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

doi:10.1093/ve/veab098

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 journal › Article › peer-review

4 Scopus citations

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.

Original language	English (US)
Article number	veab098
Journal	Virus Evolution
Volume	8
Issue number	1
DOIs	https://doi.org/10.1093/ve/veab098
State	Published - 2022
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Microbiology
Virology

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10.1093/ve/veab098

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title = "Sequencing SARS-CoV-2 genomes from saliva",

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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author = "Tara Alpert and Vogels, {Chantal B.F.} and Breban, {Mallery I.} and Petrone, {Mary E.} and Wyllie, {Anne L.} and Grubaugh, {Nathan D.} and Fauver, {Joseph R.}",

note = "Funding Information: This work was funded by CTSA Grant Number TL1 TR001864 (T.A.), a fast grant from Emergent Ventures at the Mercatus Center at George Mason University (N.D.G.), and Centers for Disease Control and Prevention (CDC) contracts 75D30120C09570 (N.D.G.). Publisher Copyright: {\textcopyright} 2022 The Author(s).",

year = "2022",

doi = "10.1093/ve/veab098",

language = "English (US)",

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AU - Vogels, Chantal B.F.

AU - Breban, Mallery I.

AU - Petrone, Mary E.

AU - Wyllie, Anne L.

AU - Grubaugh, Nathan D.

AU - Fauver, Joseph R.

N1 - Funding Information: This work was funded by CTSA Grant Number TL1 TR001864 (T.A.), a fast grant from Emergent Ventures at the Mercatus Center at George Mason University (N.D.G.), and Centers for Disease Control and Prevention (CDC) contracts 75D30120C09570 (N.D.G.). Publisher Copyright: © 2022 The Author(s).

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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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Sequencing SARS-CoV-2 genomes from saliva

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Keywords

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