tetano
Editor, Senior Moderator
Virus Evol
. 2022 Jan 3;8(1):veab098.
doi: 10.1093/ve/veab098. eCollection 2022.
Sequencing SARS-CoV-2 genomes from saliva
Tara Alpert[SUP] 1 [/SUP], Chantal B F Vogels[SUP] 1 [/SUP], Mallery I Breban[SUP] 1 [/SUP], Mary E Petrone, Anne L Wyllie[SUP] 1 [/SUP], Nathan D Grubaugh[SUP] 1 [/SUP], Joseph R Fauver[SUP] 1 [/SUP]
Affiliations
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.
Keywords: SARS-CoV-2; saliva; genomic epidemiology; next generation sequencing; oxford nanopore MinION; salivadirect.
. 2022 Jan 3;8(1):veab098.
doi: 10.1093/ve/veab098. eCollection 2022.
Sequencing SARS-CoV-2 genomes from saliva
Tara Alpert[SUP] 1 [/SUP], Chantal B F Vogels[SUP] 1 [/SUP], Mallery I Breban[SUP] 1 [/SUP], Mary E Petrone, Anne L Wyllie[SUP] 1 [/SUP], Nathan D Grubaugh[SUP] 1 [/SUP], Joseph R Fauver[SUP] 1 [/SUP]
Affiliations
- PMID: 35542310
- PMCID: PMC9074962
- DOI: 10.1093/ve/veab098
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.
Keywords: SARS-CoV-2; saliva; genomic epidemiology; next generation sequencing; oxford nanopore MinION; salivadirect.