARs, especially for regions with high incidences, which further impacts control policies and epidemiological characterization of emerging variants.
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Affiliation(s)
- Can Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaotong Huang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- Correspondence: Tim K. Tsang, PhD, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China ()
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11
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Silva DM, Secchi AR. Recursive state and parameter estimation of COVID-19 circulating variants dynamics. Sci Rep 2022; 12:15879. [PMID: 36151226 PMCID: PMC9508243 DOI: 10.1038/s41598-022-18208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
COVID-19 pandemic response with non-pharmaceutical interventions is an intrinsic control problem. Governments weigh social distancing policies to avoid overload in the health system without significant economic impact. The mutability of the SARS-CoV-2 virus, vaccination coverage, and mobility restriction measures change epidemic dynamics over time. A model-based control strategy requires reliable predictions to be efficient on a long-term basis. In this paper, a SEIR-based model is proposed considering dynamic feedback estimation. State and parameter estimations are performed on state estimators using augmented states. Three methods were implemented: constrained extended Kalman filter (CEKF), CEKF and smoother (CEKF & S), and moving horizon estimator (MHE). The parameters estimation was based on vaccine efficacy studies regarding transmissibility, severity of the disease, and lethality. Social distancing was assumed as a measured disturbance calculated using Google mobility data. Data from six federative units from Brazil were used to evaluate the proposed strategy. State and parameter estimations were performed from 1 October 2020 to 1 July 2021, during which Zeta and Gamma variants emerged. Simulation results showed that lethality increased between 11 and 30% for Zeta mutations and between 44 and 107% for Gamma mutations. In addition, transmissibility increased between 10 and 37% for the Zeta variant and between 43 and 119% for the Gamma variant. Furthermore, parameter estimation indicated temporal underreporting changes in hospitalized and deceased individuals. Overall, the estimation strategy showed to be suitable for dynamic feedback as simulation results presented an efficient detection and dynamic characterization of circulating variants.
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Affiliation(s)
- Daniel Martins Silva
- Chemical Engineering Program/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-942, Brazil.
| | - Argimiro Resende Secchi
- Chemical Engineering Program/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-942, Brazil
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12
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Hall SM, Landaverde L, Gill CJ, Yee GM, Sullivan M, Doucette-Stamm L, Landsberg H, Platt JT, White L, Hamer DH, Klapperich CM. Comparison of anterior nares CT values in asymptomatic and symptomatic individuals diagnosed with SARS-CoV-2 in a university screening program. PLoS One 2022; 17:e0270694. [PMID: 35830378 PMCID: PMC9278773 DOI: 10.1371/journal.pone.0270694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
At our university based high throughput screening program, we test all members of our community weekly using RT-qPCR. RT-qPCR cycle threshold (CT) values are inversely proportional to the amount of viral RNA in a sample and are a proxy for viral load. We hypothesized that CT values would be higher, and thus the viral loads at the time of diagnosis would be lower, in individuals who were infected with the virus but remained asymptomatic throughout the course of the infection. We collected the N1 and N2 target gene CT values from 1633 SARS-CoV-2 positive RT-qPCR tests of individuals sampled between August 7, 2020, and March 18, 2021, at the BU Clinical Testing Laboratory. We matched this data with symptom reporting data from our clinical team. We found that asymptomatic patients had CT values significantly higher than symptomatic individuals on the day of diagnosis. Symptoms were followed by the clinical team for 10 days post the first positive test. Within the entire population, 78.1% experienced at least one symptom during surveillance by the clinical team (n = 1276/1633). Of those experiencing symptoms, the most common symptoms were nasal congestion (73%, n = 932/1276), cough (60.0%, n = 761/1276), fatigue (59.0%, n = 753/1276), and sore throat (53.1%, n = 678/1276). The least common symptoms were diarrhea (12.5%, n = 160/1276), dyspnea on exertion (DOE) (6.9%, n = 88/1276), foot or skin changes (including rash) (4.2%, n = 53/1276), and vomiting (2.1%, n = 27/1276). Presymptomatic individuals, those who were not symptomatic on the day of diagnosis but became symptomatic over the following 10 days, had CT values higher for both N1 (median = 27.1, IQR 20.2-32.9) and N2 (median = 26.6, IQR 20.1-32.8) than the symptomatic group N1 (median = 21.8, IQR 17.2-29.4) and N2 (median = 21.4, IQR 17.3-28.9) but lower than the asymptomatic group N1 (median = 29.9, IQR 23.6-35.5) and N2 (median = 30.0, IQR 23.1-35.7). This study supports the hypothesis that viral load in the anterior nares on the day of diagnosis is a measure of disease intensity at that time.
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Affiliation(s)
- Samantha M. Hall
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Christopher J. Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Grace M. Yee
- Occupational Health Center, Boston University, Boston, Massachusetts, United States of America
| | - Madison Sullivan
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, United States of America
| | - Lynn Doucette-Stamm
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, United States of America
| | - Hannah Landsberg
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, United States of America
| | - Judy T. Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, United States of America
| | - Laura White
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, United States of America
| | - Davidson H. Hamer
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratory, Boston University, Boston, Massachusetts, United States of America
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA, United States of America
- Precision Diagnostics Center, Boston University, Boston, MA, United States of America
| | - Catherine M. Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, United States of America
- Precision Diagnostics Center, Boston University, Boston, MA, United States of America
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13
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Oba J, Taniguchi H, Sato M, Takanashi M, Yokemura M, Sato Y, Nishihara H. SARS-CoV-2 RT-qPCR testing of pooled saliva samples: A case study of 824 asymptomatic individuals and a questionnaire survey in Japan. PLoS One 2022; 17:e0263700. [PMID: 35550622 PMCID: PMC9098043 DOI: 10.1371/journal.pone.0263700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
From the beginning of the COVID-19 pandemic, the demand for diagnostic and screening tests has exceeded supply. Although the proportion of vaccinated people has increased in wealthier countries, breakthrough infections have occurred amid the emergence of new variants. Pooled-sample COVID-19 testing using saliva has been proposed as an efficient, inexpensive, and non-invasive method to allow larger-scale testing, especially in a screening setting. In this study, we aimed to evaluate pooled RT-qPCR saliva testing and to compare the results with individual tests. Employees of Philips Japan, Ltd. were recruited to participate in COVID-19 screening from October to December 2020. Asymptomatic individuals (n = 824) submitted self-collected saliva samples. Samples were tested for the presence of SARS-CoV-2 by RT-qPCR in both 10-sample pools and individual tests. We also surveyed participants regarding their thoughts and behaviors after the PCR screening project. Two of the 824 individuals were positive by RT-qPCR. In the pooled testing, one of these two had no measurable Ct value, but showed an amplification trend at the end of the PCR cycle. Both positive individuals developed cold-like symptoms, but neither required hospitalization. Of the 824 participants, 471 responded to our online questionnaire. Overall, while respondents agreed that PCR screening should be performed regularly, the majority were willing to undergo PCR testing only when it was provided for free or at low cost. In conclusion, pooled testing of saliva samples can support frequent large-scale screening that is rapid, efficient, and inexpensive.
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Affiliation(s)
- Junna Oba
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroaki Taniguchi
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, Innovation Medical Research Institute, Tsukuba-shi, Ibaraki, Japan
- Keio University Hospital Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- * E-mail:
| | - Masae Sato
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaki Takanashi
- LSI Medience Corporation Central Laboratory Center, Itabashi-ku, Tokyo, Japan
| | - Moe Yokemura
- LSI Medience Corporation Central Laboratory Center, Itabashi-ku, Tokyo, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Nishihara
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, Innovation Medical Research Institute, Tsukuba-shi, Ibaraki, Japan
- Keio University Hospital Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
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14
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Rice BL, Lessler J, McKee C, Metcalf CJE. Why do some coronaviruses become pandemic threats when others do not? PLoS Biol 2022; 20:e3001652. [PMID: 35576224 PMCID: PMC9135331 DOI: 10.1371/journal.pbio.3001652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
Despite multiple spillover events and short chains of transmission on at least 4 continents, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has never triggered a pandemic. By contrast, its relative, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has, despite apparently little, if any, previous circulation in humans. Resolving the unsolved mystery of the failure of MERS-CoV to trigger a pandemic could help inform how we understand the pandemic potential of pathogens, and probing it underscores a need for a more holistic understanding of the ways in which viral genetic changes scale up to population-level transmission.
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Affiliation(s)
- Benjamin L. Rice
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Justin Lessler
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Clifton McKee
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
- Wissenschaftskolleg zu Berlin, Berlin, Germany
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15
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Buitrago-Garcia D, Ipekci AM, Heron L, Imeri H, Araujo-Chaveron L, Arevalo-Rodriguez I, Ciapponi A, Cevik M, Hauser A, Alam MI, Meili K, Meyerowitz EA, Prajapati N, Qiu X, Richterman A, Robles-Rodriguez WG, Thapa S, Zhelyazkov I, Salanti G, Low N. Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis. PLoS Med 2022; 19:e1003987. [PMID: 35617363 PMCID: PMC9135333 DOI: 10.1371/journal.pmed.1003987] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/13/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Debate about the level of asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection continues. The amount of evidence is increasing and study designs have changed over time. We updated a living systematic review to address 3 questions: (1) Among people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? (2) What is the infectiousness of asymptomatic and presymptomatic, compared with symptomatic, SARS-CoV-2 infection? (3) What proportion of SARS-CoV-2 transmission in a population is accounted for by people who are asymptomatic or presymptomatic? METHODS AND FINDINGS The protocol was first published on 1 April 2020 and last updated on 18 June 2021. We searched PubMed, Embase, bioRxiv, and medRxiv, aggregated in a database of SARS-CoV-2 literature, most recently on 6 July 2021. Studies of people with PCR-diagnosed SARS-CoV-2, which documented symptom status at the beginning and end of follow-up, or mathematical modelling studies were included. Studies restricted to people already diagnosed, of single individuals or families, or without sufficient follow-up were excluded. One reviewer extracted data and a second verified the extraction, with disagreement resolved by discussion or a third reviewer. Risk of bias in empirical studies was assessed with a bespoke checklist and modelling studies with a published checklist. All data syntheses were done using random effects models. Review question (1): We included 130 studies. Heterogeneity was high so we did not estimate a mean proportion of asymptomatic infections overall (interquartile range (IQR) 14% to 50%, prediction interval 2% to 90%), or in 84 studies based on screening of defined populations (IQR 20% to 65%, prediction interval 4% to 94%). In 46 studies based on contact or outbreak investigations, the summary proportion asymptomatic was 19% (95% confidence interval (CI) 15% to 25%, prediction interval 2% to 70%). (2) The secondary attack rate in contacts of people with asymptomatic infection compared with symptomatic infection was 0.32 (95% CI 0.16 to 0.64, prediction interval 0.11 to 0.95, 8 studies). (3) In 13 modelling studies fit to data, the proportion of all SARS-CoV-2 transmission from presymptomatic individuals was higher than from asymptomatic individuals. Limitations of the evidence include high heterogeneity and high risks of selection and information bias in studies that were not designed to measure persistently asymptomatic infection, and limited information about variants of concern or in people who have been vaccinated. CONCLUSIONS Based on studies published up to July 2021, most SARS-CoV-2 infections were not persistently asymptomatic, and asymptomatic infections were less infectious than symptomatic infections. Summary estimates from meta-analysis may be misleading when variability between studies is extreme and prediction intervals should be presented. Future studies should determine the asymptomatic proportion of SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection. Without prospective longitudinal studies with methods that minimise selection and measurement biases, further updates with the study types included in this living systematic review are unlikely to be able to provide a reliable summary estimate of the proportion of asymptomatic infections caused by SARS-CoV-2. REVIEW PROTOCOL Open Science Framework (https://osf.io/9ewys/).
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Affiliation(s)
- Diana Buitrago-Garcia
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Graduate School of Health Sciences, University of Bern, Bern, Switzerland
| | - Aziz Mert Ipekci
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Leonie Heron
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Hira Imeri
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Lucia Araujo-Chaveron
- EHESP French School of Public Health, Paris and Rennes, France
- Institut Pasteur, Paris, France
| | - Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramon y Cajal, IRYCIS, CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Agustín Ciapponi
- Instituto de Efectividad Clínica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
| | - Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St. Andrews, Fife, Scotland, United Kingdom
| | - Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Kaspar Meili
- Department of Epidemiology and Global Health, Umeå University, Umeå, Sweden
| | - Eric A. Meyerowitz
- Division of Infectious Diseases, Montefiore Medical Center, Bronx, New York, New York, United States of America
| | | | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Aaron Richterman
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Shabnam Thapa
- Manchester Centre for Health Economics, University of Manchester, Manchester, United Kingdom
| | | | - Georgia Salanti
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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16
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Nakashita M, Takagi Y, Tanaka H, Nakamura H, Serizawa Y, Ukai T, Azuma K, Chiba H, Terada K, Nakanishi K, Fujikawa T, Saito K, Yamaguchi R, Mitsuhashi Y, Yano K, Shibuma T, Kuzuma A, Tsuda S, Sadamoto T, Ishii Y, Ohara T, Hitomi Y, Hiroshima T, Yamagishi T, Kamiya H, Anita S, Yahata Y, Shimada T, Arima Y, Suzuki M, Sekizuka T, Kuroda M, Sunagawa T. Singing Is a Risk Factor for SARS-CoV-2 Infection: A Case-control Study of Karaoke-related COVID-19 Outbreaks in Two Cities in Hokkaido, Japan, Linked by Whole Genome Analysis. Open Forum Infect Dis 2022; 9:ofac158. [PMID: 35531379 PMCID: PMC8992236 DOI: 10.1093/ofid/ofac158] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Singing in an indoor space may increase the risk of SARS-CoV-2 infection. We conducted a case-control study of karaoke-related COVID-19 outbreaks to reveal the risk factors for SARS-CoV-2 infection among individuals who participate in karaoke.
Methods
Cases were defined as people who enjoyed karaoke at a bar and who tested positive for SARS-CoV-2 by RT-PCR between May 16 and July 3, 2020. Controls were defined as people who enjoyed karaoke at the same bar during the same period as the cases and tested negative. Odds ratio (OR) and confidence interval (CI) were calculated. ORs were adjusted by variables with significantly high odds ratio (aOR).
Results
We identified 81 cases, the majority of whom were active elderly individuals (median age: 75 years). Six cases died (case fatality ratio: 7%). Among the cases, 68 (84%) were guests, 18 of whom had visited more than two karaoke bars. A genome analysis conducted in 30 cases showed six types of isolates within four single-nucleotide variations difference. The case-control study revealed that singing (aOR 11.0, 95% CI, 1.2-101.0), not wearing a mask (aOR 3.7, 95% CI 1.2-11.2) and time spent per visit (aOR 1.7, 95% CI 1.1-2.7) were associated with COVID-19 infection.
Conclusions
A karaoke-related COVID-19 outbreak that occurred in two different cities was confirmed by the results of genome analysis. Singing in less-ventilated, indoor and crowded environments increases the risk of acquiring SARS-CoV-2 infection. Wearing a mask and staying for only a short time can reduce the risk of infection during karaoke.
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Affiliation(s)
- Manami Nakashita
- Field Epidemiology Training Program, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuta Takagi
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | | | - Haruna Nakamura
- Field Epidemiology Training Program, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yusuke Serizawa
- Field Epidemiology Training Program, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomohiko Ukai
- Field Epidemiology Training Program, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kotaro Azuma
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | - Hiroko Chiba
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | | | | | | | - Kayoko Saito
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | - Ryo Yamaguchi
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | | | - Koichi Yano
- Public Health Office, City of Sapporo, Hokkaido, Japan
| | | | - Akemi Kuzuma
- Public Health Office, Otaru City, Hokkaido, Japan
| | | | | | - Yasuhiko Ishii
- Hokkaido Government Department of Health and Welfare, Hokkaido, Japan
| | - Tsukasa Ohara
- Hokkaido Government Department of Health and Welfare, Hokkaido, Japan
| | - Yoshiaki Hitomi
- Hokkaido Government Department of Health and Welfare, Hokkaido, Japan
| | - Takashi Hiroshima
- Hokkaido Government Department of Health and Welfare, Hokkaido, Japan
| | - Takuya Yamagishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Kamiya
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Samuel Anita
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuichiro Yahata
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoe Shimada
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuzo Arima
- Center for Surveillance, Immunization and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Center for Field Epidemiology Intelligence, Research, and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
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17
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Kang M, Xin H, Yuan J, Ali ST, Liang Z, Zhang J, Hu T, Lau EH, Zhang Y, Zhang M, Cowling BJ, Li Y, Wu P. Transmission dynamics and epidemiological characteristics of SARS-CoV-2 Delta variant infections in Guangdong, China, May to June 2021. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35272744 PMCID: PMC8915401 DOI: 10.2807/1560-7917.es.2022.27.10.2100815] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background The Delta variant of SARS-CoV-2 had become predominant globally by November 2021. Aim We evaluated transmission dynamics and epidemiological characteristics of the Delta variant in an outbreak in southern China. Methods Data on confirmed COVID-19 cases and their close contacts were retrospectively collected from the outbreak that occurred in Guangdong, China in May and June 2021. Key epidemiological parameters, temporal trend of viral loads and secondary attack rates were estimated. We also evaluated the association of vaccination with viral load and transmission. Results We identified 167 patients infected with the Delta variant in the Guangdong outbreak. Mean estimates of latent and incubation period were 3.9 days and 5.8 days, respectively. Relatively higher viral load was observed in infections with Delta than in infections with wild-type SARS-CoV-2. Secondary attack rate among close contacts of cases with Delta was 1.4%, and 73.1% (95% credible interval (CrI): 32.9–91.4) of the transmissions occurred before onset. Index cases without vaccination (adjusted odds ratio (aOR): 2.84; 95% CI: 1.19–8.45) or with an incomplete vaccination series (aOR: 6.02; 95% CI: 2.45–18.16) were more likely to transmit infection to their contacts than those who had received the complete primary vaccination series. Discussion Patients infected with the Delta variant had more rapid symptom onset compared with the wild type. The time-varying serial interval should be accounted for in estimation of reproduction numbers. The higher viral load and higher risk of pre-symptomatic transmission indicated the challenges in control of infections with the Delta variant.
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Affiliation(s)
- Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Hualei Xin
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Zimian Liang
- Foshan Center for Disease Control and Prevention, Foshan, Guangdong, China
| | - Jiayi Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Eric Hy Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
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18
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Milne GJ, Carrivick J, Whyatt D. Mitigating the SARS-CoV-2 Delta disease burden in Australia by non-pharmaceutical interventions and vaccinating children: a modelling analysis. BMC Med 2022; 20:80. [PMID: 35177062 PMCID: PMC8853841 DOI: 10.1186/s12916-022-02241-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/06/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND In countries with high COVID-19 vaccination rates the SARS-CoV-2 Delta variant resulted in rapidly increasing case numbers. This study evaluated the use of non-pharmaceutical interventions (NPIs) coupled with alternative vaccination strategies to determine feasible Delta mitigation strategies for Australia. We aimed to understand the potential effectiveness of high vaccine coverage levels together with NPI physical distancing activation and to establish the benefit of adding children and adolescents to the vaccination program. Border closure limited SARS-CoV-2 transmission in Australia; however, slow vaccination uptake resulted in Delta outbreaks in the two largest cities and may continue as international travel increases. METHODS An agent-based model was used to evaluate the potential reduction in the COVID-19 health burden resulting from alternative vaccination strategies. We assumed immunity was derived from vaccination with the BNT162b2 Pfizer BioNTech vaccine. Two age-specific vaccination strategies were evaluated, ages 5 and above, and 12 and above, and the health burden determined under alternative vaccine coverages, with/without activation of NPIs. Age-specific infections generated by the model, together with recent UK data, permitted reductions in the health burden to be quantified. RESULTS Cases, hospitalisations and deaths are shown to reduce by (i) increasing coverage to include children aged 5 to 11 years, (ii) activating moderate NPI measures and/or (iii) increasing coverage levels above 80%. At 80% coverage, vaccinating ages 12 and above without NPIs is predicted to result in 1095 additional hospitalisations per million population; adding ages 5 and above reduces this to 996 per million population. Activating moderate NPIs reduces hospitalisations to 611 for ages 12 and over, and 382 per million for ages 5 and above. Alternatively, increasing coverage to 90% for those aged 12 and above is estimated to reduce hospitalisations to 616. Combining all three measures is shown to reduce cases to 158, hospitalisations to 1 and deaths to zero, per million population. CONCLUSIONS Delta variant outbreaks may be managed by vaccine coverage rates higher than 80% and activation of moderate NPI measures, preventing healthcare facilities from being overwhelmed. If 90% coverage cannot be achieved, including young children and adolescents in the vaccination program coupled with activation of moderate NPIs appears necessary to suppress future COVID-19 Delta-like transmission and prevent intensive care unit surge capacity from being exceeded.
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Affiliation(s)
- George J Milne
- University of Western Australia, Crawley, WA, Australia.
| | | | - David Whyatt
- University of Western Australia, Crawley, WA, Australia
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19
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Donnelly MAP, Chuey MR, Soto R, Schwartz NG, Chu VT, Konkle SL, Sleweon S, Ruffin J, Haberling DL, Guagliardo SAJ, Stoddard RA, Anderson RD, Morgan CN, Rossetti R, McCormick DW, Magleby R, Sheldon SW, Dietrich EA, Uehara A, Retchless AC, Tong S, Folster JM, Drobeniuc J, Petway ME, Austin B, Stous S, McDonald E, Jain S, Hudziec MM, Stringer G, Albanese BA, Totten SE, Staples JE, Killerby ME, Hughes L, Matanock A, Beatty M, Tate JE, Kirking HL, Hsu CH. Household transmission of SARS-CoV-2 Alpha variant - United States, 2021. Clin Infect Dis 2022; 75:e122-e132. [PMID: 35147176 PMCID: PMC9047162 DOI: 10.1093/cid/ciac125] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In Spring 2021, SARS-CoV-2 B.1.1.7 (Alpha) became the predominant variant in the U.S. Research suggests that Alpha has increased transmissibility compared to non-Alpha lineages. We estimated household secondary infection risk (SIR), assessed characteristics associated with transmission, and compared symptoms of persons with Alpha and non-Alpha infections. METHODS We followed households with SARS-CoV-2 infection for two weeks in San Diego County and metropolitan Denver, January to April 2021. We collected epidemiologic information and biospecimens for serology, RT-PCR, and whole genome sequencing. We stratified SIR and symptoms by lineage, and identified characteristics associated with transmission using Generalized Estimating Equations. RESULTS We investigated 127 households with 322 household contacts; 72 households (56.7%) had member(s) with secondary infections. SIRs were not significantly higher for Alpha (61.0% [95% confidence interval (CI) 52.4-69.0%]) than non-Alpha (55.6% [CI 44.7-65.9%], P = 0.49). In households with Alpha, persons who identified as Asian or Hispanic/Latino had significantly higher SIRs than those who identified as White (P = 0.01 and 0.03, respectively). Close contact (e.g., kissing, hugging) with primary cases was associated with increased transmission for all lineages. Persons with Alpha infection were more likely to report constitutional symptoms than persons with non-Alpha (86.9% vs. 76.8%, P = 0.05). CONCLUSIONS Household SIRs were similar for Alpha and non-Alpha. Comparable SIRs may be due to saturation of transmission risk in households owing to extensive close contact, or true lack of difference in transmission rates. Avoiding close contact within households may reduce SARS-CoV-2 transmission for all lineages among household members.
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Affiliation(s)
- Marisa A P Donnelly
- CDC COVID-19 Response.,Epidemic Intelligence Service, CDC.,California Department of Public Health
| | - Meagan R Chuey
- CDC COVID-19 Response.,Epidemic Intelligence Service, CDC.,County of San Diego Health and Human Services
| | - Raymond Soto
- CDC COVID-19 Response.,Epidemic Intelligence Service, CDC
| | | | - Victoria T Chu
- CDC COVID-19 Response.,Epidemic Intelligence Service, CDC
| | | | | | | | | | | | | | | | | | | | | | - Reed Magleby
- CDC COVID-19 Response.,Epidemic Intelligence Service, CDC
| | | | | | | | | | | | | | | | | | | | - Sarah Stous
- County of San Diego Health and Human Services
| | | | | | | | | | | | | | | | | | | | | | - Mark Beatty
- County of San Diego Health and Human Services
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20
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Wang Y, Zheng K, Gao W, Lv J, Yu C, Wang L, Wang Z, Wang B, Liao C, Li L. Asymptomatic and pre-symptomatic infection in Coronavirus Disease 2019 pandemic. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:66-88. [PMID: 35658110 PMCID: PMC9047649 DOI: 10.1515/mr-2021-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
With the presence of Coronavirus Disease 2019 (COVID-19) asymptomatic infections detected, their proportion, transmission potential, and other aspects such as immunity and related emerging challenges have attracted people's attention. We have found that based on high-quality research, asymptomatic infections account for at least one-third of the total cases, whereas based on systematic review and meta-analysis, the proportion is about one-fifth. Evaluating the true transmission potential of asymptomatic cases is difficult but critical, since it may affect national policies in response to COVID-19. We have summarized the current evidence and found, compared with symptomatic cases, the transmission capacity of asymptomatic individuals is weaker, even though they have similar viral load and relatively short virus shedding duration. As the outbreak progresses, asymptomatic infections have also been found to develop long COVID-19. In addition, the role of asymptomatic infection in COVID-19 remains to be further revealed as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge. Nevertheless, as asymptomatic infections transmit the SARS-CoV-2 virus silently, they still pose a substantial threat to public health. Therefore, it is essential to conduct screening to obtain more knowledge about the asymptomatic infections and to detect them as soon as possible; meanwhile, management of them is also a key point in the fight against COVID-19 community transmission. The different management of asymptomatic infections in various countries are compared and the experience in China is displayed in detail.
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Affiliation(s)
- Yutong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Ke Zheng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Lan Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zijun Wang
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Bo Wang
- Meinian Public Health Institute, Peking University Health Science Center, Beijing, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Centre for Public Health and Epidemic Preparedness and Response, Beijing, China
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21
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COVID-19 vaccination significantly reduces morbidity and absenteeism among healthcare personnel: A prospective multicenter study. Vaccine 2021; 39:7021-7027. [PMID: 34740473 PMCID: PMC8556541 DOI: 10.1016/j.vaccine.2021.10.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 11/26/2022]
Abstract
Aim Healthcare personnel (HCP) are prioritized for coronavirus disease 2019 (COVID-19) vaccination to protect them and non-disruptive provision of healthcare services. We assessed the impact of the Pfizer-BioNTech vaccine on morbidity and absenteeism among HCP. Methods We studied 7445 HCP in five tertiary-care hospitals in Greece from November 15, 2020 through April 18, 2021. Results A total of 910 episodes of absenteeism and 9695 days of absence were recorded during the entire study period. Starting from January 4, 2021, 4823/7445 HCP (64.8%) were fully or partially vaccinated. Overall, 535 episodes of absenteeism occurred from January 4, 2021 through April 18, 2021, including 309 (57.76%) episodes among 2622 unvaccinated HCP and 226 (42.24%) episodes among 4823 vaccinated HCP (11.8 versus 4.7 episodes of absenteeism per 100 HCP, respectively; p-value < 0.001). The mean duration of absenteeism was 11.9 days among unvaccinated HCP compared with 6.9 days among vaccinated HCP (p-value < 0.001). Unvaccinated HCP more frequently developed acute respiratory infection, influenza-like illness, and COVID-19 (p-values < 0.001 for all comparisons). Vaccine effectiveness for fully vaccinated HCP was estimated at 94.16% [confidence interval (CI): 88.50%-98.05%) against COVID-19, 83.62% (CI: 73.36%-90.38%) against SARS-CoV-2 infection (asymptomatic or COVID-19), and 66.42% (CI: 56.86%-74.15%) against absenteeism. Conclusion The COVID-19 pandemic had a considerable impact on healthcare workforce. The Pfizer-BioNTech vaccine significantly reduced morbidity, COVID-19, absenteeism and duration of absenteeism among HCP during a period of high SARS-CoV-2 circulation in the community. It is expected that HCP vaccination will protect them and healthcare services and contain healthcare costs.
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22
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Lau YC, Tsang TK, Kennedy-Shaffer L, Kahn R, Lau EHY, Chen D, Wong JY, Ali ST, Wu P, Cowling BJ. Joint Estimation of Generation Time and Incubation Period for Coronavirus Disease 2019. J Infect Dis 2021; 224:1664-1671. [PMID: 34423821 PMCID: PMC8499762 DOI: 10.1093/infdis/jiab424] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/21/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has caused a heavy disease burden globally. The impact of process and timing of data collection on the accuracy of estimation of key epidemiological distributions are unclear. Because infection times are typically unobserved, there are relatively few estimates of generation time distribution. METHODS We developed a statistical framework to jointly estimate generation time and incubation period from human-to-human transmission pairs, accounting for sampling biases. We applied the framework on 80 laboratory-confirmed human-to-human transmission pairs in China. We further inferred the infectiousness profile, serial interval distribution, proportions of presymptomatic transmission, and basic reproduction number (R0) for COVID-19. RESULTS The estimated mean incubation period was 4.8 days (95% confidence interval [CI], 4.1-5.6), and mean generation time was 5.7 days (95% CI, 4.8-6.5). The estimated R0 based on the estimated generation time was 2.2 (95% CI, 1.9-2.4). A simulation study suggested that our approach could provide unbiased estimates, insensitive to the width of exposure windows. CONCLUSIONS Properly accounting for the timing and process of data collection is critical to have correct estimates of generation time and incubation period. R0 can be biased when it is derived based on serial interval as the proxy of generation time.
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Affiliation(s)
- Yiu Chung Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Lee Kennedy-Shaffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Mathematics and Statistics, Vassar College, Poughkeepsie, New York, USA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Dongxuan Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jessica Y Wong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
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23
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Tsang TK, Wang C, Yang B, Cauchemez S, Cowling BJ. Using secondary cases to characterize the severity of an emerging or re-emerging infection. Nat Commun 2021; 12:6372. [PMID: 34737277 PMCID: PMC8569220 DOI: 10.1038/s41467-021-26709-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
The methods to ascertain cases of an emerging infectious disease are typically biased toward cases with more severe disease, which can bias the average infection-severity profile. Here, we conducted a systematic review to extract information on disease severity among index cases and secondary cases identified by contact tracing of index cases for COVID-19. We identified 38 studies to extract information on measures of clinical severity. The proportion of index cases with fever was 43% higher than for secondary cases. The proportion of symptomatic, hospitalized, and fatal illnesses among index cases were 12%, 126%, and 179% higher than for secondary cases, respectively. We developed a statistical model to utilize the severity difference, and estimate 55% of index cases were missed in Wuhan, China. Information on disease severity in secondary cases should be less susceptible to ascertainment bias and could inform estimates of disease severity and the proportion of missed index cases.
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Affiliation(s)
- Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong,, Hong Kong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Can Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong,, Hong Kong, China
| | - Bingyi Yang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong,, Hong Kong, China
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong,, Hong Kong, China.
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong, China.
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24
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Bae S, Kim JY, Lim SY, Park H, Cha HH, Kwon JS, Suh MH, Lee HJ, Lim JS, Jung J, Kim MJ, Chong YP, Lee SO, Choi SH, Kim YS, Lee HY, Lee S, Park MS, Kim SH. Dynamics of Viral Shedding and Symptoms in Patients with Asymptomatic or Mild COVID-19. Viruses 2021; 13:v13112133. [PMID: 34834940 PMCID: PMC8625453 DOI: 10.3390/v13112133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/03/2022] Open
Abstract
We conducted a prospective cohort study at a community facility designated for the isolation of individuals with asymptomatic or mild COVID-19 between 10 January and 22 February 2021 to investigate the relationship of viral shedding with symptom changes of COVID-19. In total, 89 COVID-19 adult patients (12 asymptomatic, 16 presymptomatic, 61 symptomatic) were enrolled. Symptom scores, the genomic RNA and subgenomic RNA of SARS-CoV-2 from saliva samples with a cell culture were measured. Asymptomatic COVID-19 patients had a similar viral load to symptomatic patients during the early course of the disease, but exhibited a rapid decrease in viral load with the loss of infectivity. Subgenomic RNA and viable virus by cell culture in asymptomatic patients were detected only until 3 days after diagnosis, and the positivity of the subgenomic RNA and cell culture in symptomatic patients gradually decreased in both from 40% in the early disease course to 13% at 10 days and 4% at 8 days after the symptom onset, respectively. In conclusion, symptomatic patients have a high infectivity with high symptom scores during the early disease course and gradually lose infectivity depending on the symptom. Conversely, asymptomatic patients exhibit a rapid decrease in viral load with the loss of infectivity, despite a similar viral load during the early disease course.
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Affiliation(s)
- Seongman Bae
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - So Yun Lim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Heedo Park
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (H.P.); (H.Y.L.); (S.L.)
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul 02841, Korea
| | - Hye Hee Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Ji-Soo Kwon
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Mi Hyun Suh
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Hyun Jung Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Joon Seo Lim
- Clinical Research Center, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Jiwon Jung
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Sang-Oh Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Sang-Ho Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
| | - Ho Young Lee
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (H.P.); (H.Y.L.); (S.L.)
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul 02841, Korea
| | - Sohyun Lee
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (H.P.); (H.Y.L.); (S.L.)
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul 02841, Korea
| | - Man-Seong Park
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (H.P.); (H.Y.L.); (S.L.)
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, College of Medicine, Korea University, Seoul 02841, Korea
- Correspondence: (M.-S.P.); (S.-H.K.); Tel.: +82-2-2286-1312 (M.-S.P.); +82-2-3010-3305 (S.-H.K.)
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (S.B.); (J.Y.K.); (S.Y.L.); (H.H.C.); (J.-S.K.); (M.H.S.); (H.J.L.); (J.J.); (M.J.K.); (Y.P.C.); (S.-O.L.); (S.-H.C.); (Y.S.K.)
- Correspondence: (M.-S.P.); (S.-H.K.); Tel.: +82-2-2286-1312 (M.-S.P.); +82-2-3010-3305 (S.-H.K.)
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25
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Xin H, Li Y, Wu P, Li Z, Lau EHY, Qin Y, Wang L, Cowling BJ, Tsang T, Li Z. Estimating the latent period of coronavirus disease 2019 (COVID-19). Clin Infect Dis 2021; 74:1678-1681. [PMID: 34453527 DOI: 10.1093/cid/ciab746] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Indexed: 01/12/2023] Open
Abstract
Using detailed exposure information on COVID-19 cases, we estimated the mean latent period to be 5.5 days (95% confidence interval: 5.1-5.9 days), shorter than the mean incubation period (6.9 days). Laboratory testing may allow shorter quarantines since 95% of COVID-19 cases shed virus within 10.6 days (95%CI: 9.6-11.6) of infection.
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Affiliation(s)
- Hualei Xin
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yu Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Zhili Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Ying Qin
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liping Wang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Tim Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhongjie Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
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Costa R, Bueno F, Albert E, Torres I, Carbonell-Sahuquillo S, Barrés-Fernández A, Sánchez D, Padrón C, Colomina J, Lázaro Carreño MI, Bretón-Martínez JR, Martínez-Costa C, Navarro D. Upper respiratory tract SARS-CoV-2 RNA loads in symptomatic and asymptomatic children and adults. Clin Microbiol Infect 2021; 27:1858.e1-1858.e7. [PMID: 34384874 PMCID: PMC8349738 DOI: 10.1016/j.cmi.2021.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 08/01/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Studies comparing SARS-CoV-2 RNA load in the upper respiratory tract (URT) between children and adults, either presenting with COVID-19 or asymptomatic have yielded inconsistent results. Here, we conducted a retrospective, single center study to address this issue. PATIENTS AND METHODS 1,184 consecutive subjects (256 children and 928 adults) testing positive for SARS-COV-2 RNA in nasopharyngeal exudates (NP), of whom 424 (121 children and 303 adults) had COVID-19 and 760 (135 children and 625 adults) were asymptomatic close contacts of COVID-19 patients. SARS-CoV-2 RNA testing was carried out using the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, MS, USA). The AMPLIRUN® TOTAL SARS-CoV-2 RNA Control (Vircell SA, Granada, Spain) was used for estimating SARS-CoV-2 RNA loads (in copies/mL). SARS-CoV-2 RNA loads at the time of laboratory diagnosis (single specimen/patient) were used for comparison purposes. RESULTS Median initial SARS-COV-2 RNA load was lower (P=0.094) in children (6.98 log10 copies/ml; range, 3.0-11.7) than in adults (7.14 log10 copies/ml; range, 2.2.-13.4) with COVID-19. As for asymptomatic individuals, median SARS-CoV-2 RNA load was comparable (P=0.97) in children (6.20 log10 copies/ml; range, 1.8-11.6) and adults (6.48 log10 copies/ml; range, 1.9-11.8). Children with COVID-19 symptoms displayed SARS-CoV-2 RNA loads (6.98 log10 copies/ml; range, 3.0-11.7) comparable to their asymptomatic counterparts (6.20 log10 copies/ml; range, 1.8-11.6) (P=0.61). Meanwhile in adults, median SARS-CoV-2 RNA load was significantly higher in symptomatic (7.14 log10 copies/ml; range, 2.2.-13.4) than in asymptomatic subjects (6.48 log10 copies/ml; range, 1.9-11.8) (P=<0.001). Overall, a faster URT SARS-CoV-2 RNA clearance rate was observed in children than in adults. CONCLUSIONS Based on viral load data at the time of diagnosis, our results suggested that SARS-CoV-2 infected children, with or without COVID-19, may display NP viral loads of comparable magnitude to that found in their adult counterparts; However, children may have shorter viral shedding as compared to adults.
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Affiliation(s)
- Rosa Costa
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Felipe Bueno
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | | | | | - David Sánchez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Carmelo Padrón
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María Isabel Lázaro Carreño
- Pediatric Department, Hospital Clínico Universitario, Valencia, Spain; Department of Pediatrics, University of Valencia, Valencia, Spain
| | - José Rafael Bretón-Martínez
- Pediatric Department, Hospital Clínico Universitario, Valencia, Spain; Department of Pediatrics, University of Valencia, Valencia, Spain
| | - Cecilia Martínez-Costa
- Pediatric Department, Hospital Clínico Universitario, Valencia, Spain; Department of Pediatrics, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain.
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27
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Factors Associated With Household Transmission of SARS-CoV-2: An Updated Systematic Review and Meta-analysis. JAMA Netw Open 2021; 4:e2122240. [PMID: 34448865 PMCID: PMC8397928 DOI: 10.1001/jamanetworkopen.2021.22240] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
Importance A previous systematic review and meta-analysis of household transmission of SARS-CoV-2 that summarized 54 published studies through October 19, 2020, found an overall secondary attack rate (SAR) of 16.6% (95% CI, 14.0%-19.3%). However, the understanding of household secondary attack rates for SARS-CoV-2 is still evolving, and updated analysis is needed. Objective To use newly published data to further the understanding of SARS-CoV-2 transmission in the household. Data Sources PubMed and reference lists of eligible articles were used to search for records published between October 20, 2020, and June 17, 2021. No restrictions on language, study design, time, or place of publication were applied. Studies published as preprints were included. Study Selection Articles with original data that reported at least 2 of the following factors were included: number of household contacts with infection, total number of household contacts, and secondary attack rates among household contacts. Studies that reported household infection prevalence (which includes index cases), that tested contacts using antibody tests only, and that included populations overlapping with another included study were excluded. Search terms were SARS-CoV-2 or COVID-19 with secondary attack rate, household, close contacts, contact transmission, contact attack rate, or family transmission. Data Extraction and Synthesis Meta-analyses were performed using generalized linear mixed models to obtain SAR estimates and 95% CIs. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was followed. Main Outcomes and Measures Overall household SAR for SARS-CoV-2, SAR by covariates (contact age, sex, ethnicity, comorbidities, and relationship; index case age, sex, symptom status, presence of fever, and presence of cough; number of contacts; study location; and variant), and SAR by index case identification period. Results A total of 2722 records (2710 records from database searches and 12 records from the reference lists of eligible articles) published between October 20, 2020, and June 17, 2021, were identified. Of those, 93 full-text articles reporting household transmission of SARS-CoV-2 were assessed for eligibility, and 37 studies were included. These 37 new studies were combined with 50 of the 54 studies (published through October 19, 2020) from our previous review (4 studies from Wuhan, China, were excluded because their study populations overlapped with another recent study), resulting in a total of 87 studies representing 1 249 163 household contacts from 30 countries. The estimated household SAR for all 87 studies was 18.9% (95% CI, 16.2%-22.0%). Compared with studies from January to February 2020, the SAR for studies from July 2020 to March 2021 was higher (13.4% [95% CI, 10.7%-16.7%] vs 31.1% [95% CI, 22.6%-41.1%], respectively). Results from subgroup analyses were similar to those reported in a previous systematic review and meta-analysis; however, the SAR was higher to contacts with comorbidities (3 studies; 50.0% [95% CI, 41.4%-58.6%]) compared with previous findings, and the estimated household SAR for the B.1.1.7 (α) variant was 24.5% (3 studies; 95% CI, 10.9%-46.2%). Conclusions and Relevance The findings of this study suggest that the household remains an important site of SARS-CoV-2 transmission, and recent studies have higher household SAR estimates compared with the earliest reports. More transmissible variants and vaccines may be associated with further changes.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville
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28
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Role of community-based cohorts for uncovering the iceberg of disease. LANCET GLOBAL HEALTH 2021; 9:e740-e741. [PMID: 34019828 DOI: 10.1016/s2214-109x(21)00211-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022]
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29
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Wu T, Kang S, Peng W, Zuo C, Zhu Y, Pan L, Fu K, You Y, Yang X, Luo X, Jiang L, Deng M. Original Hosts, Clinical Features, Transmission Routes, and Vaccine Development for Coronavirus Disease (COVID-19). Front Med (Lausanne) 2021; 8:702066. [PMID: 34295915 PMCID: PMC8291337 DOI: 10.3389/fmed.2021.702066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to public concern worldwide. Although a variety of hypotheses about the hosts of SARS-CoV-2 have been proposed, an exact conclusion has not yet been reached. Initial clinical manifestations associated with COVID-19 are similar to those of other acute respiratory infections, leading to misdiagnoses and resulting in the outbreak at the early stage. SARS-CoV-2 is predominantly spread by droplet transmission and close contact; the possibilities of fecal-oral, vertical, and aerosol transmission have not yet been fully confirmed or rejected. Besides, COVID-19 cases have been reported within communities, households, and nosocomial settings through contact with confirmed COVID-19 patients or asymptomatic individuals. Environmental contamination is also a major driver for the COVID-19 pandemic. Considering the absence of specific treatment for COVID-19, it is urgent to decrease the risk of transmission and take preventive measures to control the spread of the virus. In this review, we summarize the latest available data on the potential hosts, entry receptors, clinical features, and risk factors of COVID-19 and transmission routes of SARS-CoV-2, and we present the data about development of vaccines.
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Affiliation(s)
- Ting Wu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Department of Cardiovascular Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Shuntong Kang
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Wenyao Peng
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Chenzhe Zuo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuhao Zhu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Liangyu Pan
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Keyun Fu
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yaxian You
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Xinyuan Yang
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Xuan Luo
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Yuanpin Cell Biotechnology Co., Ltd, Changsha, China
| | - Liping Jiang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Meichun Deng
- Department of Biochemistry and Molecular Biology, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
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30
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Chu DKW, Gu H, Chang LDJ, Cheuk SSY, Gurung S, Krishnan P, Ng DYM, Liu GYZ, Wan CKC, Tsang DNC, Peiris M, Poon LLM. SARS-CoV-2 Superspread in Fitness Center, Hong Kong, China, March 2021. Emerg Infect Dis 2021; 27:2230-2232. [PMID: 34004137 PMCID: PMC8314845 DOI: 10.3201/eid2708.210833] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To investigate a superspreading event at a fitness center in Hong Kong, China, we used genomic sequencing to analyze 102 reverse transcription PCR–confirmed cases of severe acute respiratory syndrome coronavirus 2 infection. Our finding highlights the risk for virus transmission in confined spaces with poor ventilation and limited public health interventions.
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31
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Gettings JR, Gold JAW, Kimball A, Forsberg K, Scott C, Uehara A, Tong S, Hast M, Swanson MR, Morris E, Oraka E, Almendares O, Thomas ES, Mehari L, McCloud J, Roberts G, Crosby D, Balajee A, Burnett E, Chancey RJ, Cook P, Donadel M, Espinosa C, Evans ME, Fleming-Dutra KE, Forero C, Kukielka EA, Li Y, Marcet PL, Mitruka K, Nakayama JY, Nakazawa Y, O'Hegarty M, Pratt C, Rice ME, Rodriguez Stewart RM, Sabogal R, Sanchez E, Velasco-Villa A, Weng MK, Zhang J, Rivera G, Parrott T, Franklin R, Memark J, Drenzek C, Hall AJ, Kirking HL, Tate JE, Vallabhaneni S. SARS-CoV-2 transmission in a Georgia school district - United States, December 2020-January 2021. Clin Infect Dis 2021; 74:319-326. [PMID: 33864375 PMCID: PMC8083290 DOI: 10.1093/cid/ciab332] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND To inform prevention strategies, we assessed the extent of SARS-CoV-2 transmission and settings in which transmission occurred in a Georgia public school district. METHODS During December 1, 2020-January 22, 2021, SARS-CoV-2-infected index cases and their close contacts in schools were identified by school and public health officials. For in-school contacts, we assessed symptoms and offered SARS-CoV-2 RT-PCR testing; performed epidemiologic investigations and whole-genome sequencing to identify in-school transmission; and calculated secondary attack rate (SAR) by school setting (e.g., sports, elementary school classroom), index case role (i.e., staff, student), and index case symptomatic status. RESULTS We identified 86 index cases and 1,119 contacts, 688 (63.1%) of whom received testing. Fifty-nine (8.7%) of 679 contacts tested positive; 15 (17.4%) of 86 index cases resulted in ≥2 positive contacts. Among 55 persons testing positive with available symptom data, 31 (56.4%) were asymptomatic. Highest SAR were in indoor, high-contact sports settings (23.8%, 95% confidence interval [CI] 12.7, 33.3), staff meetings/lunches (18.2%, CI 4.5-31.8), and elementary school classrooms (9.5%, CI 6.5-12.5). SAR was higher for staff (13.1%, CI 9.0-17.2) versus student index cases (5.8%, CI 3.6-8.0) and for symptomatic (10.9%, CI 8.1-13.9) versus asymptomatic index cases (3.0%, CI 1.0-5.5). CONCLUSIONS Indoor sports may pose a risk to the safe operation of in-person learning. Preventing infection in staff members, through measures that include COVID-19 vaccination, is critical to reducing in-school transmission. Because many positive contacts were asymptomatic, contact tracing should be paired with testing, regardless of symptoms.
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Affiliation(s)
- Jenna R Gettings
- Georgia Department of Public Health, Atlanta, GA, USA.,COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | - Jeremy A W Gold
- COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | - Anne Kimball
- COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | | | | | | | | | | | | | | | - Emeka Oraka
- COVID-19 Response, CDC, Atlanta, GA, USA.,General Dynamics Information Technology, Falls Church, VA, USA
| | | | | | | | | | | | | | - Abirami Balajee
- COVID-19 Response, CDC, Atlanta, GA, USA.,Maximus Federal, Reston, VA, USA
| | | | | | - Peter Cook
- COVID-19 Response, CDC, Atlanta, GA, USA
| | | | | | | | | | | | - Esther A Kukielka
- COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | - Yan Li
- COVID-19 Response, CDC, Atlanta, GA, USA
| | | | | | - Jasmine Y Nakayama
- COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | | | | | - Caroline Pratt
- COVID-19 Response, CDC, Atlanta, GA, USA.,Epidemic Intelligence Service, CDC, Atlanta, GA, USA
| | | | | | | | | | | | | | - Jing Zhang
- COVID-19 Response, CDC, Atlanta, GA, USA
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