Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
Open Access
- 1 January 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Biology Methods and Protocols
- Vol. 5 (1), bpaa014
- https://doi.org/10.1093/biomethods/bpaa014
Abstract
Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with Cq values between 20 and 31, we show that high-quality genomes can be generated with as few as 10,000 reads (approximately 5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.Keywords
This publication has 4 references indexed in Scilit:
- Detection of SARS-CoV-2 in Different Types of Clinical SpecimensJama-Journal Of The American Medical Association, 2020
- An emergent clade of SARS-CoV-2 linked to returned travellers from IranVirus Evolution, 2020
- Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samplesNature Protocols, 2017
- Data, disease and diplomacy: GISAID's innovative contribution to global healthGlobal Challenges, 2017