CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.
Dave J BakerAlp AydinThanh Le-VietGemma L KaySteven RudderLeonardo de Oliveira MartinsAna P TedimAnastasia KolyvaMaria DiazNabil-Fareed AlikhanLizzie MeadowsAndrew BellAna Victoria GutierrezAlexander J TrotterNicholas M ThomsonRachel GilroyLuke GriffithEvelien M AdriaenssensRachael StanleyIan G CharlesNgozi ElumogoJohn WainReenesh PrakashEmma MeaderAlison E MatherMark A WebberSamir DervisevicAndrew J PageJustin O'GradyPublished in: Genome medicine (2021)
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.