An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

STAR Protoc. 2021 Sep 17;2(3):100755. doi: 10.1016/j.xpro.2021.100755. Epub 2021 Aug 2.

Abstract

Sequencing of SARS-CoV-2 genomes is crucial for understanding the genetic epidemiology of the COVID-19 pandemic. It is also critical for understanding the evolution of the virus and also for the rapid development of diagnostic tools. The present protocol is a modification of the Illumina COVIDSeq test. We describe an amplicon-based next-generation sequencing approach with short turnaround time, adapted for bench-top sequencers like MiSeq, iSeq, and MiniSeq. For complete details on the use and execution of this protocol, please refer to Bhoyar et al. (2021).

Keywords: Bioinformatics; Clinical Protocol; Genomics; Immunology; Microbiology; Sequence analysis; Sequencing.

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*
  • COVID-19 Nucleic Acid Testing / statistics & numerical data*
  • Genome, Viral*
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / standards
  • Humans
  • RNA, Viral / analysis
  • RNA, Viral / genetics*
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification

Substances

  • RNA, Viral