Eleanor H Hayles, Andrew J Page, Robert A Kingsley, Javier Guitian, The Covid-Genomics Uk Consortium, Gemma C Langridge
{"title":"Genomic epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020-December 2022.","authors":"Eleanor H Hayles, Andrew J Page, Robert A Kingsley, Javier Guitian, The Covid-Genomics Uk Consortium, Gemma C Langridge","doi":"10.1099/mgen.0.001435","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 7","pages":""},"PeriodicalIF":4.0000,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282267/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbial Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/mgen.0.001435","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
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.
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.