Clinical and genomic epidemiology of Rubella virus in India – a retrospective study

Rubella virus (RuV) causes rubella, which usually occurs in children and young adults. Rubella virus is classified into two clades: Clade 1 includes 10 genotypes (1a, 1B, 1 C, 1D, 1E, 1 F, 1 G, 1H, 1I, and 1 J) and Clade 2 includes three genotypes (2 A, 2B, and 2 C). The molecular epidemiology of the Rubella virus provides valuable insights into the virus’s transmission patterns, which are crucial for tailoring targeted control efforts. The present study aims to perform the genotyping and phylogenetic analysis of the Rubella virus between 2016 and 2018, using modified Sanger sequencing. A retrospective study was conducted using archived rubella-positive throat swab samples collected between 2016 and 2018 with Ct value ≤36 by using conventional RT-PCR, followed by modified Sanger sequencing. Phylogenetic and functional studies were carried out for the sequenced region. Clinical data analysis was done using Microsoft Excel and SPSS Statistics software. The nine rubella-positive samples that were sequenced belonged to genotype 2B. Phylogenetic analysis indicated that the study strains clustered with the strain from China. Clinical data analysis revealed the age shift of rubella cases along with atypical presentation. The current study reports the circulation of rubella genotype 2B in India from 2016 to 2018. This data aids in improving knowledge of the rubella burden and dynamics of the virus circulation in India. A large-scale, prospective, population-based multicentric study is essential to monitor the current molecular epidemiology of rubella in India.