Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2013

Hepatitis C Virus genotyping testing in Western Australia using nucleic acid sequencing and a commercial line probe assay (#278)

Ian D Kay 1 , Todd M Pryce 1 , Justin P Morgan 1 , James P Flexman 1

 Introduction of antivirals specific for Hepatitis C virus (HCV), and genotypes has renewed focus on the accuracy of genotyping.Some genotypes can be misclassified when sequencing the 5’untranslated region (5’ UTR).There is the need to subtype genotype 1 for clinical trials,which again is unreliable when sequencing only the 5’ UTR.Sub-typing genotype 1 can be performed using the VERSANT HCV Genotype Assay 2.0 (LiPA).This test can help distinguish between genotypes 1 and 6 common in Asia.This study reports the genotypes for 6745 samples screened between 2006-11 using 5’ UTR.We compare this data to 992 samples recently tested (2012) using 5’ UTR with the LiPA method on all 5’ UTR genotype 1 samples.Using this approach, we were able to subtype genotype 1 samples and detect 5’ UTR genotype 1 samples that were genotype 6.Between 2006-2011 the genotypes detected by 5’NCR were genotype 1 (52.7%),2 (3.5%),3 (38.9%) 4 (1.3%),5 (0.07%),6 (0.6%),10 (0.04%) and unable to be genotyped (2.8%).For the 2012 period, the genotypes detected by 5’NCR and sub-typed by LiPA were: genotype 1 (58.3%) comprising of 1a (44.9%) and 1b (10.5%), 1a/1b genotype 6 unable to be excluded (1.6%), 1/genotype 6 unable to be excluded (1.3%), 2 (2.7%), 3 (36.6%) 4 (0.9%), 5 (0.1%), 6 (2.0%) and unable to be genotyped (2.3%).These samples reported as genotype 6 (n=20), 9 were genotype 6 detected by 5’NCR (0.9%) and 11 were 5’NCR genotype 1 samples that were subsequently identified as genotype 6 by the LiPA assay (1.1%). 
The combined assay approach is useful to screen for genotype 3 using 5’NCR (35-39%) and sub-type genotype 1a/1b.We identified some genotype 6 samples that would have been reported as genotype 1 using 5’NCR.The ability to accurately distinguish between some genotypes and sub-types of HCV genotype 1 has assisted in identifying patients for specific clinical trials and for treatment with targeted antiviral therapy