El Hadad Sahar, Al-Hamdan Hesa, Linjawi Sabah
Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Research Center of Genetic Engineering and Bioinformatics, VACSERA, Cairo, Egypt.
PLoS One. 2017 May 26;12(5):e0178225. doi: 10.1371/journal.pone.0178225. eCollection 2017.
Chronic hepatitis C virus (HCV) infection and its progression are major health problems that many countries including Saudi Arabia are facing. Determination of HCV genotypes and subgenotypes is critical for epidemiological and clinical analysis and aids in the determination of the ideal treatment strategy that needs to be followed and the expected therapy response. Although HCV infection has been identified as the second most predominant type of hepatitis in Saudi Arabia, little is known about the molecular epidemiology and genetic variability of HCV circulating in the Jeddah province of Saudi Arabia. The aim of this study was to determine the dominance of various HCV genotypes and subgenotypes circulating in Jeddah using partial sequencing of the NS5B region. To the best of our knowledge, this is the first study of its kind in Saudi Arabia. To characterize HCV genotypes and subgenotypes, serum samples from 56 patients with chronic HCV infection were collected and subjected to partial NS5B gene amplification and sequence analysis. Phylogenetic analysis of the NS5B partial sequences revealed that HCV/1 was the predominant genotype (73%), followed by HCV/4 (24.49%) and HCV/3 (2.04%). Moreover, pairwise analysis also confirmed these results based on the average specific nucleotide distance identity: ±0.112, ±0.112, and ±0.179 for HCV/1, HCV/4, and HCV/3, respectively, without any interference between genotypes. Notably, the phylogenetic tree of the HCV/1 subgenotypes revealed that all the isolates (100%) from the present study belonged to the HCV/1a subgenotype. Our findings also revealed similarities in the nucleotide sequences between HCV circulating in Saudi Arabia and those circulating in countries such as Morocco, Egypt, Canada, India, Pakistan, and France. These results indicated that determination of HCV genotypes and subgenotypes based on partial sequence analysis of the NS5B region is accurate and reliable for HCV subtype determination.
慢性丙型肝炎病毒（HCV）感染及其进展是包括沙特阿拉伯在内的许多国家面临的主要健康问题。确定HCV基因型和亚型对于流行病学和临床分析至关重要，有助于确定需要遵循的理想治疗策略以及预期的治疗反应。尽管HCV感染已被确定为沙特阿拉伯第二大最主要的肝炎类型，但对于在沙特阿拉伯吉达省流行的HCV的分子流行病学和基因变异性知之甚少。本研究的目的是通过NS5B区域的部分测序来确定在吉达流行的各种HCV基因型和亚型的优势情况。据我们所知，这是沙特阿拉伯首次此类研究。为了鉴定HCV基因型和亚型，收集了56例慢性HCV感染患者的血清样本，并进行了NS5B基因部分扩增和序列分析。对NS5B部分序列的系统发育分析表明，HCV/1是主要基因型（73%），其次是HCV/4（24.49%）和HCV/3（2.04%）。此外，成对分析也基于平均特异性核苷酸距离一致性证实了这些结果：HCV/1、HCV/4和HCV/3分别为±0.112、±0.112和±0.179，各基因型之间无任何干扰。值得注意的是，HCV/1亚型的系统发育树显示，本研究中的所有分离株（100%）均属于HCV/1a亚型。我们的研究结果还揭示了沙特阿拉伯流行的HCV与摩洛哥、埃及、加拿大、印度、巴基斯坦和法国等国家流行的HCV之间核苷酸序列的相似性。这些结果表明，基于NS5B区域部分序列分析确定HCV基因型和亚型对于HCV亚型的确定是准确可靠的。
