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. 2020 Jul:128:104438.
doi: 10.1016/j.jcv.2020.104438. Epub 2020 May 13.

Validation of SARS-CoV-2 detection across multiple specimen types

Garrett A Perchetti  1 , Arun K Nalla  1 , Meei-Li Huang  1 , Haiying Zhu  1 , Yulun Wei  1 , Larry Stensland  1 , Michelle A Loprieno  2 , Keith R Jerome  3 , Alexander L Greninger  4
Affiliations

Validation of SARS-CoV-2 detection across multiple specimen types

Garrett A Perchetti et al. J Clin Virol. 2020 Jul.

Abstract

Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused considerable disruption across the world, resulting in more than 235,000 deaths since December 2019. SARS-CoV-2 has a wide tropism and detection of the virus has been described in multiple specimen types, including various respiratory secretions, cerebrospinal fluid, and stool.

Objective: To evaluate the accuracy and sensitivity of a laboratory modified CDCbased SARS-CoV-2 N1 and N2 assay across a range of sample types. Study Design We compared the matrix effect on the analytical sensitivity of SARS-CoV-2 detection by qRT-PCR in nasal swabs collected in viral transport medium (VTM), bronchoalveolar lavage (BAL), sputum, plasma, cerebral spinal fluid (CSF), stool, VTM, phosphate buffered saline (PBS), and Hanks' Balanced Salt Solution (HBSS). Initial limits of detection (LoD) were subsequently narrowed to confirm an LoD for each specimen type and target gene.

Results: LoDs were established using a modified CDC-based laboratory developed test and ranged from a mean CT cut-off of 33.8-35.7 (10-20 copies/reaction) for the N1 gene target, and 34.0-36.2 (1-10 copies/reaction) for N2. Alternatives to VTM such as PBS and HBSS had comparable LoDs. The N2 gene target was found to be most sensitive in CSF.

Conclusion: A modified CDC-based laboratory developed test is able to detect SARSCoV- 2 accurately with similar sensitivity across all sample types tested.

Keywords: BAL; CSF; Coronavirus; SARS-CoV-2; Sensitivity; Specimen type.

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Conflict of interest statement

Declaration of Competing Interest The authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Digital droplet PCR quantification of SARS-CoV-2. A) Digital droplet PCR quantifying N1 serial dilutions with a threshold set at an amplitude of 2,600. Sample 1) 1:100,000, 2) 1:100,000, 3) 1:1,000, 4) 1:1,000, 5) 1:10,000, 6) 1:10,000, 7) extracted PBS, 8) water. B) Standard curve to establish genomic copies/reaction with a threshold set at an amplitude of 2,600. Sample 1) 1:10, 2) 1:100, 3) 1:100, 4) 1:1,000, 5) 1:1,000, 6) 1:10,000, 7) 1:10,000, 8) 1:100,000, 9) 1:100,000, 10) 1:1,000,000, 11) 1:1,000,000, 12–16) water.
See this image and copyright information in PMC

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