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Hempel EM, Bharmal A, Li G, Minhas A, Manan R, Doull K, Hamilton L, Cheung B, Chan M, Gunadasa K, Chow R, Lee T, Tsang F, Krajden M, Mooder K, Kassan T, Prystajecky N, Jassem A, Hoang LMN. Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2024; 8:283-298. [PMID: 38250616 PMCID: PMC10797771 DOI: 10.3138/jammi-2023-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/27/2023] [Accepted: 06/15/2023] [Indexed: 01/23/2024]
Abstract
Background In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative. Methods Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved. Results Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN. Conclusions TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.
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Affiliation(s)
- Eric M Hempel
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Aamir Bharmal
- British Columbia Centre for Disease Control Public Health Response, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guiyun Li
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Aileen Minhas
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Ramndip Manan
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Kathy Doull
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Lynsey Hamilton
- British Columbia Centre for Disease Control Knowledge Translation, Vancouver, British Columbia, Canada
| | - Branco Cheung
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Michael Chan
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Kingsley Gunadasa
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Ron Chow
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Tracy Lee
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Frankie Tsang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Mooder
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Trushna Kassan
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Linda MN Hoang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Callewaert C, Pezavant M, Vandaele R, Meeus B, Vankrunkelsven E, Van Goethem P, Plumacker A, Misset B, Darcis G, Piret S, De Vleeschouwer L, Staelens F, Van Varenbergh K, Tombeur S, Ottevaere A, Montag I, Vandecandelaere P, Jonckheere S, Vandekerckhove L, Tobback E, Wieers G, Marot JC, Anseeuw K, D’Hoore L, Tuyls S, De Tavernier B, Catteeuw J, Lotfi A, Melnik A, Aksenov A, Grandjean D, Stevens M, Gasthuys F, Guyot H. Sniffing out safety: canine detection and identification of SARS-CoV-2 infection from armpit sweat. Front Med (Lausanne) 2023; 10:1185779. [PMID: 37822474 PMCID: PMC10563588 DOI: 10.3389/fmed.2023.1185779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/14/2023] [Indexed: 10/13/2023] Open
Abstract
Detection dogs were trained to detect SARS-CoV-2 infection based on armpit sweat odor. Sweat samples were collected using cotton pads under the armpits of negative and positive human patients, confirmed by qPCR, for periods of 15-30 min. Multiple hospitals and organizations throughout Belgium participated in this study. The sweat samples were stored at -20°C prior to being used for training purposes. Six dogs were trained under controlled atmosphere conditions for 2-3 months. After training, a 7-day validation period was conducted to assess the dogs' performances. The detection dogs exhibited an overall sensitivity of 81%, specificity of 98%, and an accuracy of 95%. After validation, training continued for 3 months, during which the dogs' performances remained the same. Gas chromatography/mass spectrometry (GC/MS) analysis revealed a unique sweat scent associated with SARS-CoV-2 positive sweat samples. This scent consisted of a wide variety of volatiles, including breakdown compounds of antiviral fatty acids, skin proteins and neurotransmitters/hormones. An acceptability survey conducted in Belgium demonstrated an overall high acceptability and enthusiasm toward the use of detection dogs for SARS-CoV-2 detection. Compared to qPCR and previous canine studies, the detection dogs have good performances in detecting SARS-CoV-2 infection in humans, using frozen sweat samples from the armpits. As a result, they can be used as an accurate pre-screening tool in various field settings alongside the PCR test.
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Affiliation(s)
- Chris Callewaert
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maria Pezavant
- Faculty of Veterinary Medicine, Clinique Vétérinaire Universitaire (CVU), University of Liège, Liège, Belgium
| | | | | | | | | | | | - Benoit Misset
- CHU-Sart-Tilman, Intensive Care Unit, University of Liège, Liège, Belgium
| | - Gilles Darcis
- CHU-Sart-Tilman, Infectious Diseases – Internal Medicine, Public Health Sciences, University of Liège, Liège, Belgium
| | - Sonia Piret
- CHU-Bruyères, Intensive Care Unit, University of Liège, Liège, Belgium
| | | | | | | | | | | | | | | | - Stijn Jonckheere
- Laboratory of Clinical Microbiology, Jan Yperman Hospital, Ypres, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Els Tobback
- Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Gregoire Wieers
- General Internal Medicine, Clinique Saint-Pierre Ottignies, Ottignies, Belgium
- Namur Research Institute for Life Sciences (Narilis) and Department of Medicine, University of Namur, Namur, Belgium
| | | | - Kurt Anseeuw
- Department of Emergency Medicine, ZNA, Antwerp, Belgium
| | - Leen D’Hoore
- Belgian Defence, Brussels, Belgium
- Department of Emergency Medicine, ZNA, Antwerp, Belgium
| | - Sebastiaan Tuyls
- Respiratory Medicine, GasthuisZusters (GZA) Hospital Group, Antwerp, Belgium
| | - Brecht De Tavernier
- Emergency Medicine and Intensive Care, GasthuisZusters (GZA) Hospital Group, Antwerp, Belgium
| | | | - Ali Lotfi
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| | - Alexey Melnik
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| | - Alexander Aksenov
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| | - Dominique Grandjean
- Nosaïs Program, Ecole Nationale Vétérinaire d’Alfort (Alfort School of Veterinary Medicine), University Paris-Est, Maisons-Alfort, France
| | | | - Frank Gasthuys
- Department of Surgery, Anesthesiology and Orthopedics of Large Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hugues Guyot
- Faculty of Veterinary Medicine, Clinique Vétérinaire Universitaire (CVU), University of Liège, Liège, Belgium
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3
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Caffry J, Selby M, Barr K, Morgan G, McGurk D, Scully P, Park C, Caridis AM, Southworth E, Morrison J, Clark DJ, Davies BMO, Eckersley NM, Groppelli E, Kirwan DE, Monahan I, Augustin Y, Toombs C, Planche T, Staines HM, Krishna S. The QuantuMDx Q-POC SARS-CoV-2 RT-PCR assay for rapid detection of COVID-19 at point-of-care: preliminary evaluation of a novel technology. Sci Rep 2023; 13:9827. [PMID: 37330592 PMCID: PMC10276817 DOI: 10.1038/s41598-023-35479-9] [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: 01/11/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023] Open
Abstract
Accurate and rapid point-of-care (PoC) diagnostics are critical to the control of the COVID-19 pandemic. The current standard for accurate diagnosis of SARS-CoV-2 is laboratory-based reverse transcription polymerase chain reaction (RT-PCR) assays. Here, a preliminary prospective performance evaluation of the QuantuMDx Q-POC SARS-CoV-2 RT-PCR assay is reported. Between November 2020 and March 2021, 49 longitudinal combined nose/throat (NT) swabs from 29 individuals hospitalised with RT-PCR confirmed COVID-19 were obtained at St George's Hospital, London. In addition, 101 mid-nasal (MN) swabs were obtained from healthy volunteers in June 2021. These samples were used to evaluate the Q-POC SARS-CoV-2 RT-PCR assay. The primary analysis was to compare the sensitivity and specificity of the Q-POC test against a reference laboratory-based RT-PCR assay. The overall sensitivity of the Q-POC test compared with the reference test was 96.88% (83.78- 99.92% CI) for a cycle threshold (Ct) cut-off value for the reference test of 35 and 80.00% (64.35-90.95% CI) without altering the reference test's Ct cut-off value of 40. The Q-POC test is a sensitive, specific and rapid PoC test for SARS-CoV-2 at a reference Ct cut-off value of 35. The Q-POC test provides an accurate option for RT-PCR at PoC without the need for sample pre-processing and laboratory handling, enabling rapid diagnosis and clinical triage in acute care and other settings.
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Affiliation(s)
- Jessica Caffry
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Matthew Selby
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Katie Barr
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - George Morgan
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - David McGurk
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Philip Scully
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Catherine Park
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | | | - Emily Southworth
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Jack Morrison
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - David J Clark
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Benedict M O Davies
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Nicholas M Eckersley
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Elisabetta Groppelli
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Daniela E Kirwan
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Irene Monahan
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Yolanda Augustin
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
| | - Colin Toombs
- QuantuMDx, Lugano Building, 57 Melbourne St, Newcastle Upon Tyne, UK
| | - Tim Planche
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Henry M Staines
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK.
| | - Sanjeev Krishna
- Clinical Academic Group in Institute for Infection and Immunity, St George's University of London, London, UK.
- St George's University Hospitals NHS Foundation Trust, London, UK.
- Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.
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4
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Hørlyck S, Nielsen SH, Gress T, Schneider U, Martel CJM, Steenhard N, Gredal NT, Mortensen S, Cohen AS. Combined nasal- and oropharyngeal self-swab provides equivalent performance compared to professionally collected oropharyngeal swabs in detecting SARS-CoV-2 in a real-life setting. J Virol Methods 2023; 313:114667. [PMID: 36572155 PMCID: PMC9783189 DOI: 10.1016/j.jviromet.2022.114667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE To investigate the performance of a combined nasal midturbinate- and oropharyngeal (NAOP) self-swab compared to a deep oropharyngeal (OP) swab by health care workers (HCW) in detecting SARS-CoV-2 in a real-life setting. METHODS Paired swabs from 1119 participants were included. RT-PCR were used to detect SARS-CoV-2 in both swab samples. RESULTS 330 participants tested positive. The sensitivity of the combined self-swab and OP swab was 96.9 % and 95.4 % respectively, whereas the Ct-values for self-swabs were significantly lower compared to OP swabs. CONCLUSION The combined NAOP self-swab outperformed the OP swab and thus, the NAOP self-swab may be an alternative sampling method under the given circumstances.
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Affiliation(s)
- Sofie Hørlyck
- Test Center Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | | | - Tobias Gress
- Test Center Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Uffe Schneider
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Insititut, Artillerivej 5, 2300 Copenhagen, Denmark
| | | | - Nina Steenhard
- Test Center Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | | | - Shila Mortensen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Insititut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Arieh S. Cohen
- Test Center Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark,Corresponding author
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5
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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: 8] [Impact Index Per Article: 8.0] [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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6
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Prospective population-level validation of the Abbott ID NOW severe acute respiratory syndrome coronavirus 2 device implemented in multiple settings for testing asymptomatic and symptomatic individuals. Clin Microbiol Infect 2023; 29:247-252. [PMID: 36096431 PMCID: PMC9463071 DOI: 10.1016/j.cmi.2022.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Diagnostic evaluation of the ID NOW coronavirus disease 2019 (COVID-19) assay in various real-world settings among symptomatic and asymptomatic individuals. METHODS Depending on the setting, the ID NOW testing was performed using oropharyngeal swabs (OPSs) taken from patients with symptoms suggestive of COVID-19, asymptomatic close contacts, or asymptomatic individuals as part of outbreak point prevalence screening. From January to April 2021, a select number of sites switched from using OPS to combined oropharyngeal and nasal swab (O + NS) for ID NOW testing. For every individual tested, two swabs were collected by a health care worker: one swab (OPS or O + NS) for ID NOW testing and a separate swab (OPS or nasopharyngeal swab) for RT-PCR. RESULTS A total of 129 112 paired samples were analysed (16 061 RT-PCR positive). Of these, 81 697 samples were from 42 COVID-19 community collection sites, 16 924 samples were from 69 rural hospitals, 1927 samples were from nine emergency shelters and addiction treatment facilities, 23 802 samples were from six mobile units that responded to 356 community outbreaks, and 4762 O + NS swabs were collected from three community collection sites and one emergency shelter. The ID NOW assay sensitivity was the highest among symptomatic individuals presenting to community collection sites (92.5%; 95% CI, 92.0-93.0%) and the lowest for asymptomatic individuals associated with community outbreaks (73.9%; 95% CI, 69.8-77.7%). Specificity was >99% in all populations tested. DISCUSSION The sensitivity of ID NOW severe acute respiratory syndrome coronavirus 2 testing is the highest when used in symptomatic community populations not seeking medical care. Sensitivity and positive predictive value drop by approximately 10% when tested on asymptomatic populations. Using combined oropharyngeal and nasal swabs did not improve the performance of ID NOW assay.
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7
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Dos Santos PG, Vieira HCVS, Wietholter V, Gallina JP, Andrade TR, Marinowic DR, Zanirati GG, da Costa JC. When to test for COVID-19 using real-time reverse transcriptase polymerase chain reaction: a systematic review. Int J Infect Dis 2022; 123:58-69. [PMID: 35760382 PMCID: PMC9233872 DOI: 10.1016/j.ijid.2022.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the time in days between symptom onset and first positive real-time reverse transcriptase polymerase chain reaction (RT-PCR) result for COVID-19. METHODS This systematic review was conducted in the MEDLINE (PubMed), Embase, and Scopus databases using the following descriptors: "COVID-19", "SARS-CoV-2", "coronavirus", "RT-PCR", "real time PCR", and "diagnosis". RESULTS The included studies were conducted in 31 different countries and reported on a total of 6831 patients. The median age of the participants was 49.95 years. The three most common symptoms were fever, cough, and dyspnea, which affected 4012 (58.68%), 3192 (46.69%), and 2009 patients (29.38%), respectively. Among the 90 included studies, 13 were prospective cohorts, 15 were retrospective cohorts, 36 were case reports, 20 were case series, and six were cross-sectional studies. The overall mean time between symptom onset and positive test result was 6.72 days. Fourteen articles were analyzed separately for the temporal profile of RT-PCR test results; the best performance was on days 22-24, when 98% of test results were positive. CONCLUSION These findings corroborate the RT-PCR COVID-19 testing practices of some health units. In addition, the most frequently described symptoms of these patients can be considered the initial symptoms of infection and used in decision-making about RT-PCR testing.
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Affiliation(s)
- Paula Gabrielli Dos Santos
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Helena Cristina Valentini Speggiorin Vieira
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Vinícius Wietholter
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - João Pedro Gallina
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Thomás Ranquetat Andrade
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Gabriele Goulart Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil.
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8
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Tsang NNY, So HC, Cowling BJ, Leung GM, Ip DKM. Performance of saline and water gargling for SARS-CoV-2 reverse transcriptase PCR testing: a systematic review and meta-analysis. Eur Respir Rev 2022; 31:31/165/220014. [PMID: 36130785 DOI: 10.1183/16000617.0014-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/21/2022] [Indexed: 11/05/2022] Open
Abstract
The performance of gargling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcriptase (RT)-PCR testing has not been previously reviewed. This review systematically assessed the performance of saline and water gargling for SARS-CoV-2 RT-PCR testing in the settings of diagnosing and monitoring viral shedding.We included original studies comparing the performance of gargling and (oropharyngeal-)nasopharyngeal swabs for SARS-CoV-2 RT-PCR testing. Studies conducted in either suspected individuals or confirmed cases were included and analysed separately. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were examined using random-effects models.Gargles achieved a high overall sensitivity (91%), specificity (97%), PPV (95%) and NPV (91%) for SARS-CoV-2 RT-PCR testing. Studies using saline gargle and water gargle have an overall sensitivity of 97% and 86%, respectively. The sensitivity values were largely maintained for saline and water gargling on stratified analysis, for both diagnosis (96% and 92%) and viral shedding monitoring (98% and 78%). A higher sensitivity was also reported by studies using sterile saline (100%), a smaller amount of gargling solution (92% versus 87%) and a longer gargling duration (95% versus 86%).Our results supported the use of gargling as a sampling approach for SARS-CoV-2 RT-PCR testing, which achieved a high sensitivity for both diagnosis and viral shedding monitoring purposes. Further investigation on the comparative performance of different gargling mediums is needed to draw a definitive conclusion.
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Affiliation(s)
- Nicole Ngai Yung Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hau Chi So
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis Kai Ming Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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9
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Sitoe N, Sambo J, Mabunda N, Nguenha N, Chilaúle J, Rafael J, Macicame A, Chelene I, Mudenyanga C, Sacks J, Viegas S, Loquiha O, Jani I. Clinical Performance of Self-Collected Nasal Swabs and Antigen Rapid Tests for SARS-CoV-2 Detection in Resource-Poor Settings. Biomedicines 2022; 10:biomedicines10092327. [PMID: 36140429 PMCID: PMC9496276 DOI: 10.3390/biomedicines10092327] [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: 08/27/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 12/05/2022] Open
Abstract
Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3−85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3−85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2−63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5−82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.
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Affiliation(s)
- Nádia Sitoe
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
- Correspondence:
| | - Júlia Sambo
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | - Nédio Mabunda
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | - Neuza Nguenha
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | | | - Júlio Rafael
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | | | - Imelda Chelene
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | | | | | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | - Osvaldo Loquiha
- Clinton Health Access Initiative, Maputo City 592, Mozambique
| | - Ilesh Jani
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
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10
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Hernandez-Garcia A, Morales-Moreno MD, Valdés-Galindo EG, Jimenez-Nieto EP, Quezada A. Diagnostics of COVID-19 Based on CRISPR-Cas Coupled to Isothermal Amplification: A Comparative Analysis and Update. Diagnostics (Basel) 2022; 12:1434. [PMID: 35741243 PMCID: PMC9222122 DOI: 10.3390/diagnostics12061434] [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: 02/24/2022] [Revised: 04/05/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022] Open
Abstract
The emergence of the COVID-19 pandemic prompted fast development of novel diagnostic methods of the etiologic virus SARS-CoV-2. Methods based on CRISPR-Cas systems have been particularly promising because they can achieve a similar sensitivity and specificity to the benchmark RT-qPCR, especially when coupled to an isothermal pre-amplification step. Furthermore, they have also solved inherent limitations of RT-qPCR that impede its decentralized use and deployment in the field, such as the need for expensive equipment, high cost per reaction, and delivery of results in hours, among others. In this review, we evaluate publicly available methods to detect SARS-CoV-2 that are based on CRISPR-Cas and isothermal amplification. We critically analyze the steps required to obtain a successful result from clinical samples and pinpoint key experimental conditions and parameters that could be optimized or modified to improve clinical and analytical outputs. The COVID outbreak has propelled intensive research in a short time, which is paving the way to develop effective and very promising CRISPR-Cas systems for the precise detection of SARS-CoV-2. This review could also serve as an introductory guide to new labs delving into this technology.
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Affiliation(s)
- Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Coyoacan, Ciudad de Mexico C.P. 04510, Mexico; (M.D.M.-M.); (E.G.V.-G.); (E.P.J.-N.); (A.Q.)
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11
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Alonaizan F, AlHumaid J, AlJindan R, Bedi S, Dardas H, Abdulfattah D, Ashour H, AlShahrani M, Omar O. Sensitivity and Specificity of Rapid SARS-CoV-2 Antigen Detection Using Different Sampling Methods: A Clinical Unicentral Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19116836. [PMID: 35682419 PMCID: PMC9180118 DOI: 10.3390/ijerph19116836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023]
Abstract
Rapid antigen detection of SARS-CoV-2 has been widely used. However, there is no consensus on the best sampling method. This study aimed to determine the level of agreement between SARS-CoV-2 fluorescent detection and a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), using different swab methods. Fifty COVID-19 and twenty-six healthy patients were confirmed via rRT-PCR, and each patient was sampled via four swab methods: oropharyngeal (O), nasal (N), spit saliva (S), and combined O/N/S swabs. Each swab was analyzed using an immunofluorescent Quidel system. The combined O/N/S swab provided the highest sensitivity (86%; Kappa = 0.8), followed by nasal (76%; Kappa = 0.68), whereas the saliva revealed the lowest sensitivity (66%; kappa = 0.57). Further, when considering positive detection in any of the O, N, and S samples, excellent agreements with rRT-PCR were achieved (Kappa = 0.91 and 0.97, respectively). Finally, among multiple factors, only patient age revealed a significant negative association with antigenic detection in the saliva. It is concluded that immunofluorescent detection of SARS-CoV-2 antigen is a reliable method for rapid diagnosis under circumstances where at least two swabs, one nasal and one oropharyngeal, are analyzed. Alternatively, a single combined O/N/S swab would improve the sensitivity in contrast to each site swabbed alone.
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Affiliation(s)
- Faisal Alonaizan
- Department of Restorative Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Jehan AlHumaid
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia; (J.A.); (S.B.)
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Sumit Bedi
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia; (J.A.); (S.B.)
| | - Heba Dardas
- Emergency Department, King Fahad University Hospital, Al Khobar 34445, Saudi Arabia;
| | - Dalia Abdulfattah
- Clinical Nursing Supervisor Operating Room, King Fahad University Hospital, Al Khobar 34445, Saudi Arabia;
| | - Hanadi Ashour
- College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Mohammed AlShahrani
- Department of Emergency Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Omar Omar
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
- Correspondence: ; Tel.: +966-58-144-0342
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12
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Mak GC, Ng AY, Lam ET, Chan RC, Tsang DN. Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong. J Virol Methods 2022; 300:114396. [PMID: 34856306 PMCID: PMC8629508 DOI: 10.1016/j.jviromet.2021.114396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/24/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing. OBJECTIVE This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2. METHODS We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals. RESULTS This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable. CONCLUSIONS This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2.
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Affiliation(s)
- Gannon C.K. Mak
- Corresponding author at: 9/F, Public Health Laboratory Centre, 382 Nam Cheong Street, Shek Kip Mei, Kowloon, Hong Kong Special Administrative Region
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13
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Thomas HM, Mullane MJ, Ang S, Barrow T, Leahy A, Whelan A, Lombardi K, Cooper M, Stevenson PG, Lester L, Padley A, Sprigg L, Speers D, Merritt AJ, Coffin J, Cross D, Gething P, Bowen AC. Acceptability of OP/Na swabbing for SARS-CoV-2: a prospective observational cohort surveillance study in Western Australian schools. BMJ Open 2022; 12:e055217. [PMID: 35082134 PMCID: PMC8808315 DOI: 10.1136/bmjopen-2021-055217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES When the COVID-19 pandemic was declared, Governments responded with lockdown and isolation measures to combat viral spread, including the closure of many schools. More than a year later, widespread screening for SARS-CoV-2 is critical to allow schools and other institutions to remain open. Here, we describe the acceptability of a minimally invasive COVID-19 screening protocol trialled by the Western Australian Government to mitigate the risks of and boost public confidence in schools remaining open. To minimise discomfort, and optimise recruitment and tolerability in unaccompanied children, a combined throat and nasal (OP/Na) swab was chosen over the nasopharyngeal swab commonly used, despite slightly reduced test performance. DESIGN, SETTING AND PARTICIPANTS Trialling of OP/Na swabbing took place as part of a prospective observational cohort surveillance study in 79 schools across Western Australia. Swabs were collected from 5903 asymptomatic students and 1036 asymptomatic staff in 40 schools monthly between June and September 2020. OUTCOME MEASURES PCR testing was performed with a two-step diagnostic and independent confirmatory PCR for any diagnostic PCR positives. Concurrent surveys, collected online through the REDCap platform, evaluated participant experiences of in-school swabbing. RESULTS 13 988 swabs were collected from students and staff. There were zero positive test results for SARS-CoV-2, including no false positives. Participants reported high acceptability: 71% of students reported no or minimal discomfort and most were willing to be reswabbed (4% refusal rate). CONCLUSIONS OP/Na swabbing is acceptable and repeatable in schoolchildren as young as 4 years old and may combat noncompliance rates by significantly increasing the acceptability of testing. This kind of minimally-invasive testing will be key to the success of ongoing, voluntary mass screening as society adjusts to a new 'normal' in the face of COVID-19. TRIAL REGISTRATION NUMBER Australian New Zealand Clinical Trials Registry-ACTRN12620000922976.
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Affiliation(s)
- Hannah M Thomas
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Marianne J Mullane
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Sherlynn Ang
- Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Tina Barrow
- Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Adele Leahy
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Alexandra Whelan
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Karen Lombardi
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Edith Cowan University, Joondalup, Western Australia, Australia
| | - Matthew Cooper
- Telethon Kids Institute, Nedlands, Western Australia, Australia
| | | | - Leanne Lester
- University of Western Australia, Perth, Western Australia, Australia
| | - Andrea Padley
- Child and Adolescent Health Service, Perth, Western Australia, Australia
| | - Lynn Sprigg
- Child and Adolescent Health Service, Perth, Western Australia, Australia
| | - David Speers
- University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Adam J Merritt
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Juli Coffin
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- University of Western Australia, Perth, Western Australia, Australia
| | - Donna Cross
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- University of Western Australia, Perth, Western Australia, Australia
| | - Peter Gething
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Curtin University, Perth, Western Australia, Australia
| | - Asha C Bowen
- Telethon Kids Institute, Nedlands, Western Australia, Australia
- Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
- University of Western Australia, Perth, Western Australia, Australia
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14
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Euser S, Aronson S, Manders I, van Lelyveld S, Herpers B, Sinnige J, Kalpoe J, van Gemeren C, Snijders D, Jansen R, Schuurmans Stekhoven S, van Houten M, Lede I, Cohen Stuart J, Slijkerman Megelink F, Kapteijns E, den Boer J, Sanders E, Wagemakers A, Souverein D. SARS-CoV-2 viral-load distribution reveals that viral loads increase with age: a retrospective cross-sectional cohort study. Int J Epidemiol 2022; 50:1795-1803. [PMID: 34999848 PMCID: PMC8499942 DOI: 10.1093/ije/dyab145] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Describing the SARS-CoV-2 viral-load distribution in different patient groups and age categories. METHODS All results from first nasopharyngeal (NP) and oropharyngeal (OP) swabs from unique patients tested via SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) collected between 1 January and 1 December 2020 predominantly in the Public Health Services regions Kennemerland and Hollands Noorden, province of North Holland, the Netherlands, were included in this study. SARS-CoV-2 PCR crossing-point (Cp)-values were used to estimate viral loads. RESULTS In total, 278 455 unique patients were tested, of whom 9.1% (n = 25.374) were SARS-CoV-2-positive. PCRs performed by Public Health Services (n = 211 914), in which sampling and inclusion were uniform, revealed a clear relation between age and SARS-CoV-2 viral load, with especially children aged <12 years showing lower viral loads than adults (β: -0.03, 95% confidence interval: -0.03 to -0.02, p < 0.001), independently of sex and/or symptom duration. Interestingly, the median Cp-values between the >79- and <12-year-old populations differed by more than four PCR cycles, suggesting an ∼16-fold difference in viral load. In addition, the proportion of children aged <12 years with a low load (Cp-value >30) was higher compared with other patients (31.1% vs 17.2%, p-value < 0.001). CONCLUSIONS In patients tested by Public Health Services, SARS-CoV-2 viral load increases with age. Further studies should elucidate whether the lower viral load in children is indeed related to their suggested limited role in SARS-CoV-2 transmission. Moreover, as rapid antigen tests are less sensitive than PCR, these results suggest that SARS-CoV-2 antigen tests have lower sensitivity in children than in adults.
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Affiliation(s)
- Sjoerd Euser
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Sem Aronson
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Irene Manders
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
- Department of Infectious Diseases, Public Health Service Kennemerland, Haarlem, The Netherlands
| | - Steven van Lelyveld
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp/Haarlem, The Netherlands
| | - Bjorn Herpers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jan Sinnige
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Jayant Kalpoe
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Dominic Snijders
- Department of Pulmonary Disease, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ruud Jansen
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Marlies van Houten
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp/Haarlem, the Netherlands
| | - Ivar Lede
- Department of Medical Microbiology, Comicro BV Medical Microbiology, Hoorn, The Netherlands
| | - James Cohen Stuart
- Department of Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - Fred Slijkerman Megelink
- Department of Infectious Diseases, Public Health Service Hollands Noorden, Alkmaar, The Netherlands
| | - Erik Kapteijns
- Department of Pulmonary Disease, Rode Kruis Ziekenhuis, Beverwijk, The Netherlands
| | - Jeroen den Boer
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Elisabeth Sanders
- Department of Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Alex Wagemakers
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Dennis Souverein
- Department of Epidemiology, Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
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15
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Schienkiewitz A, Jordan S, Hornbacher A, Perlitz H, Zeisler ML, Sandoni A, Kubisch U, Wess B, Kuttig T, Schaffrath-Rosario A, Damerow S, Rattay P, Varnaccia G, Loer AKM, Wormsbächer J, Cohrdes C, Wetzstein M, Albrecht S, Hey I, Michel J, Schrick L, Gößwald A, Allen J, Schlaud M, Busch MA, Butschalowsky H, Wernitz J, Otte im Kampe E, Buchholz U, Haas W, Schaade L, Wieler LH, Ziese T, Lampert T, Loss J. SARS-CoV-2 Transmissibility Within Day Care Centers-Study Protocol of a Prospective Analysis of Outbreaks in Germany. Front Public Health 2021; 9:773850. [PMID: 34976930 PMCID: PMC8717701 DOI: 10.3389/fpubh.2021.773850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction: Until today, the role of children in the transmission dynamics of SARS-CoV-2 and the development of the COVID-19 pandemic seems to be dynamic and is not finally resolved. The primary aim of this study is to investigate the transmission dynamics of SARS-CoV-2 in child day care centers and connected households as well as transmission-related indicators and clinical symptoms among children and adults. Methods and Analysis: COALA ("Corona outbreak-related examinations in day care centers") is a day care center- and household-based study with a case-ascertained study design. Based on day care centers with at least one reported case of SARS-CoV-2, we include one- to six-year-old children and staff of the affected group in the day care center as well as their respective households. We visit each child's and adult's household. During the home visit we take from each household member a combined mouth and nose swab as well as a saliva sample for analysis of SARS-CoV-2-RNA by real-time reverse transcription polymerase chain reaction (real-time RT-PCR) and a capillary blood sample for a retrospective assessment of an earlier SARS-CoV-2 infection. Furthermore, information on health status, socio-demographics and COVID-19 protective measures are collected via a short telephone interview in the subsequent days. In the following 12 days, household members (or parents for their children) self-collect the same respiratory samples as described above every 3 days and a stool sample for children once. COVID-19 symptoms are documented daily in a symptom diary. Approximately 35 days after testing the index case, every participant who tested positive for SARS-CoV-2 during the study is re-visited at home for another capillary blood sample and a standardized interview. The analysis includes secondary attack rates, by age of primary case, both in the day care center and in households, as well as viral shedding dynamics, including the beginning of shedding relative to symptom onset and viral clearance. Discussion: The results contribute to a better understanding of the epidemiological and virological transmission-related indicators of SARS-CoV-2 among young children, as compared to adults and the interplay between day care and households.
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Affiliation(s)
- Anja Schienkiewitz
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Susanne Jordan
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Anselm Hornbacher
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Hanna Perlitz
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Marie-Luise Zeisler
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Anna Sandoni
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Ulrike Kubisch
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Barbara Wess
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Tim Kuttig
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | | | - Stefan Damerow
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Petra Rattay
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Gianni Varnaccia
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Anne-Kathrin M. Loer
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Jan Wormsbächer
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Carolin Cohrdes
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Matthias Wetzstein
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Stefan Albrecht
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Isabell Hey
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Livia Schrick
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Antje Gößwald
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Jennifer Allen
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Martin Schlaud
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Markus A. Busch
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Hans Butschalowsky
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Jörg Wernitz
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Eveline Otte im Kampe
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Udo Buchholz
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Walter Haas
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Lothar H. Wieler
- Leadership Robert Koch Institute, Robert Koch Institute, Berlin, Germany
- Department of Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Thomas Ziese
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Thomas Lampert
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Julika Loss
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
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16
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Boutros J, Benzaquen J, Marquette CH, Ilié M, Labaky M, Benchetrit D, Lavrut T, Leroy S, Chemla R, Carles M, Tanga V, Maniel C, Bordone O, Allégra M, Lespinet V, Fayada J, Griffonnet J, Hofman V, Hofman P. Salivary detection of COVID-19: clinical performance of oral sponge sampling for SARS-CoV-2 testing. ERJ Open Res 2021; 7:00396-2021. [PMID: 34877351 PMCID: PMC8474486 DOI: 10.1183/23120541.00396-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/17/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The current diagnostic standard for coronavirus disease 2019 (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with nasopharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. METHODS Over a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening centre. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n = 147) or by the contact tracing staff of the French public health insurance because they were considered as close contacts of a laboratory-confirmed COVID-19 case (n = 262). RESULTS In symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95% CI: 89.6-94.8) concordance with NP testing, and a 93.2% (95% CI: 89.1-97.3) sensitivity when using the IdyllaTM platform and a sensitivity of 76.3% (95% CI: 69.4-83.2) on the Synlab Barla laboratory platform. In close contacts the NP-OS concordance (93.8%, 95% CI: 90.9-96.7) and OS sensitivity (71.9%, 95% CI: 66.5-77.3) were slightly lower. CONCLUSION These results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.
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Affiliation(s)
- Jacques Boutros
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Jonathan Benzaquen
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
- Université Côte d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Nice, France
| | - Charles Hugo Marquette
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
- Université Côte d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Nice, France
| | - Marius Ilié
- Université Côte d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Nice, France
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | | | | | - Thibaut Lavrut
- Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Laboratoire de Virologie, CHU de Nice, Nice, France
| | - Sylvie Leroy
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
- CNRS UMR 7275 – Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Nice, France
| | | | - Michel Carles
- Dept of Infectious Diseases, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Charlotte Maniel
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Maryline Allégra
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Virginie Lespinet
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Julien Fayada
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Jennifer Griffonnet
- Dept of Pulmonary Medicine and Thoracic Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Véronique Hofman
- Université Côte d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Nice, France
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
| | - Paul Hofman
- Université Côte d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Nice, France
- Laboratory of Clinical and Experimental Pathology (LPCE), Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Biobank (BB-0033-00025), Nice, France
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17
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The estimated risk of SARS-CoV- 2 infection via cornea transplant in Canada. Cell Tissue Bank 2021; 22:685-695. [PMID: 34591239 PMCID: PMC8481755 DOI: 10.1007/s10561-021-09964-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 09/13/2021] [Indexed: 12/09/2022]
Abstract
In late 2019 the respiratory illness, Corona Virus Disease-19 caused by the SARS-CoV-2 virus emerged in China and quickly spread to other countries. The primary mode of transmission is person-to-person via respiratory droplets. SARS-CoV-2 has been identified in conjunctiva. Transmission by cornea transplant has not been reported but is theoretically possible. We aimed to estimate the possible risk of transmission in Canada via cornea transplant during the first wave of the pandemic, and the potential risk reduction from testing decedents. We constructed a deterministic model in which the risk of transmission was estimated as the product of three proportions: decedents with SARS-CoV-2 infection, corneas that are NAT positive, and NAT positive corneas presumed to transmit. Risk was estimated according to 3 scenarios: most likely, optimistic and pessimistic. At the peak of the first wave of the pandemic risk was estimated to be 1 in 63,031 cornea transplants in Canada but could be as low as 1 in 175,821 or as high as 1 in 10,129. It would take 16 years at the peak infection of the first wave of the pandemic to observe 1 transmission. Testing would reduce the risk of 1 in 63,031 to 1 in 210,104 assuming 70% test sensitivity. The theoretical risk of SARS-CoV-2 transmission by cornea transplant is extremely low and decedent testing is unlikely to be beneficial.
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18
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Gadenstaetter AJ, Mayer CD, Landegger LD. Nasopharyngeal versus nasal swabs for detection of SARS-CoV-2: a systematic review. Rhinology 2021; 59:410-421. [PMID: 34666340 DOI: 10.4193/rhin21.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nasopharyngeal swabbing (NPS) coupled with RT-PCR is the current gold standard for detecting SARS-CoV-2 infections. However, numerous studies have recently demonstrated the advantages of alternative nasal specimen collection approaches over NPS specifically for COVID-19 diagnosis. The present review was conducted according to PRISMA guidelines and summarises the current literature to give a clear overview of nasal specimen collection methods for SARS-CoV-2 detection. Publications investigating NPS and at least one other form of nasal specimen collection in combination with RT-PCR for viral detection in the context of COVID-19 were assessed. We identified 425 articles and ultimately included 18 studies in this systematic review. The suitable publications evaluated different forms of nasal specimen collection, with anterior nasal swabbing (ANS) and midturbinate swabbing (MTS) being the most frequently examined techniques. The analysed studies report sensitivity and specificity results (67.5-96.2% and 97.9-100.0%, respectively) similar to those achieved via NPS, especially in the early stages of disease or when paired with an oropharyngeal swab. Results from these studies suggest that ANS and MTS are suitable alternatives to NPS for COVID-19 testing. Due to their ease of collection, ANS and MTS collection techniques may facilitate broader testing strategies and allow for economization of medical staff.
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Affiliation(s)
- A J Gadenstaetter
- Department of Otolaryngology, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - C D Mayer
- Department of Otolaryngology, Vienna General Hospital, Medical University of Vienna, Vienna, Austria 2 Department of Otolaryngology, Klinik Favoriten, Wiener Gesundheitsverbund, Vienna, Austria
| | - L D Landegger
- Department of Otolaryngology, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
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19
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Kritikos A, Caruana G, Brouillet R, Miroz JP, Abed-Maillard S, Stieger G, Opota O, Croxatto A, Vollenweider P, Bart PA, Chiche JD, Greub G. Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART). Microorganisms 2021; 9:1910. [PMID: 34576805 PMCID: PMC8464722 DOI: 10.3390/microorganisms9091910] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/17/2022] Open
Abstract
Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.
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Affiliation(s)
- Antonios Kritikos
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
| | - Giorgia Caruana
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
| | - René Brouillet
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
| | - John-Paul Miroz
- Intensive Care Unit, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (J.-P.M.); (S.A.-M.); (G.S.); (J.-D.C.)
| | - Samia Abed-Maillard
- Intensive Care Unit, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (J.-P.M.); (S.A.-M.); (G.S.); (J.-D.C.)
| | - Geraldine Stieger
- Intensive Care Unit, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (J.-P.M.); (S.A.-M.); (G.S.); (J.-D.C.)
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
| | - Antony Croxatto
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
| | - Peter Vollenweider
- Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (P.V.); (P.-A.B.)
| | - Pierre-Alexandre Bart
- Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (P.V.); (P.-A.B.)
| | - Jean-Daniel Chiche
- Intensive Care Unit, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (J.-P.M.); (S.A.-M.); (G.S.); (J.-D.C.)
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (G.C.); (R.B.); (O.O.); (A.C.)
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20
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Tsang NNY, So HC, Ng KY, Cowling BJ, Leung GM, Ip DKM. Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2021. [PMID: 33857405 DOI: 10.1016/s1473-3099(1021)00146-00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods. METHODS In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv, SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation. FINDINGS Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93-100), whereas lower sensitivities were achieved by saliva (85%, 75-93) and nasal swabs (86%, 77-93) and a much lower sensitivity by throat swabs (68%, 35-94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90-100) and nasal swabs (96%, 87-100) and a slightly lower positive predictive value by saliva (93%, 88-97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45-96). Comparably high specificities (range 97-99%) and negative predictive value (range 95-99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity (I2 ≥30%) was observed in studies on saliva and nasal swabs. INTERPRETATION Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically acceptable alternative specimen collection methods. Throat swabs gave a much lower sensitivity and positive predictive value and should not be recommended. Self-collection for pooled nasal and throat swabs and nasal swabs was not associated with any significant impairment of diagnostic accuracy. Our results also provide a useful reference framework for the proper interpretation of SARS-CoV-2 testing results using different clinical specimens. FUNDING Hong Kong Research Grants Council.
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Affiliation(s)
- Nicole Ngai Yung Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hau Chi So
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ka Yan Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis Kai Ming Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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21
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De Luca P. Head and Neck Surgery Residency During Covid-19 Pandemic. Lessons from Southern Italy. TRANSLATIONAL MEDICINE AT UNISA 2021. [PMID: 33457320 PMCID: PMC8370526 DOI: 10.37825/2239-9747.1008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P De Luca
- Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
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22
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Pruidze P, Mincheva P, Weninger JT, Reissig LF, Hainfellner A, Weninger WJ. Performing nasopharyngeal swabs-Guidelines based on an anatomical study. Clin Anat 2021; 34:969-975. [PMID: 34216513 PMCID: PMC8426742 DOI: 10.1002/ca.23762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022]
Abstract
Nasopharyngeal swabs are performed to collect material for diagnosing diseases affecting the respiratory system, such as Covid‐19. Yet, no systematic anatomical study defines concrete prerequisites for successfully targeting the nasopharyngeal mucosa. We therefore aim at simulating nasopharyngeal swabs in human body donors to characterize parameters allowing and supporting to enter the nasopharynx with a swab, while avoiding endangering the cribriform plate. With the aid of metal probes and commercial swabs a total of 314 nasopharyngeal swabs in anatomical head/neck specimens stemming from 157 body donors were simulated. Important anatomical parameters were photo‐documented and measured. We provide information on angles and distances between prominent anatomical landmarks and particularly important positions the probe occupies during its advancement through the nares to the upper and lower parts of the nasopharynx and cribriform plate. Based on these data we suggest a simple and safe three‐step procedure for conducting nasopharyngeal swabs. In addition, we define easily recognizable signals for its correct performance. Evaluations prove that this procedure in all specimens without deformations of the nasal cavity allows the swab to enter the nasopharynx, whereas a widespread used alternative only succeeds in less than 50%. Our data will be the key for the successful collection of nasopharyngeal material for detecting and characterizing pathogens, such as SARS‐CoV‐2, which have a high affinity to pharyngeal mucosa. They demonstrate that the danger for damaging the cribriform plate or olfactory mucosa with swabs is unlikely, but potentially higher when performing nasal swabs.
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Affiliation(s)
- Paata Pruidze
- Division of Anatomy, Medical University of Vienna, Vienna, Austria
| | - Plamena Mincheva
- Division of Anatomy, Medical University of Vienna, Vienna, Austria
| | | | - Lukas F Reissig
- Division of Anatomy, Medical University of Vienna, Vienna, Austria
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23
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Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, Armanfard N, Sagan SM, Jahanshahi-Anbuhi S. Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021; 34:e00228-20. [PMID: 33980687 PMCID: PMC8142517 DOI: 10.1128/cmr.00228-20] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.
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Affiliation(s)
- Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
- Department of Mechanical, Industrial, and Aerospace Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Jason J LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Oyejide Damilola Oyewunmi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Carolina Camargo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Bahareh Nikpour
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
| | - Narges Armanfard
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
- Mila-Quebec AI Institute, Montréal, Québec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
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24
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LeBlanc JJ, Pettipas J, Di Quinzio M, Hatchette TF, Patriquin G. Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: A three-headed comparison on multiple molecular platforms. J Virol Methods 2021; 295:114184. [PMID: 34029634 PMCID: PMC8141269 DOI: 10.1016/j.jviromet.2021.114184] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
With increasing demands for SARS-CoV-2 testing, as well as the shortages for testing supplies, collection devices, and trained healthcare workers (HCWs) to collect specimens, self-collection is an attractive prospect to reduce the need for HCWs and expenditure of personal protective equipment. Apart from the traditional nasopharyngeal swab used for SARS-CoV-2 detection, alternative specimens have been validated such as a combined swabs of the oropharynx and anterior nares (OP/N), or throat samples using saline gargles. Both the alternative specimen types are amenable to self-collection. Objectives. This study aimed to compare the sensitivity of HCW-collected (OP/N) swabs, self-collected OP/N swabs, and self-collected saline gargles. Among 38 individuals previously testing positive for SARS-CoV-2 (or their close contacts), two self-collected specimen types (OP/N and saline gargles) were compared to HCW-collected OP/N swabs. SARS-CoV-2 testing was performed on three molecular assays: a laboratory-developed test (LDT), and two commercial assays on automated platforms: Cobas 6800 (Roche Diagnostics) and Panther (Hologic). The sensitivity of self-collected OP/N swabs was equivalent to healthcare worker (HCW)-collected OP/N swabs at 100.0 % [92.6%–100.0%] for all three molecular tests. The sensitivity of saline gargles was not significantly different than HCW-collected OP/N swabs, but varied slightly between instruments at 93.8 % [85.9%–93.8%] for the LDT, 96.8 % [88.6%–96.8%] for the Cobas assay, and 96.7 % [89.2%–96.9%] for the Panther assay. Overall, self-collection using OP/N swabs or saline gargles are reasonable alternatives to HCW-based collections for SARS-CoV-2 detection, and could facilitate broader surveillance strategies.
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Affiliation(s)
- 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; Departments of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Departments of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Janice Pettipas
- Provincial Public Health Laboratory Network of Nova Scotia (PPHLN), Halifax, Nova Scotia, Canada
| | - Melanie Di Quinzio
- Departments of Medicine, 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; Departments of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada; Departments of Microbiology and Immunology, Dalhousie University, 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.
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25
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Deitmer T, Dietz A, Chaberny IF, Pietsch C. [The nasal and pharyngeal swab techniques during the COVID-19-pandemic - the ENT-perspective - SARS-CoV-2, Coronavirus, nasal swab, pharyngeal swab, complications]. Laryngorhinootologie 2021; 100:517-525. [PMID: 34010974 DOI: 10.1055/a-1498-3549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the beginning of the SARS-CoV-2 pandemic, swabs or other samples have increasingly been taken from the upper aero-digestive tract, since high viral loads exist here, especially in the early stages of the disease. As diagnostic options, swabs from the anterior nose, from the nasopharynx, from the oropharynx or the extraction of throat rinse water or saliva are possible. The laboratory methods available are antigen tests that can be read in a few minutes or more lengthy RT-PCR methods in a lab. Swabs are carried out by physicians, medical staff, laypeople and in the self-test, in each case according to prior instructions. Many of these factors therefore have an influence on the informative value and the sensitivity of the entire diagnostic process. The PCR laboratory method is more sensitive than the antigen method; the swabs from the nasopharynx are considered the most valid smear site; correct execution of a test can be achieved even with non-professional individuals with good instructions. Complications with such swabs are reported very rarely, given the assumed number of procedures performed. Short-term nosebleeds after traumatic smears can be assumed without publications about it being found. Broken parts of swabs had to be removed by an ENT doctor. There are only very few reports on injuries to the skullbase with CSF-leaks, including 2 times with anomalies such as meningoceles. The choice of a suitable diagnostic medium depends on many parameters such as availability, the timing of the result, a smear test by knowledgeable staff or a self-test, and a number of other practical considerations.
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Affiliation(s)
- Thomas Deitmer
- Deutsche Gesellschaft für Hals-Nasen-Ohrenheilkunde, Kopf- und Hals-Chirurgie, Bonn
| | - A Dietz
- Hals-Nasen-Ohrenklinik, Universitätsklinikum Leipzig, Leipzig
| | - I F Chaberny
- Institut für Hygiene, Krankenhaushygiene und Umweltmedizin, Universitätsklinikum Leipzig, Leipzig
| | - C Pietsch
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsklinikum Leipzig, Leipzig
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Kriegova E, Fillerova R, Raska M, Manakova J, Dihel M, Janca O, Sauer P, Klimkova M, Strakova P, Kvapil P. Excellent option for mass testing during the SARS-CoV-2 pandemic: painless self-collection and direct RT-qPCR. Virol J 2021; 18:95. [PMID: 33947425 PMCID: PMC8094981 DOI: 10.1186/s12985-021-01567-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
The early identification of asymptomatic yet infectious cases is vital to curb the 2019 coronavirus (COVID-19) pandemic and to control the disease in the post-pandemic era. In this paper, we propose a fast, inexpensive and high-throughput approach using painless nasal-swab self-collection followed by direct RT-qPCR for the sensitive PCR detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This approach was validated in a large prospective cohort study of 1038 subjects, analysed simultaneously using (1) nasopharyngeal swabs obtained with the assistance of healthcare personnel and analysed by classic two-step RT-qPCR on RNA isolates and (2) nasal swabs obtained by self-collection and analysed with direct RT-qPCR. Of these subjects, 28.6% tested positive for SARS-CoV-2 using nasopharyngeal swab sampling. Our direct RT-qPCR approach for self-collected nasal swabs performed well with results similar to those of the two-step RT-qPCR on RNA isolates, achieving 0.99 positive and 0.98 negative predictive values (cycle threshold [Ct] < 37). Our research also reports on grey-zone viraemia, including samples with near-cut-off Ct values (Ct ≥ 37). In all investigated subjects (n = 20) with grey-zone viraemia, the ultra-small viral load disappeared within hours or days with no symptoms. Overall, this study underscores the importance of painless nasal-swab self-collection and direct RT-qPCR for mass testing during the SARS-CoV-2 pandemic and in the post-pandemic era.
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Affiliation(s)
- Eva Kriegova
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Regina Fillerova
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Milan Raska
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Jirina Manakova
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Martin Dihel
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Ondrej Janca
- Department of Immunology, OLGEN, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hnevotinska 3, 77900 Olomouc, Czech Republic
| | - Pavel Sauer
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | | | | | - Petr Kvapil
- Institute of Applied Biotechnologies a.s., Prague, Czech Republic
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27
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Huang C, Fei L, Xu W, Li W, Xie X, Li Q, Chen L. Efficacy Evaluation of Thymosin Alpha 1 in Non-severe Patients With COVID-19: A Retrospective Cohort Study Based on Propensity Score Matching. Front Med (Lausanne) 2021; 8:664776. [PMID: 33968969 PMCID: PMC8102900 DOI: 10.3389/fmed.2021.664776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Objective: Thymosin alpha 1 (Thymosin-α1) is a potential treatment for patients with COVID-19. We aimed to determine the effect of Thymosin-α1 in non-severe patients with COVID-19. Methods: We retrospectively enrolled 1,388 non-severe patients with COVID-19. The primary and secondary clinical outcomes were evaluated with comparisons between patients treated with or without Thymosin-α1 therapy. Results: Among 1,388 enrolled patients, 232 patients (16.7%) received both Thymosin-α1 therapy and standard therapy (Thymosin-α1 group), and 1,156 patients (83.3%) received standard therapy (control group). After propensity score matching (1:1 ratio), baseline characteristics were well-balanced between the Thymosin-α1 group and control group. The proportion of patients that progressed to severe COVID-19 is 2.17% for the Thymosin-α1 group and 2.71% for the control group (p = 0.736). The COVID-19-related mortality is 0.54% for the Thymosin-α1 group and 0 for the control group (p = 0.317). Compared with the control group, the Thymosin-α1 group had significantly shorter SARS-CoV-2 RNA shedding duration (13 vs. 16 days, p = 0.025) and hospital stay (14 vs. 18 days, p < 0.001). No statistically significant difference was found between the Thymosin-α1 group and control group in duration of symptoms (median, 4 vs. 3 days, p = 0.843) and antibiotic utilization rate (14.1% vs. 15.2%, p = 0.768). Conclusion: For non-severe patients with COVID-19, Thymosin-α1 can shorten viral RNA shedding duration and hospital stay but did not prevent COVID-19 progression and reduce COVID-19-related mortality rate.
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Affiliation(s)
- ChenLu Huang
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Ling Fei
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wei Xu
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - WeiXia Li
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - XuDong Xie
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qiang Li
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liang Chen
- Department of Liver Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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28
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Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:JCM.02881-20. [PMID: 33504593 DOI: 10.1101/2020.11.12.20230748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
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Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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29
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Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:e02881-20. [PMID: 33504593 PMCID: PMC8091856 DOI: 10.1128/jcm.02881-20] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
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Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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30
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Ryu G, Shin HW. SARS-CoV-2 Infection of Airway Epithelial Cells. Immune Netw 2021; 21:e3. [PMID: 33728096 PMCID: PMC7937510 DOI: 10.4110/in.2021.21.e3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide since its outbreak in December 2019, and World Health Organization declared it as a pandemic on March 11, 2020. SARS-CoV-2 is highly contagious and is transmitted through airway epithelial cells as the first gateway. SARS-CoV-2 is detected by nasopharyngeal or oropharyngeal swab samples, and the viral load is significantly high in the upper respiratory tract. The host cellular receptors in airway epithelial cells, including angiotensin-converting enzyme 2 and transmembrane serine protease 2, have been identified by single-cell RNA sequencing or immunostaining. The expression levels of these molecules vary by type, function, and location of airway epithelial cells, such as ciliated cells, secretory cells, olfactory epithelial cells, and alveolar epithelial cells, as well as differ from host to host depending on age, sex, or comorbid diseases. Infected airway epithelial cells by SARS-CoV-2 in ex vivo experiments produce chemokines and cytokines to recruit inflammatory cells to target organs. Same as other viral infections, IFN signaling is a critical pathway for host defense. Various studies are underway to confirm the pathophysiological mechanisms of SARS-CoV-2 infection. Herein, we review cellular entry, host-viral interactions, immune responses to SARS-CoV-2 in airway epithelial cells. We also discuss therapeutic options related to epithelial immune reactions to SARS-CoV-2.
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Affiliation(s)
- Gwanghui Ryu
- Department of Otorhinolaryngology-Head and Neck Surgery, Soonchunhyang University College of Medicine, Cheonan 31151, Korea
| | - Hyun-Woo Shin
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul 03080, Korea
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31
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Hanson KE, Caliendo AM, Arias CA, Hayden MK, Englund JA, Lee MJ, Loeb M, Patel R, El Alayli A, Altayar O, Patel P, Falck-Ytter Y, Lavergne V, Morgan RL, Murad MH, Sultan S, Bhimraj A, Mustafa RA. The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing. Clin Infect Dis 2021:ciab048. [PMID: 33480973 PMCID: PMC7929045 DOI: 10.1093/cid/ciab048] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE The IDSA's goal was to develop an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS The panel agreed on 17 diagnostic recommendations. CONCLUSIONS Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform solid organ or hematopoietic stem cell transplantation timing. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations.
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Affiliation(s)
- Kimberly E Hanson
- Department of Internal Medicine and Pathology, University of Utah, Salt Lake City, Utah
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Cesar A Arias
- Division of Infectious Diseases, Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health McGovern Medical School, Center for Infectious Diseases, University of Texas Health School of Public Health, Houston, TX
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois; Department of Pathology, Rush University Medical Center, Chicago, Illinois
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle, Washington
| | - Mark J Lee
- Department of Pathology and Clinical Microbiology Laboratory, Duke University School of Medicine, Durham, North Carolina
| | - Mark Loeb
- Divinsion of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota
| | - Abdallah El Alayli
- Outcomes and Implementation Research Unit, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Osama Altayar
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Payal Patel
- Department of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Yngve Falck-Ytter
- VA Northeast Ohio Healthcare System, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Valery Lavergne
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Rebecca L Morgan
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario
| | - M Hassan Murad
- Division of Preventive Medicine, Mayo Clinic, Rochester, Minnesota
| | - Shahnaz Sultan
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis VA Healthcare System, Minneapolis, Minnesota
| | - Adarsh Bhimraj
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio
| | - Reem A Mustafa
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
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32
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Head and Neck Surgery Residency during Covid-19 Pandemic. Lessons from Southern Italy. Transl Med UniSa 2020. [PMCID: PMC7789927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] Open
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33
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Combined Self-Collected Anterior Nasal and Oropharyngeal Specimens versus Provider-Collected Nasopharyngeal Swabs for the Detection of SARS-CoV-2. J Clin Microbiol 2020; 59:JCM.02291-20. [PMID: 33087437 PMCID: PMC7771445 DOI: 10.1128/jcm.02291-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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34
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De Luca P. Head and Neck Surgery Residency during Covid-19 Pandemic. Lessons from Southern Italy. Transl Med UniSa 2020; 23:37-38. [PMID: 33457320 PMCID: PMC8370526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- P De Luca
- Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
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