Analysis of hepatitis C virus sequence quasi species by NGS

丙型肝炎病毒（HCV）由于RNA聚合酶保真度低和病毒复制率高，基因组中积累了大量的核苷酸替换。这种准种性质被认为有助于其发病机制或病毒逃逸。我们构建了一种结合下一代测序和毛细管测序从患者血清中确定全长病毒基因组RNA种类的方法。我们发现独立的优势种共存于一个病人的血清。与干扰素敏感性的有利应答相关的多态性被收集到一个物种中。顺序种形成相同的聚类。因此，我们认为这两个物种可能是混合物，并在患者感染时的瓶颈事件中幸存下来，然后在患者中单独进化。总之，我们的研究表明，考虑患者血清中的每个全长物种对于理解HCV生命周期是重要的。

Hepatitis C Virus (HCV) genome accumulates nucleotide substitutions because of low viral RNA polymerase fidelity and high viral replication ratio. This quasispecies nature has been considered to contribute for its pathogenesis or viral escape. We constructed a method to determine the full-length viral genome RNA species from patient serum combined next-generation sequencing and capillary sequencing. We found independent dominant species co-existed in one patient serum. Polymorphisms related to the favorable response of interferon sensitivity were gathered into one species. Sequential species were formed same clusters. We thus considered that both species might have been mixture and survived the bottleneck events when the patient was infected, and then evolved individually in the patient. In conclusion, our study demonstrated that considering each full-length species in patient serum is important for understanding HCV life cycle.