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.

Identification of HCV transmission is of critical importance in implementing measures aimed at preventing virus spread. HCV transmission networks are difficult to identify for several reasons. First, acute HCV infections are usually asymptomatic; therefore, establishing when a transmission event has occurred is rather challenging. Second, the lack of laboratory tests capable of distinguishing acute from chronic infections further complicates the identification of related cases. Finally, the characteristically long incubation periods among symptomatic cases make difficult to link related cases to a common source of infection. In addition, molecular approaches required to assess the intrahost viral genetic variation are quite sophisticated, time-consuming, and expensive

Thus, straightforward, inexpensive platforms suitable for molecular epidemiology studies are much needed. Next-generation sequencing (NGS) allows for cost-effective probing of virus populations at an unprecedented level of detail. The massively parallel sequencing approach can detect low-frequency mutations, providing a snapshot of the entire virus population, which makes it a viable alternative to other conventional methodologies

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Regards,
Lucy Morgan
Editorial Coordinator
Journal of Next Generation Sequencing & Applications
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