Genetic characterization of production strains of measles, rubella, and mumps viruses by high-throughput sequencing

INTRODUCTION. Spontaneous mutations often arise and accumulate in the genome of RNA-containing viruses, for example measles, rubella and mumps. Modern requirements for the production of vaccine products containing live vaccine viruses suggest control of the genetic stability of production strains. The method of high throughput sequencing allows to determine all mutations arisen in viral population, and to assess genetic stability of production strains.

AIM. Analysis of nucleotide sequence of the genomes of seed and production strains of measles (Leningrad-16), rubella (RA27/3) and mumps (Leningrad-3) viruses, in comparison with the reference nucleotide sequences of vaccine strains genomes (submitted in the Gen-Bank database).

MATERIALS AND METHODS. Production strains of vaccines (measles culture live, rubella culture live and mumps culture live) were used in this study. Whole genome sequencing was performed using the MGI DNBSEQ G-400 and Illumina NextSeq2000 genetic analyzers. When processing and analyzing the sequencing data, the following programs and tools were used: FastQC v.0.12.1, FastP v.0.23.4, BWA-MEM2 v.2.2.1, VizCoV tool.

RESULTS. Analysis of single nucleotide polymorphisms (SNPs) within the viral population in the studied samples revealed a number of minor variants that, and after further accumulation, may lead to changes in the consensus sequences of the vaccine strains proteins. For the studied measles virus samples, no SNPs were found in the main measles virus antigen H protein, however, a nonsynonymous polymorphism was detected in the F protein, occurring in 30.0–40.9% of the viral genomes. SNPs were found in the capsid protein C and in the surface glycoprotein E2 rubella virus, occurring in the viral population with a frequency of up to 30%. SNPs were found in surface antigens hemagglutinin neuraminidase HN and fusion protein F of mumps virus, occurring in the genomes of less than 20% of viral population. Mutations in the genomes of production strains that could affect the immunogenicity of measles, rubella, and mumps vaccines were not detected.

CONCLUSIONS. The identified set of minor variants with a frequency of occurrence in viral population of more than 10%, which, with further accumulation, can lead to changes in the consensus sequences of vaccine strains, makes the monitoring of vaccine strains stability using high-throughput sequencing relevant.

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