Molecular insights into measles virus diversity in Ethiopia
PhD candidate: Eleni Kidane
Institution: Heinrich Heine University Düsseldorf, Germany (in collaboration with Ethiopian Public Health Institute (EPHI) and EpiGen-Ethiopia project)
Supervisors: Alexander Dilthey; Torsten Feldt; Anna Rommerskirchen
This PhD project investigates the genetic diversity and molecular epidemiology of measles virus (MeV) circulating in Ethiopia using genomic surveillance approaches. Despite the availability of an effective vaccine, measles remains a major public health problem in Ethiopia, with recurrent outbreaks linked to suboptimal vaccination coverage, population susceptibility, and ongoing transmission. These outbreaks continue to cause significant morbidity and mortality, highlighting gaps in current surveillance and outbreak response systems.
The study focuses on MeV strains collected from suspected and confirmed outbreak cases across Ethiopia through Integrated Disease Surveillance and Response (IDSR) sites. Clinical nasopharyngeal/throat swab samples will be analyzed using an amplicon-based approach on Oxford Nanopore or Illumina platforms. This will enable identification of circulating genotypes, their geographic distribution, and temporal dynamics across outbreaks.
A key objective is to characterize viral genetic variation, including mutations in antigenic regions that may affect transmission, immune escape, and vaccine effectiveness. Sequencing data will be processed using established bioinformatics pipelines for quality control, genome assembly, variant calling, and phylogenetic analysis, enabling comparison of Ethiopian MeV strains with global reference datasets.
The project also evaluates the feasibility of implementing genomic surveillance for measles in low-resource settings by integrating sequencing data with epidemiological and vaccination information collected through digital surveillance systems. This includes assessing outbreak drivers such as vaccine breakthrough infections, immunity gaps, and population-level risk factors.
The expected outcome is a detailed understanding of measles virus diversity in Ethiopia, including circulating genotypes and clinically relevant mutations. The findings will strengthen molecular surveillance capacity, inform outbreak response strategies, and support improvements in vaccination policy and measles elimination efforts in Ethiopia and similar resource-limited settings.