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Detection of SARS-CoV-2 in Saliva Using Tailed Amplicon Sequencing | OMICS International| Abstract
ISSN: 2332-0877

Journal of Infectious Diseases & Therapy
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  • Research Article   
  • J Infect Dis Ther,
  • DOI: 10.4172/2332-0877.1000464

Detection of SARS-CoV-2 in Saliva Using Tailed Amplicon Sequencing

Aaron Garoutte1, Tasha M Santiago-Rodriguez1, Heather L Fehling2 and Rafal Iwasiow3*
1Diversigen, Houston, USA
2Clinical Reference Laboratory, Lenexa, USA
3DNA Genotek, Ottawa, Canada
*Corresponding Author : Rafal Iwasiow, DNA Genotek, Ottawa, Canada, Email: [email protected]

Received Date: Jun 08, 2021 / Accepted Date: Jun 22, 2021 / Published Date: Jun 29, 2021

Abstract

The most recent virus from the Coronaviridae family infecting humans, SARS-CoV-2, has resulted in a global pandemic. As part of the surveillance efforts, SARS-CoV-2 genomes are increasingly being made publicly available. Methods that include both short- and long-read sequencing have been used to elucidate SARS-CoV-2 genomes; however, many of these untargeted approaches may require deeper sequencing for greater genome coverage. For this reason, sequence capture or amplicon-based approaches for SARS-CoV-2 genome sequencing have been developed. The present proof-of-concept study evaluated a modified sequence capture approach, namely, tailed amplicon sequencing, to determine SARS-CoV-2 near complete genome sequences from the saliva of infected individuals. Particularly, the suitability of saliva samples stored at room temperature using OMNIgene® •ORAL OME-505 was evaluated. The tailed amplicon sequencing approach poses the additional advantage of being a cost-effective method for library preparation. Different known SARS-CoV-2 variants were identified across the infected subjects, with an average of >99.4% genome coverage. This methodology also enabled robust genomic surveillance using phylogenetic analyses. The present study supports the suitability of saliva stored at room temperature using collection devices for SARS-CoV-2 variant detection. Importantly, the present study supports the use of tailed amplicon sequencing approaches as an alternative, cost-effective method for SARS-CoV-2 detection in saliva for genomic surveillance.

Keywords: Genomic surveillance; SARS-CoV-2; Sequence capture; Tailed amplicon sequencing

Citation: Garoutte A, Santiago-Rodriguez TM, Fehling HL, Iwasiow R (2021) Detection of SARS-CoV-2 in Saliva Using Tailed Amplicon Sequencing. J Infect Dis Ther 9:464. Doi: 10.4172/2332-0877.1000464

Copyright: © 2021 Garoutte A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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