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. 2023 Sep 20:151:e169.
doi: 10.1017/S0950268823001541.

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Katherine A Twohig  1 , Katie Harman  2 , Asad Zaidi  2 , Shirin Aliabadi  1 , Sophie G Nash  2 , Mary Sinnathamby  2 , Ian Harrison  3 , Eileen Gallagher  4 , Natalie Groves  4 , Frank Schwach  4 , Clare Pearson  1 , Alicia Thornton  1 , Richard Myers  4 , Meera Chand  4 , Simon Thelwall  2 , Gavin Dabrera  2
Affiliations

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Katherine A Twohig et al. Epidemiol Infect. .

Abstract

Whole-genome sequencing (WGS) information has played a crucial role in the SARS-CoV-2 (COVID-19) pandemic by providing evidence about variants to inform public health policy. The purpose of this study was to assess the representativeness of sequenced cases compared with all COVID-19 cases in England, between March 2020 and August 2021, by demographic and socio-economic characteristics, to evaluate the representativeness and utility of these data in epidemiological analyses. To achieve this, polymerase chain reaction (PCR)-confirmed COVID-19 cases were extracted from the national laboratory system and linked with WGS data. During the study period, over 10% of COVID-19 cases in England had WGS data available for epidemiological analysis. With sequencing capacity increasing throughout the period, sequencing representativeness compared to all reported COVID-19 cases increased over time, allowing for valuable epidemiological analyses using demographic and socio-economic characteristics, particularly during periods with emerging novel SARS-CoV-2 variants. This study demonstrates the comprehensiveness of England's sequencing throughout the COVID-19 pandemic, rapidly detecting variants of concern, and enabling representative epidemiological analyses to inform policy.

Keywords: COVID-19; England; SARS-CoV-2; deprivation; ethnicity; inequalities; sequencing; socio-economic status; travel; variants.

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Conflict of interest statement

G.D. declares that his employer’s predecessor organisation, Public Health England, received funding from GlaxoSmithKline for a previous research project related to influenza antiviral treatment. This preceded and had no relation to COVID-19, and G.D. had no role in and received no funding from the project. All other authors report no potential conflicts.

Figures

Figure 1.
Figure 1.
(a) PCR-confirmed COVID-19 cases reported in England, by pillar. (b) PCR-confirmed COVID-19 cases linked with quality-assessed whole-genome sequencing results from CLIMB. (c) 7-day rolling per cent of cases that were sequenced.
See this image and copyright information in PMC

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Supplementary concepts