Genetic characteristics of nucleoprotein of the epidemic measles virus in Xi’an, 2013-2017

Objective To know the genetic characteristics of nucleoprotein(N)of wild type measles virus in Xi’an, 2013-2017. Methods We used the pharyngeal swab specimens of suspected measles cases which were tested positive for measles virus (MV) nucleic acid by Real-time RT-PCR to isolate MV strains with Vero-SLAM cells, extracted RNA of the strains, amplified the N genes of MV strains and the pharyngeal swab specimens which had lower Ct values by One-Step RT-PCR, and analyzed the result after sequencing. Results Thirty carboxyl terminal sequences of the N genes of MV endemic strains were obtained and identified as genotype H1a. The nucleotide and amino acid homology among the epidemic strains were 97.3%-100% and 96.7%-100%, among the epidemic strains and S191 were 91.3%-92.2% and 87.3%-90.0%, while among the epidemic strains and C47 were 92.2%-92.7% and 88.0%-90.7%. The nucleotide homology among the epidemic strains and wild strains of same period in Anhui, Gansu, Shandong, Henan, Jilin were higher than that in Shanxi, Sichuan, Hunan and Guangdong. The most different amino acid sites among the epidemic strains and the two vaccine strains which had high level of entropy were 422, 457 and 497, secondly 467, thirdly 500. The mutations at the 467 site only existed in 2017. dN/dS=0.199 and no positive selection site was found. Conclusions The dominant genotype of the epidemic MV strains in Xi’an was H1a in 2013-2017, the genetic diversity of viruses decreased in 2016-2017. We should strengthen the surveillance of etiology of MV to provide evidence for elimination of measles. Key words: Measles Virus; Nucleoprotein; Genetic variation