Molecular epidemiology and phylogenetic insights into measles virus in Malaysia, 2018–2024

Measles remains a public health concern in Malaysia despite high reported vaccine coverage. Molecular surveillance is essential to distinguish endemic persistence from repeated importations and to identify immunity gaps. This study characterized the molecular epidemiology of measles virus (MeV) circulating in Malaysia from 2018 to 2024 and assessed whether the observed molecular patterns were compatible with endemic persistence or repeated introductions. A total of 1,110 MeV sequences collected nationwide between 2018 and 2024 from routine surveillance and outbreak investigations were analysed alongside 28 World Health Organization reference strains. Partial N-gene (N450) sequences were genotyped using the WHO classification framework. Temporal genotype trends were assessed using logistic regression, genotype distributions were compared using χ² tests, and phylogenetic analyses were performed using the Nextstrain Augur pipeline. Vaccination status and demographic metadata were examined to identify epidemiological patterns. Genotype D8 predominated throughout the study period (94%, n = 1,043), followed by B3 (4%) and genotype A (vaccine-associated) accounted for 2% of detections. Phylogenetic and molecular clock analyses showed that D8 sequences formed a highly conserved lineage (99.2–99.9% nucleotide identity). The presence of multiple phylogenetic distinct clusters across the study period was compatible with repeated introductions followed by local amplification. The odds of D8 detection increased nearly fourfold per year ( p < 0.0001). Within the sequenced dataset, D8 was first detected in Terengganu in 2018, with increased representation in Sabah during 2023–2024 and phylogeographic patterns compatible with inter-regional spread involving Sabah and Peninsular Malaysia. Most cases occurred among unvaccinated children and adolescents, while 29% of sequenced cases occurred in previously vaccinated individuals. MeV genotype D8 predominated in Malaysia from 2018 to 2024. The observed molecular and phylogenetic patterns were compatible with repeated introductions followed by local amplification, although uninterrupted low-level domestic transmission could not be excluded. Not applicable.