Molecular identification and characterization of measles virus genotypes circulating in Afghanistan, 2008–2018

The measles virus (MV) remains a leading cause of morbidity and mortality in children under 5 years of age. Molecular identification of circulating wild‐type MV) strains is a vital component of the measles elimination program. We received 159 oral swab samples from Afghanistan during 2008–2018. Viral RNA was extracted, followed by one‐step RT‐PCR and positive amplicons were subject to sequencing for genotype identification. Out of 159 total samples, 52% (83/159) were detected positive by RT‐PCR. Genotype D4 was identified from 2.4% (2/83), genotype H1, 4.8% (4/83), and genotype B3, 92.7% (77/83) cases, respectively. Highlights Molecular surveillance of the Measles virus is an essential tool for the elimination program. Current molecular surveillance of the measles virus is based on 450 nucleotides of the N gene. Molecular characterization of the Measles virus is efficient and useful to distinguish the chain of transmission of the measles virus.