Genetic diversity and evolution of the measles virus in Uganda (2011-2023) based on the haemagglutinin gene and matrix fusion non-coding region

Abstract

Measles is a highly contagious viral disease that remains a leading cause of childhood illness and death globally. Recent treatment advances exist, but sporadic outbreaks still occur due to factors like low vaccination rates, vaccine hesitancy, incomplete doses, and occasional vaccine ineffectiveness. This study employed Sanger sequencing technology to establish the measles virus diversity and evolution, focusing on the Matrix/Fusion-noncoding region (MF-NCR) and the hemagglutinin (H) gene, which have been demonstrated to have superior variability in contrast to the routinely used Nucleocapsid (N-450) gene. 245 samples that matched the inclusion criteria were screened for measles virus by qRT-PCR. One hundred twenty-nine Measles virus sequences (66 H gene, 63 MF-NCR) were generated from these samples, which had been collected from 29 districts during the period 2011-2023. Fifty-nine samples from 24 districts yielded Measles virus sequences for both the H gene and MF-NCR. All the study samples belonged to the B3 genotype and subgroups were seen within all 5 major clusters based on the H gene and MF-NCR. The MF-NCR showed a higher nucleotide variability of 3.3448×10⁻⁴ substitutions/site/year compared to the H gene that had 1.5521×10⁻⁴ substitutions/site/year. Fifty-two non-synonymous mutations were seen in the H gene of the study sequences, with 11 [R195I, N200D, S240N, K295R, G316S, E395G, N396D, A400V, G546S, D574N, Q575K] linked to epitope binding sites, and possibly contributing to vaccine ineffectiveness, especially those seen in the vaccinated but diseased population. Overall, these findings show that the H gene and MF-NCR can complement the routinely obtained N gene data in epidemiological classification and highlight major mutations at antigenic sites that need to further scrutiny to confirm if vaccine antibodies failed to neutralize the Measles virus due to detected mutations.