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Herdina AN, Bozdogan A, Aspermair P, Dostalek J, Klausberger M, Lingg N, Cserjan-Puschmann M, Aguilar PP, Auer S, Demirtas H, Andersson J, Lötsch F, Holzer B, Steinrigl A, Thalhammer F, Schellnegger J, Breuer M, Knoll W, Strassl R. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosens Bioelectron 2024; 267:116807. [PMID: 39341071 DOI: 10.1016/j.bios.2024.116807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/02/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024]
Abstract
This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.
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Affiliation(s)
- Anna Nele Herdina
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria
| | - Anil Bozdogan
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria; BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria
| | - Patrik Aspermair
- BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria; Life Sciences Technology, Danube Privat University, Wiener Neustadt, Austria
| | - Jakub Dostalek
- Life Sciences Technology, Danube Privat University, Wiener Neustadt, Austria; Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nico Lingg
- ACIB - Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, BOKU University, Vienna, Austria
| | - Monika Cserjan-Puschmann
- ACIB - Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, BOKU University, Vienna, Austria
| | - Patricia Pereira Aguilar
- ACIB - Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, BOKU University, Vienna, Austria
| | - Simone Auer
- BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria
| | - Halil Demirtas
- BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria
| | - Jakob Andersson
- BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria; Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Felix Lötsch
- Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria; Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Barbara Holzer
- Institute Krems Bioanalytics, IMC Krems University of Applied Sciences, Krems, Austria
| | - Adi Steinrigl
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, Mödling, Austria
| | | | - Julia Schellnegger
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria
| | - Monika Breuer
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Knoll
- BioSensor Technologies, Austrian Institute of Technology, Vienna, Austria; Life Sciences Technology, Danube Privat University, Wiener Neustadt, Austria
| | - Robert Strassl
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria.
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2
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Claveau S, Mahmood F, Amir B, Kwan JJW, White C, Vipond J, Iannattone L. COVID-19 and Cancer Care: A Review and Practical Guide to Caring for Cancer Patients in the Era of COVID-19. Curr Oncol 2024; 31:5330-5343. [PMID: 39330021 PMCID: PMC11431468 DOI: 10.3390/curroncol31090393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
COVID-19, a novel infectious disease caused by the emergence of the SARS-CoV-2 virus in 2020, has had a profound impact on healthcare, both at the individual and population level. The impact at the population level was felt most acutely during the emergency phase of the pandemic, with hospital capacity issues leading to widespread disruptions and delays in the delivery of healthcare services such as screening programs and elective surgeries. While hospitals are no longer being acutely overwhelmed by COVID-19 patients, the impact of the virus on vulnerable patient populations such as cancer patients continues to be of ongoing consequence. Cancer patients remain at high risk of hospitalization, ICU admission, and death due to COVID-19, even in the era of vaccination. Infection prevention and risk mitigation strategies such air quality control, masking, testing, vaccination, and treatment should therefore be integrated into the usual care and counseling of cancer patients moving forward to avoid preventable morbidity and mortality from this infection and ensure the safety of this vulnerable cohort as they navigate their cancer diagnosis and treatment in the era of COVID-19.
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Affiliation(s)
- Simon Claveau
- Department of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Farhan Mahmood
- Department of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Baraa Amir
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Cheryl White
- Independent Researcher, Toronto, ON M6P 3X9, Canada
| | - Joe Vipond
- Department of Emergency Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lisa Iannattone
- Department of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
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3
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Baumgart SWL, McLachlan A, Kenny H, McKew G, Maddocks S, Chen SCA, Kok J. Deisolation in the Healthcare Setting Following Recent COVID-19 Infection. Viruses 2024; 16:1131. [PMID: 39066294 PMCID: PMC11281359 DOI: 10.3390/v16071131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Deisolation of persons infected with SARS-CoV-2, the virus that causes COVID-19, presented a substantial challenge for healthcare workers and policy makers, particularly during the early phases of the pandemic. Data to guide deisolation of SARS-CoV-2-infected patients remain limited, and the risk of transmitting and acquiring infection has changed with the evolution of SARS-CoV-2 variants and population immunity from previous vaccination or infection, or both. AIMS This review examines the evidence to guide the deisolation of SARS-CoV-2-infected inpatients within the hospital setting when clinically improving and also of healthcare workers with COVID-19 prior to returning to work. METHODS A review was performed using relevant search terms in Medline, EMBASE, Google Scholar, and PubMed. RESULTS AND DISCUSSION The evidence is reviewed with regards to the nature of SARS-CoV-2 transmission, the role of testing to guide deisolation, and the impact of SARS-CoV-2-specific immunity. A paradigm and recommendations are proposed to guide deisolation for inpatients and return to work for healthcare workers.
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Affiliation(s)
- Samuel W. L. Baumgart
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Aidan McLachlan
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Hayden Kenny
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Genevieve McKew
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Susan Maddocks
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
| | - Sharon C.-A. Chen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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4
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Leibovici L, Friedman J. Clinical Microbiology and Infection: how did we do in 2023? Clin Microbiol Infect 2024:S1198-743X(24)00314-8. [PMID: 38992432 DOI: 10.1016/j.cmi.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
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5
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Kanki PJ, Hamel DJ, Riedel S, Dutta S, Cheng A, Chang CA, Arnaout R, Kirby JE. SARS-CoV-2 live virus culture and sample freeze-thaw stability. Diagn Microbiol Infect Dis 2024; 109:116282. [PMID: 38663335 DOI: 10.1016/j.diagmicrobio.2024.116282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 05/28/2024]
Abstract
The effect of freeze-thaw on SARS-CoV-2 viral viability is not well established. We isolated virus from 31 split clinical samples cultured fresh or after a 7- or 17/18-day freeze. We found that freeze-thaw did not significantly affect viral culture isolation. Therefore, frozen samples may be used to assess SARS-CoV-2 infectiousness.
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Affiliation(s)
- Phyllis J Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA.
| | - Donald J Hamel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Sanjucta Dutta
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Annie Cheng
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Charlotte A Chang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Ramy Arnaout
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
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6
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Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. THE LANCET. INFECTIOUS DISEASES 2024; 24:e453-e462. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
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Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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7
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Theel ES, Kirby JE, Pollock NR. Testing for SARS-CoV-2: lessons learned and current use cases. Clin Microbiol Rev 2024; 37:e0007223. [PMID: 38488364 PMCID: PMC11237512 DOI: 10.1128/cmr.00072-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.
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Affiliation(s)
- Elitza S. Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
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8
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Zhang YP, Bu JW, Shu RX, Liu SL. Advances in rapid point-of-care virus testing. Analyst 2024; 149:2507-2525. [PMID: 38630498 DOI: 10.1039/d4an00238e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2024]
Abstract
Outbreaks of viral diseases seriously jeopardize people's health and cause huge economic losses. At the same time, virology provides a new perspective for biology, molecular biology and cancer research, and it is important to study the discovered viruses with potential applications. Therefore, the development of immediate and rapid viral detection methods for the prevention and treatment of viral diseases as well as the study of viruses has attracted extensive attention from scientists. With the continuous progress of science and technology, especially in the field of bioanalysis, a series of new detection techniques have been applied to the on-site rapid detection of viruses, which has become a powerful approach for human beings to fight against viruses. In this paper, the latest research progress of rapid point-of-care detection of viral nucleic acids, antigens and antibodies is presented. In addition, the advantages and disadvantages of these technologies are discussed from the perspective of practical application requirements. Finally, the problems and challenges faced by rapid viral detection methods and their development prospects are discussed.
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Affiliation(s)
- Yu-Peng Zhang
- Technical Center, Shanghai Tobacco Group Co., Ltd, Shanghai 201315, P. R. China.
| | - Jin-Wei Bu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China.
| | - Ru-Xin Shu
- Technical Center, Shanghai Tobacco Group Co., Ltd, Shanghai 201315, P. R. China.
| | - Shu-Lin Liu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China.
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9
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Manten K, Katzenschlager S, Brümmer LE, Schmitz S, Gaeddert M, Erdmann C, Grilli M, Pollock NR, Macé A, Erkosar B, Carmona S, Ongarello S, Johnson CC, Sacks JA, Faehling V, Bornemann L, Weigand MA, Denkinger CM, Yerlikaya S. Clinical accuracy of instrument-based SARS-CoV-2 antigen diagnostic tests: a systematic review and meta-analysis. Virol J 2024; 21:99. [PMID: 38685117 PMCID: PMC11059670 DOI: 10.1186/s12985-024-02371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND During the COVID-19 pandemic, antigen diagnostic tests were frequently used for screening, triage, and diagnosis. Novel instrument-based antigen tests (iAg tests) hold the promise of outperforming their instrument-free, visually-read counterparts. Here, we provide a systematic review and meta-analysis of the SARS-CoV-2 iAg tests' clinical accuracy. METHODS We systematically searched MEDLINE (via PubMed), Web of Science, medRxiv, and bioRxiv for articles published before November 7th, 2022, evaluating the accuracy of iAg tests for SARS-CoV-2 detection. We performed a random effects meta-analysis to estimate sensitivity and specificity and used the QUADAS-2 tool to assess study quality and risk of bias. Sub-group analysis was conducted based on Ct value range, IFU-conformity, age, symptom presence and duration, and the variant of concern. RESULTS We screened the titles and abstracts of 20,431 articles and included 114 publications that fulfilled the inclusion criteria. Additionally, we incorporated three articles sourced from the FIND website, totaling 117 studies encompassing 95,181 individuals, which evaluated the clinical accuracy of 24 commercial COVID-19 iAg tests. The studies varied in risk of bias but showed high applicability. Of 24 iAg tests from 99 studies assessed in the meta-analysis, the pooled sensitivity and specificity compared to molecular testing of a paired NP swab sample were 76.7% (95% CI 73.5 to 79.7) and 98.4% (95% CI 98.0 to 98.7), respectively. Higher sensitivity was noted in individuals with high viral load (99.6% [95% CI 96.8 to 100] at Ct-level ≤ 20) and within the first week of symptom onset (84.6% [95% CI 78.2 to 89.3]), but did not differ between tests conducted as per manufacturer's instructions and those conducted differently, or between point-of-care and lab-based testing. CONCLUSION Overall, iAg tests have a high pooled specificity but a moderate pooled sensitivity, according to our analysis. The pooled sensitivity increases with lower Ct-values (a proxy for viral load), or within the first week of symptom onset, enabling reliable identification of most COVID-19 cases and highlighting the importance of context in test selection. The study underscores the need for careful evaluation considering performance variations and operational features of iAg tests.
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Affiliation(s)
- Katharina Manten
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephan Katzenschlager
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Lukas E Brümmer
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephani Schmitz
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mary Gaeddert
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | | | | | | | - Cheryl C Johnson
- Global HIV, Hepatitis and STIs Programmes, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Verena Faehling
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Linus Bornemann
- Institute of Virology, Faculty of Medicine, University Medical Centre, University of Freiburg, Freiburg, Germany
| | - Markus A Weigand
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Claudia M Denkinger
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| | - Seda Yerlikaya
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany.
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany.
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10
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Dong S, Jutkowitz E, Giardina J, Bilinski A. Screening Strategies to Reduce COVID-19 Mortality in Nursing Homes. JAMA HEALTH FORUM 2024; 5:e240688. [PMID: 38669030 PMCID: PMC11065177 DOI: 10.1001/jamahealthforum.2024.0688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/03/2024] [Indexed: 05/01/2024] Open
Abstract
Importance Nursing home residents continue to bear a disproportionate share of COVID-19 morbidity and mortality, accounting for 9% of all US COVID-19 deaths in 2023, despite comprising only 0.4% of the population. Objective To evaluate the cost-effectiveness of screening strategies in reducing COVID-19 mortality in nursing homes. Design and Setting An agent-based model was developed to simulate SARS-CoV-2 transmission in the nursing home setting. Parameters were determined using SARS-CoV-2 virus data and COVID-19 data from the Centers for Medicare & Medicaid Services and US Centers for Disease Control and Prevention that were published between 2020 and 2023, as well as data on nursing homes published between 2010 and 2023. The model used in this study simulated interactions and SARS-CoV-2 transmission between residents, staff, and visitors in a nursing home setting. The population used in the simulation model was based on the size of the average US nursing home and recommended staffing levels, with 90 residents, 90 visitors (1 per resident), and 83 nursing staff members. Exposure Screening frequency (none, weekly, and twice weekly) was varied over 30 days against varying levels of COVID-19 community incidence, booster uptake, and antiviral use. Main Outcomes and Measures The main outcomes were SARS-CoV-2 infections, detected cases per 1000 tests, and incremental cost of screening per life-year gained. Results Nursing home interactions were modeled between 90 residents, 90 visitors, and 83 nursing staff over 30 days, completing 4000 to 8000 simulations per parameter combination. The incremental cost-effectiveness ratios of weekly and twice-weekly screening were less than $150 000 per resident life-year with moderate (50 cases per 100 000) and high (100 cases per 100 000) COVID-19 community incidence across low-booster uptake and high-booster uptake levels. When COVID-19 antiviral use reached 100%, screening incremental cost-effectiveness ratios increased to more than $150 000 per life-year when booster uptake was low and community incidence was high. Conclusions and Relevance The results of this cost-effectiveness analysis suggest that screening may be effective for reducing COVID-19 mortality in nursing homes when COVID-19 community incidence is high and/or booster uptake is low. Nursing home administrators can use these findings to guide planning in the context of widely varying levels of SARS-CoV-2 transmission and intervention measures across the US.
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Affiliation(s)
- Shirley Dong
- Department of Health Services, Policy & Practice, Brown University School of Public Health, Providence, Rhode Island
| | - Eric Jutkowitz
- Department of Health Services, Policy & Practice, Brown University School of Public Health, Providence, Rhode Island
- Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, Rhode Island
- Evidence Synthesis Program Center Providence VA Medical Center, Providence, Rhode Island
| | - John Giardina
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston
| | - Alyssa Bilinski
- Department of Health Services, Policy & Practice, Brown University School of Public Health, Providence, Rhode Island
- Department of Biostatistics, Brown University School of Public Health, Providence, Rhode Island
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11
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Snedden CE, Lloyd-Smith JO. Predicting the presence of infectious virus from PCR data: A meta-analysis of SARS-CoV-2 in non-human primates. PLoS Pathog 2024; 20:e1012171. [PMID: 38683864 PMCID: PMC11081500 DOI: 10.1371/journal.ppat.1012171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/09/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Researchers and clinicians often rely on molecular assays like PCR to identify and monitor viral infections, instead of the resource-prohibitive gold standard of viral culture. However, it remains unclear when (if ever) PCR measurements of viral load are reliable indicators of replicating or infectious virus. The recent popularity of PCR protocols targeting subgenomic RNA for SARS-CoV-2 has caused further confusion, as the relationships between subgenomic RNA and standard total RNA assays are incompletely characterized and opinions differ on which RNA type better predicts culture outcomes. Here, we explore these issues by comparing total RNA, subgenomic RNA, and viral culture results from 24 studies of SARS-CoV-2 in non-human primates (including 2167 samples from 174 individuals) using custom-developed Bayesian statistical models. On out-of-sample data, our best models predict subgenomic RNA positivity from total RNA data with 91% accuracy, and they predict culture positivity with 85% accuracy. Further analyses of individual time series indicate that many apparent prediction errors may arise from issues with assay sensitivity or sample processing, suggesting true accuracy may be higher than these estimates. Total RNA and subgenomic RNA showed equivalent performance as predictors of culture positivity. Multiple cofactors (including exposure conditions, host traits, and assay protocols) influence culture predictions, yielding insights into biological and methodological sources of variation in assay outcomes-and indicating that no single threshold value applies across study designs. We also show that our model can accurately predict when an individual is no longer infectious, illustrating the potential for future models trained on human data to guide clinical decisions on case isolation. Our work shows that meta-analysis of in vivo data can overcome longstanding challenges arising from limited sample sizes and can yield robust insights beyond those attainable from individual studies. Our analytical pipeline offers a framework to develop similar predictive tools in other virus-host systems, including models trained on human data, which could support laboratory analyses, medical decisions, and public health guidelines.
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Affiliation(s)
- Celine E. Snedden
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, California, United States of America
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12
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Mostafa HH. Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2). Clin Lab Med 2024; 44:85-93. [PMID: 38280800 DOI: 10.1016/j.cll.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).
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Affiliation(s)
- Heba H Mostafa
- Johns Hopkins School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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13
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. Clin Infect Dis 2024; 78:301-307. [PMID: 37768707 PMCID: PMC10874267 DOI: 10.1093/cid/ciad582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. METHODS We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. RESULTS Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. CONCLUSIONS In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.
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Affiliation(s)
- Jennifer K Frediani
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Kaleb B McLendon
- Emory/Children's Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Adrianna L Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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14
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Rhee C, Klompas M, Pak TR, Köhler JR. In Support of Universal Admission Testing for SARS-CoV-2 During Significant Community Transmission. Clin Infect Dis 2024; 78:439-444. [PMID: 37463411 DOI: 10.1093/cid/ciad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023] Open
Abstract
Many hospitals have stopped or are considering stopping universal admission testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We discuss reasons why admission testing should still be part of a layered system to prevent hospital-acquired SARS-CoV-2 infections during times of significant community transmission. These include the morbidity of SARS-CoV-2 in vulnerable patients, the predominant contribution of presymptomatic and asymptomatic people to transmission, the high rate of transmission between patients in shared rooms, and data suggesting surveillance testing is associated with fewer nosocomial infections. Preferences of diverse patient populations, particularly the hardest-hit communities, should be surveyed and used to inform prevention measures. Hospitals' ethical responsibility to protect patients from serious infections should predominate over concerns about costs, labor, and inconvenience. We call for more rigorous data on the incidence and morbidity of nosocomial SARS-CoV-2 infections and more research to help determine when to start, stop, and restart universal admission testing and other prevention measures.
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Affiliation(s)
- Chanu Rhee
- Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Theodore R Pak
- Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julia R Köhler
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
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15
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Borroto-Esoda K, Wilfret D, Tong X, Plummer A, Kearney B, Kwong AD. SARS-CoV-2 viral dynamics in a placebo-controlled phase 2 study of patients infected with the SARS-CoV-2 Omicron variant and treated with pomotrelvir. Microbiol Spectr 2024; 12:e0298023. [PMID: 38197702 PMCID: PMC10845961 DOI: 10.1128/spectrum.02980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
Current guidelines recommend that individuals with moderate COVID-19 disease isolate for 5 days after the first appearance of symptoms or a positive SARS-CoV-2 test. It would be useful to understand the time course of infectious virus production and its correlation with virus detection using a rapid antigen test (RAT) or quantitative reverse transcriptase (qRT)-PCR. In a phase 2 study, 242 vaccinated patients with COVID-19 and at low risk for progression to severe disease initiated 5 days of treatment with pomotrelvir (PBI-0451, a SARS-CoV-2 main protease inhibitor) or placebo within 5 days after symptom onset. The primary endpoint, the proportion of subjects with SARS-CoV-2 viral titers below the limit of detection on Day 3 of treatment in the pomotrelvir versus placebo groups, was not met. No between-group differences in SARS-CoV-2 clearance or symptom resolution or alleviation were observed. Additional analyses evaluated the dynamics of SARS-CoV-2 replication in mid-turbinate nasal swabs and saliva samples using infectious virus assay (IVA), RAT, and qRT-PCR. SARS-CoV-2 cleared rapidly, with negative results first determined by IVA (TCID50 below the limit of detection), followed by the RAT (negative for SARS-CoV-2 N antigen), and qRT-PCR (RNA below the limit of detection), which suggests that delayed initiation of treatment (up to 5 days after symptom onset) may have contributed to the lack of treatment response. Symptom resolution lagged behind viral clearance assessed by IVA and RAT. These data support reliance on a negative RAT to determine when an individual is no longer producing infectious virus and may end isolation.IMPORTANCEA phase 2 double-blind, placebo-controlled study was performed evaluating pomotrelvir, a SARS-CoV-2 Mpro inhibitor, compared with placebo in 242 non-hospitalized, vaccinated, symptomatic adults with COVID-19 (Omicron). No improvement in the decrease of viral replication or relief of symptoms was observed between the two groups when treatment was initiated ≥3 days after symptom onset. These results suggest that future COVID-19 antiviral studies using a similar patient population may need to initiate treatment earlier, like influenza studies. This is the first study to prospectively evaluate SARS-CoV-2 viral dynamics and the time to viral clearance in a significant number of patients using concurrently obtained results from an infectious virus assay, a rapid antigen test (RAT), and a qRT-PCR assay over a 15-day time course. These results suggest that a negative RAT assay is a good indicator of loss of infectious virus and the ability to return to normal activities.
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Affiliation(s)
| | | | - Xiao Tong
- Pardes BioSciences Inc., Carlsbad, California, USA
| | | | | | - Ann D. Kwong
- Pardes BioSciences Inc., Carlsbad, California, USA
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16
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Schrank GM, Harris-Williams M, Schiavone K, Lusby MC, Dove C, Leekha S. Evaluation of an antigen-test-based strategy to reduce duration of transmission-based precautions for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in hospitalized patients. Infect Control Hosp Epidemiol 2024; 45:114-116. [PMID: 37539701 DOI: 10.1017/ice.2023.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
An academic hospital implemented a severe acute respiratory coronavirus virus 2 (SARS-CoV-2) antigen-test-based strategy to facilitate discontinuation of precautions for patients admitted with a positive SARS-CoV-2 test. Of 171 patients that underwent antigen testing, 68% had an initial negative test performed a median of 5 days after admission. Antigen testing reduced isolation time by 144 hours.
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Affiliation(s)
- Gregory M Schrank
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | | | - Martha C Lusby
- University of Maryland Medical Center, Baltimore, Maryland
| | - Cindy Dove
- University of Maryland Medical Center, Baltimore, Maryland
| | - Surbhi Leekha
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland
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17
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Kyo H, Patel SA, Yamamoto M, Matsumura Y, Ikeda T, Nagao M. A population-based study of the trend in SARS-CoV-2 diagnostic modalities from the beginning of the pandemic to the Omicron surge in Kyoto City, Kyoto, Japan. BMC Public Health 2023; 23:2551. [PMID: 38129830 PMCID: PMC10734122 DOI: 10.1186/s12889-023-17498-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) presents critical diagnostic challenges for managing the pandemic. We investigated the 30-month changes in COVID-19 testing modalities and functional testing sites from the early period of the pandemic to the most recent Omicron surge in 2022 in Kyoto City, Japan. METHODS This is a retrospective-observational study using a local anonymized population database that included patients' demographic and clinical information, testing methods and facilities from January 2020 to June 2022, a total of 30 months. We computed the distribution of symptomatic presentation, testing methods, and testing facilities among cases. Differences over time were tested using chi-square tests of independence. RESULTS During the study period, 133,115 confirmed COVID-19 cases were reported, of which 90.9% were symptomatic. Although nucleic acid amplification testing occupied 68.9% of all testing, the ratio of lateral flow devices (LFDs) rapidly increased in 2022. As the pandemic continued, the testing capability was shifted from COVID-19 designated facilities to general practitioners, who became the leading testing providers (57.3% of 99,945 tests in 2022). CONCLUSIONS There was a dynamic shift in testing modality during the first 30 months of the pandemic in Kyoto City. General practitioners increased their role substantially as the use of LFDs spread dramatically in 2022. By comprehending and documenting the evolution of testing methods and testing locations, it is anticipated that this will contribute to the establishment of an even more efficient testing infrastructure for the next pandemic.
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Affiliation(s)
- Hiroki Kyo
- MetroAtlanta Ambulance Service, Emory Healthcare Network, Atlanta, GA, USA
| | - Shivani A Patel
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Laboratory, Kyoto University Hospital, Kyoto, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Laboratory, Kyoto University Hospital, Kyoto, Japan
| | - Takeshi Ikeda
- Public Health and Welfare Bureau of Kyoto City, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
- Department of Clinical Laboratory, Kyoto University Hospital, Kyoto, Japan.
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18
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Edelstein GE, Boucau J, Uddin R, Marino C, Liew MY, Barry M, Choudhary MC, Gilbert RF, Reynolds Z, Li Y, Tien D, Sagar S, Vyas TD, Kawano Y, Sparks JA, Hammond SP, Wallace Z, Vyas JM, Barczak AK, Lemieux JE, Li JZ, Siedner MJ. SARS-CoV-2 Virologic Rebound With Nirmatrelvir-Ritonavir Therapy : An Observational Study. Ann Intern Med 2023; 176:1577-1585. [PMID: 37956428 PMCID: PMC10644265 DOI: 10.7326/m23-1756] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Data are conflicting regarding an association between treatment of acute COVID-19 with nirmatrelvir-ritonavir (N-R) and virologic rebound (VR). OBJECTIVE To compare the frequency of VR in patients with and without N-R treatment for acute COVID-19. DESIGN Observational cohort study. SETTING Multicenter health care system in Boston, Massachusetts. PARTICIPANTS Ambulatory adults with acute COVID-19 with and without use of N-R. INTERVENTION Receipt of 5 days of N-R treatment versus no COVID-19 therapy. MEASUREMENTS The primary outcome was VR, defined as either a positive SARS-CoV-2 viral culture result after a prior negative result or 2 consecutive viral loads above 4.0 log10 copies/mL that were also at least 1.0 log10 copies/mL higher than a prior viral load below 4.0 log10 copies/mL. RESULTS Compared with untreated persons (n = 55), those taking N-R (n = 72) were older, received more COVID-19 vaccinations, and more commonly had immunosuppression. Fifteen participants (20.8%) taking N-R had VR versus 1 (1.8%) who was untreated (absolute difference, 19.0 percentage points [95% CI, 9.0 to 29.0 percentage points]; P = 0.001). All persons with VR had a positive viral culture result after a prior negative result. In multivariable models, only N-R use was associated with VR (adjusted odds ratio, 10.02 [CI, 1.13 to 88.74]; P = 0.038). Virologic rebound was more common among those who started therapy within 2 days of symptom onset (26.3%) than among those who started 2 or more days after symptom onset (0%) (P = 0.030). Among participants receiving N-R, those who had VR had prolonged shedding of replication-competent virus compared with those who did not have VR (median, 14 vs. 3 days). Eight of 16 participants (50% [CI, 25% to 75%]) with VR also reported symptom rebound; 2 were completely asymptomatic. No post-VR resistance mutations were detected. LIMITATIONS Observational study design with differences between the treated and untreated groups; positive viral culture result was used as a surrogate marker for risk for ongoing viral transmission. CONCLUSION Virologic rebound occurred in approximately 1 in 5 people taking N-R, often without symptom rebound, and was associated with shedding of replication-competent virus. PRIMARY FUNDING SOURCE National Institutes of Health.
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Affiliation(s)
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts (J.B., C.M.)
| | - Rockib Uddin
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Caitlin Marino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts (J.B., C.M.)
| | - May Y Liew
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Mamadou Barry
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Manish C Choudhary
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (M.C.C., J.Z.L.)
| | - Rebecca F Gilbert
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Zahra Reynolds
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Yijia Li
- Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Y.L.)
| | - Dessie Tien
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Shruti Sagar
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Tammy D Vyas
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Yumeko Kawano
- Brigham and Women's Hospital, Boston, Massachusetts (G.E.E., Y.K., J.A.S.)
| | - Jeffrey A Sparks
- Brigham and Women's Hospital, Boston, Massachusetts (G.E.E., Y.K., J.A.S.)
| | - Sarah P Hammond
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Zachary Wallace
- Massachusetts General Hospital, Boston, Massachusetts (R.U., M.Y.L., M.B., R.F.G., Z.R., D.T., S.S., T.D.V., S.P.H., Z.W.)
| | - Jatin M Vyas
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (J.M.V.)
| | - Amy K Barczak
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (A.K.B.)
| | - Jacob E Lemieux
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts (J.E.L.)
| | - Jonathan Z Li
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (M.C.C., J.Z.L.)
| | - Mark J Siedner
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, and Africa Health Research Institute, KwaZulu-Natal, South Africa (M.J.S.)
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19
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Ota K, Kodama H, Kawamoto Y, Sasaki D, Mitsumoto-Kaseida F, Sakamoto K, Kosai K, Hasegawa H, Takazono T, Izumikawa K, Mukae H, Tun MMN, Morita K, Yanagihara K. The evaluation of a rapid microfluidic immunofluorescence antigen test in detecting the infectiousness of COVID-19 patients. BMC Infect Dis 2023; 23:823. [PMID: 37996783 PMCID: PMC10668452 DOI: 10.1186/s12879-023-08821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND A test-based strategy against coronavirus disease 2019 (COVID-19) is one of the measures to assess the need for isolation and prevention of infection. However, testing with high sensitivity methods, such as quantitative RT-PCR, leads to unnecessary isolation, whereas the lateral flow antigen test shows low sensitivity and false negative results. The purpose of this study was to evaluate the performance of the LumiraDx SARS-CoV-2 Ag test (Lumira Ag), a rapid microfluidic immunofluorescence method, in assessing infectivity. METHODS This study was performed from March 2022 to July 2022. A pair of nasopharyngeal swab samples were obtained from each patient with mild COVID-19. One swab was used for Lumira Ag testing, and the other for quantitative RT-PCR testing and virus culture. RESULTS A total of 84 patients were included in the study. Among them, PCR, Lumira Ag test, and virus culture indicated positivity for 82, 66, and 24 patients, respectively. When comparing the Lumira Ag test to virus culture, its sensitivity was 100.0% (24/24), specificity, 30.0% (18/60); positive predictive value, 36.3% (24/66); and negative predictive value (NPV), 100.0% (18/18). The positive sample for virus culture was observed until the ninth day from the onset of symptoms, while the Lumira Ag test was observed until day 11. CONCLUSIONS The Lumira Ag test showed high sensitivity and NPV (100% each) compared to virus culture. A test-based strategy using the Lumira Ag test can effectively exclude COVID-19 infectiousness.
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Affiliation(s)
- Kenji Ota
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan.
| | - Hina Kodama
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Yasuhide Kawamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Fujiko Mitsumoto-Kaseida
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
- Department of Microbiology, Graduate School of Medicine, Yamaguchi University, 1-1-1, Minami-Kogushi, Ube, 755-8505, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Takahiro Takazono
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Koichi Izumikawa
- Infection Control and Education Center, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
- Dejima Infectious Disease Research Alliance, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
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20
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Viloria Winnett A, Akana R, Shelby N, Davich H, Caldera S, Yamada T, Reyna JRB, Romano AE, Carter AM, Kim MK, Thomson M, Tognazzini C, Feaster M, Goh YY, Chew YC, Ismagilov RF. Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types. Microbiol Spectr 2023; 11:e0129523. [PMID: 37314333 PMCID: PMC10434058 DOI: 10.1128/spectrum.01295-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/21/2023] [Indexed: 06/15/2023] Open
Abstract
In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6 × 106 copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, preinfectious period of the infection. Further, the Ag-RDT detected ≤63% of presumably infectious time points. The poor observed clinical sensitivity of the Ag-RDT was similar to what was predicted based on quantitative ANS viral loads and the inferred limit of detection of the ANS Ag-RDT being evaluated, indicating high-quality self-sampling. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDTs for detection of infected or infectious individuals should be compared with a composite (multispecimen) infection status to correctly assess performance. IMPORTANCE We reveal three findings from a longitudinal study of daily nasal antigen rapid diagnostic test (Ag-RDT) evaluated against SARS-CoV-2 viral load quantification in three specimen types (saliva, nasal swab, and throat swab) in participants enrolled at the incidence of infection. First, the evaluated Ag-RDT showed low (44%) clinical sensitivity for detecting infected persons at all infection stages. Second, the Ag-RDT poorly detected (≤63%) time points that participants had high and presumably infectious viral loads in at least one specimen type. This poor clinical sensitivity to detect infectious individuals is inconsistent with the commonly held view that daily Ag-RDTs have near-perfect detection of infectious individuals. Third, use of a combination nasal-throat specimen type was inferred by viral loads to significantly improve Ag-RDT performance to detect infectious individuals.
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Affiliation(s)
| | - Reid Akana
- California Institute of Technology, Pasadena, California, USA
| | - Natasha Shelby
- California Institute of Technology, Pasadena, California, USA
| | - Hannah Davich
- California Institute of Technology, Pasadena, California, USA
| | - Saharai Caldera
- California Institute of Technology, Pasadena, California, USA
| | - Taikun Yamada
- Pangea Laboratory LLC, Tustin, California, USA
- Zymo Research Corporation, Irvine, California, USA
| | | | - Anna E. Romano
- California Institute of Technology, Pasadena, California, USA
| | | | - Mi Kyung Kim
- California Institute of Technology, Pasadena, California, USA
| | - Matt Thomson
- California Institute of Technology, Pasadena, California, USA
| | | | - Matthew Feaster
- Pasadena Public Health Department, Pasadena, California, USA
| | - Ying-Ying Goh
- Pasadena Public Health Department, Pasadena, California, USA
| | - Yap Ching Chew
- Pangea Laboratory LLC, Tustin, California, USA
- Zymo Research Corporation, Irvine, California, USA
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21
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.09.23289735. [PMID: 37214887 PMCID: PMC10197800 DOI: 10.1101/2023.05.09.23289735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
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Affiliation(s)
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Kaleb B. McLendon
- Emory/Children’s Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, GA USA
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
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22
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Chang-Graham AL, Sahoo MK, Huang C, Solis D, Sibai M, August G, Calayag L, Kenji OM, Shi RZ, Mostafa HH, Lei GS, Relich RF, Pinsky BA. Comparison of nucleocapsid antigen with strand-specific reverse-transcription PCR for monitoring SARS-CoV-2 infection. J Clin Virol 2023; 164:105468. [PMID: 37119583 PMCID: PMC10124094 DOI: 10.1016/j.jcv.2023.105468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND Tests that sensitively detect the presence of actively replicating SARS-CoV-2 may improve patient care by allowing the safe and timely discontinuation of isolation. Correlates of active replication include nucleocapsid antigen and virus minus-strand RNA. METHODS Qualitative agreement of the DiaSorin LIAISON SARS-CoV-2 nucleocapsid antigen chemiluminescent immunoassay (CLIA) with minus-strand RNA was determined using 402 upper respiratory specimens from 323 patients previously tested using a laboratory-developed SARS-CoV-2 strand-specific RT-qPCR. Nucleocapsid antigen levels, minus-strand and plus-strand cycle threshold values, as well as virus culture, were used to evaluate discordant specimens. Receiver operating characteristic curves were also used to identify virus RNA thresholds for active replication, including values harmonized to the World Health Organization International Standard. RESULTS Overall agreement was 92.0% [95% confidence interval (CI): 89.0 - 94.5], positive percent agreement was 90.6% (95% CI: 84.4 - 95.0), and negative percent agreement was 92.8% (95% CI: 89.0 - 95.6). The kappa coefficient was 0.83 (95% CI: 0.77 - 0.88). Discordant specimens contained low levels of nucleocapsid antigen and minus-strand RNA. 84.8% (28/33) were negative by culture. Sensitivity-optimized plus-strand RNA thresholds for active replication were 31.6 cycles or 3.64 log10 IU/mL; resulting in 100.0% sensitivity (95% CI: 97.6 to 100.0) and 55.9 specificity (95% CI: 49.7 to 62.0). CONCLUSIONS Detection of nucleocapsid antigen by CLIA performs equivalently to minus-strand detection via strand-specific RT-qPCR, though these methods may overestimate replication-competent virus compared to culture. Careful implementation of biomarkers for actively replicating SARS-CoV-2 has the potential to inform infection control decision-making and patient management.
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Affiliation(s)
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gianna August
- Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Lira Calayag
- Special Chemistry and Immunology Laboratory, Stanford Health Care, CA, USA
| | - Obadia M Kenji
- Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Run-Zhang Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Special Chemistry and Immunology Laboratory, Stanford Health Care, CA, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guang-Sheng Lei
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ryan F Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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23
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Widyasari K, Kim S. Rapid Antigen Tests during the COVID-19 Era in Korea and Their Implementation as a Detection Tool for Other Infectious Diseases. Bioengineering (Basel) 2023; 10:322. [PMID: 36978713 PMCID: PMC10045740 DOI: 10.3390/bioengineering10030322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Rapid antigen tests (RATs) are diagnostic tools developed to specifically detect a certain protein of infectious agents (viruses, bacteria, or parasites). RATs are easily accessible due to their rapidity and simplicity. During the COVID-19 pandemic, RATs have been widely used in detecting the presence of the specific SARS-CoV-2 antigen in respiratory samples from suspected individuals. Here, the authors review the application of RATs as detection tools for COVID-19, particularly in Korea, as well as for several other infectious diseases. To address these issues, we present general knowledge on the design of RATs that adopt the lateral flow immunoassay for the detection of the analyte (antigen). The authors then discuss the clinical utilization of the authorized RATs amidst the battle against the COVID-19 pandemic in Korea and their role in comparison with other detection methods. We also discuss the implementation of RATs for other, non-COVID-19 infectious diseases, the challenges that may arise during the application, the limitations of RATs as clinical detection tools, as well as the possible problem solving for those challenges to maximize the performance of RATs and avoiding any misinterpretation of the test result.
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Affiliation(s)
- Kristin Widyasari
- Gyeongsang Institute of Health Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Sunjoo Kim
- Gyeongsang Institute of Health Sciences, Gyeongsang National University, Jinju 52727, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon 51472, Republic of Korea
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24
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Viloria Winnett A, Akana R, Shelby N, Davich H, Caldera S, Yamada T, Reyna JRB, Romano AE, Carter AM, Kim MK, Thomson M, Tognazzini C, Feaster M, Goh YY, Chew YC, Ismagilov RF. Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods. PNAS NEXUS 2023; 2:pgad033. [PMID: 36926220 PMCID: PMC10013338 DOI: 10.1093/pnasnexus/pgad033] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 03/16/2023]
Abstract
SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 109 copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat-nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.
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Affiliation(s)
| | - Reid Akana
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Natasha Shelby
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Hannah Davich
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Saharai Caldera
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Taikun Yamada
- Pangea Laboratory LLC, 14762 Bentley Cir, Tustin, CA 92780, USA.,Zymo Research Corp., 17062 Murphy Ave, Irvine, CA 92614, USA
| | | | - Anna E Romano
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Alyssa M Carter
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Mi Kyung Kim
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Matt Thomson
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Colten Tognazzini
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Matthew Feaster
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Ying-Ying Goh
- Pasadena Public Health Department, 1845 N. Fair Oaks Ave, Pasadena, CA 91103, USA
| | - Yap Ching Chew
- Pangea Laboratory LLC, 14762 Bentley Cir, Tustin, CA 92780, USA.,Zymo Research Corp., 17062 Murphy Ave, Irvine, CA 92614, USA
| | - Rustem F Ismagilov
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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25
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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26
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Wagester S, Smith P, Lutz CT, Chung A, Tanis MD, O'Hare C, Mallon A, Minnier TE, Silvaggio T, Ruscetti A, Chrisman M, Zapf RL, Kip PL, Snyder GM. COVID-19 contagious health care personnel 5-day early return-to-work program. Am J Infect Control 2022:S0196-6553(22)00808-2. [PMID: 36410551 PMCID: PMC9674395 DOI: 10.1016/j.ajic.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND COVID-19 contagious health care personnel (HCP) who are self-isolating for a 10-day period increases burden to workforce shortages. Implementation of a 5-day early return-to-work (RTW) program may reduce self-isolation periods, without increasing transmission risk, during the COVID-19 pandemic. DESIGN AND METHODS This observational cohort quality improvement study included newly diagnosed COVID-19 HCP at a multifacility health care system. The program allowed HCP to return to work 6 days after date of a positive test result if they were not immunocompromised, had mild and improving symptoms, and self-reported a SARS-CoV-2 antigen negative test on day 5. RESULTS Between January 4 and April 3, 2022, 1,023 HCP self-enrolled and 344 (33.6%) self-reported negative test results. Among these, 161 (46.8%) self-reported negative test results on day 5 and were eligible for early RTW on day 6. A total of 714 days were saved from missed work in self-isolation. The number of tests purchased, dispensed, and reported per day of HCP time saved was 4.4. No transmission events were observed originating from HCP who participated in early RTW. CONCLUSION Implementing a 5-day early RTW program that includes HCP self-reporting SARS-CoV-2 antigen test results can increase staffing availability, while maintaining a low risk of SARS-CoV-2 transmission.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Teresa Silvaggio
- Wolff Center, UPMC, Pittsburgh, PA,Workpartners, UPMC, Pittsburgh, PA,Laboratory Service Center, UPMC, Pittsburgh, PA,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA,Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA
| | | | | | | | | | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA,Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA,Address correspondence to Graham M. Snyder MD, MS, Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, 3601 Fifth Ave, Suite 150, Pittsburgh, PA 15213
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27
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Neukam K, Lucero A, Gutiérrez-Valencia A, Amaya L, Echegoyen N, Martelli A, Videla C, Di Lello FA, Martínez AP. Point-of-care detection of SARS-CoV-2 antigen among symptomatic vs. asymptomatic persons: Testing for COVID-19 vs. infectivity. Front Public Health 2022; 10:995249. [PMID: 36324442 PMCID: PMC9619045 DOI: 10.3389/fpubh.2022.995249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023] Open
Abstract
Background Management of the coronavirus disease 2019 (COVID-19) pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires rapid and simple methods to detect COVID-19 patients and identify potential infectors. This study aimed to evaluate the utility of a point-of-care (PoC) rapid antigen diagnostic test (Ag-RDT) in these settings. Patients and methods Individuals who consecutively presented for SARS-CoV-2 testing at a tertiary care center in Buenos Aires, Argentina, underwent PoC Ag-RDT testing and real-time RT-PCR (qRT-PCR) on the same day during June 2021. Results Of 584 included subjects, 108 (18.5%) were symptomatic for COVID-19 while the remaining presented for miscellaneous reasons unrelated to possible or confirmed contact with a SARS-CoV-2-infected individual. A positive Ag-RDT result was obtained in 26 (24.1%) symptomatic and 7 (1.5%) asymptomatic persons (p < 0.001), which was concordant with qRT-PCR in 105/108 [97.2%, Cohen's kappa coefficient (κ) = 0.927] symptomatic and 467/476 (98.1% κ = 0.563) asymptomatic participants, with a positive percentage agreement (PPA; 95% confidence interval) of 89.7% (71.5-97.3%) and 42.9% (18.8-70.4%), respectively. None of the 11 false-negative diagnoses showed a Ct-value ≤20. Considering only failures with a Ct-value below 31 as hypothetical infectivity threshold of 105 SARS-CoV-2 RNA copies/mL, concordance was observed in 98.1% (κ = 0.746) in the asymptomatic population, accounting for a PPA of 66.7% (30.9-91%). Conclusions PoC Ag-RDT accurately detected active SARS-CoV-2 infection and showed acceptable diagnostic performance in asymptomatic persons potentially spreading infectious virus. Ag-RDT may therefore be useful to slow down or stop transmission by enabling adequate decisions on isolation at a public health level.
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Affiliation(s)
- Karin Neukam
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain,Instituto de Biomedicina de Sevilla, University of Seville, Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain,*Correspondence: Karin Neukam
| | - Alicia Lucero
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Alicia Gutiérrez-Valencia
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain,Instituto de Biomedicina de Sevilla, University of Seville, Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Lucas Amaya
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Natalia Echegoyen
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Antonella Martelli
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Cristina Videla
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Federico A. Di Lello
| | - Alfredo P. Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno “CEMIC”, Buenos Aires, Argentina
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