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Sequencing SARS-CoV-2 Genomes from Saliva

By Tara Alpert, Chantal BF Vogels, Mallery I. Breban, Mary Petrone, Yale IMPACT Research Team, Anne L Wyllie, Nathan Grubaugh, Joseph R Fauver

Posted 29 Jun 2021
medRxiv DOI: 10.1101/2021.06.21.21259289

Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal 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 nasopharyngeal 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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