Evaluation of self‐collected nasal, urine, and saliva samples for molecular detection of SARS‐CoV‐2 using an EUA approved RT‐PCR assay and a laboratory developed LAMP SARS‐CoV‐2 test

TL;DR

This study compares self-collected nasal, saliva, and urine samples for detecting SARS-CoV-2, finding saliva to be the most effective and introducing a rapid LAMP test as a viable alternative to RT-PCR.

Contribution

The study introduces a rapid, colorimetric LAMP test for SARS-CoV-2 and demonstrates the effectiveness of self-collected saliva samples for molecular testing.

Findings

Saliva samples showed higher viral load and moderate agreement with nasal samples.

The LAMP test demonstrated 90% concordance with the RT-PCR test.

Saliva-based testing is a superior and practical alternative for community-based SARS-CoV-2 detection.

Abstract

As the SARS‐CoV‐2 virus spread throughout the world, millions of positive cases of COVID‐19 were registered and, even though there are millions of people already vaccinated against SARS‐CoV‐2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS‐CoV‐2 molecular testing availability, we evaluated the diagnostic accuracy of self‐collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit to detect SARS‐CoV‐2. We also created a colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS‐CoV‐2, as another strategy to increase the availability of molecular testing in community‐based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS‐CoV‐2 on the 7500 Fast Dx RT‐PCR using the TaqPath RT‐PCR COVID‐19 molecular test. Data was interpreted by the COVID‐19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene‐Biomarks' SARS‐CoV‐2 Rapid Colorimetric LAMP LDT and the TaqPath RT‐PCR COVID‐19 test. Our results suggest that self‐collected saliva is superior to nasal and urine samples for COVID‐19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT‐PCR tests for the detection of SARS‐CoV‐2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.

The objective of this study was to evaluate the diagnostic accuracy of the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit in paired nasopharyngeal, saliva, and urine samples, as well as a loop‐mediated isothermal amplification (LAMP) SARS‐CoV‐2 laboratory developed test (LDT) in nasopharyngeal samples. Our findings suggest that utilizing saliva samples for RT‐PCR TaqPath and LifeGene‐Biomarks SARS‐CoV‐2 rapid colorimetric LAMP LDT holds promise as an effective alternative method for diagnosing COVID‐19.

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