PrimalScheme: open-source community resources for low-cost viral genome sequencing

• Published in: bioRxiv 2024-12
• Main Authors: Kent, Chris, Smith, Andrew D, Tyson, John, Stepniak, Dominika, Eddy Kinganda-Lusamaki, Lee, Tracy, Weaver, Mia, Sparks, Natalie, Landsdowne, Lauren, Wilkinson, Sam Aj, Brier, Thomas, Colquhoun, Rachel, O'toole, Aine N, Placide Mbala Kingebeni, Goodfellow, Ian G, Rambaut, Andrew, Loman, Nicholas James, Quick, Joshua
• Format: Article
• Language: English
• Subjects: COVID-19; Genomes; Genomics; Genotypes; Mpox; Primers; Severe acute respiratory syndrome coronavirus 2; Surveillance; Viruses
• ISSN: 2692-8205
• DOI: 10.1101/2024.12.20.629611

Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its low cost and high sensitivity. Here, we describe PrimalScheme, an open-source toolkit and website that allows users to easily design primer schemes for amplicon sequencing of viruses and has generated over 67,000 primer schemes for a global community since 2017. In January 2020, PrimalScheme was used to rapidly generate a primer scheme for SARS-CoV-2, with primer pools distributed to researchers from 44 countries to help scale-up genomic surveillance efforts. Overall, these primers were used to generate an estimated 18M genome sequences and the protocols were viewed online ~250K times. To complement PrimalScheme, we have built PrimalScheme Labs, a scheme repository which allows users to find and share primers schemes as well as establishing a set of data standards. Through improvements to the primer design process, including the use of discrete primer clouds, we have expanded the use of amplicon sequencing to include diverse virus species. We demonstrate the utility of this approach through a high diversity pan-genotype Measles virus (MeV) scheme. We also demonstrate its use on a high sensitivity, short amplicon Monkeypox virus (MPXV) scheme with over 1000 primers, showing high genome recovery on low-titre clinical samples. These developments have implications for sequencing from samples such as wastewater, for genomic surveillance of endemic pathogens and in preparing for future pandemics.Competing Interest StatementJ.Q., J.T, and N.J.L. have all received travel expenses and accommodation from Oxford Nanopore Technologies to speak at organised events. C.K has received an honorarium from Illumina for participating in a webinar series.