Sequencing SARS-CoV-2 genomes from saliva

Tara Alpert, Chantal B.F. Vogels, Mallery I. Breban, Mary E. Petrone, Anne L. Wyllie, Nathan D. Grubaugh, Joseph R. Fauver

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish (US)
Article numberveab098
JournalVirus Evolution
Issue number1
StatePublished - 2022
Externally publishedYes


  • SARS-CoV-2; saliva
  • genomic epidemiology
  • next generation sequencing
  • oxford nanopore MinION
  • salivadirect

ASJC Scopus subject areas

  • Microbiology
  • Virology


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