Landmark Study Maps 406 Rare Diseases and COVID-19 Infection Across 62.5 Million People in England

Rare diseases are individually uncommon, but together they touch millions of lives, and until now England has lacked a truly national picture of how their burden is distributed across ethnic groups. A new cross-sectional study published in Scientific Reports has drawn on the linked primary care, hospital, and mortality records of 62.5 million people alive on 31 July 2023 to estimate the prevalence of 406 rare diseases by ethnicity and to describe recorded COVID-19 infection rates within these communities. The analysis, conducted within the NHS England Secure Data Environment through the British Heart Foundation Data Science Centre’s CVD-COVID-UK/COVID-IMPACT Consortium, offers one of the most comprehensive ethnicity-resolved maps of rare disease burden ever assembled for a single country.

The scale of the data infrastructure behind the study is itself remarkable. Rather than relying on surveys or small clinical cohorts, the researchers accessed anonymised electronic health records spanning general practice, hospital episode statistics for admitted patient care and outpatient care, and mortality records, all linked at the individual level within a secure research environment. This allowed the team to calculate age- and sex-standardised prevalence for each of the 406 rare diseases and to compute recorded COVID-19 infection rates for the overall rare disease group, for each individual condition, and across both the six-group Office for National Statistics ethnicity classification and the more granular 19-group NHS classification.

The headline finding is that 1.05 million people in England, or 1.7 percent of the population studied, had at least one of the 406 rare diseases captured in the analysis. While that proportion may appear modest, it represents a substantial population whose healthcare needs are often fragmented across specialties and whose conditions may go unrecognised for years. By standardising prevalence estimates for age and sex, the researchers accounted for the demographic differences between ethnic groups, ensuring that observed variations reflect genuine differences in disease occurrence rather than differences in population structure.

Perhaps the most striking technical insight of the study concerns the way ethnic categories are constructed. When the researchers used broad aggregate categories, patterns of rare disease prevalence appeared relatively uniform. But when these categories were disaggregated into the finer-grained NHS classifications, substantial heterogeneity emerged that had been completely hidden. A vivid example is discoid lupus erythematosus, an autoimmune condition affecting the skin: its prevalence was markedly elevated among people recorded as Black Caribbean but not among those recorded as Black African, a distinction that vanishes entirely when both groups are folded into a single aggregate Black category. This finding has direct implications for how health systems collect and report ethnicity data, suggesting that coarse classifications can mask clinically meaningful differences in disease distribution.

The COVID-19 component of the analysis adds a pandemic-era dimension to the picture. Recorded COVID-19 infection was higher among people with rare diseases than in the rest of the population, at 32.8 percent compared with 29.0 percent. This elevation could reflect a combination of factors, including greater contact with healthcare settings where infections were detected, potentially increased susceptibility related to underlying conditions, and differences in testing behaviour. Because the study measured recorded infections rather than confirmed biological incidence, some caution is warranted in interpreting the absolute rates, but the relative patterns remain informative.

Within the rare disease group, infection rates varied considerably by ethnicity. People in the Pakistani group had a recorded infection rate of 27.7 percent, and those in the Black African group 23.8 percent, compared with 33.7 percent in the White British group. Infection rates also varied by specific rare disease, ranging from 24.6 to 41.2 percent among the 25 most common conditions in the dataset. The observation that the highest recorded rates appeared in the ONS White and NHS White British groups is noteworthy, as it runs counter to some earlier pandemic-era findings that reported higher recorded infection rates in several minority ethnic groups, and it underscores how the intersection of rare disease status and ethnicity produces patterns that neither factor alone would predict.

The study’s methodology deserves attention for how it handled the complexity of rare disease identification. Rare diseases are defined individually by low prevalence, often affecting fewer than one in 2,000 people, which means that even a dataset of 62.5 million people yields small counts for many individual conditions. The researchers used coded diagnostic criteria drawn from ICD-10 and SNOMED CT terminologies to identify cases across primary care, hospital, and mortality records, and they reported confidence intervals alongside their prevalence estimates to convey the precision of each figure. The breadth of the approach, covering 406 distinct conditions, means the resulting dataset functions as a baseline reference that clinicians, commissioners, and researchers can consult when assessing whether specific communities are being diagnosed fairly.

The implications for health equity are significant. If the prevalence of certain rare diseases is genuinely higher in particular ethnic groups, whether because of genetic ancestry, environmental exposures, or a combination of factors, then diagnostic pathways, screening programmes, and specialist services need to be designed with that distribution in mind. Conversely, if prevalence appears lower in some groups, this may signal underdiagnosis rather than true protection, a possibility that the authors suggest their findings can help interrogate. The study’s authors frame their work as providing a baseline to support earlier, fairer diagnosis and more targeted care, positioning the national map as a tool for identifying where diagnostic effort should be concentrated.

There are also important caveats that shape how the findings should be read. The cross-sectional design captures a snapshot rather than tracking individuals over time, so it cannot establish when diagnoses were made or how incidence has changed. Recorded infection status depends on testing uptake and recording practices, which themselves varied across the pandemic and across communities. Ethnicity recording in health records is imperfect, and some individuals will have missing or inconsistently coded ethnicity. The study also covers England specifically, and healthcare system differences mean the findings may not generalise directly to other countries, though the methodological framework is broadly transferable.

Nevertheless, the study stands as a landmark in the use of national-scale linked health records to address questions that smaller datasets simply cannot answer. By demonstrating that rare disease prevalence varies substantially across ethnic groups and that much of this variation is invisible within broad categories, the research makes a compelling case for finer-grained ethnicity data collection throughout health systems. As genomic medicine, newborn screening, and personalised therapies expand the possibilities for rare disease care, ensuring that these advances reach all communities equitably will depend on exactly the kind of evidence this study provides: a detailed, ethnicity-resolved accounting of who has which conditions, and how they fared during one of the most disruptive public health emergencies in recent history.

Subject of Research: Prevalence of 406 rare diseases by ethnicity and recorded COVID-19 infection rates in England

Article Title: Prevalence of 406 rare diseases by ethnicity and recorded COVID-19 infection rates among 62.5 million people in England

Article References: Gu, Q., Hasheminasab, S. A., Pineda-Moncusí, M., Chilala, C., Thygesen, J. H., Wu, H., Khalid, S., Coombe, A., & CVD-COVID-UK/COVID-IMPACT Consortium (2026). Prevalence of 406 rare diseases by ethnicity and recorded COVID-19 infection rates among 62.5 million people in England. Scientific Reports. https://doi.org/10.1038/s41598-026-70531-4

Image Credits: AI Generated

DOI: 10.1038/s41598-026-70531-4

Keywords: rare diseases, ethnicity, COVID-19, electronic health records, prevalence, health inequalities, NHS England, epidemiology, population health, health equity, discoid lupus erythematosus, data linkage