Abstract
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.
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