Evidence map›Paper›PMID 37726109›Full record

ArticleEpidemiology and infection2023

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 and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Epidemiology and infection, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Katherine A TwohigCOVID-19 National Epidemiology Cell, UKHSA, London, UK.ORCID 0000-0001-9514-0097
Katie HarmanCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0003-1387-0200
Asad ZaidiCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0002-6420-2539
Shirin AliabadiCOVID-19 National Epidemiology Cell, UKHSA, London, UK.ORCID 0000-0003-3611-7377
Sophie G NashCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0002-7717-6982
Mary SinnathambyCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0001-6212-4672
Ian HarrisonPathogen Genomics, Science Group, UKHSA, London, UK.ORCID 0000-0003-4117-961X
Eileen GallagherTARZET Division, Clinical and Emerging Infections Directorate, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0009-0007-9223-5542
Natalie GrovesTARZET Division, Clinical and Emerging Infections Directorate, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0002-3832-3484
Frank SchwachTARZET Division, Clinical and Emerging Infections Directorate, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0001-5495-7535
Clare PearsonCOVID-19 National Epidemiology Cell, UKHSA, London, UK.ORCID 0000-0002-1941-4735
Alicia ThorntonCOVID-19 National Epidemiology Cell, UKHSA, London, UK.
Richard MyersTARZET Division, Clinical and Emerging Infections Directorate, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0003-4269-1164
Meera ChandTARZET Division, Clinical and Emerging Infections Directorate, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0001-9697-0340
Simon ThelwallCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0002-0434-2724
Gavin DabreraCOVID-19 Vaccines and Epidemiology Division, Public Health Programmes, Clinical and Public Health Group, UKHSA, London, UK.ORCID 0000-0003-4606-5945

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

COVID-19EnglandHumansPandemicsSARS-CoV-2COVID-19deprivationEnglandethnicityinequalitiesSARS-CoV-2sequencingsocio-economic statustravelvariants

Identifiers

PMID37726109
PMCPMC10600896

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.