Nowcasting cases and trends during the measles 2023/24 outbreak in England

Background From 2023 to 2024, England had the largest measles outbreak in over a decade. Lags from suspected cases’ symptom onset to the availability of test results mean laboratory-confirmed case data are inherently retrospective rather than real-time. Reporting lags vary by measles prevalence and whether testing was for diagnostic or surveillance purposes. Nowcasting models predict future backfilling of reported cases and can estimate recent trends.

We developed a generalised additive model framework accounting for reporting delays, location, and day-of-week effects in line-list data by onset date. The model was re-fit weekly providing real-time nowcasts and directional trends for national and regional users. Retrospectively, we tested alternative specifications to optimise structure and confirm predictive performance, evaluating with log weighted interval score (WIS) and ranked probability score (RPS).

For case count estimates, the operational and retrospective models outperformed the baseline model, with a lower average daily national log WIS by 42% and 41%, respectively, and similar regional improvements. For four-week trend direction, the operational and retrospective models provided better national estimates than the baseline with an average RPS lower by 69% and 6% respectively. Regionally, they also outperformed the baseline model in London, but the baseline model offered better performance for the smoother single-peak West Midlands epidemic. An alternative model indexed by report date instead sometimes outperformed the other nowcasting models for trend direction but also lagged changes in trend. Interpretation Our work highlights the utility for real-time nowcasting models during outbreaks to inform fast-evolving trends, and the need for early access of accurate reporting delay data to facilitate effective modelling. Competing Interest Statement The authors have declared no competing interest. Funding Statement This study did not receive any funding. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: UK Health Security Agency have an exemption under Regulation 3 of Section 251 of the National Health Service Act (2006) to allow identifiable patient information to be processed to diagnose, control, prevent, or recognise trends in, communicable diseases and other risks to public health. Individual-level data was de-identified before use in this study. This study uses the de-identified and aggregated data. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes Add link to GitHub repository with code for the paper - updated in supplementary material and data availability statement and link Data Availability Code for the paper is available at: https://github.com/maria-tang/measles-nowcast Aggregate annual measles cases are provided on the gov.uk website https://www.gov.uk/government/publications/measles-epidemiology-2023. Individual-level data including reporting delays have not been shared due to patient identifiability. UKHSA operates a robust governance process for applying to access protected data that considers: - the benefits and risks of how the data will be used - compliance with policy, regulatory and ethical obligations - data minimisation - how the confidentiality, integrity, and availability will be maintained - retention, archival, and disposal requirements - best practice for protecting data, including the application of "privacy by design and by default", emerging privacy conserving technologies and contractual controls. Access to protected data is always strictly controlled using legally binding data sharing contracts. UKHSA welcomes data applications from organisations looking to use protected data for public health purposes. To request an application pack or discuss a request for UKHSA data you would like to submit, contact DataAccess{at}ukhsa.gov.uk. Data Availability Aggregate annual measles cases are provided on the gov.uk website https://www.gov.uk/government/publications/measles-epidemiology-2023. Individual-level data including reporting delays have not been shared due to patient identifiability. UKHSA operates a robust governance process for applying to access protected data that considers: - the benefits and risks of how the data will be used - compliance with policy, regulatory and ethical obligations - data minimisation - how the confidentiality, integrity, and availability will be maintained - retention, archival, and disposal requirements - best practice for protecting data, including the application of "privacy by design and by default", emerging privacy conserving technologies and contractual controls. Access to protected data is always strictly controlled using legally binding data sharing contracts. UKHSA welcomes data applications from organisations looking to use protected data for public health purposes. To request an application pack or discuss a request for UKHSA data you would like to submit, contact DataAccess{at}ukhsa.gov.uk.