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bioRxiv · 10.1101/2020.09.04.283077

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Tyson, J. R.·James, P.·Stoddart, D.·Sparks, N.·Wickenhagen, A.·Hall, G.·Choi, J. H.·Lapointe, H.·Kamelian, K.·Smith, A. D.·Prystajecky, N.·Goodfellow, I.·Wilson, S. J.·Harrigan, R.·Snutch, T. P.·Loman, N. J.·Quick, J.
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Abstract

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to {pound}10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.

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Tyson, J. R., James, P., Stoddart, D., Sparks, N., Wickenhagen, A., Hall, G., Choi, J. H., Lapointe, H., Kamelian, K., Smith, A. D., Prystajecky, N., Goodfellow, I., Wilson, S. J., Harrigan, R., Snutch, T. P., Loman, N. J., Quick, J.. 2020-09-04. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. https://doi.org/10.1101/2020.09.04.283077

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