Wellcome open research · 2025
Enabling genomic surveillance from 30 years of linked English sentinel network data: The Wellcome Quinquagenarian (QQG) Biomedical Resource.
СтатьяНазвание и аннотация: Перевод пока не подготовлен
Обработка статьи · этапы, ошибки и управление
Загрузка состояния…
Ошибки и ограничения
История · было → стало
Состояние обновляется каждые 5 секунд, пока блок открыт. Процент показывается только там, где известен объём работы. Пауза останавливает продолжение этапа; текущий запрос к источнику может завершиться.
de Lusignan Simon, SebastianPillai Praveen, Parvizi Omid, Okusi Cecilia, Joy Mark, Banik Shuma, Batool Fatima, Hoschler Katja, Kele Beatrix, Lackenby Angie, Ellis Joanna, Pebody Richard, Watson Conall, Lopez Bernal Jamie, Zambon Maria
Аннотация
BACKGROUND: The 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).
METHODS: We 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.
RESULTS: We 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.
CONCLUSION: We 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.
METHODS: We 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.
RESULTS: We 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.
CONCLUSION: We 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.