A preliminary molecular snapshot of measles virus genotypes circulating in Rabat, Morocco, during 2024-2025

Abstract

<title>Abstract</title> Background Measles remains a major public health challenge globally, particularly in regions with low vaccination coverage. Since late 2023, Morocco has experienced renewed measles virus (MeV) circulation, but genomic data on the responsible strains remain scarce. Methods We analyzed 25 RT-PCR confirmed measles cases admitted to the Virology and Infectious and Tropical Diseases Center of the Mohammed V Military Teaching Hospital in Rabat between 2024 and early 2025. The WHO-recommended 450-nt C-terminal region of the nucleoprotein gene (N-450) was sequenced and compared with reference MeV strain and contemporaneous international sequences. Results Compared with previous reports from Morocco, this study provides the first molecular documentation of the 2024–2025 epidemic and reveals limited intra-genotype diversification. Phylogenetic analysis showed that 24 of 25 Moroccan strains belonged to genotype B3, confirming it as the dominant lineage during the recent epidemic wave. Within B3, 23 sequences formed a single, well-supported Moroccan cluster with minor sub-grouping, consistent with sustained local transmission. These sequences showed very high nucleotide similarity (99.69–99.83%) to the locally obtained genome MVi/Rabat.MAR/29.24/[B3], which was itself closely related to MVs/Virginia.USA/35.21/[B3], indicating that the epidemic strain circulating in Morocco is part of broader international B3 circulation. One B3 sequence, MVs/Rabat.MAR/33.24/, branched outside the main Moroccan cluster and was closer to a French 2016 strain, pointing to occasional, independent introductions. A single strain 1 of 25 was classified as genotype D8 and showed 100% identity with MVs/Kobe.JPN/31.24/157, strongly suggesting a recent importation rather than local diversification. This study confirms B3 as the main MeV lineage currently circulating in Rabat and highlights the need to maintain routine N-450, and where feasible whole-genome, sequencing to detect introductions and monitor microevolution. Conclusion The findings underscore the urgency of strengthening genomic surveillance nationally and expanding epidemiological metadata collection to better track transmission chains and assess the public health implications of emerging substitutions.