Analysis for nucleoprotein gene of measles virus strains isolated in Huangpu district of Shanghai, 2013-2016

Abstract

Objective To analyze the molecular characteristics of nucleoprotein genes of measles virus strains isolated from 2013 to 2016 in Huangpu district, Shanghai. Methods A total of 72 suspected measles cases were collected by Huangpu district measles network laboratory from 2013 to 2016. Measles virus isolation was performed using Vero/hSLAM cells. The positive isolations of measles virus strains were confirmed by real-time RT-PCR and was amplified by RT-PCR for a 450 bp-segment in N gene. The PCR products were sequenced for gene characterization. Results Of the 72 suspected measles cases, 40 viral strains were isolated. Among the 40 confirmed measles cases, 23 were males (57.5%) and 17 were females (42.5%). The mean and standard deviation of age were 19.07±16.52 years old. The phylogenetic analysis showed that 39 strains belonged to H1a sub-genotype and formed obviously two branches. The other one strain belonged to genotype B3. The nucleotide and amino acid divergences between 39 strains of H1a measles virus and reference strain of H1 genotype, MVi/Hunan CHN/0.93/7 (AF045212), were 0.0%-2.2% and 0.0%-3.4%, respectively. The nucleotide and amino acid similarity among 39 strains H1a genotype were 97.8%-100.0% and 96.6%-100.0% respectively. Conclusions H1a sub-genotype was predominant in Shanghai in 2013-2016. There existed different chains of transmission in one year. Measles strains were highly conserved in nucleic acid and amino acid sequences. No variation of important functional sites was observed. Key words: Measles virus; Nucleoproteins; Genotype; Sequence analysis