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

BioRxiv : the Preprint Server for Biology
J. R. TysonJoshua Quick

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 £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.

Citations

Apr 3, 2021·Viruses·Rachel L TullochJohn-Sebastian Eden
May 1, 2021·Bioengineering·Tina Shaffaf, Ebrahim Ghafar-Zadeh
May 29, 2021·Nature Reviews. Genetics·Wouter De CosterFritz J Sedlazeck
Jun 9, 2021·BMC Infectious Diseases·Grit SchubertANDEMIA consortium

Methods Mentioned

BETA
amplicon sequencing
PCR
FCS
Assay

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