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Related Experiment Video

Updated: Sep 23, 2025

Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots

Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots

Published on: February 11, 2022

Sequencing SARS-CoV-2 genomes from saliva.

Tara Alpert¹, Chantal B F Vogels¹, Mallery I Breban¹

¹Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT 06510, USA.

Virus Evolution

|May 11, 2022

Summary

Saliva is a viable specimen for Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequencing. RNA extraction from saliva yields SARS-CoV-2 genomes comparable to those from nasopharyngeal swabs.

Keywords:

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

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Last Updated: Sep 23, 2025

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Published on: February 11, 2022

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Published on: June 30, 2023

Area of Science:

Virology
Genomics
Epidemiology

Background:

Genomic sequencing of SARS-CoV-2 is vital for tracking its evolution and spread.
Nasopharyngeal (NP) swabs are the traditional specimen source for SARS-CoV-2 whole-genome sequencing.
Saliva is a known reliable specimen for SARS-CoV-2 RNA detection but is underutilized for genomic studies.

Purpose of the Study:

To evaluate saliva as a specimen type for SARS-CoV-2 genomic sequencing.
To compare the quality of SARS-CoV-2 genomes generated from saliva versus NP swabs.
To determine the necessity of RNA extraction for saliva-based SARS-CoV-2 sequencing.

Main Methods:

Utilized the ARTIC Network amplicon-generation method.
Employed Oxford Nanopore MinION for sequencing.
Compared genomic data derived from saliva and NP swabs, with and without RNA extraction.

Main Results:

SARS-CoV-2 genomes generated from saliva were comparable in quality to those from NP swabs.
Complete SARS-CoV-2 genomes could be generated from saliva, but only after RNA extraction.
Saliva proved to be a stable and effective specimen for SARS-CoV-2 sequencing.

Conclusions:

Saliva is a suitable alternative specimen for SARS-CoV-2 genomic sequencing.
RNA extraction is a critical step for obtaining complete SARS-CoV-2 genomes from saliva.
This finding expands the options for specimen collection in SARS-CoV-2 genomic surveillance efforts.