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.
Show 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.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols 96%
- Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals 96%
- High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with Next Generation Sequencing 96%
Similar papers in this journal
Similar papers in this journal
- ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics. 94%
- vsgseq2: an updated pipeline for analysis of the diversity and abundance of population-wide Trypanosoma brucei VSG expression 93%
- Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer 91%
Similar papers in this journal
- Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens 94%
- Development and Implementation of a scalable and versatile test for COVID-19 diagnostics in rural communities 94%
- A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome 94%
Similar papers in this journal
- Comparison of long read methods for sequencing and assembly of a plant genome 95%
- Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans 95%
- IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.