Publication date: Jul 01, 2025
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.
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Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | COVID-19 |
| drug | DRUGBANK | Pentaerythritol tetranitrate |
| disease | IDO | pathogen |
| disease | IDO | country |
| disease | IDO | intervention |
| disease | IDO | algorithm |
| drug | DRUGBANK | Etoperidone |
| drug | DRUGBANK | L-Phenylalanine |
| disease | MESH | aids |
| drug | DRUGBANK | Trestolone |
| disease | MESH | pneumonia |
| drug | DRUGBANK | Coenzyme M |
| disease | MESH | infection |
| disease | IDO | history |