First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing.

Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189-3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2) and Azerbaijan (n = 1), the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment

BootScan plot of percentage permuted trees over nucleotide position across the full length of one of the HCV 2k/1b recombinant strains.

<p>Different colors represent sequences of different genotypes/subtypes.</p

BootScan plot of percentage permuted trees over nucleotide position across the full length of one of the HCV 2k/1b recombinant strains.

<p>Different colors represent sequences of different genotypes/subtypes.</p

Phylogenetic analysis of the 5'UTR through NS1/p7.

<p>Maximum Likelihood tree constructed using MEGA 6.0 using the GTR model of evolution, incorporating assumed rate heterogeneity (Γ, gamma) across sites and invariant sites (I). The four patient samples S1-S4 clustered most closely with genotype 2 and subtype 2k.</p

Phylogenetic analysis of the NS3 through NS5B genes.

<p>The Maximum Likelihood tree was constructed using MEGA 6.0 using the GTR model of evolution, incorporating assumed rate heterogeneity (Γ, gamma) across sites and invariant sites (I). The four patient samples S1-S4 clustered most closely with genotype 1 and subtype 1b.</p