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Campos M, Sempere JM, Galán JC, Moya A, Llorens C, de-Los-Angeles C, Baquero-Artigao F, Cantón R, Baquero F. Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model. ACTA ACUST UNITED AC 2021; 2:uqab011. [PMID: 34642663 PMCID: PMC8499911 DOI: 10.1093/femsml/uqab011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/03/2021] [Indexed: 01/08/2023]
Abstract
Epidemics caused by microbial organisms are part of the natural phenomena of increasing biological complexity. The heterogeneity and constant variability of hosts, in terms of age, immunological status, family structure, lifestyle, work activities, social and leisure habits, daily division of time and other demographic characteristics make it extremely difficult to predict the evolution of epidemics. Such prediction is, however, critical for implementing intervention measures in due time and with appropriate intensity. General conclusions should be precluded, given that local parameters dominate the flow of local epidemics. Membrane computing models allows us to reproduce the objects (viruses and hosts) and their interactions (stochastic but also with defined probabilities) with an unprecedented level of detail. Our LOIMOS model helps reproduce the demographics and social aspects of a hypothetical town of 10 320 inhabitants in an average European country where COVID-19 is imported from the outside. The above-mentioned characteristics of hosts and their lifestyle are minutely considered. For the data in the Hospital and the ICU we took advantage of the observations at the Nursery Intensive Care Unit of the Consortium University General Hospital, Valencia, Spain (included as author). The dynamics of the epidemics are reproduced and include the effects on viral transmission of innate and acquired immunity at various ages. The model predicts the consequences of delaying the adoption of non-pharmaceutical interventions (between 15 and 45 days after the first reported cases) and the effect of those interventions on infection and mortality rates (reducing transmission by 20, 50 and 80%) in immunological response groups. The lockdown for the elderly population as a single intervention appears to be effective. This modeling exercise exemplifies the application of membrane computing for designing appropriate multilateral interventions in epidemic situations.
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Affiliation(s)
- M Campos
- Department of Microbiology, Ramón y Cajal University Hospital, M-607, km 9,1 28034 Madrid, Spain
| | - J M Sempere
- Valencian Research Institute for Artificial Intelligence (VRAIN), Universitat Politècnica de Valencia, Camí de Vera s/n, 46022 Valencia, Spain
| | - J C Galán
- Department of Microbiology, Ramón y Cajal University Hospital, M-607, km 9,1 28034 Madrid, Spain
| | - A Moya
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, M-607, km 9,1. 28034 Madrid, Spain
| | - C Llorens
- Biotechvana, Valencia, CEEI Building, Valencia Technological Park., C. agustín Escardino 9, 46980, Paterna, Valencia, Spain
| | - C de-Los-Angeles
- Nursery Unit, Intensive Care Unit and Pain Therapy, Consortium University General Hospital (CHGUV)., Av. Tres Cruces 2, 46014 Valencia, Spain
| | - F Baquero-Artigao
- Department of Infectious Diseases and Tropical Pediatrics, La Paz University Hospital., Av. Monforte de Lemos 2D, 28029 Madrid, Spain
| | - R Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, M-607, km 9,1 28034 Madrid, Spain
| | - F Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, M-607, km 9,1 28034 Madrid, Spain
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152
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Zhang K, Shoukat A, Crystal W, Langley JM, Galvani AP, Moghadas SM. Routine saliva testing for the identification of silent coronavirus disease 2019 (COVID-19) in healthcare workers. Infect Control Hosp Epidemiol 2021; 42:1189-1193. [PMID: 33427141 PMCID: PMC7870913 DOI: 10.1017/ice.2020.1413] [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] [Received: 08/15/2020] [Revised: 10/29/2020] [Accepted: 12/24/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Current COVID-19 guidelines recommend symptom-based screening and regular nasopharyngeal (NP) testing for healthcare personnel in high-risk settings. We sought to estimate case detection percentages with various routine NP and saliva testing frequencies. DESIGN Simulation modeling study. METHODS We constructed a sensitivity function based on the average infectiousness profile of symptomatic coronavirus disease 2019 (COVID-19) cases to determine the probability of being identified at the time of testing. This function was fitted to reported data on the percent positivity of symptomatic COVID-19 patients using NP testing. We then simulated a routine testing program with different NP and saliva testing frequencies to determine case detection percentages during the infectious period, as well as the presymptomatic stage. RESULTS Routine biweekly NP testing, once every 2 weeks, identified an average of 90.7% (SD, 0.18) of cases during the infectious period and 19.7% (SD, 0.98) during the presymptomatic stage. With a weekly NP testing frequency, the corresponding case detection percentages were 95.9% (SD, 0.18) and 32.9% (SD, 1.23), respectively. A 5-day saliva testing schedule had a similar case detection percentage as weekly NP testing during the infectious period, but identified ~10% more cases (mean, 42.5%; SD, 1.10) during the presymptomatic stage. CONCLUSION Our findings highlight the utility of routine noninvasive saliva testing for frontline healthcare workers to protect vulnerable patient populations. A 5-day saliva testing schedule should be considered to help identify silent infections and prevent outbreaks in nursing homes and healthcare facilities.
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Affiliation(s)
- Kevin Zhang
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Affan Shoukat
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, United States
| | - William Crystal
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, United States
| | - Joanne M. Langley
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre and Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, United States
| | - Seyed M. Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
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153
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Kim KS, Iwanami S, Oda T, Fujita Y, Kuba K, Miyazaki T, Ejima K, Iwami S. Incomplete antiviral treatment may induce longer durations of viral shedding during SARS-CoV-2 infection. Life Sci Alliance 2021; 4:e202101049. [PMID: 34344719 PMCID: PMC8340032 DOI: 10.26508/lsa.202101049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
The duration of viral shedding is determined by a balance between de novo infection and removal of infected cells. That is, if infection is completely blocked with antiviral drugs (100% inhibition), the duration of viral shedding is minimal and is determined by the length of virus production. However, some mathematical models predict that if infected individuals are treated with antiviral drugs with efficacy below 100%, viral shedding may last longer than without treatment because further de novo infections are driven by entry of the virus into partially protected, uninfected cells at a slower rate. Using a simple mathematical model, we quantified SARS-CoV-2 infection dynamics in non-human primates and characterized the kinetics of viral shedding. We counterintuitively found that treatments initiated early, such as 0.5 d after virus inoculation, with intermediate to relatively high efficacy (30-70% inhibition of virus replication) yield a prolonged duration of viral shedding (by about 6.0 d) compared with no treatment.
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Affiliation(s)
- Kwang Su Kim
- Interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shoya Iwanami
- Interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takafumi Oda
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhisa Fujita
- Interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
| | - Taiga Miyazaki
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Keisuke Ejima
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA
| | - Shingo Iwami
- Interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan
- Science Groove Inc., Fukuoka, Japan
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154
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Chung E, Chow EJ, Wilcox NC, Burstein R, Brandstetter E, Han PD, Fay K, Pfau B, Adler A, Lacombe K, Lockwood CM, Uyeki TM, Shendure J, Duchin JS, Rieder MJ, Nickerson DA, Boeckh M, Famulare M, Hughes JP, Starita LM, Bedford T, Englund JA, Chu HY. Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting. JAMA Pediatr 2021; 175:e212025. [PMID: 34115094 PMCID: PMC8491103 DOI: 10.1001/jamapediatrics.2021.2025] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023]
Abstract
Importance The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. Objective To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. Design, Setting, and Participants This cross-sectional study used a respiratory virus surveillance platform in persons of all ages to detect community COVID-19 cases from March 23 to November 9, 2020. A population-based convenience sample of children younger than 18 years and adults in King County, Washington, who enrolled online for home self-collection of upper respiratory samples for SARS-CoV-2 testing were included. Exposures Detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) from participant-collected samples. Main Outcomes and Measures RT-PCR-confirmed SARS-CoV-2 infection, with Ct values stratified by age and symptoms. Results Among 555 SARS-CoV-2-positive participants (mean [SD] age, 33.7 [20.1] years; 320 were female [57.7%]), 47 of 123 children (38.2%) were asymptomatic compared with 31 of 432 adults (7.2%). When symptomatic, fewer symptoms were reported in children compared with adults (mean [SD], 1.6 [2.0] vs 4.5 [3.1]). Symptomatic individuals had lower Ct values (which corresponded to higher viral RNA levels) than asymptomatic individuals (adjusted estimate for children, -3.0; 95% CI, -5.5 to -0.6; P = .02; adjusted estimate for adults, -2.9; 95% CI, -5.2 to -0.6; P = .01). The difference in mean Ct values was neither statistically significant between symptomatic children and symptomatic adults (adjusted estimate, -0.7; 95% CI, -2.2 to 0.9; P = .41) nor between asymptomatic children and asymptomatic adults (adjusted estimate, -0.6; 95% CI, -4.0 to 2.8; P = .74). Conclusions and Relevance In this community-based cross-sectional study, SARS-CoV-2 RNA levels, as determined by Ct values, were significantly higher in symptomatic individuals than in asymptomatic individuals and no significant age-related differences were found. Further research is needed to understand the role of SARS-CoV-2 RNA levels and viral transmission.
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Affiliation(s)
- Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Eric J. Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Naomi C. Wilcox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Roy Burstein
- Institute for Disease Modeling, Seattle, Washington
| | - Elisabeth Brandstetter
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle, Washington
| | | | - Christina M. Lockwood
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Timothy M. Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Jeffrey S. Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Public Health—Seattle & King County, Seattle, Washington
| | - Mark J. Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Deborah A. Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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155
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Sell SL, Prough DS, Weisz HA, Widen SG, Hellmich HL. Leveraging publicly available coronavirus data to identify new therapeutic targets for COVID-19. PLoS One 2021; 16:e0257965. [PMID: 34587192 PMCID: PMC8480897 DOI: 10.1371/journal.pone.0257965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023] Open
Abstract
Many important questions remain regarding severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the viral pathogen responsible for COVID-19. These questions include the mechanisms explaining the high percentage of asymptomatic but highly infectious individuals, the wide variability in disease susceptibility, and the mechanisms of long-lasting debilitating effects. Bioinformatic analysis of four coronavirus datasets representing previous outbreaks (SARS-CoV-1 and MERS-CoV), as well as SARS-CoV-2, revealed evidence of diverse host factors that appear to be coopted to facilitate virus-induced suppression of interferon-induced innate immunity, promotion of viral replication and subversion and/or evasion of antiviral immune surveillance. These host factors merit further study given their postulated roles in COVID-19-induced loss of smell and brain, heart, vascular, lung, liver, and gut dysfunction.
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Affiliation(s)
- Stacy L. Sell
- Department of Anesthesiology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Donald S. Prough
- Department of Anesthesiology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Harris A. Weisz
- Department of Anesthesiology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Steve G. Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Helen L. Hellmich
- Department of Anesthesiology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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156
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Cheng HM, Zhao X, Lim WS, Tan BJM, Tey HL. Factors affecting duration of SARS-Cov-2 viral shedding in mildly symptomatic patients isolated in a community facility. PLoS One 2021; 16:e0257565. [PMID: 34570805 PMCID: PMC8476038 DOI: 10.1371/journal.pone.0257565] [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: 05/20/2021] [Accepted: 09/05/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction Mildly symptomatic cases of Covid-19 in previously-well individuals form the majority of infections and also serve as potent vectors of transmission. The factors affecting the duration of SARS-CoV-2 RNA viral shedding (DVS) in these patients remain largely unknown. Objectives To perform a systematic analysis of the clinical, radiologic, laboratory investigations in patients with few comorbidities infected with mild Covid-19 to identify factors associated with the DVS. Methods In this retrospective cohort study, patients with mild or asymptomatic Covid-19 were included. Baseline characteristics including age, nationality, comorbidities, concomitant medications, and type of isolation arrangement in the facility (single or in pairs) were collected. Clinical features and radiologic/haematologic findings were also collected. Taking day 28 as the cut-off, 187 patients who had a negative swab result up to day 28 (no prolonged DVS) were compared to 126 patients with a persistently positive result on or after day 28 (prolonged DVS). Results Of 964 consecutive patients included, 851 (88.3%) patients were symptomatic. 266 patients had a documented negative RT-PCR assay with a median DVS of 25 days (range: 13 to 96 days; interquartile range (IQR): 22 to 33 days). Patients isolated in pairs were associated with prolonged DVS (OR: 2.7; 95% CI: 1.7 to 4.5; p<0.0001) compared to those isolated individually. Among vital signs, only tachycardia was associated with prolonged DVS (OR: 2.6; 95% CI: 1.0 to 7.1; p = 0.03). Amongst investigations, only a raised CRP was associated with prolonged DVS (OR: 2.7; 95% CI: 1.1 to 6.8; p = 0.02). Conclusions In young, mildly symptomatic Covid-19 patients, prolonged DVS was associated with being isolated in pairs compared to individually. In situations where a negative RT-PCR test result is required, retesting in patients who were not isolated individually, or who had baseline tachycardia or a raised CRP, may be delayed to increase the yield of a negative result.
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Affiliation(s)
| | | | - Wei Shyann Lim
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Beatrice Jia Min Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hong Liang Tey
- National Skin Centre, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- * E-mail: ,
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157
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Fröberg J, Gillard J, Philipsen R, Lanke K, Rust J, van Tuijl D, Teelen K, Bousema T, Simonetti E, van der Gaast-de Jongh CE, Bos M, van Kuppeveld FJ, Bosch BJ, Nabuurs-Franssen M, van der Geest-Blankert N, van Daal C, Huynen MA, de Jonge MI, Diavatopoulos DA. SARS-CoV-2 mucosal antibody development and persistence and their relation to viral load and COVID-19 symptoms. Nat Commun 2021; 12:5621. [PMID: 34556667 PMCID: PMC8460778 DOI: 10.1038/s41467-021-25949-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022] Open
Abstract
Although serological studies have shown that antibodies against SARS-CoV-2 play an important role in protection against (re)infection, the dynamics of mucosal antibodies during primary infection and their potential impact on viral load and the resolution of disease symptoms remain unclear. During the first pandemic wave, we assessed the longitudinal nasal antibody response in index cases with mild COVID-19 and their household contacts. Nasal and serum antibody responses were analysed for up to nine months. Higher nasal receptor binding domain and spike protein-specific antibody levels at study inclusion were associated with lower viral load. Older age was correlated with more frequent COVID-19 related symptoms. Receptor binding domain and spike protein-specific mucosal antibodies were associated with the resolution of systemic, but not respiratory symptoms. Finally, receptor binding domain and spike protein-specific mucosal antibodies remained elevated up to nine months after symptom onset.
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Affiliation(s)
- Janeri Fröberg
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Joshua Gillard
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
- Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Ria Philipsen
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
- RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen, The Netherlands
| | - Kjerstin Lanke
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Joyce Rust
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
- RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen, The Netherlands
| | - Diana van Tuijl
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
- RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen, The Netherlands
| | - Karina Teelen
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Teun Bousema
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Elles Simonetti
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Christa E van der Gaast-de Jongh
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Mariska Bos
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Frank J van Kuppeveld
- Utrecht University, Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Utrecht University, Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Utrecht, The Netherlands
| | - Marrigje Nabuurs-Franssen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Charlotte van Daal
- Department of Occupational Health, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Dimitri A Diavatopoulos
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, 6525 GA, Nijmegen, The Netherlands.
- Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands.
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158
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Bailie CR, Leung VK, Orr E, Singleton E, Kelly C, Buising KL, Cowie BC, Kirk MD, Sullivan SG, Marshall C. Performance of hospital-based contact tracing for COVID-19 during Australia's second wave. Infect Dis Health 2021; 27:15-22. [PMID: 34563476 PMCID: PMC8457622 DOI: 10.1016/j.idh.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/26/2021] [Accepted: 09/04/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Hospital-based contact tracing aims to limit spread of COVID-19 within healthcare facilities. In large outbreaks, this can stretch resources and workforce due to quarantine of uninfected staff. We analysed the performance of a manual contact tracing system for healthcare workers (HCW) at a multi-site healthcare facility in Melbourne, Australia, from June-September 2020, during an epidemic of COVID-19. METHODS All HCW close contacts were quarantined for 14 days, and tested around day 11, if not already diagnosed with COVID-19. We examined the prevalence and timing of symptoms in cases detected during quarantine, described this group as proportions of all close contacts and of all cases, and used logistic regression to assess factors associated with infection. RESULTS COVID-19 was diagnosed during quarantine in 52 furloughed HCWs, from 483 quarantine episodes (11%), accounting for 19% (52/270) of total HCW cases. In 361 exposures to a clear index case, odds of infection were higher after contact with an infectious patient compared to an infectious HCW (aOR: 4.69, 95% CI: 1.98-12.14). Contact with cases outside the workplace increased odds of infection compared to workplace contact only (aOR: 7.70, 95% CI: 2.63-23.05). We estimated 30%, 78% and 95% of symptomatic cases would develop symptoms by days 3, 7, and 11 of quarantine, respectively. CONCLUSION In our setting, hospital-based contact tracing detected and contained a significant proportion of HCW cases, without excessive quarantine of uninfected staff. Effectiveness of contact tracing is determined by a range of dynamic factors, so system performance should be monitored in real-time.
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Affiliation(s)
- Christopher R Bailie
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne VIC, Australia; National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia.
| | - Vivian K Leung
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne VIC, Australia
| | - Elizabeth Orr
- The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | | | - Cate Kelly
- The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Kirsty L Buising
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin C Cowie
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Melbourne, VIC, Australia; Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Reference Laboratory, Melbourne, VIC, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne VIC, Australia; Doherty Department, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne VIC, Australia
| | - Caroline Marshall
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Melbourne, VIC, Australia; Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
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de la Guardia C, Rangel G, Villarreal A, Goodridge A, Fernández PL, Lleonart R. Development of in-house, indirect ELISAs for the detection of SARS-CoV-2 spike protein-associated serology in COVID-19 patients in Panama. PLoS One 2021; 16:e0257351. [PMID: 34520491 PMCID: PMC8439474 DOI: 10.1371/journal.pone.0257351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/27/2021] [Indexed: 12/18/2022] Open
Abstract
COVID-19 is the name of the acute respiratory disease caused by the new coronavirus SARS-CoV-2, a close relative of those that caused the severe outbreaks of SARS and MERS several years ago. Since first appearance on December of 2019, the COVID-19 pandemic has cause extremely high levels of mortality, morbidity, global economic breakdown, and the consequent human suffering. The main diagnostic test for the confirmation of symptomatic individuals is the detection of viral RNA by reverse transcriptase-quantitative real time PCR (RT-PCR). Additionally, serology techniques, such as ELISA are useful to measure the antibodies produced in humans after contact with the virus, as well as the direct presence of viral antigens. In this study we aim to assemble and evaluate four ELISA assays to measure the presence of IgG or IgM specific for the viral Spike protein in COVID-19 patients, using either the full recombinant SARS-CoV-2 Spike protein or the fragment corresponding to the receptor binding domain. As a control, we analyzed a group of pre-pandemic serum samples obtained before 2017. Strong reactivity was observed against both antigens. A few pre-pandemic samples displayed high OD values, suggesting the possibility of some cross reactivity. All four assays show very good repeatability, both intra- and inter-assay. Receiver operating characteristic analysis allowed the definition of cutoffs and evaluation of performance for each ELISA by estimation of the area under the curve. This performance parameter was high for all tests (AUC range: 0.98-0.99). Multiple comparisons between tests revealed no significant difference between each other (P values: 0.24-0.95). Our results show that both antigens are effective to detect both specific IgG and IgM antibodies, with high sensitivity (range 0.92-0.99), specificity (range 0.93-0.97) and congruence with the RT-PCR test (Cohen´s Kappa range 0.87-0.93). These assays will allow health authorities to have a new tool to estimate seroprevalence, in order to manage and improve the severe sanitary situation caused by this virus.
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Affiliation(s)
- Carolina de la Guardia
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
| | - Giselle Rangel
- Centro de Neurociencias y Unidad de Investigación Clínica, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
| | - Alcibiades Villarreal
- Centro de Neurociencias y Unidad de Investigación Clínica, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
| | - Amador Goodridge
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
| | - Patricia L. Fernández
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad de Panama, Panama
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160
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Olearo F, Nörz D, Hoffman A, Grunwald M, Gatzemeyer K, Christner M, Both A, Campos CEB, Braun P, Andersen G, Pfefferle S, Zapf A, Aepfelbacher M, Knobloch JKM, Lütgehetmann M. Clinical performance and accuracy of a qPCR-based SARS-CoV-2 mass-screening workflow for healthcare-worker surveillance using pooled self-sampled gargling solutions: A cross-sectional study. J Infect 2021; 83:589-593. [PMID: 34499947 PMCID: PMC8420133 DOI: 10.1016/j.jinf.2021.08.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
Introduction The large number of asymptomatic SARS-CoV-2 infections necessitates general screening of employees. We evaluate the performance of a SARS-CoV-2 screening program in asymptomatic healthcare-workers (HCW), utilizing self-sampled gargling-solution and sample pooling for RT-qPCR. Methods We conducted a cross-sectional retrospective study to collect real-life data on the performance of a screening-workflow based on automated-pooling and high-throughput qPCR testing over a 3-month-period at the University Hospital Hamburg. Results Matrix validation reveals that lower limit of detection for SARS-CoV-2 RNA in gargling-solution was 180 copies/mL (5-sample-pool). A total of 55,122 self-collected gargle samples (= 7513 HCWs) was analyzed. The median time to result was 8.5 hours (IQR 7.2–10.8). Of 11,192 pools analyzed, 11,041 (98.7%) were negative, 69 (0.6%) were positive and 82 (0.7%) were invalid. Individual testing of pool participants revealed 57 SARS-CoV-2 previously unrecognized infections. All 57 HCWs were either pre-symptomatic or asymptomatic (prevalence 0.76%,CI95%0.58–0.98%). Accuracy based on HCWs with gargle-solution and NP-swab available within 3-day-interval (N = 521) was 99.5% (CI95%98.3–99.9%), sensitivity 88.9% (CI95%65.3–98.6%) while specificity 99.8% (CI95%98.9–99.9). Conclusion This workflow was highly effective in identifying SARS-CoV-2 positive HCWs, thereby lowering the potential of inter-HCW and HCW-patient transmissions. Automated-sample-pooling helped to conserve qPCR reagents and represents a promising alternative strategy to antigen testing in mass-screening programs.
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Affiliation(s)
- Flaminia Olearo
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Dominik Nörz
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Armin Hoffman
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Moritz Grunwald
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Kimani Gatzemeyer
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Martin Christner
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Anna Both
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Cristina Elena Belmar Campos
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Platon Braun
- Department of Occupational Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Andersen
- Department of Occupational Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Pfefferle
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Antonia Zapf
- Center for Experimental Medicine, Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Johannes K M Knobloch
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany
| | - Marc Lütgehetmann
- Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, Hamburg D-20246, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany.
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161
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O'Connor SL, O'Connor DH. Initial Evaluation of a Mobile SARS-CoV-2 RT-LAMP Testing Strategy. J Biomol Tech 2021; 32:137-147. [PMID: 35035293 PMCID: PMC8730517 DOI: 10.7171/jbt.21-32-03-009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16, 2020, to November 19, 2020, surveillance samples (n = 4704) were collected from volunteers and tested for SARS-CoV-2 at 5 sites. Twenty-one samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, whereas 8 tested negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the false-negative rate of the RT-LAMP assay only from July 16, 2020, to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or fewer and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP-negative pools (2493 total samples) testing positive in the more-sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and that can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M. Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D. Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T. McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A. Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M. Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Mason I. Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A. Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G. Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K. Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S. Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E. Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R. Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E. Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V. Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M. Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M. Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M. Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K. Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D. Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B. Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L. Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M. Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C. Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L. O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H. O'Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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Roque M, Proudfoot K, Mathys V, Yu S, Krieger N, Gernon T, Gokli K, Hamilton S, Cook C, Fong Y. A review of nasopharyngeal swab and saliva tests for SARS-CoV-2 infection: Disease timelines, relative sensitivities, and test optimization. J Surg Oncol 2021; 124:465-475. [PMID: 34091905 PMCID: PMC8242677 DOI: 10.1002/jso.26561] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022]
Abstract
Testing is an essential part of containment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This review summarizes studies for SARS-CoV-2 infection and testing. Nasopharyngeal samples are best at sensitivity detection, especially in early stages of disease and in asymptomatic individuals. Current swab processing involves a 100- to 1000-fold dilution of the patient sample. Future optimization of testing should focus on using smaller volumes of viral transport media and swab designs to increase comfort and increased viral adhesion.
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Affiliation(s)
- Marylin Roque
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Kevin Proudfoot
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Vadim Mathys
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Sophie Yu
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Natalie Krieger
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Thomas Gernon
- Department of SurgeryCity of Hope Medical CenterDuarteCaliforniaUSA
| | - Kash Gokli
- Department of EngineeringHarvey Mudd CollegeClaremontCaliforniaUSA
| | - Stanley Hamilton
- Department of PathologyCity of Hope Medical CenterDuarteCaliforniaUSA
| | - Colin Cook
- Department of SurgeryCity of Hope Medical CenterDuarteCaliforniaUSA
| | - Yuman Fong
- Department of SurgeryCity of Hope Medical CenterDuarteCaliforniaUSA
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Pickering S, Batra R, Merrick B, Snell LB, Nebbia G, Douthwaite S, Reid F, Patel A, Kia Ik MT, Patel B, Charalampous T, Alcolea-Medina A, Lista MJ, Cliff PR, Cunningham E, Mullen J, Doores KJ, Edgeworth JD, Malim MH, Neil SJD, Galão RP. Comparative performance of SARS-CoV-2 lateral flow antigen tests and association with detection of infectious virus in clinical specimens: a single-centre laboratory evaluation study. THE LANCET. MICROBE 2021; 2:e461-e471. [PMID: 34226893 PMCID: PMC8245061 DOI: 10.1016/s2666-5247(21)00143-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Lateral flow devices (LFDs) for rapid antigen testing are set to become a cornerstone of SARS-CoV-2 mass community testing, although their reduced sensitivity compared with PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is, therefore, essential for successful implementation. We evaluated six commercial LFDs and assessed their correlation with infectious virus culture and PCR cycle threshold (Ct) values. METHODS In a single-centre, laboratory evaluation study, we did a head-to-head comparison of six LFDs commercially available in the UK: Innova Rapid SARS-CoV-2 Antigen Test, Spring Healthcare SARS-CoV-2 Antigen Rapid Test Cassette, E25Bio Rapid Diagnostic Test, Encode SARS-CoV-2 Antigen Rapid Test Device, SureScreen COVID-19 Rapid Antigen Test Cassette, and SureScreen COVID-19 Rapid Fluorescence Antigen Test. We estimated the specificities and sensitivities of the LFDs using stored naso-oropharyngeal swabs collected at St Thomas' Hospital (London, UK) for routine diagnostic SARS-CoV-2 testing by real-time RT-PCR (RT-rtPCR). Swabs were from inpatients and outpatients from all departments of St Thomas' Hospital, and from health-care staff (all departments) and their household contacts. SARS-CoV-2-negative swabs from the same population (confirmed by RT-rtPCR) were used for comparative specificity determinations. All samples were collected between March 23 and Oct 27, 2020. We determined the limit of detection (LOD) for each test using viral plaque-forming units (PFUs) and viral RNA copy numbers of laboratory-grown SARS-CoV-2. Additionally, LFDs were selected to assess the correlation of antigen test result with RT-rtPCR Ct values and positive viral culture in Vero E6 cells. This analysis included longitudinal swabs from five infected inpatients with varying disease severities. Furthermore, the sensitivities of available LFDs were assessed in swabs (n=23; collected from Dec 4, 2020, to Jan 12, 2021) confirmed to be positive (RT-rtPCR and whole-genome sequencing) for the B.1.1.7 variant, which was the dominant genotype in the UK at the time of study completion. FINDINGS All LFDs showed high specificity (≥98·0%), except for the E25Bio test (86·0% [95% CI 77·9-99·9]), and most tests reliably detected 50 PFU/test (equivalent SARS-CoV-2 N gene Ct value of 23·7, or RNA copy number of 3 × 106/mL). Sensitivities of the LFDs on clinical samples ranged from 65·0% (55·2-73·6) to 89·0% (81·4-93·8). These sensitivities increased to greater than 90% for samples with Ct values of lower than 25 for all tests except the SureScreen fluorescence (SureScreen-F) test. Positive virus culture was identified in 57 (40·4%) of 141 samples; 54 (94·7%) of the positive cultures were from swabs with Ct values lower than 25. Among the three LFDs selected for detailed comparisons (the tests with highest sensitivity [Innova], highest specificity [Encode], and alternative technology [SureScreen-F]), sensitivity of the LFDs increased to at least 94·7% when only including samples with detected viral growth. Longitudinal studies of RT-rtPCR-positive samples (tested with Innova, Encode, and both SureScreen-F and the SureScreen visual [SureScreen-V] test) showed that most of the tests identified all infectious samples as positive. Test performance (assessed for Innova and SureScreen-V) was not affected when reassessed on swabs positive for the UK variant B.1.1.7. INTERPRETATION In this comprehensive comparison of antigen LFDs and virus infectivity, we found a clear relationship between Ct values, quantitative culture of infectious virus, and antigen LFD positivity in clinical samples. Our data support regular testing of target groups with LFDs to supplement the current PCR testing capacity, which would help to rapidly identify infected individuals in situations in which they would otherwise go undetected. FUNDING King's Together Rapid COVID-19, Medical Research Council, Wellcome Trust, Huo Family Foundation, UK Department of Health, National Institute for Health Research Comprehensive Biomedical Research Centre.
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Affiliation(s)
- Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Fiona Reid
- School of Population Health and Environmental Sciences, King's College London, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mark Tan Kia Ik
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Bindi Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Penelope R Cliff
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Emma Cunningham
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jane Mullen
- Viapath Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
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Mishra B, Ranjan J, Purushotham P, Saha S, Payal P, Kar P, Das S, Deshmukh V. High proportion of low cycle threshold value as an early indicator of COVID-19 surge. J Med Virol 2021; 94:240-245. [PMID: 34460115 PMCID: PMC8661879 DOI: 10.1002/jmv.27307] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/05/2021] [Accepted: 08/26/2021] [Indexed: 12/23/2022]
Abstract
Many countries in the world are experiencing a recent surge in COVID‐19 cases. This is mainly attributed to the emergence of new SARS‐CoV‐2 variants. Genome sequencing is the only means to detect the evolving virus mutants and emerging variants. Cycle threshold values have an inverse relationship with viral load and lower Ct values are also found to be associated with increased infectivity. In this study, we propose to use Ct values as an early indicator for upcoming COVID‐19 waves. A retrospective cross‐sectional study was carried out to analyze the Ct values of positive samples reported during the first wave and second wave (April 2020–May 2021). Median Ct values of confirmatory genes were taken into consideration for comparison. Ct values below 25, >25–30, and >30 were categorized as high, moderate, and low viral load respectively. Our study found a significantly higher proportion of positive samples with a low Ct value (<25) across age groups and gender during the second wave of the COVID‐19 pandemic. A higher proportion of positive samples with a low Ct value (high viral load) may act as an early indicator of an upcoming surge. A surge in COVID‐19 cases is predominantly due to emergence of new SARS‐CoV‐2 variants. Cycle threshold values have an inverse relationship with viral load and also associated with infectivity. Our study found a significantly higher proportion of positive samples with low Ct value (<25) across age groups and gender during the second wave of COVID‐19 pandemic. Higher proportion of positive samples with low Ct value (high viral load) may act as an early indicator of an upcoming surge.
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Affiliation(s)
- Baijayantimala Mishra
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Jai Ranjan
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Prashanth Purushotham
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Swarnatrisha Saha
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Poesy Payal
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Punyatoya Kar
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Sivasankar Das
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Vaishnavi Deshmukh
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
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Lubart E, Gal G, Mizrahi EH, Tzabary A, Baumohl E, Pinco E, Idkiedek Z, Ali EH, Berger M, Goltsman G. Time to resolution of infection in COVID-19 patients: the experience of a tertiary medical center in Israel. Jpn J Infect Dis 2021; 75:144-147. [PMID: 34470961 DOI: 10.7883/yoken.jjid.2021.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the coronavirus disease spreading, reports indicated that young patients are usually asymptomatic with a short convalescence period. The current study compares the time to resolution of infection in symptomatic versus asymptomatic patients. Seventy- six patients aged 44.4±23.3 years were admitted to the COVID-19 Unit during the study period. Data was collected from patients' records. Throat and nasal swabs for the RT-PCR COVID-19 were collected. Time to resolution of infection was defined as the number of days from the date of the first COVID-19 positive outcome to the second consecutive negative PCR results. Most patients showed between 1-6 COVID-19 signs and symptoms (71.1%) and the rest were asymptomatic. No association was found between the time to resolution of infection and the presence of COVID-19 signs and symptoms (symptomatic: Md 10.0 95% CI 8.4-11.6; asymptomatic: Md 15.0 95% CI 10.5-15.5; p=0.54). Age was not correlated with the number of COVID-19 signs and symptoms (r=0.13, p=0.37) and with the time to resolution of infection (r=0.06, p=0.58). In mild to moderate symptomatic patients, the time to resolution of infection from COVID-19 is not different from asymptomatic patients.
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Affiliation(s)
- Emily Lubart
- Internal medicine department. The Sackler Faculty of Medicine, Tel Aviv University, Israel.,Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Gilad Gal
- School of Behavioral Sciences, Tel Aviv-Yaffo Academic College, Israel
| | - Eliyahu H Mizrahi
- Internal medicine department. The Sackler Faculty of Medicine, Tel Aviv University, Israel.,Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Ahuva Tzabary
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Ehuda Baumohl
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Erica Pinco
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Zuhdi Idkiedek
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Eisa Haj Ali
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Maya Berger
- Acute Geriatric Department A. Shmuel Harofe Geriatric Medical Center, Israel
| | - Galina Goltsman
- Internal medicine department. The Sackler Faculty of Medicine, Tel Aviv University, Israel.,Internal medicne G department, Asaf Harofeh Medical Center, Israel
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166
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Kanta P, Singh S, Chhikara K, Goyal K, Ghosh A, Verma V, Suri V, Singh MP. Correlation of SARS-CoV-2 Viral Load in Different Population Subsets: A Study from a Tertiary Care North Indian Hospital. Int J Appl Basic Med Res 2021; 11:182-187. [PMID: 34458122 PMCID: PMC8360218 DOI: 10.4103/ijabmr.ijabmr_61_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/15/2021] [Indexed: 11/04/2022] Open
Abstract
Background The correlation of SARS-CoV-2 viral load with disease severity in different population subsets is still elusive. There is a scarcity of literature regarding this aspect in Indian Population. Aim To study retrospectively the risk factors and the role of viral load with disease severity among different age groups of North Indian population. Methods Here we quantified the viral load of 239 positive participants and collected data retrospectively from April 2020 to May 2020 and categorised the patients as per disease severity and population subsets. Results Asymptomatic patients were found to have higher viral load than the symptomatic patients, though the difference was not found to be statistically significant. The logistic regression analysis showed that contact with laboratory confirmed cases, SARI and ILI were independent risk factors for acquiring COVID-19 infection. Conclusion SARS-CoV-2 viral load is not significantly associated with disease severity among different population subsets. However, there is a need to carry out more studies with a larger number of patients to validate and confirm the above findings.
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Affiliation(s)
- Poonam Kanta
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shashank Singh
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Komal Chhikara
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Kapil Goyal
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Arnab Ghosh
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikas Verma
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikas Suri
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mini Pritam Singh
- Department of Virology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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167
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Iqbal B, Khan M, Shah N, Dawood MM, Jehanzeb V, Shafi M. Comparison of SARS-CoV-2 antigen electrochemiluminescence immunoassay to RT-PCR assay for laboratory diagnosis of COVID-19 in Peshawar. Diagnosis (Berl) 2021; 9:364-368. [PMID: 34455727 DOI: 10.1515/dx-2021-0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Antigen based rapid diagnostic tests possesses a potential to be utilized along with Gold standard methods to detect Covid-19 infection to cope with the demand of testing. The aim of this study was to determine diagnostic accuracy of electrochemiluminescence based automated antigen detection immunoassay comparing with molecular based test RT-PCR (Covid-19). METHODS It was a cross-sectional study conducted in RMI Peshawar, from 1st April 2021 till 30th April 2021. The study comprised 170 individuals who were suspected of having Covid-19. Nasopharyngeal samples taken from suspected individuals were analyzed by RT-PCR and automated antigen test (Elecsys SARS-CoV-2 Antigen) simultaneously. The correlation of SARS-CoV-2 antigen with PCR positive and negative cases was analyzed for specificity, sensitivity respectively. RESULTS The ECLIA based Elecsys antigen test (Roche) revealed overall sensitivity 72%, specificity 95% and accuracy of 94.9%. Sensitivity of antigen test progressively declined from 94.3% in Ct <25 to 70.8% in Ct 26-29 and then to 47.2% in Ct 30-35. CONCLUSIONS Based on the findings of our study we conclude that automated antigen testing (Elecsys SARS-CoV-2 Antigen) cannot replace molecular based testing like RT PCR. Elecsys SARS-CoV-2 Ag test should be used complementary to RT-PCR in testing algorithms. Frequent testing strategy should be adopted while using automated antigen testing to overcome its limitation in individuals with low viral loads.
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Affiliation(s)
- Bilal Iqbal
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | - Maria Khan
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | - Noman Shah
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | | | | | - Mohsin Shafi
- Khyber Medical College Peshawar, Peshawar, Pakistan
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168
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Bodini A, Pasquali S, Pievatolo A, Ruggeri F. Underdetection in a stochastic SIR model for the analysis of the COVID-19 Italian epidemic. STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT : RESEARCH JOURNAL 2021; 36:137-155. [PMID: 34483725 PMCID: PMC8397881 DOI: 10.1007/s00477-021-02081-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
We propose a way to model the underdetection of infected and removed individuals in a compartmental model for estimating the COVID-19 epidemic. The proposed approach is demonstrated on a stochastic SIR model, specified as a system of stochastic differential equations, to analyse data from the Italian COVID-19 epidemic. We find that a correct assessment of the amount of underdetection is important to obtain reliable estimates of the critical model parameters. The adaptation of the model in each time interval between relevant government decrees implementing contagion mitigation measures provides short-term predictions and a continuously updated assessment of the basic reproduction number.
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169
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Esteban I, Bergero G, Alves C, Bronstein M, Ziegler V, Wood C, Caballero MT, Wappner D, Libster R, Perez Marc G, Polack FP. Asymptomatic COVID-19 in the elderly: dementia and viral clearance as risk factors for disease progression. Gates Open Res 2021; 5:143. [PMID: 35441127 PMCID: PMC8987012 DOI: 10.12688/gatesopenres.13357.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND SARS-CoV-2 infected individuals ≥60 years old have the highest hospitalization rates and represent >80% fatalities. Within this population, those in long-term facilities represent >50% of the total COVID-19 related deaths per country. Among those without symptoms, the rate of pre-symptomatic illness is unclear, and potential predictors of progression for symptom development are unknown. Our objective was to delineate the natural evolution of asymptomatic SARS-CoV-2 infection in elders and identify determinants of progression. METHODS We established a medical surveillance team monitoring 63 geriatric institutions. When an index COVID-19 case emerged, we tested all other eligible asymptomatic elders ≥75 or >60 years old with at least 1 comorbidity. SARS-CoV-2 infected elders were followed for 28 days. Disease was diagnosed when any COVID-19 manifestation occurred. SARS-CoV-2 load at enrollment, shedding on day 15, and antibody responses were also studied. RESULTS After 28 days of follow-up, 74/113(65%) SARS-CoV-2-infected elders remained asymptomatic. 21/39(54%) pre-symptomatic patients developed hypoxemia and ten pre-symptomatic patients died(median day 13.5,IQR 12). Dementia was the only clinical risk factor associated with disease(OR 2.41(95%CI=1.08, 5.39). In a multivariable logistic regression model, dementia remained as a risk factor for COVID-19 severe disease. Furthermore, dementia status showed a statistically significant different trend when assessing the cumulative probability of developing COVID-19 symptoms(log-rank p=0.027). On day 15, SARS-CoV-2 was detectable in 30% of the asymptomatic group while in 61% of the pre-symptomatic(p=0.012). No differences were observed among groups in RT-PCR mean cycle threshold at enrollment(p=0.391) and in the rates of antibody seropositivity(IgM and IgG against SARS-CoV-2 nucleocapsid protein). CONCLUSIONS In summary, 2/3 of our cohort of SARS-CoV-2 infected elders from vulnerable communities in Argentina remained asymptomatic after 28 days of follow-up with high mortality among those developing symptoms. Dementia and persistent SARS-CoV-2 shedding were associated with progression from asymptomatic to symptomatic infection.
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Affiliation(s)
| | | | | | | | | | | | - Mauricio T. Caballero
- INFANT Foundation, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Wappner
- iTrials, Buenos Aires, Argentina
- Swiss Medical Group, Buenos Aires, Argentina
| | - Romina Libster
- INFANT Foundation, Buenos Aires, Argentina
- iTrials, Buenos Aires, Argentina
| | - Gonzalo Perez Marc
- Hospital Militar Central, Buenos Aires, Argentina
- iTrials, Buenos Aires, Argentina
| | - Fernando P. Polack
- INFANT Foundation, Buenos Aires, Argentina
- iTrials, Buenos Aires, Argentina
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170
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Martín-Sánchez V, Fernández-Villa T, Carvajal Urueña A, Rivero Rodríguez A, Reguero Celada S, Sánchez Antolín G, Fernández-Vázquez JP. Role of Rapid Antigen Testing in Population-Based SARS-CoV-2 Screening. J Clin Med 2021; 10:3854. [PMID: 34501297 PMCID: PMC8432187 DOI: 10.3390/jcm10173854] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022] Open
Abstract
This study evaluates a population-based screening of asymptomatic people, using a rapid antigen diagnostic test (RADT), in areas of high transmission. To detect sources of SARS-CoV-2 infection, nasopharyngeal samples were taken and were tested using RADT. Confirmatory RT-qPCR tests were performed in both positive and negative cases. The internal validity of the RADT, the prevalence of infection, and the positive and negative predictive values (PPV and NPV) were estimated, based on the percentages of confirmed cases with 95% confidence interval. Of the 157,920 people registered, 50,492 participated in the screening; 50,052 were negative, and 440 were positive on the RADT (0.87%). A total of 221 positive RADT samples were reanalysed using RT-qPCR and 214 were confirmed as positive (96.8%; 95% CI: 93.5-98.7%), while 657 out of 660 negative RADT samples were confirmed as RT-qPCR negative (99.5%; 95% CI 98.7-99.9%). The sensitivity obtained was 65.1% (38.4-90.2%) and the specificity was 99.97% (99.94-99.99%). The prevalence of infection was 1.30% (0.95-2.13%). The PPVs were 95.4% (85.9-98.9%) and 97.9% (93.3-99.5%), respectively, while the NPVs were 99.7% (99.4-100%) and 99.2% (98.7-100%), respectively. The high specificity found allow us to report a high screening performance in asymptomatic patients, even in areas where the prevalence of infection was less than 2%.
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Affiliation(s)
- Vicente Martín-Sánchez
- Research Group on Gene-Environment Interactions and Health (GIIGAS), Institute of Biomedicine (IBIOMED), Universidad de León, 24071 León, Spain;
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública—CIBERESP), 28029 Madrid, Spain
| | - Tania Fernández-Villa
- Research Group on Gene-Environment Interactions and Health (GIIGAS), Institute of Biomedicine (IBIOMED), Universidad de León, 24071 León, Spain;
| | | | - Ana Rivero Rodríguez
- Gerencia de Atención Primaria, 24008 León, Spain; (A.R.R.); (S.R.C.); (J.P.F.-V.)
| | - Sofía Reguero Celada
- Gerencia de Atención Primaria, 24008 León, Spain; (A.R.R.); (S.R.C.); (J.P.F.-V.)
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171
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Alafeef M, Moitra P, Dighe K, Pan D. Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity. ACS NANO 2021; 15:13742-13758. [PMID: 34279093 PMCID: PMC8315249 DOI: 10.1021/acsnano.1c05226] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 05/02/2023]
Abstract
Efficient monitoring of SARS-CoV-2 outbreak requires the use of a sensitive and rapid diagnostic test. Although SARS-CoV-2 RNA can be detected by RT-qPCR, the molecular-level quantification of the viral load is still challenging, time-consuming, and labor-intensive. Here, we report an ultrasensitive hyperspectral sensor (HyperSENSE) based on hafnium nanoparticles (HfNPs) for specific detection of COVID-19 causative virus, SARS-CoV-2. Density functional theoretical calculations reveal that HfNPs exhibit higher changes in their absorption wavelength and light scattering when bound to their target SARS-CoV-2 RNA sequence relative to the gold nanoparticles. The assay has a turnaround time of a few seconds and has a limit of detection in the yoctomolar range, which is 1 000 000-fold times higher than the currently available COVID-19 tests. We demonstrated in ∼100 COVID-19 clinical samples that the assay is highly sensitive and has a specificity of 100%. We also show that HyperSENSE can rapidly detect other viruses such as influenza A H1N1. The outstanding sensitivity indicates the potential of the current biosensor in detecting the prevailing presymptomatic and asymptomatic COVID-19 cases. Thus, integrating hyperspectral imaging with nanomaterials establishes a diagnostic platform for ultrasensitive detection of COVID-19 that can potentially be applied to any emerging infectious pathogen.
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Affiliation(s)
- Maha Alafeef
- Bioengineering Department, The University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health
Sciences Research Facility III, 670 W. Baltimore Street, Baltimore, Maryland 21201,
United States
- Biomedical Engineering Department, Jordan
University of Science and Technology, Irbid 22110,
Jordan
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County,
Interdisciplinary Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland
21250, United States
| | - Parikshit Moitra
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health
Sciences Research Facility III, 670 W. Baltimore Street, Baltimore, Maryland 21201,
United States
| | - Ketan Dighe
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health
Sciences Research Facility III, 670 W. Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County,
Interdisciplinary Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland
21250, United States
| | - Dipanjan Pan
- Bioengineering Department, The University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health
Sciences Research Facility III, 670 W. Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County,
Interdisciplinary Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland
21250, United States
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172
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Bruxvoort K, Tenggardjaja CF, Slezak J, Gullett JC, Broder B, Park CH, Aragones M, Mercado C, Wong K, McLaren S, Jacobsen SJ. Variation in SARS-CoV-2 molecular test sensitivity by specimen types in a large sample of emergency department patients. Am J Emerg Med 2021; 50:381-387. [PMID: 34478943 PMCID: PMC8367656 DOI: 10.1016/j.ajem.2021.08.034] [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: 03/24/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 10/30/2022] Open
Abstract
BACKGROUND Provider-collected nasopharyngeal specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular testing are the standard of care in many clinical settings, but patient-collected saliva and anterior nares specimens are less invasive and more flexible alternatives. Prior studies comparing specimen types for SARS-CoV-2 molecular testing have been limited by small sample sizes and low pretest probability. We conducted a large observational study among symptomatic adults at 7 emergency departments of Kaiser Permanente Southern California to examine sensitivity of SARS-CoV-2 molecular tests by specimen type and patient characteristics. METHODS Provider-collected nasopharyngeal/oropharyngeal (NP/OP) specimens and patient-collected saliva and anterior nares specimens were collected at the same visit and analyzed with the Roche cobas® SARS-CoV-2 assay. Patients were considered truly positive for SARS-CoV-2 if any of the three specimens was positive and negative if all three specimens were negative. Factors associated with discordant and missed positive results were examined with multivariable logistic regression. RESULTS Of 2112 patients, 350 (16.6%) were positive for SARS-CoV-2. Sensitivity of NP/OP was 93.7% (95% confidence interval [CI] 90.6%-96.0%), sensitivity of saliva was 87.7% (83.8%-91.0%), and sensitivity of anterior nares was 85.4% (81.3%-89.0%). Patients ages 18-39 years versus ≥40 years were more likely to have discordant results [adjusted odds ratio (aOR) 1.97 (1.12-3.45)], as were patients with <4 symptoms versus ≥4 [aOR 2.43 (1.39-4.25)]. Cycle threshold values were higher for saliva and anterior nares than NP/OP specimens, as well as for specimens in discordant versus concordant sets and patients with fewer symptoms. CONCLUSION This study provides robust evidence that patient-collected saliva and anterior nares are sensitive for SARS-CoV-2 molecular testing in emergency department settings, particularly among adults ages ≥40 years and those with multiple symptoms. Higher sensitivity of provider-collected NP/OP specimens must be weighed against the benefits of patient-collected specimens in tailored strategies for SARS-CoV-2 testing.
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Affiliation(s)
- Katia Bruxvoort
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA.
| | - Christopher F Tenggardjaja
- Department of Urology, Southern California Permanente Medical Group, 4867 Sunset Boulevard, Los Angeles, CA 90027, USA
| | - Jeff Slezak
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Jonathan C Gullett
- Regional Reference Laboratories, Southern California Permanente Medical Group, 11668 Sherman Way, North Hollywood, CA 91605, USA
| | - Benjamin Broder
- Department of Quality and Clinical Analysis, Southern California Permanente Medical Group, 393 East Walnut Street, Pasadena, CA 91188, USA
| | - Claire H Park
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA; Currently with the Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, 313 North Figueroa Street, Los Angeles, California 90012, USA
| | - Michael Aragones
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Cheryl Mercado
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Katherine Wong
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Steven McLaren
- Regional Reference Laboratories, Southern California Permanente Medical Group, 11668 Sherman Way, North Hollywood, CA 91605, USA
| | - Steven J Jacobsen
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
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Nishimura T, Uwamino Y, Uno S, Kashimura S, Shiraki T, Kurafuji T, Morita M, Noguchi M, Azegami T, Yamada-Goto N, Murai-Takeda A, Yokoyama H, Kuwabara K, Kato S, Matsumoto M, Hirata A, Iida M, Harada S, Ishizaka T, Misawa K, Murata M, Saya H, Amagai M, Kitagawa Y, Takeuchi T, Mori M, Takebayashi T, Hasegawa N. SARS-CoV-2 Infection among Medical Institution Faculty and Healthcare Workers in Tokyo, Japan. Intern Med 2021; 60:2569-2575. [PMID: 34148952 PMCID: PMC8429286 DOI: 10.2169/internalmedicine.7033-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Objective To consider effective measures against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in medical institutions, this study estimated the SARS-CoV-2 infection rate among healthcare workers (HCWs) in Tokyo, Japan, and determined the specific findings for mild coronavirus disease 2019 (COVID-19) cases. Methods This study analyzed the results of serologic tests to detect immunoglobulin G antibodies against SARS-CoV-2 and evaluated the demographic and clinical characteristics of the faculty and HCWs at a Tokyo medical institution in August 2020. The demographic and clinical characteristics of participants with antibody-positive results were compared to those of participants with antibody-negative results. Materials This study recruited 2,341 faculty and HCWs at a Tokyo medical institution, 21 of whom had a COVID-19 history. Results Of the 2,320 participants without a COVID-19 history, 20 (0.862%) had positive serologic test results. A fever and dysgeusia or dysosmia occurred with greater frequency among the participants with positive test results than in those with negative results [odds ratio (OR), 5.475; 95% confidence interval (CI), 1.960-15.293 and OR, 24.158; 95% CI, 2.693-216.720, respectively]. No significant difference was observed in the positivity rate between HCWs providing medical care for COVID-19 patients using adequate protection and other HCWs (OR, 2.514; 95% CI, 0.959-6.588). Conclusion To reduce the risk of COVID-19 spread in medical institutions, faculty and HCWs should follow standard and necessary transmission-based precautions, and those with a fever and dysgeusia or dysosmia should excuse themselves from work as soon as possible.
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Affiliation(s)
- Tomoyasu Nishimura
- Keio University Health Center, Japan
- Department of Infectious Diseases, Keio University School of Medicine, Japan
| | - Yoshifumi Uwamino
- Department of Infectious Diseases, Keio University School of Medicine, Japan
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | - Shunsuke Uno
- Department of Infectious Diseases, Keio University School of Medicine, Japan
| | - Shoko Kashimura
- Department of Infectious Diseases, Keio University School of Medicine, Japan
| | - Toshikimi Shiraki
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | - Toshinobu Kurafuji
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | - Maasa Morita
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | - Masayo Noguchi
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | | | | | | | | | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Minako Matsumoto
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Tamami Ishizaka
- Department of Infectious Diseases, Keio University School of Medicine, Japan
| | - Kana Misawa
- Department of Infectious Diseases, Keio University School of Medicine, Japan
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, Japan
| | - Mitsuru Murata
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
| | - Hideyuki Saya
- Institute for Advanced Medical Research, Keio University School of Medicine, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Medicine, Keio University School of Medicine, Japan
| | | | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Japan
| | - Naoki Hasegawa
- Department of Laboratory Medicine, Keio University School of Medicine, Japan
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174
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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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175
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Astatke M, Tiburzi O, Connolly A. A novel RNA detection technique for point-of-care identification of pathogens. J Immunoassay Immunochem 2021; 43:1955380. [PMID: 34355634 DOI: 10.1080/15321819.2021.1955380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite significant progress in recent years to improve capabilities to diagnose infections at point-of-care (POC), there are still technical hurdles that need to be overcome to ensure proper medical interventions. Current microbial POC tests involve polymerase chain reaction (PCR) or sandwich immunoassay (IA) based detection formats. PCR is highly sensitive but requires complex instrumentation, whereas lateral flow (LF) based IA tests are handheld but lack sensitivity. We present here a portable and sensitive technique by integrating an isothermal RNA amplification approach with IA detection format. The technique comprises i) Nucleic Acid Sequence Based isothermal Amplification (NASBA), ii) amplicon tagging with hapten labeled probes, iii) capturing the amplicon and iv) formation of a sandwich complex with an antibody (Ab) that selectively recognizes the DNA-RNA duplex. The results can be extended to develop an automated, portable and highly sensitive diagnostic platform suitable for POC applications.
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Affiliation(s)
- Mekbib Astatke
- Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, United States
| | - Olivia Tiburzi
- Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, United States
| | - Amy Connolly
- Fina Biosolutions, LLC, Rockville, United States
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176
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Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, Schwab J, Martinez J, Jones D, Black D, Gandhi M, Kerkhoff AD, Jain V, Sergi F, Jacobo J, Rojas S, Tulier-Laiwa V, Gallardo-Brown T, Appa A, Chiu C, Rodgers M, Hackett J, Kistler A, Hao S, Kamm J, Dynerman D, Batson J, Greenhouse B, DeRisi J, Havlir DV. Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco. Clin Infect Dis 2021; 73:S127-S135. [PMID: 32821935 PMCID: PMC7499499 DOI: 10.1093/cid/ciaa1234] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background There is urgent need to understand the dynamics and risk factors driving ongoing SARS-CoV-2 transmission during shelter-in-place mandates. Methods We offered SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (≥4 years) and workers in a San Francisco census tract (population: 5,174) at outdoor, community-mobilized events over four days. We estimated SARS-CoV-2 point prevalence (PCR-positive) and cumulative incidence (antibody or PCR-positive) in the census tract and evaluated risk factors for recent (PCR-positive/antibody-negative) versus prior infection (antibody-positive/PCR-negative). SARS-CoV-2 genome recovery and phylogenetics were used to measure viral strain diversity, establish viral lineages present, and estimate number of introductions. Results We tested 3,953 persons: 40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black. Overall, 2.1% (83/3,871) tested PCR-positive: 95% were Latinx and 52% asymptomatic when tested. 1.7% of census tract residents and 6.0% of workers (non-census tract residents) were PCR-positive. Among 2,598 tract residents, estimated point prevalence of PCR-positives was 2.3% (95%CI: 1.2-3.8%): 3.9% (95%CI: 2.0-6.4%) among Latinx vs. 0.2% (95%CI: 0.0-0.4%) among non-Latinx persons. Estimated cumulative incidence among residents was 6.1% (95%CI: 4.0-8.6%). Prior infections were 67% Latinx, 16% White, and 17% other ethnicities. Among recent infections, 96% were Latinx. Risk factors for recent infection were Latinx ethnicity, inability to shelter-in-place and maintain income, frontline service work, unemployment, and household income &$50,000/year. Five SARS-CoV-2 phylogenetic lineages were detected. Conclusion SARS-CoV-2 infections from diverse lineages continued circulating among low-income, Latinx persons unable to work from home and maintain income during San Francisco’s shelter-in-place ordinance.
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Affiliation(s)
- Gabriel Chamie
- University of California, San Francisco, San Francisco, California, USA
| | - Carina Marquez
- University of California, San Francisco, San Francisco, California, USA
| | - Emily Crawford
- University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - James Peng
- University of California, San Francisco, San Francisco, California, USA
| | - Maya Petersen
- University of California, Berkeley, Berkeley, California, USA
| | - Daniel Schwab
- College of the Holy Cross, Worcester, Massachusetts, USA
| | - Joshua Schwab
- University of California, Berkeley, Berkeley, California, USA
| | - Jackie Martinez
- University of California, San Francisco, San Francisco, California, USA
| | - Diane Jones
- Unidos en Salud/United in Health, San Francisco, California, USA
| | - Douglas Black
- University of California, San Francisco, San Francisco, California, USA
| | - Monica Gandhi
- University of California, San Francisco, San Francisco, California, USA
| | - Andrew D Kerkhoff
- University of California, San Francisco, San Francisco, California, USA
| | - Vivek Jain
- University of California, San Francisco, San Francisco, California, USA
| | - Francesco Sergi
- University of California, San Francisco, San Francisco, California, USA
| | - Jon Jacobo
- Latino Task Force for COVID-19, San Francisco, California, USA
| | - Susana Rojas
- Latino Task Force for COVID-19, San Francisco, California, USA
| | | | | | - Ayesha Appa
- University of California, San Francisco, San Francisco, California, USA
| | - Charles Chiu
- University of California, San Francisco, San Francisco, California, USA
| | | | | | | | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Samantha Hao
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Bryan Greenhouse
- University of California, San Francisco, San Francisco, California, USA
| | - Joe DeRisi
- University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Diane V Havlir
- University of California, San Francisco, San Francisco, California, USA
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177
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Sakano T, Urashima M, Takao H, Takeshita K, Kobashi H, Fujiwara T. Differential Kinetics of Cycle Threshold Values during Admission by Symptoms among Patients with Mild COVID-19: A Prospective Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8181. [PMID: 34360473 PMCID: PMC8346104 DOI: 10.3390/ijerph18158181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/12/2023]
Abstract
In the coronavirus disease 2019 (COVID-19) pandemic, more than half of the cases of transmission may occur via asymptomatic individuals, which makes it difficult to contain. However, whether viral load in the throat during admission is different between asymptomatic and symptomatic patients is not well known. By conducting a prospective cohort study of patients with asymptomatic or mild COVID-19, cycle threshold (Ct) values of the polymerase chain reaction test for COVID-19 were examined every other day during admission. The Ct values during admission increased more steadily in symptomatic patients and febrile patients than in asymptomatic patients, with significance (p = 0.01 and p = 0.004, respectively), although the Ct values as a whole were not significantly different between the two groups. Moreover, the Ct values as a whole were higher in patients with dysosmia/dysgeusia than in those without it (p = 0.02), whereas they were lower in patients with a headache than those without (p = 0.01). Patients who were IgG-positive at discharge maintained higher Ct values, e.g., more than 35, during admission than those with IgG-negative (p = 0.03). Assuming that viral load and Ct values are negatively associated, the viral loads as a whole and their changes by time may be different by symptoms and immune reaction, i.e., IgG-positive at discharge.
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Affiliation(s)
- Teppei Sakano
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
- Allm, Inc., Yushin Bldg. Shinkan 2F, 3-27-11 Shibuya, Shibuya-ku, Tokyo 150-0002, Japan
| | - Mitsuyoshi Urashima
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Hiroyuki Takao
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
- Department of Neurosurgery, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Kohei Takeshita
- Division of Innovation for Medical Information Technology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; (T.S.); (H.T.); (K.T.)
| | - Hiroe Kobashi
- Infectious Disease Department, Team Medical Clinic, Tokyo 105-0003, Japan;
| | - Takeo Fujiwara
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
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178
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Brümmer LE, Katzenschlager S, Gaeddert M, Erdmann C, Schmitz S, Bota M, Grilli M, Larmann J, Weigand MA, Pollock NR, Macé A, Carmona S, Ongarello S, Sacks JA, Denkinger CM. Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis. PLoS Med 2021; 18:e1003735. [PMID: 34383750 PMCID: PMC8389849 DOI: 10.1371/journal.pmed.1003735] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/26/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) are increasingly being integrated in testing strategies around the world. Studies of the Ag-RDTs have shown variable performance. In this systematic review and meta-analysis, we assessed the clinical accuracy (sensitivity and specificity) of commercially available Ag-RDTs. METHODS AND FINDINGS We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 up until 30 April 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity in comparison to reverse transcription polymerase chain reaction (RT-PCR) testing. We assessed heterogeneity by subgroup analyses, and rated study quality and risk of bias using the QUADAS-2 assessment tool. From a total of 14,254 articles, we included 133 analytical and clinical studies resulting in 214 clinical accuracy datasets with 112,323 samples. Across all meta-analyzed samples, the pooled Ag-RDT sensitivity and specificity were 71.2% (95% CI 68.2% to 74.0%) and 98.9% (95% CI 98.6% to 99.1%), respectively. Sensitivity increased to 76.3% (95% CI 73.1% to 79.2%) if analysis was restricted to studies that followed the Ag-RDT manufacturers' instructions. LumiraDx showed the highest sensitivity, with 88.2% (95% CI 59.0% to 97.5%). Of instrument-free Ag-RDTs, Standard Q nasal performed best, with 80.2% sensitivity (95% CI 70.3% to 87.4%). Across all Ag-RDTs, sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values, i.e., <20 (96.5%, 95% CI 92.6% to 98.4%) and <25 (95.8%, 95% CI 92.3% to 97.8%), in comparison to those with Ct ≥ 25 (50.7%, 95% CI 35.6% to 65.8%) and ≥30 (20.9%, 95% CI 12.5% to 32.8%). Testing in the first week from symptom onset resulted in substantially higher sensitivity (83.8%, 95% CI 76.3% to 89.2%) compared to testing after 1 week (61.5%, 95% CI 52.2% to 70.0%). The best Ag-RDT sensitivity was found with anterior nasal sampling (75.5%, 95% CI 70.4% to 79.9%), in comparison to other sample types (e.g., nasopharyngeal, 71.6%, 95% CI 68.1% to 74.9%), although CIs were overlapping. Concerns of bias were raised across all datasets, and financial support from the manufacturer was reported in 24.1% of datasets. Our analysis was limited by the included studies' heterogeneity in design and reporting. CONCLUSIONS In this study we found that Ag-RDTs detect the vast majority of SARS-CoV-2-infected persons within the first week of symptom onset and those with high viral load. Thus, they can have high utility for diagnostic purposes in the early phase of disease, making them a valuable tool to fight the spread of SARS-CoV-2. Standardization in conduct and reporting of clinical accuracy studies would improve comparability and use of data.
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Affiliation(s)
- Lukas E. Brümmer
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mary Gaeddert
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Stephani Schmitz
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Bota
- Agaplesion Bethesda Hospital, Hamburg, Germany
| | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Jan Larmann
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | | | | | | | | | - Claudia M. Denkinger
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Partner Site Heidelberg University Hospital, German Center for Infection Research (DZIF), Heidelberg, Germany
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179
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Modeling of network based digital contact tracing and testing strategies, including the pre-exposure notification system, for the COVID-19 pandemic. Math Biosci 2021; 338:108645. [PMID: 34147516 PMCID: PMC8214465 DOI: 10.1016/j.mbs.2021.108645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022]
Abstract
With more than 1.7 million COVID-19 deaths, identifying effective measures to prevent COVID-19 is a top priority. We developed a mathematical model to simulate the COVID-19 pandemic with digital contact tracing and testing strategies. The model uses a real-world social network generated from a high-resolution contact data set of 180 students. This model incorporates infectivity variations, test sensitivities, incubation period, and asymptomatic cases. We present a method to extend the weighted temporal social network and present simulations on a network of 5000 students. The purpose of this work is to investigate optimal quarantine rules and testing strategies with digital contact tracing. The results show that the traditional strategy of quarantining direct contacts reduces infections by less than 20% without sufficient testing. Periodic testing every 2 weeks without contact tracing reduces infections by less than 3%. A variety of strategies are discussed including testing second and third degree contacts and the pre-exposure notification system, which acts as a social radar warning users how far they are from COVID-19. The most effective strategy discussed in this work was combining the pre-exposure notification system with testing second and third degree contacts. This strategy reduces infections by 18.3% when 30% of the population uses the app, 45.2% when 50% of the population uses the app, 72.1% when 70% of the population uses the app, and 86.8% when 95% of the population uses the app. When simulating the model on an extended network of 5000 students, the results are similar with the contact tracing app reducing infections by up to 79%.
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180
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Antonara S, Ozbolt P, Landon L, Fatica L, Pleasant T, Swickard J, Drury A, Wongchaowart N, Cradic KW. Detection of SARS-CoV-2 infection in asymptomatic populations using the DiaSorin molecular Simplexa and Roche Cobas EUA assays. Diagn Microbiol Infect Dis 2021; 102:115513. [PMID: 34649190 PMCID: PMC8324421 DOI: 10.1016/j.diagmicrobio.2021.115513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/03/2022]
Abstract
Identification of asymptomatic patients is necessary to control the COVID-19 pandemic and testing is one of the measures to detect this population. We evaluated the clinical correlation of the DiaSorin Molecular Simplexa COVID-19 Direct (DiaSorin Molecular) and Roche Cobas 6800 SARS-CoV-2 (Roche) assays using 253 oropharyngeal (OP) swab specimens collected from asymptomatic patients. Agreement between DiaSorin Molecular and Roche was 97% (95% CI, 0.94 to 0.99), with a κ statistic of 0.90 (95% CI, 0.83 to 0.97) and a PPA of 89% (95% CI, 0.76 to 0.96) and NPA of 99% (95% CI, 0.97 to 0.99). Simple regression analysis of Ct values revealed a regression line of y = 1.065*X - 5.537 with a Pearson's r of 0.8542, indicating a good correlation between both platforms. The DiaSorin Molecular assay demonstrates clinical performance comparable to that of Roche in this population.
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Affiliation(s)
- Stella Antonara
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA; CORPath Pathology Services, LLC, Columbus, OH, USA.
| | - Patrick Ozbolt
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA
| | - Lorie Landon
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA
| | - Lisa Fatica
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA
| | - Tamra Pleasant
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA
| | | | - Andrew Drury
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA
| | - Nicholas Wongchaowart
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA; CORPath Pathology Services, LLC, Columbus, OH, USA
| | - Kendall W Cradic
- OhioHealth Laboratory Services, OhioHealth, Columbus, OH, USA; CORPath Pathology Services, LLC, Columbus, OH, USA
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181
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Wachinger J, Olaru ID, Horner S, Schnitzler P, Heeg K, Denkinger CM. The potential of SARS-CoV-2 antigen-detection tests in the screening of asymptomatic persons. Clin Microbiol Infect 2021; 27:1700.e1-1700.e3. [PMID: 34325065 PMCID: PMC8310783 DOI: 10.1016/j.cmi.2021.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 10/25/2022]
Abstract
OBJECTIVES The aim was to assess the performance of antigen-based rapid diagnostic tests (Ag-RDTs) for SARS CoV-2 when implemented for large-scale universal screening of asymptomatic individuals. METHODS This study was a pragmatic implementation study for universal Ag-RDT-based screening at a tertiary care hospital in Germany where patients presenting for elective procedures and selected personnel without symptoms suggestive of SARS-CoV-2 were screened with an Ag-RDT since October 2020. Test performance was calculated on an individual patient level. RESULTS In total, 49 542 RDTs were performed in 27 421 asymptomatic individuals over a duration of 5 and a half months. Out of 222 positive results, 196 underwent in-house confirmatory testing with PCR, out of which 170 were confirmed positive, indicating a positive predictive value of 86.7% (95% CI 81.2-91.1%). Negative Ag-RDTs were not routinely tested with PCR, but a total of 94 cases of false negative Ag-RDTs were detected due to PCR tests being performed within the following 5 days with a median cycle threshold value of 33 (IQR 29-35). DISCUSSION This study provides evidence that Ag-RDTs can have a high diagnostic yield for transmission relevant infections with limited false positives when utilized at the point of care on asymptomatic patients and thus can be a suitable public health test for universal screening.
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Affiliation(s)
- Jonas Wachinger
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Ioana Diana Olaru
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susanne Horner
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Paul Schnitzler
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Klaus Heeg
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Claudia M Denkinger
- Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; German Center of Infection Research, Site Heidelberg, Heidelberg, Germany.
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182
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Isolation thresholds for curbing SARS-CoV-2 resurgence. Epidemiol Infect 2021; 149:e168. [PMID: 34289920 PMCID: PMC8353193 DOI: 10.1017/s0950268821001692] [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] [Indexed: 11/18/2022] Open
Abstract
Self-instigated isolation is heavily relied on to curb severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Accounting for uncertainty in the latent and prepatent periods, as well as the proportion of infections that remain asymptomatic, the limits of this intervention at different phases of infection resurgence are estimated. We show that by October 2020, SARS-CoV-2 transmission rates in England had already begun exceeding levels that could be interrupted using this intervention alone, lending support to the second national lockdown on 5th November 2020.
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183
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Gertler M, Krause E, van Loon W, Krug N, Kausch F, Rohardt C, Rössig H, Michel J, Nitsche A, Mall MA, Nikolai O, Hommes F, Burock S, Lindner AK, Mockenhaupt FP, Pison U, Seybold J. Self-collected oral, nasal and saliva samples yield sensitivity comparable to professionally collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis among symptomatic outpatients. Int J Infect Dis 2021; 110:261-266. [PMID: 34302962 PMCID: PMC8295057 DOI: 10.1016/j.ijid.2021.07.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 12/19/2022] Open
Abstract
Introduction Containing COVID-19 requires broad-scale testing. However, sample collection requires qualified personnel and protective equipment and may cause transmission. We assessed the sensitivity of SARS-CoV-2-rtPCR applying three self-sampling techniques as compared to professionally collected oro-nasopharyngeal samples (cOP/NP). Methods From 62 COVID-19 outpatients, we obtained: (i) multi-swab, MS; (ii) saliva sponge combined with nasal vestibula, SN; (iii) gargled water, GW; (iv) professionally collected cOP/NP (standard). We compared ct-values for E-gene and ORF1ab and analysed variables reducing sensitivity of self-collecting procedures. Results The median ct-values for E-gene and ORF1ab obtained in cOP/NP samples were 20.7 and 20.2, in MS samples 22.6 and 21.8, in SN samples 23.3 and 22.3, and in GW samples 30.3 and 29.8, respectively. MS and SN samples showed sensitivities of 95.2% (95%CI, 86.5-99.0) and GW samples of 88.7% (78.1-95.3). Sensitivity was inversely correlated with ct-values, and became <90% for samples obtained more than 8 days after symptom onset. For MS and SN samples, false negativity was associated with language problems, sampling errors, and symptom duration. Conclusion Conclusions from this study are limited to the sensitivity of self-sampling in mildly to moderately symptomatic patients. Still, self-collected oral/nasal/saliva samples can facilitate up-scaling of testing in early symptomatic COVID-19 patients if operational errors are minimized.
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Affiliation(s)
- Maximilian Gertler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany.
| | - Eva Krause
- Robert Koch Institute - center for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany
| | - Welmoed van Loon
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Niklas Krug
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Franka Kausch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Chiara Rohardt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Heike Rössig
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin; Medical Directorate, Berlin, Germany
| | - Janine Michel
- Robert Koch Institute - center for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany
| | - Andreas Nitsche
- Robert Koch Institute - center for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany
| | - Marcus A Mall
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin; Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Berlin, Germany
| | - Olga Nikolai
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Franziska Hommes
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Susen Burock
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité Comprehensive Cancer Center, Berlin, Germany
| | - Andreas K Lindner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Frank P Mockenhaupt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Ulrich Pison
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin; Department of Anaesthesiology and Intensive Care Medicine, Berlin, Germany
| | - Joachim Seybold
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin; Medical Directorate, Berlin, Germany
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Pollmann TR, Schönert S, Müller J, Pollmann J, Resconi E, Wiesinger C, Haack C, Shtembari L, Turcati A, Neumair B, Meighen-Berger S, Zattera G, Neumair M, Apel U, Okolie A. The impact of digital contact tracing on the SARS-CoV-2 pandemic-a comprehensive modelling study. EPJ DATA SCIENCE 2021; 10:37. [PMID: 34306910 PMCID: PMC8290404 DOI: 10.1140/epjds/s13688-021-00290-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/22/2021] [Indexed: 05/08/2023]
Abstract
Contact tracing is one of several strategies employed in many countries to curb the spread of SARS-CoV-2. Digital contact tracing (DCT) uses tools such as cell-phone applications to improve tracing speed and reach. We model the impact of DCT on the spread of the virus for a large epidemiological parameter space consistent with current literature on SARS-CoV-2. We also model DCT in combination with random testing (RT) and social distancing (SD). Modelling is done with two independently developed individual-based (stochastic) models that use the Monte Carlo technique, benchmarked against each other and against two types of deterministic models. For current best estimates of the number of asymptomatic SARS-CoV-2 carriers (approximately 40%), their contagiousness (similar to that of symptomatic carriers), the reproductive number before interventions ( R 0 at least 3) we find that DCT must be combined with other interventions such as SD and/or RT to push the reproductive number below one. At least 60% of the population would have to use the DCT system for its effect to become significant. On its own, DCT cannot bring the reproductive number below 1 unless nearly the entire population uses the DCT system and follows quarantining and testing protocols strictly. For lower uptake of the DCT system, DCT still reduces the number of people that become infected. When DCT is deployed in a population with an ongoing outbreak where O (0.1%) of the population have already been infected, the gains of the DCT intervention come at the cost of requiring up to 15% of the population to be quarantined (in response to being traced) on average each day for the duration of the epidemic, even when there is sufficient testing capability to test every traced person.
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Affiliation(s)
- Tina R. Pollmann
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Stefan Schönert
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Johannes Müller
- Center for Mathematical Sciences, Technical University of Munich, 85748 Garching, Germany
- Institute for Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Julia Pollmann
- Department of Medical Oncology, University Hospital Heidelberg, National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Elisa Resconi
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | | | - Christian Haack
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | | | - Andrea Turcati
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Birgit Neumair
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | | | - Giovanni Zattera
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Matthias Neumair
- Department of Mathematics, Technical University of Munich, 85748 Garching, Germany
| | - Uljana Apel
- Center for Mathematical Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Augustine Okolie
- Center for Mathematical Sciences, Technical University of Munich, 85748 Garching, Germany
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185
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Nakajo K, Nishiura H. Exploring secondary SARS-CoV-2 transmission from asymptomatic cases using contact tracing data. Theor Biol Med Model 2021; 18:12. [PMID: 34271962 PMCID: PMC8284042 DOI: 10.1186/s12976-021-00144-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/24/2021] [Indexed: 12/23/2022] Open
Abstract
Background Individuals with asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can propagate the virus unknowingly and thus have been a focus of public health attentions since the early stages of the pandemic. Understanding viral transmissibility among asymptomatic individuals is critical for successful control of coronavirus disease 2019 (COVID-19). The present study aimed to understand SARS-CoV-2 transmissibility among young asymptomatic individuals and to assess whether symptomatology was associated with transmission of symptomatic vs. asymptomatic infections. Methods We analyzed one of the first-identified clusters of SARS-CoV-2 infections with multiple chains of transmission that occurred among university students in March 2020 in Kyoto prefecture, Japan, using discrete and two-type branching process models. Assuming that the number of secondary cases resulting from either primary symptomatic or asymptomatic cases independently followed negative binomial distributions, we estimated the relative reproduction numbers of an asymptomatic case compared with a symptomatic case. To explore the potential association between symptomatology and transmission of symptomatic vs. asymptomatic incident infections, we also estimated the proportion of secondary symptomatic cases produced by primary symptomatic and asymptomatic cases. Results The reproduction number for a symptomatic primary case was estimated at 1.14 (95% confidence interval [CI]: 0.61–2.09). The relative reproduction number for asymptomatic cases was estimated at 0.19 (95% CI: 0.03–0.66), indicating that asymptomatic primary cases did not result in sufficient numbers of secondary infections to maintain chains of transmission. There was no apparent tendency for symptomatic primary cases to preferentially produce symptomatic secondary cases. Conclusions Using data from a transmission network during the early epidemic in Japan, we successfully estimated the relative transmissibility of asymptomatic cases of SARS-CoV-2 infection at 0.22. These results suggest that contract tracing focusing on symptomatic index cases may be justified given limited testing capacity. Supplementary Information The online version contains supplementary material available at 10.1186/s12976-021-00144-z.
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Affiliation(s)
- Ko Nakajo
- Graduate, School of Medicine, Hokkaido University, Kita 15 Jo Nishi 7 Chome, Kita-ku, Sapporo-shi, Hokkaido, 060-8638, Japan.,Kyoto University School of Public Health, Yoshidakonoecho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8503, Japan
| | - Hiroshi Nishiura
- Graduate, School of Medicine, Hokkaido University, Kita 15 Jo Nishi 7 Chome, Kita-ku, Sapporo-shi, Hokkaido, 060-8638, Japan. .,Kyoto University School of Public Health, Yoshidakonoecho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8503, Japan.
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186
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Gitman MR, Shaban MV, Paniz-Mondolfi AE, Sordillo EM. Laboratory Diagnosis of SARS-CoV-2 Pneumonia. Diagnostics (Basel) 2021; 11:diagnostics11071270. [PMID: 34359353 PMCID: PMC8306256 DOI: 10.3390/diagnostics11071270] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence and rapid proliferation of Coronavirus Disease-2019, throughout the past year, has put an unprecedented strain on the global schema of health infrastructure and health economy. The time-sensitive agenda of identifying the virus in humans and delivering a vaccine to the public constituted an effort to flatten the statistical curve of viral spread as it grew exponentially. At the forefront of this effort was an exigency of developing rapid and accurate diagnostic strategies. These have emerged in various forms over the past year—each with strengths and weaknesses. To date, they fall into three categories: (1) those isolating and replicating viral RNA in patient samples from the respiratory tract (Nucleic Acid Amplification Tests; NAATs), (2) those detecting the presence of viral proteins (Rapid Antigen Tests; RATs) and serology-based exams identifying antibodies to the virus in whole blood and serum. The latter vary in their detection of immunoglobulins of known prevalence in early-stage and late-stage infection. With this review, we delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.
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Affiliation(s)
- Melissa R. Gitman
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
- Correspondence: ; Tel.: +1-212-659-8173
| | - Maryia V. Shaban
- Emerging Pathogens and Zoonoses Network, Incubadora Venezolana de la Ciencia, Cabudare 3023, Venezuela;
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
| | - Emilia M. Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
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187
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Margolin L, Luchins J, Margolin D, Margolin M, Lefkowitz S. 20-Week Study of Clinical Outcomes of Over-the-Counter COVID-19 Prophylaxis and Treatment. J Evid Based Integr Med 2021; 26:2515690X211026193. [PMID: 34225463 PMCID: PMC8264737 DOI: 10.1177/2515690x211026193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Objectives and Setting. As the lethal COVID-19 pandemic enters its second year, the need for effective modalities of alleviation remains urgent. This includes modalities that can readily be used by the public to reduce disease spread and severity. Such preventive measures and early-stage treatments may temper the immediacy of demand for advanced anti-COVID measures (drugs, antibodies, vaccines) and help relieve strain also on other health system resources. Design and Participants. We present results of a clinical study with a multi-component OTC “core formulation” regimen used in a multiply exposed adult population. Analysis of clinical outcome data from our sample of over 100 subjects − comprised of roughly equal sized regimen-compliant (test) and non-compliant (control) groups meeting equivalent inclusion criteria − demonstrates a strong statistical significance in favor of use of the core formulations. Results. While both groups were moderate in size, the difference between them in outcomes over the 20-week study period was large and stark: Just under 4% of the compliant test group presented flu-like symptoms, but none of the test group was COVID-positive; whereas 20% of the non-compliant control group presented flu-like symptoms, three-quarters of whom (15% overall of the control group) were COVID-positive. Conclusions. Offering a low cost, readily implemented anti-viral approach, the study regimen may serve, at the least, as a stopgap modality and, perhaps, as a useful tool in combatting the pandemic.
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Affiliation(s)
- Leon Margolin
- Comprehensive Pain Management Institute, LLC, Columbus, OH, USA
| | - Jeremy Luchins
- Comprehensive Pain Management Institute, LLC, Columbus, OH, USA
| | - Daniel Margolin
- Comprehensive Pain Management Institute, LLC, Columbus, OH, USA
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188
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Lennon NJ, Bhattacharyya RP, Mina MJ, Rehm HL, Hung DT, Smole S, Woolley A, Lander ES, Gabriel SB. Cross-sectional assessment of SARS-CoV-2 viral load by symptom status in Massachusetts congregate living facilities. J Infect Dis 2021; 224:1658-1663. [PMID: 34255846 PMCID: PMC8420626 DOI: 10.1093/infdis/jiab367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 11/14/2022] Open
Abstract
Transmission of COVID-19 from people without symptoms confounds societal mitigation strategies. From April to June 2020, we tested nasopharyngeal swabs by RT-qPCR from 15,514 staff and 16,966 residents of nursing homes and assisted living facilities in Massachusetts. Cycle threshold (Ct) distributions were very similar between populations with (N = 739) and without (N = 2179) symptoms at the time of sampling (mean Ct 25.7 versus 26.4, ranges 12-38). However, as local cases waned, those without symptoms shifted towards higher Ct. With such similar viral load distributions, existing testing modalities should perform comparably regardless of symptoms, contingent upon time since infection.
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Affiliation(s)
| | - Roby P Bhattacharyya
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Massachusetts General Hospital, Boston, MA, USA
| | - Michael J Mina
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Massachusetts General Hospital, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Massachusetts General Hospital, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Sandra Smole
- State Public Health Laboratory, Massachusetts Department of Public Health, Boston, MA, USA
| | - Ann Woolley
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
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189
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Walker AS, Pritchard E, House T, Robotham JV, Birrell PJ, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Hay J, Vihta KD, Peto TEA, Stoesser N, Matthews PC, Eyre DW, Pouwels KB. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. eLife 2021; 10:e64683. [PMID: 34250907 PMCID: PMC8282332 DOI: 10.7554/elife.64683] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Methods We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. Results Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. Conclusions Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. Funding Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
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Affiliation(s)
- A Sarah Walker
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- MRC Clinical Trials Unit at UCL, UCLLondonUnited Kingdom
| | - Emma Pritchard
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Thomas House
- Department of Mathematics, University of ManchesterManchesterUnited Kingdom
- IBM Research, Hartree CentreSci-Tech DaresburyUnited Kingdom
| | - Julie V Robotham
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- National Infection Service, Public Health EnglandLondonUnited Kingdom
| | - Paul J Birrell
- National Infection Service, Public Health EnglandLondonUnited Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public HealthCambridgeUnited Kingdom
| | - Iain Bell
- Office for National StatisticsNewportUnited Kingdom
| | - John I Bell
- Office of the Regius Professor of Medicine, University of OxfordOxfordUnited Kingdom
| | - John N Newton
- Health Improvement Directorate, Public Health EnglandLondonUnited Kingdom
| | | | - Ian Diamond
- Office for National StatisticsNewportUnited Kingdom
| | - Ruth Studley
- Office for National StatisticsNewportUnited Kingdom
| | - Jodie Hay
- University of GlasgowGlasgowUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
| | - Karina-Doris Vihta
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Timothy EA Peto
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - David W Eyre
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
- Big Data Institute, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - Koen B Pouwels
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Health Economics Research Centre, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
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190
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Characteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic. PLoS One 2021; 16:e0253941. [PMID: 34242243 PMCID: PMC8270193 DOI: 10.1371/journal.pone.0253941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Accurate SARS-CoV-2 diagnosis is essential to guide prevention and control of COVID-19. Here we examine SARS-CoV-2 molecular-based test performance characteristics and summarize case-level data related to COVID-19 diagnosis. From January 11 through April 22, 2020, Public Health Ontario conducted SARS-CoV-2 testing of 86,942 specimens collected from 80,354 individuals, primarily using real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods. We analyzed test results across specimen types and for individuals with multiple same-day and multi-day collected specimens. Nasopharyngeal compared to throat swabs had a higher positivity (8.8% vs. 4.8%) and an adjusted estimate 2.9 Ct lower (SE = 0.5, p<0.001). Same-day specimens showed high concordance (98.8%), and the median Ct of multi-day specimens increased over time. Symptomatic cases had rRT-PCR results with an adjusted estimate 3.0 Ct (SE = 0.5, p<0.001) lower than asymptomatic/pre-symptomatic cases. Overall test sensitivity was 84.6%, with a negative predictive value of 95.5%. Molecular testing is the mainstay of SARS-CoV-2 diagnosis and testing protocols will continue to be dynamic and iteratively modified as more is learned about this emerging pathogen.
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191
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Jones TC, Biele G, Mühlemann B, Veith T, Schneider J, Beheim-Schwarzbach J, Bleicker T, Tesch J, Schmidt ML, Sander LE, Kurth F, Menzel P, Schwarzer R, Zuchowski M, Hofmann J, Krumbholz A, Stein A, Edelmann A, Corman VM, Drosten C. Estimating infectiousness throughout SARS-CoV-2 infection course. Science 2021; 373:eabi5273. [PMID: 34035154 PMCID: PMC9267347 DOI: 10.1126/science.abi5273] [Citation(s) in RCA: 297] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/21/2021] [Indexed: 12/20/2022]
Abstract
Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Germany, including 6110 from test centers attended by presymptomatic, asymptomatic, and mildly symptomatic (PAMS) subjects, 9519 who were hospitalized, and 1533 B.1.1.7 lineage infections. The viral load of the youngest subjects was lower than that of the older subjects by 0.5 (or fewer) log10 units, and they displayed an estimated ~78% of the peak cell culture replication probability; in part this was due to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 109 copies per swab were found in 8% of subjects, one-third of whom were PAMS, with a mean age of 37.6 years. We estimate 4.3 days from onset of shedding to peak viral load (108.1 RNA copies per swab) and peak cell culture isolation probability (0.75). B.1.1.7 subjects had mean log10 viral load 1.05 higher than that of non-B.1.1.7 subjects, and the estimated cell culture replication probability of B.1.1.7 subjects was higher by a factor of 2.6.
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Affiliation(s)
- Terry C Jones
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, U.K
| | - Guido Biele
- Norwegian Institute of Public Health, 0473 Oslo, Norway
- University of Oslo, 0315 Oslo, Norway
| | - Barbara Mühlemann
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Talitha Veith
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Julia Schneider
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Julia Tesch
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine I, University Medical Centre Hamburg-Eppendorf, 20359 Hamburg, Germany
| | - Peter Menzel
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Rolf Schwarzer
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Marta Zuchowski
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Jörg Hofmann
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Labor Dr. Krause und Kollegen MVZ GmbH, 24106 Kiel, Germany
| | - Angela Stein
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Anke Edelmann
- Labor Berlin-Charité Vivantes GmbH, Sylter Straße 2, 13353 Berlin, Germany
| | - Victor Max Corman
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité--Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
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192
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Shi L, Ding R, Zhang T, Wu W, Wang Z, Jia X, Li K, Liang Y, Li J, Zhu M, Huang B, Wu L, Wu M, Chen J, Wang C, Huang B, Liu C, Shen H, Wang Q, Xia X, Li P, Lyu S, Xiao Y. Comparative Characterization and Risk Stratification of Asymptomatic and Presymptomatic Patients With COVID-19. Front Immunol 2021; 12:700449. [PMID: 34305939 PMCID: PMC8301218 DOI: 10.3389/fimmu.2021.700449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
The identification of asymptomatic, non-severe presymptomatic, and severe presymptomatic coronavirus disease 2019 (COVID-19) in patients may help optimize risk-stratified clinical management and improve prognosis. This single-center case series from Wuhan Huoshenshan Hospital, China, included 2,980 patients with COVID-19 who were hospitalized between February 4, 2020 and April 10, 2020. Patients were diagnosed as asymptomatic (n = 39), presymptomatic (n = 34), and symptomatic (n = 2,907) upon admission. This study provided an overview of asymptomatic, presymptomatic, and symptomatic COVID-19 patients, including detection, demographics, clinical characteristics, and outcomes. Upon admission, there was no significant difference in clinical symptoms and CT image between asymptomatic and presymptomatic patients for diagnosis reference. The mean area under the receiver operating characteristic curve (AUC) of the differential diagnosis model to discriminate presymptomatic patients from asymptomatic patients was 0.89 (95% CI, 0.81-0.98). Importantly, the severe and non-severe presymptomatic patients can be further stratified (AUC = 0.82). In conclusion, the two-step risk-stratification model based on 10 laboratory indicators can distinguish among asymptomatic, severe presymptomatic, and non-severe presymptomatic COVID-19 patients on admission. Moreover, single-cell data analyses revealed that the CD8+T cell exhaustion correlated to the progression of COVID-19.
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Affiliation(s)
- Lei Shi
- Affiliated First People’s Hospital of Kunshan, Gusu College of Nanjing Medical University, Suzhou, China
| | - Rong Ding
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Tingting Zhang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziyu Wang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Xiuzhi Jia
- Central Lab of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Kening Li
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Yuan Liang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Jie Li
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Mengyan Zhu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Bin Huang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Lingxiang Wu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Min Wu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Jing Chen
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Chaochen Wang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Bin Huang
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Caidong Liu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Qianghu Wang
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing, China
| | - Xinyi Xia
- COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing Clinical College of Southern Medical University, Nanjing, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, Wuhan, China
| | - Pengping Li
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Sali Lyu
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Ying Xiao
- Central Lab of Biomedical Research Center, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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193
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Camargo JF, Lin RY, Komanduri KV. Lack of correlation between the SARS-CoV-2 cycle threshold (C t ) value and clinical outcomes in patients with COVID-19. J Med Virol 2021; 93:6059-6062. [PMID: 34196409 PMCID: PMC8427039 DOI: 10.1002/jmv.27171] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022]
Abstract
Problem The utility of the polymerase chain reaction (PCR) cycle threshold (Ct) values in the management of patients with coronavirus disease 2019 (COVID‐19) remains controversial. Methods We assessed the correlation of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Ct values in nasopharyngeal swab samples with the oxygen requirements at the time of sample collection. Specimens were tested with the Simplexa PCR platform, which targets the SARS‐CoV‐2 ORF1ab and S genes. Results We identified 23 COVID‐19 patients with 49 Ct values available. While Ct values from ORF1ab and S genes were highly correlated for a given specimen, there was no correlation between Ct values for any of these target genes and the oxygen requirements of the patient at the time of sample collection. We found no differences in the initial nor the nadir Ct values between survivors and non‐survivors or mild/moderate versus severe/critical illness at the maximum point of illness. Conclusion SARS‐CoV‐2 Ct values have limited value in the management of COVID‐19.
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Affiliation(s)
- Jose F Camargo
- Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Rick Y Lin
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Krishna V Komanduri
- Division of Transplantation and Cellular Therapy, Sylvester Comprehensive Cancer Center, Miami, Florida, USA
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194
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Silverstein NJ, Wang Y, Manickas-Hill Z, Carbone C, Dauphin A, Boribong BP, Loiselle M, Davis J, Leonard MM, Kuri-Cervantes L, Meyer NJ, Betts MR, Li JZ, Walker B, Yu XG, Yonker LM, Luban J. Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33469605 PMCID: PMC7814851 DOI: 10.1101/2021.01.14.21249839] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Risk of severe COVID-19 increases with age, is greater in males, and is associated with lymphopenia, but not with higher burden of SARS-CoV-2. It is unknown whether effects of age and sex on abundance of specific lymphoid subsets explain these correlations. This study found that the abundance of innate lymphoid cells (ILCs) decreases more than 7-fold over the human lifespan — T cell subsets decrease less than 2-fold — and is lower in males than in females. After accounting for effects of age and sex, ILCs, but not T cells, were lower in adults hospitalized with COVID-19, independent of lymphopenia. Among SARS-CoV-2-infected adults, the abundance of ILCs, but not of T cells, correlated inversely with odds and duration of hospitalization, and with severity of inflammation. ILCs were also uniquely decreased in pediatric COVID-19 and the numbers of these cells did not recover during follow-up. In contrast, children with MIS-C had depletion of both ILCs and T cells, and both cell types increased during follow-up. In both pediatric COVID-19 and MIS-C, ILC abundance correlated inversely with inflammation. Blood ILC mRNA and phenotype tracked closely with ILCs from lung. Importantly, blood ILCs produced amphiregulin, a protein implicated in disease tolerance and tissue homeostasis, and the percentage of amphiregulin-producing ILCs was higher in females than in males. These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance accounts for increased COVID-19 severity with age and in males.
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Affiliation(s)
- Noah J Silverstein
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Yetao Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Zachary Manickas-Hill
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Claudia Carbone
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brittany P Boribong
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Maggie Loiselle
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA
| | - Jameson Davis
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA
| | - Maureen M Leonard
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Nuala J Meyer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Z Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bruce Walker
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA
| | - Xu G Yu
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lael M Yonker
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
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195
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Chen YC, Yang HP, Li HC, Huang PY, Chen CL, Chiu CH. Features and transmission dynamics of SARS-CoV-2 superspreading events in Taiwan: Implications for effective and sustainable community-centered control. Pediatr Neonatol 2021; 62:437-440. [PMID: 34120866 PMCID: PMC8164498 DOI: 10.1016/j.pedneo.2021.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/10/2021] [Accepted: 05/19/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Yi-Ching Chen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Ping Yang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Chieh Li
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Po-Yen Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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196
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Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol 2021; 19:e3001333. [PMID: 34252080 PMCID: PMC8297933 DOI: 10.1371/journal.pbio.3001333] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/22/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
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Affiliation(s)
- Stephen M. Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christina Mack
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott W. Olesen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline Tai
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
| | - Kristin Y. Shiue
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sarah Jednak
- Department of Health Management and Policy, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jay Wohlgemuth
- Quest Diagnostics, San Juan Capistrano, California, United States of America
| | - James Weisberger
- Bioreference Laboratories, Elmwood Park, New Jersey, United States of America
| | - John DiFiori
- Hospital for Special Surgery, New York, New York, United States of America
- National Basketball Association, New York, New York, United States of America
| | - Deverick J. Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, United States of America
| | - Jimmie Mancell
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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197
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Okoh M, Onyia N, Okoh DS, Abah AA, Otakhoigbogie U, Adedapo HA, Oyetola EO, Agho ET, Owotade FJ. Awareness of COVID-19 and the Dental Implications of its Oral Manifestations among Dental Health Practitioners in Nigeria. Niger Med J 2021; 62:194-201. [PMID: 38694212 PMCID: PMC11058442 DOI: 10.60787/nmj-62-4-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024] Open
Abstract
Background There are many aspects of COVID-19 that are related to dental practice. Hence, this study aimed to assess the level of awareness of COVID-19 concerning its symptoms, transmission and prevention and the dental implications of its oral manifestations among dentists in Nigeria. Methodology This is a cross-sectional study that sampled dentists who work in Nigeria regardless of their place of work with an online questionnaire using Google forms to collect the data. The questionnaire was anonymous to maintain the privacy and confidentiality of all information collected in the study. The survey was a structured questionnaire divided into three sections: Dentists' demographics, knowledge of the disease and dental implications of COVID-19. Results This study included 206 dentists practising in Nigeria, with 126 (61.2%) males and 80 (38.8%) females. A total of 191 (92.7%) dentists perceived COVID-19 as highly contagious and deadly. Almost all the participants (n=205, 99.5%) were knowledgeable about the mode of transmission of the disease through respiratory droplets. A total of 204 (99.0%) affirmed that dental practitioners were at risk of becoming infected with COVID-19. About 84.5% reported that salivary glands can serve as a potential reservoir for COVID-19. Conclusion The awareness of COVID-19 concerning the mode of transmission, symptoms and prevention among the dental professionals was encouraging. This would lead to enhanced infection control in dental settings. The majority of the participants reported that saliva can be used as a promising non-invasive specimen for diagnosis, monitoring and infection control in patients with COVID-19.
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Affiliation(s)
- Mercy Okoh
- Department of Oral and Maxillofacial Pathology and Medicine, School of Dentistry, University of Benin, Nigeria
| | - Nonso Onyia
- Department Oral Pathology and Medicine, University of Benin Teaching Hospital, Benin, Nigeria
| | | | - Aderonke Adebowun Abah
- Department of Oral Pathology and Oral Medicine, Faculty of Dentistry, Lagos State University College of Medicine, Lagos, Nigeria
| | - Uwaila Otakhoigbogie
- Department of Oral Pathology and Oral Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Happy Adeyinka Adedapo
- Department of Oral Pathology and Oral Medicine, University College Hospital, Ibadan, Nigeria
| | - Elijah Olufemi Oyetola
- Department of Oral Pathology and Oral Medicine, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Foluso John Owotade
- Department of Oral Pathology and Oral Medicine, Obafemi Awolowo University, Ile-Ife, Nigeria
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198
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La Regina DP, Nenna R, Schramm D, Freitag N, Goussard P, Eber E, Midulla F. The use of pediatric flexible bronchoscopy in the COVID-19 pandemic era. Pediatr Pulmonol 2021; 56:1957-1966. [PMID: 33730395 PMCID: PMC8251429 DOI: 10.1002/ppul.25358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/01/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
On March 11, 2020, the World Health Organization (WHO) declared the pandemic because of a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In January 2020, the first transmission to healthcare workers (HCWs) was described. SARS-CoV-2 is transmitted between people because of contact, droplets, and airborne. Airborne transmission is caused by aerosols that remain infectious when suspended in air over long distances and time. In the clinical setting, airborne transmission may occur during aerosol generating procedures like flexible bronchoscopy. To date, although the role of children in the transmission of SARS-CoV-2 is not clear the execution of bronchoscopy is associated with a considerably increased risk of SARS-CoV-2 transmission to HCWs. The aim of this overview is to summarize available recommendations and to apply them to pediatric bronchoscopy. We performed systematic literature searches using the MEDLINE (accessed via PubMed) and Scopus databases. We reviewed major recommendations and position statements published at the moment by the American Association for Bronchology and Interventional Pulmonology, WHO, European Center for Disease Prevention and Control and expert groups on the management of patients with COVID-19 to limit transmission among HCWs. To date there is a lack of recommendations for safe bronchoscopy during the pandemic period. The main indications concern adults and little has been said about children. We have summarized available recommendations and we have applied them to pediatric bronchoscopy.
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Affiliation(s)
- Domenico Paolo La Regina
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Raffaella Nenna
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Dirk Schramm
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children's Hospital Duesseldorf, Duesseldorf, Germany
| | - Nadine Freitag
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children's Hospital Duesseldorf, Duesseldorf, Germany
| | - Pierre Goussard
- Department of Pediatrics and Child Health, Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - Ernst Eber
- Division of Pediatric Pulmonology and Allergology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Fabio Midulla
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
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Medina J, Cessa-Rojas R, Umpaichitra V. Reducing COVID-19 Cases and Deaths by Applying Blockchain in Vaccination Rollout Management. IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY 2021; 2:249-255. [PMID: 35257096 PMCID: PMC8769009 DOI: 10.1109/ojemb.2021.3093774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 01/10/2023] Open
Abstract
Goal: Because a fast vaccination rollout against coronavirus disease 2019 (COVID-19) is critical to restore daily life and avoid virus mutations, it is tempting to have a relaxed vaccination-administration management system. However, a rigorous management system can support the enforcement of preventive measures, and in turn, reduce incidence and deaths. Here, we model a trustable and reliable management system based on blockchain for vaccine distribution by extending the Susceptible-Exposed-Infected-Recovery (SEIR) model. The model includes prevention measures such as mask-wearing, social distancing, vaccination rate, and vaccination efficiency. It also considers negative social behavior, such as violations of social distance and attempts of using illegitimate vaccination proofs. By evaluating the model, we show that the proposed system can reduce up to 2.5 million cases and half a million deaths in the most demanding scenarios.
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Affiliation(s)
- Jorge Medina
- New Jersey Institute of TechnologyNewarkNJ07102USA
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200
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Choi W, Shim E. Vaccine Effects on Susceptibility and Symptomatology Can Change the Optimal Allocation of COVID-19 Vaccines: South Korea as an Example. J Clin Med 2021; 10:jcm10132813. [PMID: 34202324 PMCID: PMC8268243 DOI: 10.3390/jcm10132813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
The approved coronavirus disease (COVID-19) vaccines reduce the risk of disease by 70–95%; however, their efficacy in preventing COVID-19 is unclear. Moreover, the limited vaccine supply raises questions on how they can be used effectively. To examine the optimal allocation of COVID-19 vaccines in South Korea, we constructed an age-structured mathematical model, calibrated using country-specific demographic and epidemiological data. The optimal control problem was formulated with the aim of finding time-dependent age-specific optimal vaccination strategies to minimize costs related to COVID-19 infections and vaccination, considering a limited vaccine supply and various vaccine effects on susceptibility and symptomatology. Our results suggest that “susceptibility-reducing” vaccines should be relatively evenly distributed among all age groups, resulting in more than 40% of eligible age groups being vaccinated. In contrast, “symptom-reducing” vaccines should be administered mainly to individuals aged 20–29 and ≥60 years. Thus, our study suggests that the vaccine profile should determine the optimal vaccination strategy. Our findings highlight the importance of understanding vaccine’s effects on susceptibility and symptomatology for effective public health interventions.
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