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

Author:

Banada Padmapriya1ORCID,Elson David1,Daivaa Naranjargal1,Park Claire1ORCID,Desind Samuel1ORCID,Montalvan Ibsen2ORCID,Kwiatkowski Robert3ORCID,Chakravorty Soumitesh31,Alland David1ORCID,Xie Yingda L.1ORCID

Affiliation:

1. The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA

2. University Hospital, Newark, NJ 07103, USA

3. Cepheid, Sunnyvale, CA, USA

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.

Funder

National Institute of Allergy and Infectious Diseases

Rutgers, The State University of New Jersey

Publisher

Microbiology Society

Subject

Microbiology (medical),General Medicine,Microbiology

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