Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan.
PLoS One. 2013 Sep 17;8(9):e73615. doi: 10.1371/journal.pone.0073615. eCollection 2013.
Hepatitis C virus (HCV) subgenotypes 1a and 1b have different impacts on the treatment response to peginterferon plus ribavirin with direct-acting antivirals (DAAs) against patients infected with HCV genotype 1, as the emergence rates of resistance mutations are different between these two subgenotypes. In Japan, almost all of HCV genotype 1 belongs to subgenotype 1b.
To determine HCV subgenotype 1a or 1b in Japanese patients infected with HCV genotype 1, real-time PCR-based method and Sanger method were used for the HCV NS5B region. HCV subgenotypes were determined in 90% by real-time PCR-based method. We also analyzed the specific probe regions for HCV subgenotypes 1a and 1b using ultra-deep sequencing, and uncovered mutations that could not be revealed using direct-sequencing by Sanger method. We estimated the prevalence of HCV subgenotype 1a as 1.2-2.5% of HCV genotype 1 patients in Japan.
Although real-time PCR-based HCV subgenotyping method seems fair for differentiating HCV subgenotypes 1a and 1b, it may not be sufficient for clinical practice. Ultra-deep sequencing is useful for revealing the resistant strain(s) of HCV before DAA treatment as well as mixed infection with different genotypes or subgenotypes of HCV.
丙型肝炎病毒 (HCV) 1 型亚基因型 1a 和 1b 对聚乙二醇干扰素加利巴韦林联合直接作用抗病毒药物 (DAA) 治疗的反应有不同的影响，因为这两种亚基因型的耐药突变发生率不同。在日本，几乎所有的 HCV 1 型都属于 1b 亚型。
为了确定日本 HCV 1 型感染患者的 HCV 1a 或 1b 亚基因型，使用基于实时 PCR 的方法和 Sanger 法对 HCV NS5B 区进行检测。90%的 HCV 亚基因型通过基于实时 PCR 的方法确定。我们还使用超深度测序分析了 HCV 1a 和 1b 亚基因型的特定探针区域，并发现了 Sanger 法直接测序无法揭示的突变。我们估计日本 HCV 1 型患者中 HCV 1a 亚基因型的流行率为 1.2-2.5%。
虽然基于实时 PCR 的 HCV 亚基因型检测方法似乎可以很好地区分 HCV 1a 和 1b 亚基因型，但对于临床实践可能还不够。超深度测序对于在 DAA 治疗前揭示 HCV 的耐药株以及不同基因型或亚基因型 HCV 的混合感染非常有用。
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