Important Factors in Reliable Determination of Hepatitis C Virus Genotype by Use of the 5′ Untranslated Region
Important Factors in Reliable Determination of Hepatitis C Virus Genotype by Use of the 5′ Untranslated Region
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DOI：
10.1128/jcm.03344-12
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发表时间：
2013-05-01
影响因子：
9.4
通讯作者：
Heller, Theo
中科院分区：
文献类型：
--
作者：
Hara, Koji;Rivera, Maria M.;Heller, Theo
准确的丙型肝炎病毒（HCV）基因分型对于确定慢性HCV感染抗病毒治疗的最佳方案、剂量和持续时间以及估计反应率非常重要。HCV RNA的5'非翻译区（UTR）用于商业基因分型，但探针和扩增子的长度是专有的，并且在不同的检测中有所不同。在这项研究中，评估了利用5' UTR可靠地确定HCV基因型所涉及的因素。分析了4名慢性HCV感染受试者的血清样本以及商业基因分型的不同结果和4名对照。从血清中提取HCV RNA，对其5′UTR和NS5B区进行测序。每个区域的10个克隆与原型序列进行比较，并使用5个程序进行基因型分配分析。结果与商业分析结果进行了比较。5‘ UTR序列依次从5’端、3'端或两端缩短，并对所得片段进行基因分型。获得了所有8名受试者的5' UTR和5名受试者的NS5B区域的序列。完整测序的5名受试者的两个区域基因型分配相同。在4个实验样本中，测序的基因分型结果与商业分析的结果不同，但在4个对照中一致。序列的缩短影响了结果，而序列的缩短影响了结果
Accurate genotyping of hepatitis C virus (HCV) is important for determining the optimal regimen, dose, and duration of antiviral therapy for chronic HCV infection, as well as for estimating the response rate. The 5' untranslated region (UTR) of HCV RNA is used in commercial genotyping, but the probes and the lengths of the amplicons are proprietary and vary among the assays. In this study, factors involved in the reliable determination of HCV genotypes utilizing the 5' UTR were evaluated. Serum samples from four subjects with chronic HCV infection and disparate results on commercial genotyping and four controls were analyzed. HCV RNA was extracted from serum samples, and the 5' UTR and NS5B region were sequenced. Ten clones from each region were compared to prototype sequences and analyzed for genotype assignment using five programs. The results were compared to those from commercial assays. 5' UTR sequences were sequentially shortened from either the 5' end, the 3' end, or both ends, with genotyping of the resultant fragments. Sequences were obtained for the 5' UTR in all eight subjects and for the NS5B region in five subjects. The genotype assignments were identical between the two regions in the five subjects with complete sequencing. Genotyping by sequencing gave different results than those from the commercial assays in the four experimental samples but agreed in the four controls. Shortening of the sequences affected the results, and the results for sequences of