McCormick Adele L, Macartney Malcolm J, Abdi-Abshir Ikran, Labbett Wendy, Smith Colette, Irish Dianne, Webster Daniel P, Haque Tanzina
Department of Virology, Royal Free London NHS Foundation Trust, London, UK.
Department of Virology, Royal Free London NHS Foundation Trust, London, UK.
J Clin Virol. 2015 May;66:56-9. doi: 10.1016/j.jcv.2015.03.006. Epub 2015 Mar 10.
Hepatitis C virus (HCV) genotyping is required for tailoring the dose and duration of antiviral therapy, predicting virological response rates, and selecting future treatment options.
To establish whether baseline genotypes, performed by INNO-LiPA Version 1.0 (v1.0), before 2008, were valid for making treatment decisions now or whether genotypic determination should be repeated. Furthermore, to evaluate concordance between Abbott RealTime genotype II assay (RT) and genotyping by sequencing HCV C/E1, NS5A, NS5B.
Genotyping by RT and sequencing was performed on paired historic and current specimens from 50 patients previously baseline genotyped using INNO-LiPA.
Of 100 samples from 50 patients, ≥ 2 of HCV genomic target regions yielded a sequence that was suitable for genotyping, with 100% concordance, providing no evidence of recombination events. Genotype and subtype prediction based on RT and sequencing agreed in 62.8% historic and 72.7% current specimens, with a kappa coefficient score of 0.48 and 0.76, respectively. LiPA could not subtype 46% of HCV gt1 infections, and LiPA subgenotype was only in agreement with RT and sequencing in 28.6% cases, where matched baseline and historic specimens were available. Three patients were indeterminate by RT, and five patients with HCV gt1 infections could not be subtyped by RT. However, RT revealed mixed infections in five patients where sequencing detected only single HCV infection at 20% threshold.
Genotyping by sequencing, exhibited excellent concordance, with moderate to good agreement with RT, and could resolve RT indeterminates and subtype HCV-gt1 infections not possible by LiPA.
丙型肝炎病毒（HCV）基因分型对于确定抗病毒治疗的剂量和疗程、预测病毒学应答率以及选择未来治疗方案至关重要。
确定2008年前采用INNO-LiPA 1.0版本（v1.0）进行的基线基因分型是否仍适用于当前的治疗决策，还是应重新进行基因分型测定。此外，评估雅培实时基因II型检测法（RT）与通过对HCV C/E1、NS5A、NS5B进行测序的基因分型之间的一致性。
对50例先前使用INNO-LiPA进行基线基因分型的患者的配对历史和当前标本进行RT基因分型和测序。
在50例患者的100份样本中，≥2个HCV基因组靶区域产生了适合基因分型的序列，一致性为100%，未发现重组事件的证据。基于RT和测序的基因型和亚型预测在62.8%的历史标本和72.7%的当前标本中一致，kappa系数评分分别为0.48和0.76。LiPA无法对46%的HCV gt1感染进行亚型分型，在有匹配的基线和历史标本的情况下，LiPA亚型仅在28.6%的病例中与RT和测序一致。3例患者通过RT无法确定，5例HCV gt1感染患者无法通过RT进行亚型分型。然而，RT显示5例患者存在混合感染，而测序在20%阈值下仅检测到单一HCV感染。
测序基因分型表现出极佳的一致性，与RT的一致性为中度至良好，并且可以解决RT无法确定的情况以及LiPA无法进行亚型分型的HCV-gt1感染。
