Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic

Smith, Kenneth P.; Cheng, Annie; Chopelas, Amber; DuBois-Coyne, Sarah; Mezghani, Ikram; Rodriguez, Shade; Talay, Mustafa

doi:10.1101/2020.04.29.20085514

Cited by 4 publications

(4 citation statements)

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“…Repeat tests were excluded to estimate the range of Ct values of the infected population upon presentation at our medical center. In our internal validation, we determined that the detection rate was 100% for the Abbott m2000 platform at 100 copies/mL (n = 80), with Ct mean and standard deviation at this LoD of 26.06 ± 1.03 [ 4 ], including 20 replicates each on 4 separate M2000 platforms on different dates. The genome copy number was based on the reference standard produced by SeraCare (AccuPlex SARS-CoV-2 Reference Material Kit, catalog number 0505-0126).…”

Section: Methodsmentioning

confidence: 99%

“…Here we report on (1) the reproducibility of Ct values from the Abbott SARS-CoV-2 EUA [ 4 ] obtained by sampling the same patients within 6 and 12 hours; (2) conversion from Ct to viral load; (3) the distribution of viral loads in sampling of 4700 first-time positive patients; and (4) based on these findings, an estimate of clinical sensitivity of testing in relation to assay LoD. These findings have clear implications for patient care, epidemiology, and the social and economic management of the ongoing pandemic.…”

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confidence: 99%

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The Limit of Detection Matters: The Case for Benchmarking Severe Acute Respiratory Syndrome Coronavirus 2 Testing

Arnaout

Lee

et al. 2021

Clinical Infectious Diseases

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111

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Background Resolving the coronavirus disease 2019 (COVID-19) pandemic requires diagnostic testing to determine which individuals are infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The current gold standard is to perform reverse-transcription polymerase chain reaction (PCR) on nasopharyngeal samples. Best-in-class assays demonstrate a limit of detection (LoD) of approximately 100 copies of viral RNA per milliliter of transport media. However, LoDs of currently approved assays vary over 10,000-fold. Assays with higher LoDs will miss infected patients. However, the relative clinical sensitivity of these assays remains unknown. Methods Here we model the clinical sensitivities of assays based on their LoD. Cycle threshold (Ct) values were obtained from 4700 first-time positive patients using the Abbott RealTime SARS-CoV-2 Emergency Use Authorization test. We derived viral loads from Ct based on PCR principles and empiric analysis. A sliding scale relationship for predicting clinical sensitivity was developed from analysis of viral load distribution relative to assay LoD. Results Ct values were reliably repeatable over short time testing windows, providing support for use as a tool to estimate viral load. Viral load was found to be relatively evenly distributed across log10 bins of incremental viral load. Based on these data, each 10-fold increase in LoD is expected to lower assay sensitivity by approximately 13%. Conclusions The assay LoD meaningfully impacts clinical performance of SARS-CoV-2 tests. The highest LoDs on the market will miss a majority of infected patients. Assays should therefore be benchmarked against a universal standard to allow cross-comparison of SARS-CoV-2 detection methods.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

The Limit of Detection Matters: The Case for Benchmarking Severe Acute Respiratory Syndrome Coronavirus 2 Testing

Arnaout

Lee

et al. 2021

Clinical Infectious Diseases

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111

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“…NP specimens were collected per standard protocol. Briefly, the NP swab was inserted into the nasopharynx and rotated for 10 seconds, removed, and placed in a vial containing viral transport media [17].…”

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confidence: 99%

Saliva Is Comparable to Nasopharyngeal Swabs for Molecular Detection of SARS-CoV-2

Callahan¹,

Ditelberg²,

Dutta³

et al. 2021

Preprint

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BackgroundThe continued need for molecular testing for SARS-CoV-2 and potential for self-collected saliva as an alternative to nasopharyngeal (NP) swabs for sample acquisition led us to compare saliva to NP swabs in an outpatient setting, without restrictions to avoid food, drink, smoking, or tooth-brushing.MethodsA total of 385 pairs of NP and saliva specimens were obtained, the majority from individuals presenting for initial evaluation, and were tested on two high-sensitivity RT-PCR platforms: the Abbott m2000 and Abbott Alinity m (both with limits of detection [LoD] of 100 copies of viral RNA/mL).ResultsConcordance between saliva and NP was excellent overall (Cohen’s κ=0.93), for both initial and followup testing, for both platforms, and for specimens treated with guanidinium transport medium as preservative as well as for untreated saliva (κ=0.88-0.95). Viral loads were on average 16x higher in NP specimens than saliva specimens, suggesting that only the relatively small fraction of outpatients (∼8% in this study) who present with very low viral loads (<1,600 copies/mL from NP swabs) would be missed by testing saliva instead of NP swabs, when using sensitive testing platforms. Special attention was necessary to ensure leak-resistant specimen collection and transport.ConclusionsThe advantages of self-collection of saliva, without behavioral restrictions, will likely outweigh a minor potential decrease in clinical sensitivity in individuals less likely to pose an infectious risk to others for many real-world scenarios, especially for initial testing.Key pointsSaliva has comparable sensitivity and specificity to nasopharyngeal swabs for RT-PCR-based COVID-19 testing (concordance, κ=0.93; n=385 participants), albeit with slightly lower recovery of viral RNA. Treatment with a readily available guanidinium preservative within 24 hours of sample collection improves recovery.

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“…Testing for COVID-19 has thus been limited by worldwide shortages of critical components, including RNA extraction kits, PCR reagents, transport media, and nasopharyngeal swabs. [6][7][8] While 3-dimensionally printed nasopharyngeal swabs (3DP swabs) have been reported to be used during COVID-19, to our knowledge, clinical validation has been limited to singleinstitution experiences in suspected COVID-19 cases 9 and, in some instances, using human gene targets, such as RNase-P, as a surrogate for effectiveness. 10 In this article, we report our experience in designing a novel 3DP nasopharyngeal swab (the Python swab) and its clinical validation across 2 health care institutions for the identification of SARS-CoV-2.…”

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confidence: 99%

Design and Multicenter Clinical Validation of a 3-Dimensionally Printed Nasopharyngeal Swab for SARS-CoV-2 Testing

Tay

Cross

Toh

et al. 2021

JAMA Otolaryngol Head Neck Surg

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IMPORTANCE Three-dimensionally printed nasopharyngeal swabs (3DP swabs) have been used to mitigate swab shortages during the coronavirus disease 2019 (COVID-19) pandemic. Clinical validation for diagnostic accuracy and consistency, as well as patient acceptability, is crucial to evaluate the swab's performance.OBJECTIVE To determine the accuracy and acceptability of the 3DP swab for identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). DESIGN, SETTING, AND PARTICIPANTSA diagnostic study was conducted from May to July 2020 at 2 tertiary care centers in Singapore with different reference swabs (FLOQSwab [COPAN Diagnostics] or Dacron swab [Deltalab]) and swab processing techniques (wet or dry) to evaluate the performance of the 3DP swab compared with traditional, standard-of-care nasopharyngeal swabs used in health care institutions. The participants were patients with COVID-19 in the first 2 weeks of illness and controls with acute respiratory illness with negative test results for SARS-CoV-2. Paired nasopharyngeal swabs were obtained from the same nostril and tested for SARS-CoV-2 by reverse-transcriptase polymerase chain reaction. The sequence of swabs was randomized based on odd and even participant numbers.MAIN OUTCOMES AND MEASURES Primary outcome measures were overall agreement (OA), positive percentage agreement (PPA), and negative percentage agreement of the 3DP swab compared with reference swabs. Secondary outcome measures were the correlation of cycle threshold (Ct) values of both swabs. RESULTSThe mean (SD) age of participants was 45.4 (13.1) years, and most participants were men (87 of 89 [97.8%]), in keeping with the epidemiology of the COVID-19 pandemic in Singapore. A total of 79 patients with COVID-19 and 10 controls were recruited. Among the patients with COVID-19, the overall agreement and PPA of the 3DP swab was 91.1% and 93.5%, respectively, compared with reference swabs. The PPA was 100% for patients with COVID-19 who were tested within the first week of illness. All controls tested negative. The reverse-transcriptase polymerase chain reaction Ct values for the ORF1ab and E-gene targets showed a strong correlation (intraclass correlations coefficient, 0.869-0.920) between the 3DP and reference swab on independent testing at each institution despite differences in sample processing. Discordant results for both gene targets were observed only at high Ct values. CONCLUSIONS AND RELEVANCEIn this diagnostic study of 79 patients with COVID-19 and 10 controls, the 3DP swab performed accurately and consistently across health care institutions and could help mitigate strained resources in the escalating COVID-19 pandemic.

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Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic

Cited by 4 publications

References 5 publications

The Limit of Detection Matters: The Case for Benchmarking Severe Acute Respiratory Syndrome Coronavirus 2 Testing

The Limit of Detection Matters: The Case for Benchmarking Severe Acute Respiratory Syndrome Coronavirus 2 Testing

Saliva Is Comparable to Nasopharyngeal Swabs for Molecular Detection of SARS-CoV-2

Design and Multicenter Clinical Validation of a 3-Dimensionally Printed Nasopharyngeal Swab for SARS-CoV-2 Testing

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