Virology Department, Centre Pasteur of Cameroon, 451 rue 2005 Yaounde 2, Po Box 1274, Yaounde, Cameroon.
Virol J. 2019 Aug 9;16(1):101. doi: 10.1186/s12985-019-1214-9.
Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients.
All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences.
A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region.
We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1-4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
目前的 HCV 治疗方法是针对基因型的，尽管最近已经描述了潜在的泛基因型治疗方法。因此，基因分型是 HCV 感染治疗管理的重要工具，已经开发了多种技术来确定 HCV 基因型。HCV 亚基因组区域的序列分析被认为是金标准，并广泛用于 HCV 基因分型。在这里，我们比较了在 HCV 阳性喀麦隆患者中常规实践中使用核心和 NS5B 区域进行 HCV 基因分型的方法。
本研究纳入了 2016 年期间在喀麦隆巴斯德中心（CPC）接收的所有用于 HCV 基因分型的血浆样本。使用 Abbott Real Time 测定法测定病毒载量。此外，基于核心和 NS5B 区域的扩增和测序，对相应序列进行系统发育分析，进行基因分型。
在研究期间共收到 369 份样本，病毒载量值较高（中位数：930,952IU/ml；IQR：281,833-2,861,179）。所有样本至少在一个基因组区域（核心或 NS5B）中获得了阳性扩增，两个基因组区域的扩增率相似（p=0.34）。系统发育分析显示，在 369 个样本中，146 个（39.6%）被分类为基因型 4，132 个（35.8%）为基因型 1，89 个（24.1%）为基因型 2，在核心和 NS5B 区域均为如此。有趣的是，对于两个样本（0.54%），在两个区域中均获得了不一致的基因型，核心区域分类为基因型 4，而 NS5B 鉴定为基因型 1，表明这些样本中存在可能的 HCV 重组病毒或多重感染。与核心区域相比，使用 NS5B 更有可能区分 HCV 亚型。
我们发现核心和 NS5B 区域中 HCV 的扩增率都很高，除了两个样本中检测到可能的 1-4 重组/多重感染外，在基因型水平上使用这两个区域获得了良好的一致性。因此，基于至少两个基因组区域的 HCV 基因分型有助于识别可能的重组体，并改善 HCV 感染的治疗管理。
