Sequencing SARS-CoV-2 Genomes From Saliva

Authors

Tara Alpert, Yale School of Public Health
Chantal B. F. Vogels, Yale School of Public Health
Mallery I. Breban, Yale School of Public Health
Mary E. Petrone, Yale School of Public Health
Anne L. Wyllie, Yale School of Public Health
Nathan D. Grubaugh, Yale School of Public Health
Joseph R. Fauver, University of Nebraska Medical CenterFollow

Document Type

Article

Journal Title

Virus Evolution

Publication Date

2022

Volume

8

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.

DOI Link

10.1093/ve/veab098

ISSN

2057-1577

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Recommended Citation

Alpert, Tara; Vogels, Chantal B. F.; Breban, Mallery I.; Petrone, Mary E.; Wyllie, Anne L.; Grubaugh, Nathan D.; and Fauver, Joseph R., "Sequencing SARS-CoV-2 Genomes From Saliva" (2022). Journal Articles: Epidemiology. 165.
https://digitalcommons.unmc.edu/coph_epidem_articles/165