GSE176224
Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection
The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing worldwide has led to major issues in scaling the efforts of diagnostic labs and even in securing basic supplies for collection and processing of samples. This has in turn led to worldwide efforts by the scientific community to establish improved protocols that are cheaper, more scalable, and not as resource intensive. One such effort resulted in an assay called “Swab-Seq”, which was so named because it was originally developed to work with dry nasal swab samples, but is actually flexible in terms of the sample type it can accommodate for testing. The assay adapts the existing gold standard (RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction, “qRT-PCR”) to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques it is possible to achieve high scalability at low cost per sample, and a reasonable turnaround time for reporting results. We evaluated the effectiveness of this assay both on samples collected from asymptomatic individuals using the traditional NP swab and using alternative extraction-free sampling techniques, including saliva and a saline mouth gargle protocol, and found the assay to be highly sensitive (comparable to the standard qRT-PCR assay), flexible (adaptable to saliva and gargle samples stored at room temperature up to a week), and scalable (easily accommodating hundreds of samples at a time). Continued development in the future will lead to more effective testing regimes that reduce the burden of transmissible respiratory infections on the global community. Overall design: Through a series of experiments, we evaluated the performance of Swab-Seq in detecting SARS-CoV-2 in various sample types, including: extracted RNA samples from asymptomatic individuals, extration-free saliva samples, and extraction-free saline gargle samples. This project involves a total of 9 different experiments.