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 more than 146,000 cases and 1200 deaths, primarily among children under 15 years of age. This epidemic occurred in a context of low vaccination coverage. Prior to this outbreak, no genotyping data were available for the measles virus (MeV) or rubella virus (RuV) in 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 cases with a mean age of 11.4 years. Viral detection was performed using real-time RT-PCR, followed by conventional RT-PCR and sequencing of the N and H genes for MeV and of the E1 gene for RuV. Co-circulation of the two viruses was observed, with positivity 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 showed that all MeV strains belonged to genotype [B3], and they were highly similar to strains circulating globally in 2018–2019, suggesting recent introduction. In contrast, all RuV strains belonged to genotype [2B] and displayed greater genetic diversity, consistent with endemic rubella circulation 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.