Identification of hepatitis C virus transmission using a next-generation sequencing approach

Abstract

Here, we describe a transmission event of hepatitis C virus (HCV) among injection drug users. Next-generation sequencing (NGS) was used to assess the intrahost viral genetic variation. Deep amplicon sequencing of HCV hypervariable region 1 allowed for a detailed analysis of the structure of the viral population. Establishment of the genetic relatedness between cases was accomplished by phylogenetic analysis. NGS is a powerful tool with applications in molecular epidemiology studies and outbreak investigations.

Fig 1

Phylogenetic analysis. Genetic distances (Kimura 2-parameter) were used to conduct the corresponding phylogenetic analysis (neighbor-joining method) of HCV HVR-1 sequences from all HCV cases studied. Sequences from related cases are color coded (patient A, light gray; patient B, dark gray) and magnified in the window in the lower left corner. Unrelated local HCV cases are indicated by solid black lines. HVR-1 sequences from the Los Alamos National Laboratory HCV database are shown in black discontinuous lines.