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Fomenko A, Dähne T, Weibel S, Panning M, Grummich K, Schlesinger S, Rücker G, Hengel H. Test accuracy of rapid diagnostic tests and reverse-transcription polymerase chain reaction against virus isolation in cell culture for assessing SARS-CoV-2 infectivity: Systematic review and meta-analysis. Rev Med Virol 2024; 34:e2569. [PMID: 38986606 DOI: 10.1002/rmv.2569] [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: 01/25/2024] [Revised: 04/25/2024] [Accepted: 06/23/2024] [Indexed: 07/12/2024]
Abstract
We aimed to assess the performance of Ag-RDT and RT-qPCR with regard to detecting infectious SARS-CoV-2 in cell cultures, as their diagnostic test accuracy (DTA) compared to virus isolation remains largely unknown. We searched three databases up to 15 December 2021 for DTA studies. The bivariate model was used to synthesise the estimates. Risk of bias was assessed using QUADAS-2/C. Twenty studies (2605 respiratory samples) using cell culture and at least one molecular test were identified. All studies were at high or unclear risk of bias in at least one domain. Three comparative DTA studies reported results on Ag-RDT and RT-qPCR against cell culture. Two studies evaluated RT-qPCR against cell culture only. Fifteen studies evaluated Ag-RDT against cell culture as reference standard in RT-qPCR-positive samples. For Ag-RDT, summary sensitivity was 93% (95% CI 78; 98%) and specificity 87% (95% CI 70; 95%). For RT-qPCR, summary sensitivity (continuity-corrected) was 98% (95% CI 95; 99%) and specificity 45% (95% CI 28; 63%). In studies relying on RT-qPCR-positive subsamples (n = 15), the summary sensitivity of Ag-RDT was 93% (95% CI 92; 93%) and specificity 63% (95% CI 63; 63%). Ag-RDT show moderately high sensitivity, detecting most but not all samples demonstrated to be infectious based on virus isolation. Although RT-qPCR exhibits high sensitivity across studies, its low specificity to indicate infectivity raises the question of its general superiority in all clinical settings. Study findings should be interpreted with caution due to the risk of bias, heterogeneity and the imperfect reference standard for infectivity.
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Affiliation(s)
- Alexey Fomenko
- Institute of Virology, Medical Center, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department Clinical Medicine, Institute of General Practice and Health Services Research, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Theo Dähne
- Institute of Virology, Medical Center, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Stephanie Weibel
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Kathrin Grummich
- Institute for Evidence in Medicine, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Cochrane Germany, Cochrane Germany Foundation, Freiburg, Germany
| | - Sabrina Schlesinger
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DDZ), Partner Düsseldorf, Munich-Neuherberg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
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Popova G, Jakjovska T, Arnaudova-Danevska I, Boskovska K, Spasovska OS. Multiplex PCR in Diagnosing Respiratory Tract Infections in Hospitalized Children. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2024; 45:61-68. [PMID: 38575379 DOI: 10.2478/prilozi-2024-0007] [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: 04/06/2024]
Abstract
OBJECTIVES To elaborate the utility of multiplex quantitative polymerase chain reaction (multiplex qPCR) for the accurate diagnosis of severe respiratory tract infections (RTIs) in hospitalized children. METHODS In two separate periods during 2022, 76 respiratory specimens (combined throat/nasopharyngeal swabs) were submitted for multiplex qPCR regarding 26 respiratory pathogens. The specimens were obtained from children with severe RTIs hospitalized in the Institute for Respiratory Diseases in Children, Skopje. RESULTS Multiplex qPCR detected at least one respiratory pathogen in all examined specimens (76/76), with 83% (63/76) rate of co-infections. Considering that positive results are only the ones with Ct value below 28, the rates of detected pathogens and co-infections decrease to 75% and 22%, respectively. The most commonly detected pathogens during the spring period were Parainfluenza type 3 (PIV3) followed by Adenovirus (AdV) and Respiratory syncytial virus type B (RSVB) with frequency rate of 23%, 19% and 19%, respectively. During the autumn period, the most common were RSVB and Streptococcus pneumoniae with frequency rate of 31% and 17%, respectively. CONCLUSION Multiplex qPCR is a powerful tool for diagnosing RTIs. Semi-quantification of the viral load by reporting Ct values added higher level of evidence for accurate diagnosis. Seasonal detection of the examined viruses was notable with higher prevalence of PIV3 in spring and RSVB in autumn period.
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Affiliation(s)
- Gorica Popova
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medical Sciences, Goce Delcev University, Stip, RN Macedonia
| | - Tatjana Jakjovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Ivana Arnaudova-Danevska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Katerina Boskovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
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Plachouras D, Kacelnik O, Rodríguez-Baño J, Birgand G, Borg MA, Kristensen B, Kubele J, Lyytikäinen O, Presterl E, Reilly J, Voss A, Zingg W, Suetens C, Monnet DL. Revisiting the personal protective equipment components of transmission-based precautions for the prevention of COVID-19 and other respiratory virus infections in healthcare. Euro Surveill 2023; 28:2200718. [PMID: 37561052 PMCID: PMC10416576 DOI: 10.2807/1560-7917.es.2023.28.32.2200718] [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: 08/30/2022] [Accepted: 05/10/2023] [Indexed: 08/11/2023] Open
Abstract
The COVID-19 pandemic highlighted some potential limitations of transmission-based precautions. The distinction between transmission through large droplets vs aerosols, which have been fundamental concepts guiding infection control measures, has been questioned, leading to considerable variation in expert recommendations on transmission-based precautions for COVID-19. Furthermore, the application of elements of contact precautions, such as the use of gloves and gowns, is based on low-quality and inconclusive evidence and may have unintended consequences, such as increased incidence of healthcare-associated infections and spread of multidrug-resistant organisms. These observations indicate a need for high-quality studies to address the knowledge gaps and a need to revisit the theoretical background regarding various modes of transmission and the definitions of terms related to transmission. Further, we should examine the implications these definitions have on the following components of transmission-based precautions: (i) respiratory protection, (ii) use of gloves and gowns for the prevention of respiratory virus infections, (iii) aerosol-generating procedures and (iv) universal masking in healthcare settings as a control measure especially during seasonal epidemics. Such a review would ensure that transmission-based precautions are consistent and rationally based on available evidence, which would facilitate decision-making, guidance development and training, as well as their application in practice.
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Affiliation(s)
| | | | - Jesús Rodríguez-Baño
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases and Microbiology division, Hospital Universitario Virgen Macarena and Department of Medicine, University of Seville/CSIC, Biomedicine Institute of Seville, Seville, Spain
| | - Gabriel Birgand
- Health Protection Research Unit, Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, London, United Kingdom
- Regional Centre for Infection Prevention and Control, Region of Pays de la Loire, Nantes, France
| | - Michael A Borg
- Infection Control Department, Mater Dei Hospital, Msida, Malta
| | | | - Jan Kubele
- Clinical Microbiology and ATB centre, Na Homolce Hospital, Prague, Czechia
| | | | - Elisabeth Presterl
- Department for Hospital Epidemiology and Infection Control, Medical University of Vienna, Vienna, Austria
| | - Jacqui Reilly
- Research Centre for Health, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University Medical Centre Groningen, Groningen, the Netherlands
| | - Walter Zingg
- Charité Universitätsmedizin, Berlin, Germany
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Carl Suetens
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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Jefferson T, Spencer E, Conly J, Rosca E, Maltoni S, Brassey J, Onakpoya I, Evans D, Heneghan C, Plüddemann A. Viral cultures, cycle threshold values and viral load estimation for assessing SARS-CoV-2 infectiousness in haematopoietic stem cell and solid organ transplant patients: a systematic review. J Hosp Infect 2023; 132:62-72. [PMID: 36473552 PMCID: PMC9721162 DOI: 10.1016/j.jhin.2022.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Solid organ and haematopoietic stem cell transplant recipients are more vulnerable to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) than non-transplant recipients due to immunosuppression, and may pose a continued transmission risk, especially within hospital settings. Detailed case reports including symptoms, viral load and infectiousness, defined by the presence of replication-competent viruses in culture, provide an opportunity to examine the relationship between clinical course, burden and contagiousness, and provide guidance on release from isolation. OBJECTIVES To investigate the relationship between serial SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) value or cycle of quantification value, or other measures of viral burden and the likelihood and duration of the presence of infectious virus based on viral culture, including the influence of age, sex, underlying pathologies, degree of immunosuppression, and/or vaccination on this relationship, in transplant recipients. METHODS LitCovid, medRxiv, Google Scholar and the World Health Organization COVID-19 database were searched from 1st November 2019 to 26th October 2022. Studies reporting relevant data (results from serial RT-PCR testing and viral culture data from the same respiratory samples) for transplant recipients with SARS-CoV-2 infection were included in this systematic review: Methodological quality was assessed using five criteria, and the data were synthesized narratively and graphically. RESULTS Thirteen case reports and case series reporting on 41 transplant recipients (22 renal, five cardiac, one bone marrow, two liver, one bilateral lung and 10 blood stem cell) were included in this review. A relationship was observed between proxies of viral burden and likelihood of shedding replication-competent SARS-CoV-2. Three individuals shed replication-competent viruses for >100 days after symptom onset. Lack of standardization of testing and reporting platforms precludes establishing a definitive viral burden cut-off. However, the majority of transplant recipients stopped shedding replication-competent viruses when the Ct value was >30 despite differences across platforms. CONCLUSIONS Viral burden is a reasonable proxy for infectivity when considered within the context of the clinical status of each patient. Standardized study design and reporting are essential to standardize guidance based on an increasing evidence base.
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Affiliation(s)
- T. Jefferson
- Department for Continuing Education, University of Oxford, Oxford, UK
| | - E.A. Spencer
- Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - J.M. Conly
- Departments of Medicine, Microbiology, Immunology & Infectious Diseases, and Pathology & Laboratory Medicine, Synder Institute for Chronic Diseases and O'Brien Institute for Public Health, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada
| | - E.C. Rosca
- Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - S. Maltoni
- Division of Research and Innovation, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - I.J. Onakpoya
- Department for Continuing Education, University of Oxford, Oxford, UK
| | - D.H. Evans
- Li Ka Shing Institute of Virology and Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - C.J. Heneghan
- Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - A. Plüddemann
- Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK,Corresponding author. Address: Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Primary Care Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
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Rosca EC, Heneghan C, Spencer EA, Brassey J, Plüddemann A, Onakpoya IJ, Evans D, Conly JM, Jefferson T. Transmission of SARS-CoV-2 Associated with Cruise Ship Travel: A Systematic Review. Trop Med Infect Dis 2022; 7:290. [PMID: 36288031 PMCID: PMC9610645 DOI: 10.3390/tropicalmed7100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Maritime and river travel may be associated with respiratory viral spread via infected passengers and/or crew and potentially through other transmission routes. The transmission models of SARS-CoV-2 associated with cruise ship travel are based on transmission dynamics of other respiratory viruses. We aimed to provide a summary and evaluation of relevant data on SARS-CoV-2 transmission aboard cruise ships, report policy implications, and highlight research gaps. Methods: We searched four electronic databases (up to 26 May 2022) and included studies on SARS-CoV-2 transmission aboard cruise ships. The quality of the studies was assessed based on five criteria, and relevant findings were reported. Results: We included 23 papers on onboard SARS-CoV-2 transmission (with 15 reports on different aspects of the outbreak on Diamond Princess and nine reports on other international cruises), 2 environmental studies, and 1 systematic review. Three articles presented data on both international cruises and the Diamond Princess. The quality of evidence from most studies was low to very low. Index case definitions were heterogeneous. The proportion of traced contacts ranged from 0.19 to 100%. Studies that followed up >80% of passengers and crew reported attack rates (AR) up to 59%. The presence of a distinct dose−response relationship was demonstrated by findings of increased ARs in multi-person cabins. Two studies performed viral cultures with eight positive results. Genomic sequencing and phylogenetic analyses were performed in individuals from three cruises. Two environmental studies reported PCR-positive samples (cycle threshold range 26.21−39.00). In one study, no infectious virus was isolated from any of the 76 environmental samples. Conclusion: Our review suggests that crowding and multiple persons per cabin were associated with an increased risk of transmission on cruise ships. Variations in design, methodology, and case ascertainment limit comparisons across studies and quantification of transmission risk. Standardized guidelines for conducting and reporting studies on cruise ships of acute respiratory infection transmission should be developed.
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Affiliation(s)
- Elena Cecilia Rosca
- Department of Neurology, Victor Babes University of Medicine and Pharmacy, Piata Eftimie Murgu 2, 300041 Timisoara, Romania
| | - Carl Heneghan
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Elizabeth A. Spencer
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Jon Brassey
- Trip Database Ltd., Glasllwch Lane, Newport NP20 3PS, UK
| | - Annette Plüddemann
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK
| | - Igho J. Onakpoya
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK
| | - David Evans
- Li Ka Shing Institute of Virology, and Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - John M. Conly
- Departments of Medicine, Microbiology, Immunology & Infectious Diseases, and Pathology & Laboratory Medicine, Synder Institute for Chronic Diseases and O’Brien Institute for Public Health, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
| | - Tom Jefferson
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK
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Viral Cultures for Assessing Fomite Transmission of SARS-CoV-2: a Systematic Review and Meta-Analysis. J Hosp Infect 2022; 130:63-94. [PMID: 36115620 PMCID: PMC9473144 DOI: 10.1016/j.jhin.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 01/01/2023]
Abstract
Background The role of fomites in the transmission of SARS-CoV-2 is unclear. Aim To assess whether SARS-CoV-2 can be transmitted through fomites, using evidence from viral culture studies. Methods Searches were conducted in the World Health Organization COVID-19 Database, PubMed, LitCovid, medRxiv, and Google Scholar to December 31st, 2021. Studies that investigated fomite transmission and performed viral culture to assess the cytopathic effect (CPE) of positive fomite samples and confirmation of SARS-CoV-2 as the cause of the CPE were included. The risk of bias using a checklist modified from the modified Quality Assessment of Diagnostic Accuracy Studies – 2 (QUADAS-2) criteria was assessed. Findings Twenty-three studies were included. The overall risk of bias was moderate. Five studies demonstrated replication-competent virus from fomite cultures and three used genome sequencing to match fomite samples with human clinical specimens. The mean cycle threshold (CT) of samples with positive viral culture was significantly lower compared with cultured samples that returned negative results (standardized mean difference: –1.45; 95% confidence interval (CI): –2.00 to –0.90; I2 = 0%; P < 0.00001). The likelihood of isolating replication-competent virus was significantly greater when CT was <30 (relative risk: 3.10; 95% CI: 1.32 to 7.31; I2 = 71%; P = 0.01). Infectious specimens were mostly detected within seven days of symptom onset. One study showed possible transmission of SARS-CoV-2 from fomites to humans. Conclusion The evidence from published studies suggests that replication-competent SARS-CoV-2 is present on fomites. Replication-competent SARS-CoV-2 is significantly more likely when the PCR CT for clinical specimens and fomite samples is <30. Further studies should investigate the duration of infectiousness of SARS-CoV-2 and the frequency of transmission from fomites.
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