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

  • Katherine A. Twohig, Katie Harman, Asad Zaidi, Shirin Aliabadi, Sophie G. Nash, Mary Sinnathamby, Ian Harrison, Eileen Gallagher, Natalie Groves, Frank Schwach, Clare Pearson, Alicia Thornton, Richard Myers, Meera Chand, Simon Thelwall, Gavin Dabrera
  • Journal:
    Epidemiology & Infection / Volume 151 / 2023
    Published online by Cambridge University Press:
    20 September 2023, e169
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  • 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.

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