RT Journal Article
SR Electronic
T1 Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.28.122648
DO 10.1101/2020.05.28.122648
A1 Nikki E. Freed
A1 Markéta Vlková
A1 Muhammad B. Faisal
A1 Olin K. Silander
YR 2020
UL http://biorxiv.org/content/early/2020/06/02/2020.05.28.122648.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.