Impact of the COVID-19 pandemic on reported malaria incidence in children under five years of age in Cameroon: an interrupted time series analysis with regional heterogeneity (2017–2022)

Malaria remains a major cause of childhood morbidity and mortality in Cameroon. The COVID-19 pandemic disrupted access to healthcare and the continuity of malaria control programmes; however, its impact on reported incidence among children under 5 years of age, and its regional heterogeneity, remain insufficiently studied. We aimed to estimate the impact of the COVID-19-related interruption on reported malaria incidence among children under five years of age in Cameroon, nationally and by region, using routine DHIS2 surveillance data from 2017 to 2022. We conducted an interrupted time series (ITS) study using monthly DHIS2 data from January 2017 to December 2022. Reported malaria incidence among children under 5 years of age was modelled using negative binomial regression (NB2) with a population offset. Two interruption points were defined a priori: March 2020 and January 2022. The model controlled for monthly fixed effects, long-lasting insecticidal net (LLIN) distribution activity, seasonal malaria chemoprevention (SMC) activity, the paediatric consultation rate, and one-month lagged rainfall. Inference relied on Newey–West HAC-robust standard errors (lag = 12). Regional ITS models, counterfactual analysis, and sensitivity analyses complemented the primary analysis. In March 2020, reported incidence showed an immediate 36.9% decline relative to the pre-pandemic trend (D1: IRR = 0.631; 95% CI 0.539–0.738; p < 0.001), followed by a positive slope change of 3.1% per month (P1: IRR = 1.031; 95% CI 1.017–1.045; p < 0.001). The second interruption point was not associated with any significant change in level or slope. The LLIN distribution indicator was inversely associated with reported incidence (IRR = 0.978; 95% CI 0.960–0.997; p = 0.024). Counterfactual analysis estimated a deficit of 69,708 notifications over 2020–2021, followed by an excess of 74,831 in 2022. Marked regional heterogeneity was observed, with particularly severe initial declines in the Centre (IRR = 0.467) and East (IRR = 0.544) regions. The COVID-19 pandemic was associated with a substantial initial disruption in reported childhood malaria incidence in Cameroon, followed by a progressive recovery with marked territorial disparities. These findings support strengthening the continuity of malaria services during crises and maintaining high-quality surveillance systems to enable regionally tailored programmatic decision-making.