Genetic characteristic analysis on 33 strains of rubella virus isolated in Chaoyang district of Beijing, 2012–2016

Objective To identify the genotype and the genetic characteristics of rubella virus isolated from throat swabs of suspected rubella cases in Chaoyang district of Beijing during 2012–2016.

Methods Vero/SLAM cells were used to isolate rubella viruses from throat swabs collected from rubella cases in rubella outbreak and sporadic cases in Chaoyang during this period. The fragments of E1 genes of the isolates were amplified by RT-PCR and then the PCR products were directly sequenced and analyzed. The phylogenetic tree based on the 739 nucleotide sequences of E1 genes were conducted using the rubella virus strains isolated in Chaoyang and 32 WHO reference strain sequences representing 13 genotypes, another phylogenetic tree was also conducted with the 33 rubella virus strains isolated in Chaoyang and 16 rubella virus strains isolated in other provinces in China for the multiple sequence comparison.

Results A total of 33 strains of rubella virus strains were isolated, which belonged to two different genotypes, i.e. 1E (8 strains) and 2B (25 strains). The genotype 1E strains were detected during 2012–2013, and the genotype 2B strains were detected during 2012–2016. The intra and inter genetic distance of genotype 2B strains were less than those of genotype 1E strains.

Conclusion Two genotypes of rubella virus (1E and 2B) were detected in Chaoyang during 2012–2016. The nucleotide sequence of genotype 2B strain was more stable and genotype 2B strain has gradually become predominant.