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Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

View ORCID ProfileNikki E. Freed, View ORCID ProfileMarkéta Vlková, View ORCID ProfileMuhammad B. Faisal, View ORCID ProfileOlin K. Silander
doi: https://doi.org/10.1101/2020.05.28.122648
Nikki E. Freed
School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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  • For correspondence: n.freed@massey.ac.nz olinsilander@gmail.com
Markéta Vlková
School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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Muhammad B. Faisal
School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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Olin K. Silander
School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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  • For correspondence: n.freed@massey.ac.nz olinsilander@gmail.com
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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.

Competing Interest Statement

The authors have declared no competing interest.

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Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 02, 2020.
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Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
Nikki E. Freed, Markéta Vlková, Muhammad B. Faisal, Olin K. Silander
bioRxiv 2020.05.28.122648; doi: https://doi.org/10.1101/2020.05.28.122648
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Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
Nikki E. Freed, Markéta Vlková, Muhammad B. Faisal, Olin K. Silander
bioRxiv 2020.05.28.122648; doi: https://doi.org/10.1101/2020.05.28.122648

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