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Rubella RNA was detected in 41 samples from 26 infants by both real\u2010time and block based PCR. The PCR results correlated well with the presence of anti\u2010rubella IgM\/IgG (23\/27 cases with rubella IgM were PCR positive). Whereas, only 17 of 26 infants met the WHO CRS case definition. Amongst the various specimens tested from the sero\u2010confirmed cases (n\u2009=\u200927), a high percentage of positives were detected in lens (92%) and oral fluid (60%) specimens, when compared to other samples. The quantification of viral load by real\u2010time PCR demonstrated higher copy number of virus in lens samples of 0\u201311 months infants. The rubella viruses were characterized and revealed the circulation of genotype 2B in three South Indian states. The integrated analysis of clinical manifestations, serological and molecular data in the study has generated baseline information of rubella infection and CRS in infants with ocular anomalies. J. Med. 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