Detecting SARS-CoV-2 variants with SNP genotyping

Research output: Contribution to journalArticlepeer-review

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Detecting SARS-CoV-2 variants with SNP genotyping. / The COVID-19 Genomics UK (COG-UK) Consortium ; Beggs, Andrew.

In: PLOS One, Vol. 16, No. 2, e0243185, 24.02.2021.

Research output: Contribution to journalArticlepeer-review

Harvard

The COVID-19 Genomics UK (COG-UK) Consortium & Beggs, A 2021, 'Detecting SARS-CoV-2 variants with SNP genotyping', PLOS One, vol. 16, no. 2, e0243185. https://doi.org/10.1371/journal.pone.0243185

APA

The COVID-19 Genomics UK (COG-UK) Consortium, & Beggs, A. (2021). Detecting SARS-CoV-2 variants with SNP genotyping. PLOS One, 16(2), [e0243185]. https://doi.org/10.1371/journal.pone.0243185

Vancouver

The COVID-19 Genomics UK (COG-UK) Consortium, Beggs A. Detecting SARS-CoV-2 variants with SNP genotyping. PLOS One. 2021 Feb 24;16(2). e0243185. https://doi.org/10.1371/journal.pone.0243185

Author

The COVID-19 Genomics UK (COG-UK) Consortium ; Beggs, Andrew. / Detecting SARS-CoV-2 variants with SNP genotyping. In: PLOS One. 2021 ; Vol. 16, No. 2.

Bibtex

@article{7d03473b2e74411c882f45544acf195e,
title = "Detecting SARS-CoV-2 variants with SNP genotyping",
abstract = "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 SARS-CoV-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.",
author = "{The COVID-19 Genomics UK (COG-UK) Consortium} and Helen Harper and Amanda Burridge and Mark Winfield and Adam Finn and Andrew Davidson and David Matthews and Stephanie Hutchings and Barry Vipond and Nisha Jain and Keith Edwards and Gary Barker and Andrew Beggs",
year = "2021",
month = feb,
day = "24",
doi = "10.1371/journal.pone.0243185",
language = "English",
volume = "16",
journal = "PLOS One",
issn = "1932-6203",
publisher = "Public Library of Science (PLOS)",
number = "2",

}

RIS

TY - JOUR

T1 - Detecting SARS-CoV-2 variants with SNP genotyping

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Harper, Helen

AU - Burridge, Amanda

AU - Winfield, Mark

AU - Finn, Adam

AU - Davidson, Andrew

AU - Matthews, David

AU - Hutchings, Stephanie

AU - Vipond, Barry

AU - Jain, Nisha

AU - Edwards, Keith

AU - Barker, Gary

AU - Beggs, Andrew

PY - 2021/2/24

Y1 - 2021/2/24

N2 - 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 SARS-CoV-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.

AB - 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 SARS-CoV-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.

U2 - 10.1371/journal.pone.0243185

DO - 10.1371/journal.pone.0243185

M3 - Article

VL - 16

JO - PLOS One

JF - PLOS One

SN - 1932-6203

IS - 2

M1 - e0243185

ER -