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.

Hepatitis C virus genetic variability and evolution

“…NGS approaches are powerful methods that allow a rather comprehensive analysis of the intra-host viral genetic variation [107] . Moreover, these technologies are becoming rapidly accessible all around the world which will likely revolutionise the field of molecular epidemiology [110] . It is worth mentioning that these technologies offer, as already discussed, several advantages over conventional methods, such as consensus sequencing, bacterial cloning, and endpoint limiting dilution [107] .…”

“…It is worth mentioning that these technologies offer, as already discussed, several advantages over conventional methods, such as consensus sequencing, bacterial cloning, and endpoint limiting dilution [107] . Furthermore, as the development of a variety of software and algorithms capable of handling the massive amount of data generated by NGS platforms is increasing in parallel with the advances in these technologies, it will likely expedite the implementation of such approaches in a variety of settings in the near future [110] . Taking this into consideration, the use of NGS in HCV outbreak investigations will presumably improve molecular epidemiology studies as well as provide a vast amount of information that will need to be handled appropriately both for the benefit of infected patients and the management of public health systems.…”

“…In addition, NGS technology has already been implemented in order to study the transmission event of HCV among injection drug users. In this case NGS was used to determine intra-host viral genetic variation by deep sequencing the HCV hypervariable region, which allowed a detailed analysis of the structure of the viral quasispecies in the patients' population under study [110] . NGS approaches are powerful methods that allow a rather comprehensive analysis of the intra-host viral genetic variation [107] .…”

Rapid Hepatitis C Virus Divergence among Chronically Infected Individuals

“…The HCV mutation rate has been estimated to be 2.5 ϫ 10 5 mutations per nucleotide per genome replication (6). This characteristic high mutation rate is consistent with the high degree of intrahost genetic diversity commonly observed among infected individuals (7,8). The high degree of genetic variability allows rapid evolution that ultimately favors escape from immune and antiviral drug pressures (9,10).…”

“…Different HCV subgenomic regions exhibit different degrees of variability (13). As a consequence, several regions of the viral genome have been used for molecular studies (7,14,15). However, the HCV hypervariable region 1 (HVR1) of the envelope (E) 2 gene has been the region of choice to conduct relatedness studies due to its greater variability (16).…”