Enabling genomic surveillance from 30 years of linked English sentinel network data: The Wellcome Quinquagenarian (QQG) Biomedical Resource

de Lusignan, S; SebastianPillai, P; Parvizi, O; Okusi, C; Joy, M; Banik, S; Batool, F; Hoschler, K; Kele, B; Lackenby, A; Ellis, J; Pebody, R; Watson, C; Lopez Bernal, J; Zambon, M

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Journal article

Enabling genomic surveillance from 30 years of linked English sentinel network data: The Wellcome Quinquagenarian (QQG) Biomedical Resource

Abstract:: BackgroundThe World Health Organisation recommends integrating viral genome sequences and sentinel surveillance data. We report progress in linking clinical, virology, and sequence data to enable genomic surveillance of influenza, respiratory syncytial virus (RSV), and severe-acute-respiratory-syndrome coronavirus-2 (SARS-CoV-2).MethodsWe linked individual-level clinical data from the Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) sentinel network to virology results from the UK Health Security Agency (UKHSA) reference virology laboratory. We identify where publicly accessible repositories, the Global Initiative on Sharing All Influenza Data (GISAID), or others hold viral genome sequence data from test-positive cases. Our metadata also identifies test-negative controls contemporaneous to test-positive cases. We summarise the scope of data availability in the Wellcome Quinquagenarian (QQG) biomedical resource.ResultsWe report respiratory virus sampling for influenza, RSV, and SARS-CoV-2 between 1992 and 2023. Samples were collected from a nationally representative subset of RSC general practices participating in the virological surveillance programme.QQG contains 13,665 positive influenza samples, 3,791 positive RSV samples, and 5,068 positive SARS-CoV2 samples. There were 2,819 sequenced influenza genomes, of which 97.1% were linked to clinical records, 1,251 sequenced RSV genomes of which 96.8 were linked to clinical records, and 2,486 sequenced SARS-CoV-2 genomes of which 98.9% were linked to clinical records.ConclusionWe have described the scale of QQG, created to enable genomic surveillance linked to clinical metadata to facilitate research on the impact of different viral variants on clinical outcomes, vaccine effectiveness, and therapeutic strategies.

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

de Lusignan, S., SebastianPillai, P., Parvizi, O., Okusi, C., Joy, M., Banik, S., Batool, F., Hoschler, K., Kele, B., Lackenby, A., Ellis, J., Pebody, R., Watson, C., Lopez Bernal, J., & Zambon, M. (2025). Enabling genomic surveillance from 30 years of linked English sentinel network data: The Wellcome Quinquagenarian (QQG) Biomedical Resource. Wellcome Open Research, 10, 411.

MLA Style

de Lusignan, S, et al. “Enabling Genomic Surveillance from 30 Years of Linked English Sentinel Network Data: The Wellcome Quinquagenarian (QQG) Biomedical Resource.” Wellcome Open Research, vol. 10, 2025, p. 411.

Chicago Style

Lusignan, S de, P SebastianPillai, O Parvizi, et al. 2025. “Enabling Genomic Surveillance from 30 Years of Linked English Sentinel Network Data: The Wellcome Quinquagenarian (QQG) Biomedical Resource.” Wellcome Open Research 10: 411.
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