Sequencing SARS-CoV-2 from antigen tests

PLoS One. 2022 Feb 8;17(2):e0263794. doi: 10.1371/journal.pone.0263794. eCollection 2022.

Abstract

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 / genetics
  • COVID-19 / virology
  • COVID-19 Nucleic Acid Testing / methods*
  • Culture Media / analysis*
  • Culture Media / metabolism
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification
  • Specimen Handling / methods*
  • Whole Genome Sequencing / methods*

Substances

  • Culture Media

Grants and funding

This study was funded 59th Medical Wing Clinical Investigations Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The views expressed are those of the authors and do not reflect the official views of the Department of Defense or its Components.