Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding

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dc.citation.issue1
dc.citation.volume5
dc.contributor.authorFreed NE
dc.contributor.authorVlková M
dc.contributor.authorFaisal MB
dc.contributor.authorSilander OK
dc.date.accessioned2024-01-09T01:55:19Z
dc.date.accessioned2024-07-25T06:41:17Z
dc.date.available2020-07-18
dc.date.available2024-01-09T01:55:19Z
dc.date.available2024-07-25T06:41:17Z
dc.date.issued2020-07-18
dc.description.abstractRapid and cost-efficient whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, 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 (∼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.
dc.description.confidentialfalse
dc.identifier.citationFreed NE, Vlková M, Faisal MB, Silander OK. (2021). Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biology Methods and Protocols. 5. 1.
dc.identifier.doi10.1093/biomethods/bpaa014
dc.identifier.eissn2396-8923
dc.identifier.elements-typejournal-article
dc.identifier.numberbpaa014
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70682
dc.languageEnglish
dc.publisherOxford University Press
dc.publisher.urihttps://academic.oup.com/biomethods/article/5/1/bpaa014/5873518
dc.relation.isPartOfBiology Methods and Protocols
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectNanopore
dc.subjectSARS-CoV-2
dc.subjectamplicon
dc.subjectgenome
dc.titleRapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
dc.typeJournal article
pubs.elements-id440092
pubs.organisational-groupOther
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