Optimization and application of subtype specific polymerase chain reaction for detection and identification of mixed subtypes of hepatitis C virus in patients with renal disease

The main objective of the study is to optimize a subtype specific polymerase chain reaction (PCR) for identification of hepatitis C virus (HCV) subtypes in patients with renal disease. Thirty two peripheral blood specimens obtained from 28 patients (post renal transplant N = 14, chronic kidney disease N = 14) were subjected to HCV viral load determination followed by genotyping analysis. Based on the mixed genotypes and subtypes (>one subtype) obtained by type specific PCR, specific patterns from Pattern I through Pattern X were assigned. All the 32 peripheral blood specimens revealed mixed HCV subtype patterns (>one subtype). The detection of Pattern I in 12 (42.8%) out of 28 patients was statistically significant (Chi square test, P value < 0.001). HCV subtyping assay developed using stringent thermal profile revealed the presence of mixed subtype patterns (>one subtype) which is for the first time being reported in literature.

► Optimization of PCR to identify mixed HCV subtypes. ► A novel methodology developed to identify mixed HCV genotypes. ► Mixed HCV subtypes (more than five subtypes) are described. ► HCV genotypes 1, 2 and 3 were detected in all the specimens.