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. 2022 Jun:304:114522.
doi: 10.1016/j.jviromet.2022.114522. Epub 2022 Mar 9.

Concordance in RT-PCR detection of SARS-CoV-2 between samples preserved in viral and bacterial transport medium

Bia Peña  1 , Mayra Ochoa  2 , Omar Flores  2 , Ana I Gil  2 , Lucie Ecker  2 , Rubelio Cornejo  2 , Claudio F Lanata  3 , Leigh M Howard  4 , Carlos G Grijalva  4
Affiliations

Concordance in RT-PCR detection of SARS-CoV-2 between samples preserved in viral and bacterial transport medium

Bia Peña et al. J Virol Methods. 2022 Jun.

Abstract

Background: While the detection of SARS-CoV-2 in samples preserved in viral transport medium (VTM) by RT-PCR is a standard diagnostic method, this may preclude the study of bacterial respiratory pathogens from the same specimen. It is unclear if the use of skim milk, tryptone, glucose, and glycerin (STGG) transport media, used for study of respiratory bacteria, allows an efficient and concurrent study of SARS-CoV-2 infections.

Objectives: To determine the concordance in SARS-CoV-2 detection by real time RT-PCR between paired nasopharyngeal (NP) swabs preserved in STGG and nasal (NS) swabs preserved in VTM.

Study design: Paired samples of NP and NS swabs were collected between December 2020 and March 2021 from a prospective longitudinal cohort study of 44 households and 132 participants from a peri-urban community (Lima, Peru). NP and NS swabs were taken from all participants once and twice per week, respectively, independent of respiratory symptoms. STGG medium was used for NP samples and VTM for NS samples. Samples were analyzed for SARS-CoV-2 by RT-PCR for N, S and ORF1ab targets. We calculated the concordance in detections between sample types and compared the RT-PCR cycle thresholds (Ct).

Results: Among the 148 paired samples, we observed a high concordance in detections between NP and NS samples (agreement = 94.59%; Kappa = 0.79). Median Ct values were statistically similar between sample types for each RT-PCR target: N, S and ORF1ab (p = 0.11, p = 0.71 and p = 0.11, respectively).

Conclusions: NP swabs collected in STGG medium are reliable alternatives to nasal swabs collected in VTM for the study of SARS-CoV-2.

Keywords: Nasal swab; Nasopharyngeal swab; SARS-CoV-2.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Ct comparisons of the phage MS2 from NS and NP swabs (n = 148) using a Wilcoxon signed-rank test. The analysis showed; NS samples, median = 28.98 and IQR = 2.01, for NP swabs; median = 26.86 and IQR = 2.56.
Fig. 2
Fig. 2
Differences in Ct of NP and NS versus their mean using the Bland-Altman graphs for each evaluated gene with the TaqPath™ COVID-19 CE-IVD RT-PCR kit. (A) N gene target, 20 paired samples analyzed (B) ORF1ab gene target, 16 paired samples analyzed (C) S gene target, 19 paired samples analyzed. When the Ct difference in the y-axis is above 0, NS samples were more sensitive, Ct differences under 0 indicates NP swabs were more sensitive.
See this image and copyright information in PMC

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