Genomic epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020-December 2022.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
Eleanor H Hayles, Andrew J Page, Robert A Kingsley, Javier Guitian, The Covid-Genomics Uk Consortium, Gemma C Langridge
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Abstract

In the UK, the COVID-19 Genomics UK Consortium (COG-UK) established a real-time national genomic surveillance system during the COVID-19 pandemic, producing centralized data for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a COG-UK partner, Quadram Institute Bioscience in Norfolk sequenced over 87,000 SARS-CoV-2 genomes as part of the national effort, contributing to the region becoming densely sequenced. Retrospective analysis of SARS-CoV-2 lineage dynamics in this region may contribute to preparedness for future pandemics. In total, 29,406 SARS-CoV-2 whole genome sequences and corresponding metadata from Norfolk were extracted from the COG-UK dataset, sampled between March 2020 and December 2022, representing 9.9% of regional COVID-19 cases. Sequences were lineage typed using Pangolin, with subsequent lineage analysis carried out in R using RStudio and related packages, including graphical analysis using ggplot2. In total, 401 global lineages were identified, with 69.8% appearing more than once and 31.2% over ten times. Temporal clustering identified six lineage communities based on first lineage emergence. Alpha, Delta and Omicron variants of concern (VOCs) accounted for 8.6, 34.9 and 48.5% of sequences, respectively. These formed four regional epidemic waves alongside the remaining lineages which were observed in the early pandemic prior to VOC designation and were termed 'pre-VOC' lineages. Regional comparison highlighted variability in VOC epidemic wave dates dependent on location. This study is the first to assess SARS-CoV-2 diversity in Norfolk across a large timescale within the COVID-19 pandemic. SARS-CoV-2 was both highly diverse and dynamic throughout the Norfolk region between March 2020 and December 2022, with a strong VOC presence within the latter two-thirds of the study period. The study also displays the utility of incorporating genomic epidemiological methods into pandemic response.

2020年3月- 2022年12月英国诺福克市SARS-CoV-2基因组流行病学分析
在英国,COVID-19基因组学英国联盟(COG-UK)在COVID-19大流行期间建立了实时国家基因组监测系统,为监测严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)提供集中数据。作为COG-UK的合作伙伴,诺福克的Quadram生物科学研究所对超过87,000个SARS-CoV-2基因组进行了测序,作为国家努力的一部分,为该地区变得密集测序做出了贡献。对该地区SARS-CoV-2谱系动态的回顾性分析可能有助于为未来的大流行做好准备。在2020年3月至2022年12月期间,从COG-UK数据集中提取了诺福克郡的29,406个SARS-CoV-2全基因组序列和相应的元数据,占该地区COVID-19病例的9.9%。序列使用穿山甲进行谱系分型,随后使用RStudio及相关软件包在R语言中进行谱系分析,包括使用ggplot2进行图形分析。总共确定了401个全球血统,其中69.8%出现了一次以上,31.2%出现了10次以上。基于第一谱系出现的时间聚类鉴定出6个谱系群落。α、δ和Omicron变体分别占8.6%、34.9%和48.5%的序列。这些形成了四个区域流行波,以及在VOC指定之前早期大流行中观察到的剩余谱系,称为“前VOC”谱系。区域比较突出了VOC流行波日期随地点的变化。这项研究是第一个在COVID-19大流行期间评估诺福克郡SARS-CoV-2多样性的研究。在2020年3月至2022年12月期间,SARS-CoV-2在整个诺福克地区既高度多样化又充满活力,在研究期间的后三分之二时间内,挥发性有机化合物的存在很强。该研究还显示了将基因组流行病学方法纳入大流行应对的效用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Microbial Genomics
Microbial Genomics Medicine-Epidemiology
CiteScore
6.60
自引率
2.60%
发文量
153
审稿时长
12 weeks
期刊介绍: Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.
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