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

Jinhua Song; Zhen Zhu; Huiling Wang; Manli Hu; Baicheng Xia; Yan Zhang

doi:10.1016/j.virol.2024.110104

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

Virology. 2024 May 10:596:110104. doi: 10.1016/j.virol.2024.110104. Online ahead of print.

Authors

Jinhua Song¹, Zhen Zhu¹, Huiling Wang¹, Manli Hu¹, Baicheng Xia¹, Yan Zhang²

Affiliations

¹ WHO Western Pacific Regional Measles/Rubella Reference Laboratory, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
² WHO Western Pacific Regional Measles/Rubella Reference Laboratory, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. Electronic address: zhangyan@ivdc.chinacdc.cn.

PMID: 38761640
DOI: 10.1016/j.virol.2024.110104

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.

Keywords: M-F NCR; Measles elimination; Measles virus.