Detecting SARS-CoV-2 variants with SNP genotyping.

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 ope...

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Autores principales:	Helen Harper, Amanda Burridge, Mark Winfield, Adam Finn, Andrew Davidson, David Matthews, Stephanie Hutchings, Barry Vipond, Nisha Jain, COVID-19 Genomics UK (COG-UK) Consortium, Keith Edwards, Gary Barker
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/593eab5eb7f44ded88636344488e8b3e
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spelling	oai:doaj.org-article:593eab5eb7f44ded88636344488e8b3e2021-12-02T20:18:56ZDetecting SARS-CoV-2 variants with SNP genotyping.1932-620310.1371/journal.pone.0243185https://doaj.org/article/593eab5eb7f44ded88636344488e8b3e2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0243185https://doaj.org/toc/1932-6203Tracking 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.Helen HarperAmanda BurridgeMark WinfieldAdam FinnAndrew DavidsonDavid MatthewsStephanie HutchingsBarry VipondNisha JainCOVID-19 Genomics UK (COG-UK) ConsortiumKeith EdwardsGary BarkerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 2, p e0243185 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Helen Harper Amanda Burridge Mark Winfield Adam Finn Andrew Davidson David Matthews Stephanie Hutchings Barry Vipond Nisha Jain COVID-19 Genomics UK (COG-UK) Consortium Keith Edwards Gary Barker Detecting SARS-CoV-2 variants with SNP genotyping.
description	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.
format	article
author	Helen Harper Amanda Burridge Mark Winfield Adam Finn Andrew Davidson David Matthews Stephanie Hutchings Barry Vipond Nisha Jain COVID-19 Genomics UK (COG-UK) Consortium Keith Edwards Gary Barker
author_facet	Helen Harper Amanda Burridge Mark Winfield Adam Finn Andrew Davidson David Matthews Stephanie Hutchings Barry Vipond Nisha Jain COVID-19 Genomics UK (COG-UK) Consortium Keith Edwards Gary Barker
author_sort	Helen Harper
title	Detecting SARS-CoV-2 variants with SNP genotyping.
title_short	Detecting SARS-CoV-2 variants with SNP genotyping.
title_full	Detecting SARS-CoV-2 variants with SNP genotyping.
title_fullStr	Detecting SARS-CoV-2 variants with SNP genotyping.
title_full_unstemmed	Detecting SARS-CoV-2 variants with SNP genotyping.
title_sort	detecting sars-cov-2 variants with snp genotyping.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/593eab5eb7f44ded88636344488e8b3e
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Detecting SARS-CoV-2 variants with SNP genotyping.

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