Molecular Characterization of Measles and Rubella Virus Strains from the 2018–2019 Epidemic in Madagascar

Madagascar experienced a severe measles epidemic between September 2018 and mid-2019, resulting in over 146,000 cases and 1,200 deaths, primarily among children under 15. This epidemic occurred in a context of low vaccination coverage. Prior to this epidemic, no genotyping data for the measles virus (MeV) or rubella virus (RuV) were available for Madagascar. This study aimed to molecularly characterize MeV and RuV strains circulating during the epidemic. A total of 310 biological samples (gingival swabs, urine, and stool) were collected from 288 suspected patients with a mean age of 11.4 years. Viral detection was performed by real-time RT-PCR, followed by conventional RT-PCR and sequencing for genotyping of the N and H genes of MeV and the E1 gene of RuV. The results revealed co-circulation of the two viruses, with detection rates of 39.9% (115/288) for MeV and 40.0% (70/175) for RuV. The mean age differed significantly between MeV-positive (12.0 years) and RuV-positive (7.2 years) patients, with 35.1% and 43.8% of cases occurring in children under five years of age, respectively. Phylogenetic analysis identified all MeV strains as belonging to genotype B3, showing high similarity to strains circulating globally in 2018-2019, suggesting recent importation. Meanwhile, the phylogenetic profile of RuV strains, all belonging to genotype 2B and displaying greater genetic diversity, was characteristic of endemic rubella in a partially vaccinated or unvaccinated population. This study provides the first genotyping data for Madagascar, essential for monitoring virus circulation and supporting elimination efforts in the African region.