Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection

Hyunjin Kang,Sheilah Allison,Amber Spangenberg,Tara Carr,Ryan Sprissler,Marilyn Halonen,Darren A Cusanovich

doi:10.1038/s41598-022-06901-5

Hyunjin Kang, Sheilah Allison + Show 5 more

Open Access

https://doi.org/10.1038/s41598-022-06901-5

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Abstract

The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples. This has motivated efforts by the scientific community to establish improved protocols that are more scalable, less resource intensive, and less expensive. One such developmental effort has resulted in an assay called “Swab-Seq”, so named because it was originally developed to work with dry nasal swab samples. The existing gold standard test consists of RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR). Swab-Seq adapts this method to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques, Swab-Seq achieves high scalability, low cost per sample, and a reasonable turnaround time. We evaluated the effectiveness of this assay in a community surveillance setting by testing samples collected from both symptomatic and asymptomatic individuals using the traditional NP swab. In addition, we evaluated extraction-free sampling techniques (both saliva and saline mouth gargle samples). We found the assay to be as clinically sensitive as the qRT-PCR assay, adaptable to multiple sample types, and able to easily accommodate hundreds of samples at a time. We thus provide independent validation of Swab-Seq and extend its utility regarding sample type and sample stability. Assays of this type greatly expand the possibility of routine, noninvasive, repeated testing of asymptomatic individuals suitable for current and potential future needs.

Highlights

The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples
We found that the assay was easy to implement, comparable to quantitative reverse transcription polymerase chain reaction (qRT-PCR) in terms of clinical sensitivity in asymptomatic individuals, and that it is flexible to various sampling methods
With synthetic RNA, we estimated that the assay had a limit of detection (LOD) of approximately 10 copies of viral genome per reaction: 10 of 12 replicates were distinguishable from the negative controls at this viral load in our initial experiments with the AB TaqPath 1-step Multiplex Master Mix kit, and an additional 12 of 12 replicates at this load were distinguishable from negatives regardless of whether we used synthetic RNA or inactivated viral particles in a subsequent experiment (Supplementary Fig. S2, Supplementary Table S3)