CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

Genome Med. 2021 Feb 9;13(1):21. doi: 10.1186/s13073-021-00839-5.

Abstract

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

Keywords: ARTIC; Genetic; Genome; Multiplexing; NGS; Nanopore; SARS-CoV-2; Sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / genetics*
  • COVID-19 / virology
  • Genome, Viral / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Pandemics*
  • RNA, Viral / genetics
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / pathogenicity
  • Whole Genome Sequencing

Substances

  • RNA, Viral