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Phillips D, da Conceicao F, Jong JBDC, Rawlin G, Mee P. Stability of Genotube ® Swabs for African Swine Fever Virus Detection Using Loop-Mediated Isothermal (LAMP) Laboratory Testing on Samples Stored without Refrigeration. Viruses 2024; 16:263. [PMID: 38400038 PMCID: PMC10892491 DOI: 10.3390/v16020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
African swine fever (ASF) is a transboundary viral disease which causes high mortality in pigs. In many low- and middle-income countries and in remote areas where diagnostic surveillance for ASF virus (ASFV) is undertaken, access to trained animal health technicians, sample collection, cold chain storage and transport of samples to suitably equipped laboratories can be limiting when traditional sampling and laboratory tests are used. Previously published studies have demonstrated that alternative sampling matrices such as swabs and filter papers can be tested using PCR without refrigeration for up to a week. This study used Genotube® swabs stored in temperate and tropical climates without refrigeration for four weeks after collection to demonstrate there was no change in test performance and results using loop-mediated isothermal amplification (LAMP) ASFV detection on a series of pig serum samples including serum spiked with a synthetic ASFV positive control, naturally acquired ASFV positive serum from Timor-Leste and negative ASFV serum samples. The use of Genotube® swabs for ASFV detection for surveillance purposes, coupled with testing platforms such as LAMP, can provide an alternative to traditional testing methodology where resources are limited and time from collection to testing of samples is prolonged.
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Affiliation(s)
- Dianne Phillips
- Agriculture Victoria, Biosecurity and Agriculture Services, Bairnsdale, VIC 3857, Australia
| | - Felisiano da Conceicao
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Joanita Bendita da Costa Jong
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili 0332, Timor-Leste; (F.d.C.); (J.B.d.C.J.)
| | - Grant Rawlin
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (G.R.); (P.M.)
| | - Peter Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (G.R.); (P.M.)
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Swain RK, Mohanty SS, Thakor M, Sharma AK. Assessment of thermal and temporal stability of SARS-CoV-2 samples using real-time qRT-PCR. Mol Biol Rep 2023; 50:8565-8573. [PMID: 37644371 DOI: 10.1007/s11033-023-08740-7] [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: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND As per the guidelines of the Indian Council of Medical Research, nasopharyngeal and oropharyngeal swabs in viral transport medium (VTM) are to be stored at 4 °C for less than 5 days and for more than 5 days at -70 °C. Samples are not transported or stored as per prescribed conditions because of the limitations, resulting in an apprehensive diagnosis. The aim of the study was to test the stability of the SARS-CoV-2 sample stored in VTM at different temperatures. METHODS In this study, the stability of 21 positive and 9 negative samples for SARS-CoV-2 was evaluated in commercial VTM at different temperatures (-80 °C, -20 °C, 4 °C, and 25 to 30 °C). Stability was checked for up to 50 days in the above storage conditions at different intervals. PathoDetect™ and Hi-PCR® kits were used for the detection of the four genes of SARS-CoV-2. The Cycle Threshold (Ct) value for determining the positivity of samples for PathoDetect™ was < 40 and for Hi-PCR® was < 38. RESULTS The SARS-CoV-2 confirmatory genes (RdRp and E genes) and the internal housekeeping gene remained detectable even on the 50th day of the study. The Ct of the RdRp and E genes were found to increase with storage duration, but all positive samples remained positive till the end of the study, or the Ct value remained below the cut-off level. The negative samples gave consistent results until the end of the study. When the differences in Ct values were compared between the days in a set of experiments, they were not significantly different except in a few samples. CONCLUSION The SARS-CoV-2 genetic materials in commercial VTM were stable at room temperature to -80 °C for 50 days.
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Affiliation(s)
- Rohit Kumar Swain
- Department of Biological Sciences and Engineering, MANIT, Bhopal, India
| | - S S Mohanty
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India.
| | - Mahendra Thakor
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India
| | - A K Sharma
- Virology Laboratory, Indian Council of Medical Research- National Institute for Implementation Research on Non-Communicable Diseases (ICMR-NIIRNCD), New Pali Road, Jodhpur, 342005, Rajasthan, India
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Hassouneh SAD, Trujillo A, Ali S, Cella E, Johnston C, DeRuff KC, Sabeti PC, Azarian T. Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2. Sci Rep 2023; 13:11255. [PMID: 37438412 DOI: 10.1038/s41598-023-37893-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Viral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and use of rapid antigen tests, which could lead to gaps in future monitoring efforts. As such, genomic surveillance strategies must adapt to include laboratory workflows that are robust to sample type. To that end, we compare the results of RT-qPCR and viral genome sequencing using samples from positive BinaxNOW COVID-19 Antigen Card swabs (N = 555) to those obtained from nasopharyngeal (NP) swabs used for nucleic acid amplification testing (N = 135). We show that swabs obtained from antigen cards are comparable in performance to samples from NP swabs, providing a viable alternative and allowing for the potential expansion of viral genomic surveillance to outpatient clinic as well as other settings where rapid antigen tests are often used.
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Affiliation(s)
| | - Alexa Trujillo
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Sobur Ali
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Catherine Johnston
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, 32816-2993, USA.
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Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
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Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
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Clinical Validation of GenBody COVID-19 Ag, Nasal and Nasopharyngeal Rapid Antigen Tests for Detection of SARS-CoV-2 in European Adult Population. Biomedicines 2023; 11:biomedicines11020493. [PMID: 36831028 PMCID: PMC9953360 DOI: 10.3390/biomedicines11020493] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Accurate and rapid identification of COVID-19 is critical for effective patient treatment and disease outcomes, as well as the prevention of SARS-CoV-2 transmission. Rapid antigen tests (RATs) for identifying SARS-CoV-2 are simpler, faster and less expensive than molecular assays. Any new product to be considered a medical device is subject to evaluation and data analysis to verify the in vitro diagnostic ability to achieve its intended purpose. Clinical validation of such a test is a prerequisite before clinical application. This study was a clinical validation on adult Europeans of GenBody COVID-19 Ag, nasal and nasopharyngeal RATs. A set of 103 positive and 301 negative from nose and nasopharynx samples confirmed by RT-qPCR were examined. The tests were safe to use and showed 100% specificity in both specimens, and high sensitivity of 94.17% (95%CI 87.75% to 97.83%) and 97.09% (95%CI 91.72% to 99.4%), respectively. The parameters were significantly better for samples with higher virus loads (the highest for CT ≤ 25). The GenBody COVID-19 Ag RATs are inexpensive (compared to RT-qPCR), reliable and rapid with high sensitivity and specificity, making them suitable for diagnosis and timely isolation and treatment of COVID-19 patients, contributing to the better control of virus spread.
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Kandel C, Lee Y, Taylor M, Llanes A, McCready J, Crowl G, Powis J, Li AX, Shigayeva A, Yip L, Katz K, Kozak R, Mubareka S, McGeer A. Viral dynamics of the SARS-CoV-2 Omicron Variant among household contacts with 2 or 3 COVID-19 vaccine doses. J Infect 2022; 85:666-670. [PMID: 36283495 PMCID: PMC9595488 DOI: 10.1016/j.jinf.2022.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES SARS-CoV-2 shedding has changed as new variants have emerged. It is important to understand the trajectory of PCR positivity due to Omicron in vaccinated populations. METHODS Double- or triple-vaccinated adult household contacts of individuals with COVID-19 self-collected oral-nasal swabs for 14 days. A hierarchical linear model estimated viral load trajectories and an exploratory logistic regression model assessed for factors associated with viral detection before symptom onset. RESULTS Forty-one participants developed COVID-19 with 37 (90%) symptomatic. Viral load peaked 3 days after symptom onset at a median concentration of 8.83 log10 copies/milliliter (range 5.95-10.32) and the mean difference between participants with two or three COVID-19 vaccine doses was 0.02 log10 copies/milliliter (95% CI -0.13 to 0.16). PCR positivity began with a range of 4 days prior to 3 days after symptom onset and was positive on the day of symptom onset in 76% (28/37). SARS-CoV-2 detection on the day of symptom onset was less likely among those with 2 vaccine doses (OR 0.13, 95%CI 0.02-0.79). 68% (25/37) of infected participants had detectable SARS-CoV-2 with Ct<30 at 7 days after symptom onset. CONCLUSIONS Peak viral load and duration of PCR positivity were similar in participants with COVID-19 after two versus three COVID-19 vaccine doses. Onset of viral detection relative to symptom onset was variable.
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Affiliation(s)
- Christopher Kandel
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada.
| | - Yaejin Lee
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Maureen Taylor
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Andrea Llanes
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Janine McCready
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Gloria Crowl
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Jeff Powis
- Toronto East Health Network, Michael Garron Hospital, 825 Coxwell Avenue, Toronto, Ontario M4C 3E7, Canada
| | - Angel Xinliu Li
- Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Altynay Shigayeva
- Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Lily Yip
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada
| | - Kevin Katz
- Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada,North York General Hospital, 4001 Leslie St, North York, Ontario M2K 1E1, Canada,Shared Hospital Laboratory, 555 Finch Ave W, Toronto, Ontario M2R 1N5, Canada
| | - Robert Kozak
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Samira Mubareka
- Sunnybrook Health Sciences Centre, 2075 Bayview Ave, Toronto, Ontario M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, King's College Cir, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Sinai Health System, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
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Gordhan BG, Ealand CS, Kana BD. Survival and detection of SARS-CoV-2 variants on dry swabs post storage. Front Cell Infect Microbiol 2022; 12:1031775. [PMID: 36467724 PMCID: PMC9715580 DOI: 10.3389/fcimb.2022.1031775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022] Open
Abstract
COVID-19 has resulted in nearly 598 million infections and over 6.46 million deaths since the start of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in 2019. The rapid onset of the pandemic, combined with the emergence of viral variants, crippled many health systems particularly from the perspective of coping with massive diagnostic loads. Shortages of diagnostic kits and capacity forced laboratories to store clinical samples resulting in huge backlogs, the effects of this on diagnostic pickup have not been fully understood. Herein, we investigated the impact of storing SARS-CoV-2 inoculated dry swabs on the detection and viability of four viral strains over a period of 7 days. Viral load, as detected by qRT-PCR, displayed no significant degradation during this time for all viral loads tested. In contrast, there was a ca. 2 log reduction in viral viability as measured by the tissue culture infectious dose (TCID) assay, with 1-3 log viable virus detected on dry swabs after 7 days. When swabs were coated with 102 viral copies of the Omicron variant, no viable virus was detected after 24 hours following storage at 4°C or room temperature. However there was no loss of PCR signal over 7 days. All four strains showed comparable growth kinetics and survival when cultured in Vero E6 cells. Our data provide information on the viability of SARS-CoV-2 on stored swabs in a clinical setting with important implications for diagnostic pickup and laboratory processing protocols. Survival after 7 days of SARS-CoV-2 strains on swabs with high viral loads may impact public health and biosafety practices in diagnostic laboratories.
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Blackwell AD, Garcia AR. Ecoimmunology in the field: Measuring multiple dimensions of immune function with minimally invasive, field-adapted techniques. Am J Hum Biol 2022; 34:e23784. [PMID: 35861267 PMCID: PMC9786696 DOI: 10.1002/ajhb.23784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Immune function is multifaceted and characterizations based on single biomarkers may be uninformative or misleading, particularly when considered across ecological contexts. However, measuring the many facets of immunity in the field can be challenging, since many measures cannot be obtained on-site, necessitating sample preservation and transport. Here we assess state-of-the-art methods for measuring immunity, focusing on measures that require a minimal blood sample obtained from a finger prick, which can be: (1) dried on filter paper, (2) frozen in liquid nitrogen, or (3) stabilized with chemical reagents. RESULTS We review immune measures that can be obtained from point-of-care devices or from immunoassays of dried blood spots (DBSs), field methods for flow cytometry, the use of RNA or DNA sequencing and quantification, and the application of immune activation assays under field conditions. CONCLUSIONS Stable protein products, such as immunoglobulins and C-reactive protein are reliably measured in DBSs. Because less stable proteins, such as cytokines, may be problematic to measure even in fresh blood, mRNA from stabilized blood may provide a cleaner measure of cytokine and broader immune-related gene expression. Gene methylation assays or mRNA sequencing also allow for the quantification of many other parameters, including the inference of leukocyte subsets, though with less accuracy than with flow cytometry. Combining these techniques provides an improvement over single-marker studies, allowing for a more nuanced understanding of how social and ecological variables are linked to immune measures and disease risk in diverse populations and settings.
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Affiliation(s)
- Aaron D. Blackwell
- Department of AnthropologyWashington State UniversityPullmanWashingtonUSA
| | - Angela R. Garcia
- Research DepartmentPhoenix Children's HospitalPhoenixArizonaUSA,Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
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Bangalee A, Govender K, Bangalee V. A pandemic guided by the SARS-CoV-2 PCR test: What should the clinician know? S Afr Fam Pract (2004) 2022; 64:e1-e4. [PMID: 36226952 PMCID: PMC9559189 DOI: 10.4102/safp.v64i1.5492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/09/2022] [Accepted: 05/14/2022] [Indexed: 12/03/2022] Open
Abstract
Amidst an ever-evolving pandemic, the demand for timely and accurate diagnosis of coronavirus disease 2019 (COVID-19) continues to increase. Critically, managing and containing the spread of the disease requires expedient testing of infected individuals. Presently, the gold standard for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains the polymerase chain reaction (PCR) test. Potential vulnerabilities of this testing methodology can range from preanalytical variables to laboratory-related analytical factors and, ultimately, to the interpretation of results.
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Affiliation(s)
- Avania Bangalee
- Department of Medical Virology, Faculty of Health Sciences, Prinshof Campus, University of Pretoria, South Africa; and, National Health Laboratory Services, Johannesburg.
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Evaluation of the Diagnostic Accuracy of Nasal Cavity and Nasopharyngeal Swab Specimens for SARS-CoV-2 Detection via Rapid Antigen Test According to Specimen Collection Timing and Viral Load. Diagnostics (Basel) 2022; 12:diagnostics12030710. [PMID: 35328263 PMCID: PMC8947492 DOI: 10.3390/diagnostics12030710] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 11/24/2022] Open
Abstract
The rapid diagnosis of SARS-CoV-2 is an essential aspect in the detection and control of the spread of COVID-19. We evaluated the accuracy of the rapid antigen test (RAT) using samples from the nasal cavity and nasopharynx based on sample collection timing and viral load. We enrolled 175 patients, of which 71 patients and 104 patients had tested positive and negative, respectively, based on real time-PCR. Nasal cavity and nasopharyngeal swab samples were tested using STANDARD Q COVID-19 Ag tests (Q Ag, SD Biosensor, Korea). The sensitivity of the Q Ag test was 77.5% (95% confidence interval [CI], 67.8−87.2%) for the nasal cavity and 81.7% (95% [CI, 72.7−90.7%) for the nasopharyngeal specimens. The RAT results showed a substantial agreement between the nasal cavity and nasopharyngeal specimens (Cohen’s kappa index = 0.78). The sensitivity of the RAT for nasal cavity specimens exceeded 89% for <5 days after symptom onset (DSO) and 86% for Ct of E and RdRp < 25. The Q Ag test performed fairly well, especially in the early DSO when a high viral load was present, and the nasal cavity swab can be considered an alternative site for the rapid diagnosis of COVID-19.
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Campbell ST, Orner EP, Reyes Gil M, Fox AS, Goldstein DY, Wolgast LR, Cadoff EM, Freedman VH, Akabas MH, Prystowsky MB, Szymczak WA. Mater Artium Necessitas: The Birth of a COVID-19 Command Center. Acad Pathol 2021; 8:23742895211015347. [PMID: 34046523 PMCID: PMC8138285 DOI: 10.1177/23742895211015347] [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: 01/15/2021] [Revised: 03/08/2021] [Accepted: 04/16/2021] [Indexed: 01/29/2023] Open
Abstract
In February of 2020, New York City was unprepared for the COVID-19 pandemic. Cases of SARS-CoV-2 infection appeared and spread rapidly. Hospitals had to repurpose staff and establish diagnostic testing for this new viral infection. In the background of the usual respiratory pathogen testing performed in the clinical laboratory, SARS-CoV-2 testing at the Montefiore Medical System grew exponentially, from none to hundreds per day within the first week of testing. The job of appropriately routing SARS-CoV-2 viral specimens became overwhelming. Additional staff was required to triage these specimens to multiple in-house testing platforms as well as external reference laboratories. Since medical school classes and many research laboratories shut down at the Albert Einstein College of Medicine and students were eager to help fight the pandemic, we seized the opportunity to engage and train senior MD-PhD students to assist in triaging specimens. This volunteer force enabled us to establish the "Pathology Command Center," staffed by these students as well as residents and furloughed dental associates. The Pathology Command Center staff were tasked with the accessioning and routing of specimens, answering questions from clinical teams, and updating ever evolving protocols developed in collaboration with a team of Infectious Disease clinicians. Many lessons were learned during this process, including how best to restructure an accessioning department and how to properly onboard students and repurpose staff while establishing safeguards for their well-being during these unprecedented times. In this article, we share some of our challenges, successes, and what we ultimately learned as an organization.
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Affiliation(s)
- Sean T. Campbell
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Erika P. Orner
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | | | - Amy S. Fox
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | | | - Lucia R. Wolgast
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Evan M. Cadoff
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Victoria H. Freedman
- Graduate Division of Biomedical Sciences, Department of Microbiology
and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Myles H. Akabas
- Departments of Physiology & Biophysics, Neuroscience, and
Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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