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. 2021 Sep;70(9):001380.
doi: 10.1099/jmm.0.001380.

Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing

Padmapriya Banada  1 , David Elson  1 , Naranjargal Daivaa  1 , Claire Park  1 , Samuel Desind  1 , Ibsen Montalvan  2 , Robert Kwiatkowski  3 , Soumitesh Chakravorty  1   3 , David Alland  1 , Yingda L Xie  1
Affiliations

Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing

Padmapriya Banada et al. J Med Microbiol. 2021 Sep.

Abstract

Introduction. Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR).Gap statement. The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared.Aim. We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system.Methods. We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard.Results. Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, P=0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, P<0.001) or eNAT (67.8 %, P=0.0012) and oral swabs in VTM (50 %, P<0.0001) or eNAT (58 %, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases.Conclusion. Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.

Keywords: Inactivation; Nasal; Oral; Saliva; eNAT.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
Study flowchart.
Fig. 2.
Fig. 2.
Comparative testing of different respiratory specimens using the Xpert Xpress SARS-CoV-2 test. (A) Percent positive rate and (B) N2 gene cycle threshold (Ct) values of samples from all participants with at least one SARS-CoV-2 positive sample (N=84 for all samples and N=37 for NP swab). NP=Nasopharyngeal: VTM=Viral transport medium; eNAT=eNAT transport media, Copan diagnostics. ns=not statistically different. ****P<0.0001; ***P<0.001, **P=0.02.
Fig. 3.
Fig. 3.
eNAT as a transport media for saliva. Saliva diluted with eNAT at 1 : 1, 1 : 2, and 1 : 4 ratio showing (A) Percent positive rate and (B) N2-Ct values from patient saliva samples tested directly (N=44), as a swab in eNAT (N=44), diluted 1 : 1 (N=44), 1 : 2 (N=42), and 1 : 4 (N=42) in eNAT transport media. ns=not statistically significant.
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