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Exner HM, Gregorchuk BSJ, Castor AG, Crisostomo L, Kolsun K, Giesbrecht S, Dust K, Alexander DC, Bolaji A, Quill Z, Head BM, Meyers AFA, Sandstrom P, Becker MG. Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants. Microbiol Spectr 2024:e0016324. [PMID: 38757955 DOI: 10.1128/spectrum.00163-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product quality, manufacturing processes over time, or the evolution of new variants may impact product performance. During the COVID-19 pandemic, a plethora of point-of-care tests (POCTs) was released onto the Canadian market. This study evaluated the performance characteristics of several of the most widely distributed POCTs in Canada, including four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT). All tests were challenged with 149 SARS-CoV-2 clinical positives, including multiple variants up to and including Omicron XBB.1.5, as well as 29 clinical negatives. Results were stratified based on whether the isolate was Omicron or pre-Omicron as well as by reverse transcriptase quantitative PCR Ct value. The test performance of each POCT was consistent with the manufacturers' claims and showed no significant decline in clinical performance against any of the variants tested. These findings provide continued confidence in the results of these POCTs as they continue to be used to support decentralized COVID-19 testing. This work demonstrates the essential role of post-market surveillance in ensuring reliability in diagnostic tools.IMPORTANCEPost-market surveillance of diagnostic test performance is critical to ensure their reliability after regulatory approval. This is especially critical in the context of the COVID-19 pandemic as the use of point-of-care tests (POCTs) became widespread. Our study focused on four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT) that were widely distributed across Canada, assessing their performance using many SARS-CoV-2 variants, including up to Omicron subvariant XBB.1.5. Overall, we found no significant difference in performance against any variant, reinforcing confidence in their use. As concerns in test efficacy have been raised by news outlets, particularly regarding the BTNX Rapid Response, this work is even more timely and crucial. Our research offers insights into the performance of widely used COVID-19 POCTs but also highlights the necessity for post-market surveillance.
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Affiliation(s)
- Hannah M Exner
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Branden S J Gregorchuk
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ac-Green Castor
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Leandro Crisostomo
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kurt Kolsun
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shayna Giesbrecht
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kerry Dust
- Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada
| | | | | | - Zoe Quill
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Breanne M Head
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Adrienne F A Meyers
- Office of Population and Public Health, Indigenous Services Canada, Ottawa, Ontario, Canada
| | - Paul Sandstrom
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael G Becker
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Burtniak J, Hedley A, Dust K, Van Caeseele P, Bullard J, Stein DR. Dorfman pooling enhances SARS-CoV-2 large-scale community testing efficiency. PLOS Glob Public Health 2023; 3:e0001793. [PMID: 37071604 PMCID: PMC10112776 DOI: 10.1371/journal.pgph.0001793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023]
Abstract
PCR-based analysis is the gold standard for detection of SARS-CoV-2 and was used broadly throughout the pandemic. However, heightened demand for testing put strain on diagnostic resources and the adequate amount of PCR-based testing required exceeded existing testing capacity. Pooled testing strategies presented an effective method to increase testing capacity by decreasing the number of tests and resources required for laboratory PCR analysis of SARS-CoV-2. We sought to conduct an analysis of SARS-CoV-2 pooling schemes to determine the sensitivity of various sized Dorfman pooling strategies and evaluate the utility of using such pooling strategies in diagnostic laboratory settings. Overall, a trend of decreasing sensitivity with larger pool sizes was observed, with modest sensitivity losses in the largest pools tested, and high sensitivity in all other pools. Efficiency data was then calculated to determine the optimal Dorfman pool sizes based on test positivity rate. This was correlated with current presumptive test positivity to maximize the number of tests saved, thereby increasing testing capacity and resource efficiency in the community setting. Dorfman pooling methods were evaluated and found to offer a high-throughput solution to SARS-CoV-2 clinical testing that improve resource efficiency in low-resource environments.
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Affiliation(s)
| | - Adam Hedley
- University of Manitoba, Winnipeg, Canada
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Kerry Dust
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Paul Van Caeseele
- University of Manitoba, Winnipeg, Canada
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Jared Bullard
- University of Manitoba, Winnipeg, Canada
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Derek R Stein
- University of Manitoba, Winnipeg, Canada
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
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Garnett L, Tse C, Funk D, Dust K, Tran KN, Hedley A, Poliquin G, Bullard J, Strong JE. Differential Infectivity of Original and Delta Variants of SARS-CoV-2 in Children Compared to Adults. Microbiol Spectr 2022; 10:e0039522. [PMID: 35972128 PMCID: PMC9602606 DOI: 10.1128/spectrum.00395-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
Although children of all ages are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, they have not been implicated as major drivers of transmission thus far. However, it is still unknown if this finding holds true with new variants of concern (VOC), such as Delta (B.1.617.2). This study aimed to examine differences in both viral RNA (as measured by cycle threshold [CT]) and viable-virus levels from children infected with Delta and those infected with original variants (OV). Furthermore, we aimed to compare the pediatric population infection trends to those in adults. We obtained 690 SARS-CoV-2 RT-PCR positive nasopharyngeal swabs from across Manitoba, Canada, which were further screened for mutations characteristic of VOC. Aliquots of sample were then provided for TCID50 (50% tissue culture infective dose) assays to determine infectious titers. Using a variety of statistical analyses we compared CT and infectivity of VOC in different age demographics. Comparing 122 Delta- to 175 OV-positive nasopharyngeal swab samples from children, we found that those infected with Delta are 2.7 times more likely to produce viable SARS-CoV-2 with higher titers (in TCID50 per milliliter), regardless of viral RNA levels. Moreover, comparing the pediatric samples to 130 OV- and 263 Delta-positive samples from adults, we found only that the Delta pediatric culture-positive samples had titers (TCID50 per milliliter) similar to those of culture-positive adult samples. IMPORTANCE These important findings show that children may play a larger role in viral transmission of Delta than for previously circulating SARS-CoV-2 variants. Additionally, they may suggest a mechanism for why Delta has evolved to be the predominant circulating variant.
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Affiliation(s)
- Lauren Garnett
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carmen Tse
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Duane Funk
- Departments of Anaesthesiology and Medicine, Section of Critical Care, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kerry Dust
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
| | - Kaylie N. Tran
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Adam Hedley
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
| | - Guillaume Poliquin
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jared Bullard
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James E. Strong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
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Funk DJ, Bullard J, Lother S, Grande GV, Garnett L, Doan K, Dust K, Kumar A, Poliquin G, Strong J. Persistence of live virus in critically ill patients infected with SARS-COV-2: a prospective observational study. Crit Care 2022; 26:10. [PMID: 34983614 PMCID: PMC8724747 DOI: 10.1186/s13054-021-03884-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/27/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Research on the duration of infectivity of ICU patients with COVID-19 has been sparse. Tests based on Reverse Transcriptase polymerase chain reaction (RT-PCR) detect both live virus and non-infectious viral RNA. We aimed to determine the duration of infectiousness based on viral culture of nasopharyngeal samples of patients with COVID-19. METHODS Prospective observational study in adult intensive care units with a diagnosis of COVID-19 Pneumonia. Patients had repeated nasopharyngeal sampling performed after day 10 of ICU admission. Culture positive rate (based on viral culture on Vero cells in a level 4 lab) and Cycle threshold from RT-PCR were measured. RESULTS Nine patients of the 108 samples (8.3%, 95% CI 3.9-15.2%) grew live virus at a median of 13 days (interquartile range 11-19) after their initial positive test. 74.1% of patients were RT-PCR positive but culture negative, and the remaining (17.6%) were RT-PCR and culture negative. Cycle threshold showed excellent ability to predict the presence of live virus, with a Ct < 25 with an AUC of 0.90 (95% CI 0.83-0.97, p < 0.001). The specificity of a Ct > 25 to predict negative viral culture was 100% (95% CI 70-100%). CONCLUSION 8.3% of our ICU patients with COVID-19 grew live virus at a median of 13 days post-initial positive RT-PCR test. Severity of illness, use of mechanical ventilation, and time between tests did not predict the presence of live virus. Cycle threshold of > 25 had the best ability to determine the lack of live virus in these patents.
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Affiliation(s)
- Duane J Funk
- Departments of Anesthesiology and Medicine, Section of Critical Care, Max Rady College of Medicine, University of Manitoba, 2nd Floor Harry Medovy House, 671 William Avenue, Winnipeg, MB, R3E 0Z2, Canada. .,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
| | - Jared Bullard
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, MB, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Sylvan Lother
- Department of Medicine, Sections of Infectious Disease and Critical Care, University of Manitoba, Winnipeg, MB, Canada
| | - Gloria Vazquez Grande
- Department of Medicine, Sections of Infectious Disease and Critical Care, University of Manitoba, Winnipeg, MB, Canada
| | - Lauren Garnett
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kaylie Doan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kerry Dust
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Anand Kumar
- Department of Medicine, Sections of Infectious Disease and Critical Care, University of Manitoba, Winnipeg, MB, Canada
| | - Guillaume Poliquin
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jim Strong
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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Bullard J, Funk D, Dust K, Garnett L, Tran K, Bello A, Strong JE, Lee SJ, Waruk J, Hedley A, Alexander D, Van Caeseele P, Loeppky C, Poliquin G. Comparaison de l’infectivité du coronavirus du syndrome respiratoire aigu sévère 2 chez les enfants et les adultes. CMAJ 2021; 193:E870-E877. [PMID: 34099475 PMCID: PMC8203260 DOI: 10.1503/cmaj.210263-f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 12/11/2022] Open
Abstract
CONTEXTE: Le rôle des enfants dans la propagation et la transmission communautaire du coronavirus du syndrome respiratoire aigu sévère 2 (SRAS-CoV-2) est encore mal compris. Nous visons à quantifier l’infectivité du SRAS-CoV-2 d’échantillons nasopharyngés provenant d’enfants comparativement à ceux provenant d’adultes. MÉTHODES: Nous avons obtenu des écouvillons nasopharyngés de cas adultes et pédiatriques de la maladie à coronavirus 2019 (COVID-19) ainsi que de leurs contacts qui ont obtenu un résultat positif à la présence du SRAS-CoV-2 lors d’un test de dépistage au Manitoba entre les mois de mars et décembre 2020. Nous avons comparé la croissance virale en culture cellulaire, les valeurs de cycle seuil de test d’amplification en chaîne par polymérase couplé à une transcription inverse (RT-PCR) de l’enveloppe (E) du gène du SRAS-CoV-2 et de la dose infectieuse pour 50 % de la culture tissulaire (DICT50/mL) entre les adultes et les enfants. RÉSULTATS: Parmi les 305 échantillons positifs à la présence du SRAS-CoV-2 validés par RT-PCR, 97 échantillons provenaient d’enfants de 10 ans et moins, 78 échantillons d’enfants de 11–17 ans et 130 échantillons d’adultes (≥ 18 ans). On a observé une croissance virale en culture dans 31 % des échantillons, dont 18 (19 %) échantillons d’enfants de 10 ans et moins, 18 (23 %) d’enfants de 11–17 ans et 57 (44 %) d’adultes (enfants c. adultes, rapport de cotes 0,45; intervalle de confiance [IC] à 95 % 0,28–0,72). Le cycle seuil était de 25,1 (IC à 95 % 17,7–31,3) chez les enfants de 10 ans et moins, 22,2 (IC à 95 % 18,3–29,0) chez les enfants de 11–17 ans et 18,7 (IC à 95 % 17,9–30,4) chez les adultes (p < 0,001). La DICT50/mL médiane était considérablement plus faible chez les enfants de 11–17 ans (316, écart interquartile [EI] 178–2125) que chez les adultes (5620, EI 1171–17 800, p < 0,001). Le cycle seuil était un indicateur exact d’une culture positive chez les enfants et les adultes (aire sous la courbe de la fonction d’efficacité du récepteur, 0,87, IC à 95 % 0,81–0,93 c. 0,89, IC à 95 % 0,83–0,96, p = 0,6). INTERPRÉTATION: Comparés aux adultes, les enfants qui ont obtenu un résultat positif à un test de dépistage du SRAS-CoV-2 à l’aide d’un écouvillon nasopharyngé étaient moins susceptibles de présenter une croissance du virus en culture et obtenaient un cycle seuil plus élevé et une concentration virale moins élevée, indiquant que les enfants ne sont pas les principaux vecteurs de la transmission du SRAS-CoV-2.
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Affiliation(s)
- Jared Bullard
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man.
| | - Duane Funk
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Kerry Dust
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Lauren Garnett
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Kaylie Tran
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Alex Bello
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - James E Strong
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Santina J Lee
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Jillian Waruk
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Adam Hedley
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - David Alexander
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Paul Van Caeseele
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Carla Loeppky
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
| | - Guillaume Poliquin
- Laboratoire provincial Cadham (Bullard, Dust, Hedley, Alexander, Van Caeseele), Santé Manitoba, Département de pédiatrie et de santé de l'enfant (Bullard, Strong, Lee, Van Caeseele, Poliquin), Université du Manitoba; Laboratoire national de microbiologie (Funk, Garnett, Tran, Bello, Strong, Poliquin), Agence de la santé publique du Canada; Département d'anesthésiologie et de médecine (Funk), section des soins intensifs, Université du Manitoba; Département de microbiologie médicale et des maladies infectieuses (Garnett, Tran, Bello, Alexander), Université du Manitoba; Contrôle des maladies transmissibles, Santé publique (Lee), Santé Manitoba; Unité d'épidémiologie et de surveillance (Waruk, Loeppky), Santé Manitoba; Département des sciences en santé communautaire (Loeppky), University of Manitoba, Winnipeg, Man
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Bullard J, Funk D, Dust K, Garnett L, Tran K, Bello A, Strong JE, Lee SJ, Waruk J, Hedley A, Alexander D, Van Caeseele P, Loeppky C, Poliquin G. Infectivity of severe acute respiratory syndrome coronavirus 2 in children compared with adults. CMAJ 2021; 193:E601-E606. [PMID: 33837039 PMCID: PMC8101972 DOI: 10.1503/cmaj.210263] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND: The role of children in the transmission and community spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unclear. We aimed to quantify the infectivity of SARS-CoV-2 in nasopharyngeal samples from children compared with adults. METHODS: We obtained nasopharyngeal swabs from adult and pediatric cases of coronavirus disease 2019 (COVID-19) and from their contacts who tested positive for SARS-CoV-2 in Manitoba between March and December 2020. We compared viral growth in cell culture, cycle threshold values from the reverse transcription polymerase chain reaction (RT-PCR) of the SARS-CoV-2 envelope (E) gene and the 50% tissue culture infective dose (TCID50/mL) between adults and children. RESULTS: Among 305 samples positive for SARS-CoV-2 by RT-PCR, 97 samples were from children aged 10 years or younger, 78 were from children aged 11–17 years and 130 were from adults (≥ 18 yr). Viral growth in culture was present in 31% of samples, including 18 (19%) samples from children 10 years or younger, 18 (23%) from children aged 11–17 years and 57 (44%) from adults (children v. adults, odds ratio 0.45, 95% confidence interval [CI] 0.28–0.72). The cycle threshold was 25.1 (95% CI 17.7–31.3) in children 10 years or younger, 22.2 (95% CI 18.3–29.0) in children aged 11–17 years and 18.7 (95% CI 17.9–30.4) in adults (p < 0.001). The median TCID50/mL was significantly lower in children aged 11–17 years (316, interquartile range [IQR] 178–2125) than adults (5620, IQR 1171 to 17 800, p < 0.001). Cycle threshold was an accurate predictor of positive culture in both children and adults (area under the receiver-operator curve, 0.87, 95% CI 0.81–0.93 v. 0.89, 95% CI 0.83–0.96, p = 0.6). INTERPRETATION: Compared with adults, children with nasopharyngeal swabs that tested positive for SARS-CoV-2 were less likely to grow virus in culture, and had higher cycle thresholds and lower viral concentrations, suggesting that children are not the main drivers of SARS-CoV-2 transmission.
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Affiliation(s)
- Jared Bullard
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man.
| | - Duane Funk
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Kerry Dust
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Lauren Garnett
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Kaylie Tran
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Alex Bello
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - James E Strong
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Santina J Lee
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Jillian Waruk
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Adam Hedley
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - David Alexander
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Paul Van Caeseele
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Carla Loeppky
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
| | - Guillaume Poliquin
- Cadham Provincial Laboratory (Bullard, Dust, Hedley, Alexander, Van Caeseele), Manitoba Health; Department of Pediatrics & Child Health (Bullard, Strong, Lee, Van Caeseele, Poliquin), University of Manitoba; National Microbiology Laboratory (Funk, Garnett, Tran, Bello, Strong, Poliquin), Public Health Agency of Canada; Departments of Anesthesiology and Medicine (Funk), Section of Critical Care, University of Manitoba; Department of Medical Microbiology & Infectious Diseases (Garnett, Tran, Bello, Alexander), University of Manitoba; Communicable Disease Control, Public Health (Lee), Manitoba Health; Epidemiology and Surveillance Unit (Waruk, Loeppky), Manitoba Health; Department of Community Health Science (Loeppky), University of Manitoba. Winnipeg, Man
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7
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Bullard J, Dust K, Funk D, Strong JE, Alexander D, Garnett L, Boodman C, Bello A, Hedley A, Schiffman Z, Doan K, Bastien N, Li Y, Van Caeseele PG, Poliquin G. Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples. Clin Infect Dis 2021; 71:2663-2666. [PMID: 32442256 PMCID: PMC7314198 DOI: 10.1093/cid/ciaa638] [Citation(s) in RCA: 870] [Impact Index Per Article: 290.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/21/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Reverse-transcription polymerase chain reaction (RT-PCR) has become the primary method to diagnose viral diseases, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RT-PCR detects RNA, not infectious virus; thus, its ability to determine duration of infectivity of patients is limited. Infectivity is a critical determinant in informing public health guidelines/interventions. Our goal was to determine the relationship between E gene SARS-CoV-2 RT-PCR cycle threshold (Ct) values from respiratory samples, symptom onset to test (STT), and infectivity in cell culture. METHODS In this retrospective cross-sectional study, we took SARS-CoV-2 RT-PCR-confirmed positive samples and determined their ability to infect Vero cell lines. RESULTS Ninety RT-PCR SARS-CoV-2-positive samples were incubated on Vero cells. Twenty-six samples (28.9%) demonstrated viral growth. Median tissue culture infectious dose/mL was 1780 (interquartile range, 282-8511). There was no growth in samples with a Ct > 24 or STT > 8 days. Multivariate logistic regression using positive viral culture as a binary predictor variable, STT, and Ct demonstrated an odds ratio (OR) for positive viral culture of 0.64 (95% confidence interval [CI], .49-.84; P < .001) for every 1-unit increase in Ct. Area under the receiver operating characteristic curve for Ct vs positive culture was OR, 0.91 (95% CI, .85-.97; P < .001), with 97% specificity obtained at a Ct of > 24. CONCLUSIONS SARS-CoV-2 Vero cell infectivity was only observed for RT-PCR Ct < 24 and STT < 8 days. Infectivity of patients with Ct > 24 and duration of symptoms > 8 days may be low. This information can inform public health policy and guide clinical, infection control, and occupational health decisions. Further studies of larger size are needed.
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Affiliation(s)
- Jared Bullard
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Kerry Dust
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Duane Funk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Anaesthesiology and Medicine, Section of Critical Care, University of Manitoba, Winnipeg, Canada
| | - James E Strong
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Alexander
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Lauren Garnett
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Carl Boodman
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Alexander Bello
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Adam Hedley
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada
| | - Zachary Schiffman
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kaylie Doan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Nathalie Bastien
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yan Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Paul G Van Caeseele
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Guillaume Poliquin
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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8
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Dust K, Hedley A, Nichol K, Stein D, Adam H, Karlowsky JA, Bullard J, Van Caeseele P, Alexander DC. Comparison of commercial assays and laboratory developed tests for detection of SARS-CoV-2. J Virol Methods 2020; 285:113970. [PMID: 32920028 PMCID: PMC7482591 DOI: 10.1016/j.jviromet.2020.113970] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 02/02/2023]
Abstract
Choice of test does not compromise SARS-CoV-2 detection. Commercial assays and lab developed tests for detection of SARS-CoV-2 exhibited 100 % positive and negative agreement. Nucleic acid extraction method influenced the analytical sensitivity (limit of detection) of the lab developed RT-PCR test.
The global COVID-19 pandemic has led to the rapid development of tests for detection of SARS-CoV-2. Studies are required to assess the relative performance of different assays. Here, we compared the performance of two commercial assays, the cobas® SARS-CoV-2 (Roche Diagnostics) and Xpert® Xpress SARS-CoV-2 (Cepheid®) tests, and a laboratory developed RT-PCR test adapted for use on the Hologic® Panther Fusion® (Hologic®) instrument as well as Bio-Rad and QIAGEN real-time PCR detection systems. Performance characteristics for each test were determined by testing clinical specimens and reference material. All assays detect the pan-Sarbecovirus E (envelope structural protein) gene plus a SARS-CoV-2-specific target. The limit of detection for the E gene target varied from ∼2 copies/reaction to >30 copies/reaction. Due to assay-specific differences in sample processing and nucleic acid extraction, the overall analytical sensitivity ranged from 24 copies/mL specimen to 574 copies/mL specimen. Despite these differences, there was 100 % agreement between the commercial and laboratory developed tests. No false-negative or false-positive SARS-CoV-2 results were observed and there was no cross-reactivity with common respiratory viruses, including endemic coronaviruses.
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Affiliation(s)
- Kerry Dust
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
| | - Adam Hedley
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
| | - Kim Nichol
- Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada
| | - Derek Stein
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada
| | - Heather Adam
- Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James A Karlowsky
- Diagnostic Services, Shared Health, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jared Bullard
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paul Van Caeseele
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David C Alexander
- Cadham Provincial Laboratory, Manitoba Health, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.
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9
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LeBlanc JJ, Gubbay JB, Li Y, Needle R, Arneson SR, Marcino D, Charest H, Desnoyers G, Dust K, Fattouh R, Garceau R, German G, Hatchette TF, Kozak RA, Krajden M, Kuschak T, Lang ALS, Levett P, Mazzulli T, McDonald R, Mubareka S, Prystajecky N, Rutherford C, Smieja M, Yu Y, Zahariadis G, Zelyas N, Bastien N. Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories. J Clin Virol 2020; 128:104433. [PMID: 32405254 PMCID: PMC7219382 DOI: 10.1016/j.jcv.2020.104433] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/09/2020] [Indexed: 12/21/2022]
Abstract
With emergence of pandemic COVID-19, rapid and accurate diagnostic testing is essential. This study compared laboratory-developed tests (LDTs) used for the detection of SARS-CoV-2 in Canadian hospital and public health laboratories, and some commercially available real-time RT-PCR assays. Overall, analytical sensitivities were equivalent between LDTs and most commercially available methods.
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Affiliation(s)
- Jason J LeBlanc
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Room 404B, MacKenzie Building, 5788 University Avenue, Halifax, Nova Scotia B3H 1V8, Canada; Departments of Pathology, Medicine, and Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Jonathan B Gubbay
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Public Health Ontario Laboratories, Toronto, Ontario, Canada; Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yan Li
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Robert Needle
- Public Health and Microbiology Laboratory, St. John's, Newfoundland, Canada
| | - Sandra Radons Arneson
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Dionne Marcino
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Hugues Charest
- Laboratoire De Santé Publique Du Québec/INSPQ, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Guillaume Desnoyers
- Centre Hospitalier Universitaire Dr. Georges L. Dumont, Moncton, New-Brunswick, Canada
| | - Kerry Dust
- Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada
| | - Ramzi Fattouh
- Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Richard Garceau
- Centre Hospitalier Universitaire Dr. Georges L. Dumont, Moncton, New-Brunswick, Canada
| | - Gregory German
- Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada
| | - Todd F Hatchette
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Room 404B, MacKenzie Building, 5788 University Avenue, Halifax, Nova Scotia B3H 1V8, Canada; Departments of Pathology, Medicine, and Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert A Kozak
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Mel Krajden
- Public Health Laboratory, British Columbia Centre for Disease Control (BCCDC), Vancouver, British Columbia, Canada
| | - Theodore Kuschak
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Amanda L S Lang
- Roy Romanow Provincial Laboratory (RRPL), Saskatchewan Health Authority (SHA), Regina, Saskatchewan, Canada
| | - Paul Levett
- Public Health Laboratory, British Columbia Centre for Disease Control (BCCDC), Vancouver, British Columbia, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Microbiology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ryan McDonald
- Roy Romanow Provincial Laboratory (RRPL), Saskatchewan Health Authority (SHA), Regina, Saskatchewan, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Natalie Prystajecky
- Public Health Laboratory, British Columbia Centre for Disease Control (BCCDC), Vancouver, British Columbia, Canada
| | | | - Marek Smieja
- St Joseph's Healthcare, Hamilton, Ontario, Canada
| | - Yang Yu
- Public Health and Microbiology Laboratory, St. John's, Newfoundland, Canada
| | - George Zahariadis
- Public Health and Microbiology Laboratory, St. John's, Newfoundland, Canada
| | - Nathan Zelyas
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Room 404B, MacKenzie Building, 5788 University Avenue, Halifax, Nova Scotia B3H 1V8, Canada; Provincial Laboratory for Public Health (ProvLab), Calgary, Alberta, Canada
| | - Nathalie Bastien
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
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Affiliation(s)
- Kaien Gu
- Section of Nephrology, Department of Internal Medicine (Gu, Ho), University of Manitoba; Cadham Provincial Laboratory (Van Caeseele, Dust), Manitoba Health; Departments of Medical Microbiology (Van Caeseele); and Immunology (Ho), University of Manitoba, Winnipeg, Man
| | - Paul Van Caeseele
- Section of Nephrology, Department of Internal Medicine (Gu, Ho), University of Manitoba; Cadham Provincial Laboratory (Van Caeseele, Dust), Manitoba Health; Departments of Medical Microbiology (Van Caeseele); and Immunology (Ho), University of Manitoba, Winnipeg, Man
| | - Kerry Dust
- Section of Nephrology, Department of Internal Medicine (Gu, Ho), University of Manitoba; Cadham Provincial Laboratory (Van Caeseele, Dust), Manitoba Health; Departments of Medical Microbiology (Van Caeseele); and Immunology (Ho), University of Manitoba, Winnipeg, Man
| | - Julie Ho
- Section of Nephrology, Department of Internal Medicine (Gu, Ho), University of Manitoba; Cadham Provincial Laboratory (Van Caeseele, Dust), Manitoba Health; Departments of Medical Microbiology (Van Caeseele); and Immunology (Ho), University of Manitoba, Winnipeg, Man.
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11
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Abstract
Human bocavirus was detected by PCR in 65 (5.1%) of 1,265 respiratory specimens collected in 2002 and 2003 from the Stollery Children's Hospital from children <17 years of age. The spectrum of illness included upper respiratory infection, croup, bronchiolitis, and pneumonia with a prominence of cough and fever.
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Affiliation(s)
- Nathalie Bastien
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St., Winnipeg, Manitoba R3E 3R2, Canada
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12
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Abstract
Human Bocavirus was detected in 18 (1.5%) of 1,209 respiratory specimens collected in 2003 and 2004 in Canada. The main symptoms of affected patients were cough (78%), fever (67%), and sore throat (44%). Nine patients were hospitalized; of these, 8 (89%) were <5 years of age.
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Affiliation(s)
- Nathalie Bastien
- National Science Center for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Ken Brandt
- Saskatchewan Health, Regina, Saskatchewan, Canada
| | - Kerry Dust
- National Science Center for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Diane Ward
- National Science Center for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Yan Li
- National Science Center for Human and Animal Health, Winnipeg, Manitoba, Canada
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