Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

Abstract Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing...

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Autores principales:	Altar M. Munis, Monique Andersson, Alexander Mobbs, Stephen C. Hyde, Deborah R. Gill
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0f5350e19d5d4b4dbc98ab52f66eb2ac
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spelling	oai:doaj.org-article:0f5350e19d5d4b4dbc98ab52f66eb2ac2021-11-08T10:52:54ZGenomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown10.1038/s41598-021-01022-x2045-2322https://doaj.org/article/0f5350e19d5d4b4dbc98ab52f66eb2ac2021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-01022-xhttps://doaj.org/toc/2045-2322Abstract Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.Altar M. MunisMonique AnderssonAlexander MobbsStephen C. HydeDeborah R. GillNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Altar M. Munis Monique Andersson Alexander Mobbs Stephen C. Hyde Deborah R. Gill Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
description	Abstract Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.
format	article
author	Altar M. Munis Monique Andersson Alexander Mobbs Stephen C. Hyde Deborah R. Gill
author_facet	Altar M. Munis Monique Andersson Alexander Mobbs Stephen C. Hyde Deborah R. Gill
author_sort	Altar M. Munis
title	Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
title_short	Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
title_full	Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
title_fullStr	Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
title_full_unstemmed	Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
title_sort	genomic diversity of sars-cov-2 in oxford during united kingdom’s first national lockdown
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0f5350e19d5d4b4dbc98ab52f66eb2ac
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Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

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