Measles Virus Genotypes Causing Outbreaks in Tanzania, 2022-2024

Globally, 24 measles virus genotypes have been detected, and these genotypes have been classified into eight clades based on 450 nucleotides of the C-terminal region of the nucleoprotein gene. Genotype B3 is predominant in Africa, but there are limited data from Tanzania since the introduction of the second dose of measles-containing vaccine in 2014. A total of 129 nasopharyngeal samples and corresponding sera were collected during measles outbreaks between 2022 and 2024. Viral RNA was extracted from nasopharyngeal swabs prior to RT-qPCR and sequencing of a 450-nucleotide segment of the nucleoprotein (N) gene. Out of 129 nasopharyngeal samples, 73 (56%) were successfully amplified and identified as endemic measles virus genotype B3. Nine distinct sequence identifiers were detected, with seven reported for the first time in the MeaNS database. All the Tanzanian B3 sequences were closely related and clustered with genotype B3, similar to those reported from Kenya, Ethiopia, Rwanda, Uganda, Burundi, and South Africa. On multivariate analysis, only inpatient admission status (p = 0.014) and positive measles IgM (p = 0.003) were found to be associated with positive measles RT-qPCR. Our results indicate that genotype B3 remains endemic in Tanzania and is closely related to other genotype B3 reported globally, indicating its high stability and transmissibility.