Detecting SARS-CoV-2 variants with SNP genotyping

Helen Harper*, Amanda Burridge, Mark Winfield, Adam Finn, Andrew Davidson, David Matthews, Stephanie Hutchings, Barry Vipond, Nisha Jain, The COVID-19 Genomics UK (COG-UK) Consortium, John Allan, Matthew Bashton, Joshua Loh, Andrew Nelson, Darren L. Smith, Wen C. Yew, Gregory R. Young, Keith Edwards, Gary Barker

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

32 Citations (Scopus)
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Tracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARSCoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system, we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020 and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 61.9% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with a marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

Original languageEnglish
Article numbere0243185
Pages (from-to)1-12
Number of pages12
JournalPLoS One
Issue number2
Publication statusPublished - 24 Feb 2021


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