Sequencing SARS-CoV-2 genomes from saliva

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Abstract

Genomic sequencing is crucial to understanding the epidemiology and evolution of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal (NP) swabs, as input into whole-genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays; however, saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from NP swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.

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Alpert, T., Vogels, C. B. F., Breban, M. I., Petrone, M. E., Wyllie, A. L., Grubaugh, N. D., & Fauver, J. R. (2022). Sequencing SARS-CoV-2 genomes from saliva. Virus Evolution, 8(1). https://doi.org/10.1093/ve/veab098

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