Genomic epidemiology of invasive meningococcal disease in Scotland before, during, and after the COVID-19 pandemic: a retrospective observational study

Abstract

Background Invasive meningococcal disease (IMD) remains a major global health threat. Despite vaccination,
meningococcal genetic diversity means disease, including epidemics at various scales, still occurs unpredictably,
highlighting the need for real-time genomic surveillance. The COVID-19 pandemic reduced invasive respiratory
diseases, but its effect on IMD distribution remains unassessed. We aimed to investigate the effect of the COVID-19
pandemic and consequent social restrictions on genomic and demographic characteristics of IMD in Scotland to
inform public health policy.
Methods In this retrospective, observational analysis, we used genomic and epidemiological surveillance data of cases
of IMD reported in Scotland between July 1, 2009, and April 20, 2026. Genomic data (from whole genome
characterisation of culture-confirmed IMD cases) were obtained from the public databases for molecular typing and
microbial genome diversity (PubMLST) and demographic data were obtained from the Meningococcal Invasive
Disease Augmented Surveillance database. The pre-COVID-19 period was defined as July 1, 2009, to March 23, 2020,
the COVID-19 period was March 24, 2020, to March 18, 2022, and the post-COVID-19 period was March 19, 2022, to
April 20, 2026. A total of 27 binary outcomes derived from the genomic and demographic variables were prespecified
before model fitting. We assessed associations with interrupted time-series analyses to establish changes related to
the COVID-19 pandemic.
Findings Between July 1, 2009, and April 20, 2026, 1143 IMD cases were reported in Scotland. Of these, 512 (44·8%)
were culture-confirmed cases with a corresponding meningococcal genome. High-risk groups (including children
aged <1 year, children aged 1–4 years, adolescents and young adults aged 15–24 years, and people aged 65 years or
older) were affected across all time periods with no demographic changes associated with the COVID-19 pandemic.
Of the 27 genomic and demographic variables analysed, six showed changes in their contribution to IMD between the
pre-COVID-19 and COVID-19 periods. During the COVID-19 period, the contributions of genogroup B and MenB
FHbp-preventable status to IMD both increased and the contributions of genogroups W and C, clonal complex 11,
and polysaccharide-preventable status all decreased.
Interpretation The COVID-19 pandemic was associated with changes in IMD capsular distribution in Scotland,
concomitant with a decline in clonal complex 11. In 2025–26, 4 years after physical restrictions eased, genogroup and
lineages returned towards pre-COVID-19 patterns, from a new baseline, expected with a host-associated pathogen
causing human disease. Age, sex, and deprivation status did not differ over time, highlighting that ongoing efforts are
needed to deploy vaccinations to protect high-risk groups based on data from integrated genomic epidemiological
surveillance and cost-effectiveness evaluation.

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© Public Health Scotland 2026

This publication is licenced for re-use under the Open Government Licence v3.0. For more information visit publichealthscotland.scot/ogl

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DOI

https://doi.org/10.1016/S1473-3099(26)00284-7