M-F noncoding region sequences of H1 genotype measles virus provide higher resolution for virus transmission tracing

As countries and regions move toward measles elimination, extended sequence window including noncoding region located between the matrix and fusion protein genes (M-F NCR) was considered to be used in molecular surveillance. The molecular resolution of M-F NCR was evaluated with 192 genotype H1 strains circulating during 2011-2018 in China. Phylogenetic analyses of the N450 and M-F NCR targets indicated that both two targets could confirm epi-linked outbreak, while M-F NCR target could further improve resolution of the molecular characterization: (1) it could differentiate the strains with identical N450 circulated in one county within one month of disease onset; (2) different transmission chains could be distinguished for strains with identical N450; (3) better spatial-temporal consistency with topology could be provided among sporadic cases with inconsistent N450. Accordingly, M-F NCR could be used to complement the information from N450 to address the specific questions in tracking the virus transmission chains.