Tracking the phylogenetic profile of the MF-non-coding region of measles virus

Introduction: The highly variable non-coding region (NCR) between the matrix (M) and fusion (F) protein coding sequences (MF-NCR) has been proposed as a novel target for measles virus (MeV) molecular characterization and has been linked with cytopathogenicity and modulation of M and F protein expression. This study aimed to further characterize the MF-NCR of the four MeV genotypes (B3, D4, D8, and H1) that were most widely distributed before the COVID-19 pandemic, across different locations and collection periods, using phylogenetic analysis.Methods: Maximum likelihood phylogenetic analysis was performed using Phyml and average evolutionary divergence was estimated using MEGA X. Maximum likelihood analysis combined with genetic distance calculations provided information for understanding the evolutionary dynamics and genetic diversity of the MF-NCR of MeV.Results: Phylogenetic analysis highlighted a higher number of supported internal clusters in MeV genotype H1, followed by D8, B3 and finally by D4. Intermixing was detected both among different locations and years of collection. The MF-NCR of MeV genotype D8 had the highest proportion of variable sites (47%), followed by B3 (31.8%), H1 (29%), and D4 (13.4%). The estimates of the average evolutionary divergences showed that the MF-NCR of MeV genotypes D8, B3 and H1 have higher variability (3%) compared to MF-NCR of MeV genotype D4 (1%).Conclusions: In conclusion, this study provides a comprehensive overview of the evolution of the MF-NCR and its clustering. It highlights changes in sequence variability across the most prevalent genotypes, as well as across different locations and over time.