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Götz V, Mathé P, Agarwal P, Hornuss D, Pfau S, Panning M, Prager E, Voll RE, Engelhardt M, Frye BC, Bamberg F, Fuchs J, Müller M, Wagner D, Rieg S. Clinical phenotype and outcome of persistent SARS-CoV-2 replication in immunocompromised hosts: a retrospective observational study in the Omicron era. Infection 2024; 52:923-933. [PMID: 38095753 PMCID: PMC11142974 DOI: 10.1007/s15010-023-02138-0] [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: 08/15/2023] [Accepted: 11/10/2023] [Indexed: 06/02/2024]
Abstract
PURPOSE This study aims to describe clinical, virological and radiological characteristics as well as treatment strategies and outcomes of immunocompromised patients with persistent SARS-CoV-2 replication. METHODS We performed a retrospective cohort study of immunocompromised patients at the University Medical Center Freiburg between 01/2022 and 05/2023. Patients with substantial immunosuppression and persistent SARS-CoV-2 detection (Ct-value < 30 after 14 days) were included. RESULTS 36 patients in our cohort reported mainly fever, dyspnoea or continuous cough. Viral load was significantly higher in concurrent samples taken from the lower respiratory tract (Ct-value = 26) than from the upper respiratory tract (Ct-value = 34). Time of detectable viral RNA after start of antiviral treatment was shorter in patients receiving two antivirals (median 15 days vs. 31 days with one antiviral agent). Short-course antiviral therapy (≤ 5 days) was less efficient in reduction of symptoms and viral load than prolonged therapy > 10 days. In 30% (8/27) of patients with repeated CT scans, we found the emergence of chronic pulmonary changes, which were more frequently in patients with B cell depletion (37%, 7/19) compared to patients with organ transplantation (12%, 2/17). CONCLUSION Ongoing SARS-CoV-2 replication in the lower respiratory tract is a relevant differential diagnosis in patients with severe immunosuppression and continuous cough, fever or dyspnoea even if nasopharyngeal swabs test negative for SARS-CoV-2. Especially in B cell-depleted patients, this may lead to inflammatory or fibrotic-like pulmonary changes, which are partially reversible after inhibition of viral replication. Antiviral therapy seems to be most effective in combination and over a prolonged period of time of > 10 days. TRIAL REGISTRATION NUMBER DRKS 00027299.
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Affiliation(s)
- Veronika Götz
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
| | - Philipp Mathé
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
| | - Prerana Agarwal
- Faculty of Medicine, Department of Radiology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel Hornuss
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Stefanie Pfau
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Marcus Panning
- Faculty of Medicine, Institute of Virology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Eric Prager
- Faculty of Medicine, Department of Nephrology, University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Reinhard E Voll
- Faculty of Medicine, Department of Rheumatology and Clinical Immunology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Monika Engelhardt
- Faculty of Medicine, Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Björn C Frye
- Faculty of Medicine, Department of Pneumology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Jonas Fuchs
- Faculty of Medicine, Institute of Virology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Matthias Müller
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
- Department of Infection Medicine, Medical Service Centre Clotten, 79106, Freiburg, Germany
| | - Dirk Wagner
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Siegbert Rieg
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
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McCracken GR, Patriquin G, Hatchette TF, Davidson RJ, Goodall B, Barrett L, MacDonald J, Heinstein C, Pettipas J, Ross J, LeBlanc JJ. Taqman PACMAN: a simple molecular approach for positive rapid antigen test confirmation during periods of low prevalence. Microbiol Spectr 2024; 12:e0407323. [PMID: 38567975 PMCID: PMC11064490 DOI: 10.1128/spectrum.04073-23] [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: 12/11/2023] [Accepted: 03/13/2024] [Indexed: 05/03/2024] Open
Abstract
Antigen-based rapid diagnostic tests (Ag-RDTs) were widely deployed to enhance SARS-CoV-2 testing capacity during the COVID-19 pandemic. Consistent with national guidance for low prevalence settings, positive Ag-RDTs were confirmed using nucleic acid amplification tests (NAATs) to avoid false positive results. However, increasing demands for positive Ag-RDT confirmation competed with other testing priorities in clinical laboratories. This work hypothesized that real-time RT-PCR without nucleic acid extraction (NAE) would be sufficiently sensitive to support positive Ag-RDT confirmation. Ag-RDT and NAAT results from community-based asymptomatic testing sites prior to the omicron variant wave were compared to calculate the weekly false positive rate (FPR) and false detection rate (FDR). Real-time RT-PCR was compared with and without NAE using 752 specimens previously tested positive for SARS-CoV-2 using commercial NAATs and 344 specimens from Ag-RDT-positive individuals. The impact of SARS-CoV-2 prevalence on laboratory resources required to sustain Ag-RDT confirmation was modeled for the RT-PCR with and without NAE. Overall, FPR was low [0.07% (222/330,763)] in asymptomatic testing sites, but FDR was high [30.7% (222/724)]. When RT-PCR was compared with and without NAE, 100% concordance was obtained with NAAT-positive specimens, including those from Ag-RDT-positive individuals. NAE-free RT-PCR significantly reduced time to results, human resources, and overall costs. A 30.7% FDR reaffirms the need for NAAT-based confirmation of positive Ag-RDT results during low SARS-CoV-2 prevalence. NAE-free RT-PCR was shown to be a simple and cost-sparing NAAT-based solution for positive Ag-RDT confirmation, and its implementation supported data-driven broader Ag-RDT deployment into communities, workplaces, and households. IMPORTANCE Rapid antigen testing for SARS-CoV-2 was widely deployed during the COVID-19 pandemic. In settings of low prevalence, national guidance recommends that positive antigen test results be confirmed with molecular testing. Given the high testing burden on clinical laboratories during the COVID-19 pandemic, the high volume of positive antigen tests submitted for confirmatory testing posed challenges for laboratory workflow. This study demonstrated that a simple PCR method without prior nucleic acid purification is an accurate and cost-effective solution for positive rapid antigen test confirmation. Implementing this method allowed molecular confirmatory testing for positive antigen tests to be sustained as antigen testing was expanded into large populations such as workplaces, schools, and households.
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Affiliation(s)
- Gregory R. McCracken
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Glenn Patriquin
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Todd F. Hatchette
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ross J. Davidson
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Barbara Goodall
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lisa Barrett
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - James MacDonald
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Charles Heinstein
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Janice Pettipas
- Nova Scotia Provincial Public Health Laboratory Network (PPHLN), Halifax, Nova Scotia, Canada
| | - John Ross
- Praxes Medical Group, Halifax, Nova Scotia, Canada
| | - Jason J. LeBlanc
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
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Kurniawan SJ, Kaisar MMM, Kristin H, Ali S. Comparable performance of antigen-detecting rapid test by healthcare worker-collected and self-collected swabs for SARS-CoV-2 diagnostic: A systematic review and meta-analysis. Rev Med Virol 2024; 34:e2492. [PMID: 37989714 DOI: 10.1002/rmv.2492] [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: 04/09/2023] [Revised: 09/24/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023]
Abstract
Usage of self-screening tests has become increasingly relevant in public health perspective for early detection of SARS-CoV-2 infection in the transitioning era of the COVID-19 pandemic into an endemic. This study was designed to compare the diagnostic accuracy of self-conducted and health professional-conducted SARS-CoV-2 rapid antigen tests (Ag-RDTs) and whether the sample was taken from anterior nasal or nasal mid-turbinate. Eligible comparative Ag-RDTs accuracy studies were retrieved from electronic databases systematically, in accordance with PRISMA. Selected studies were assessed for risk of bias using QUADAS-2 and QUADAS-C. In total, we selected five out of 1952 studies retrieved using the keywords. The overall sensitivity for the self-collected nasal swab method and healthcare worker-collected nasopharyngeal swab method was 79% (95% CI 68-87; I2 = 62%) and 83% (95% CI 75-89; I2 = 32%), respectively, which was not statistically different (p = 0.499). Nasal mid-turbinate swabs have a significantly higher sensitivity compared to anterior nasal swabs (p < 0.01). Both sampling methods represent high and comparable specificity values of 98% (95% CI 97-99; I2 = 0%) and 99% (95% CI 98-99; I2 = 0%). Positive predictive value (range 90%-99%) and negative predictive value (range 87%-98%) were equivalent for both methods. Our findings indicated the accuracy of self-collected Ag-RDT on nasal swabs was comparable to those performed by healthcare worker-collected on nasopharyngeal swabs. Self-collected Ag-RDT could be considered as a transmission prevention method in the transition of COVID-19 pandemic.
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Affiliation(s)
- Samuel Johnson Kurniawan
- Undergraduate Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Maria Mardalena Martini Kaisar
- Department of Parasitology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
- Master in Biomedicine Study Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Helen Kristin
- Department of Parasitology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Soegianto Ali
- Master in Biomedicine Study Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
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Wettengel JM, Strehle K, von Lucke C, Roggendorf H, Jeske SD, Christa C, Zelger O, Haller B, Protzer U, Knolle PA. Improved detection of infection with SARS-CoV-2 Omicron variants of concern in healthcare workers by a second-generation rapid antigen test. Microbiol Spectr 2023; 11:e0176823. [PMID: 37831440 PMCID: PMC10714798 DOI: 10.1128/spectrum.01768-23] [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: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE The results from this study demonstrate the usefulness of a second-generation rapid antigen test for early detection of infection with the SARS-CoV-2 Omicron variant of concern (VoC) and reveal a higher sensitivity to detect immune escape Omicron VoCs compared to a first-generation rapid antigen test (89.4% vs 83.7%) in the high-risk group of healthcare workers.
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Affiliation(s)
- Jochen M. Wettengel
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
| | - Katharina Strehle
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Catharina von Lucke
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Hedwig Roggendorf
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Samuel D. Jeske
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Catharina Christa
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Otto Zelger
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Bernhard Haller
- Institute for AI and Informatics in Medicine Statistics, School of Medicine and Health, TUM, München, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Virology, Helmholtz Munich, München, Germany
| | - Percy A. Knolle
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
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