Gul Amina, Zahid Nabeela, Ahmed Jawad, Zahir Fazli, Khan Imtiaz Ali, Ali Ijaz
Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.
Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad, Pakistan.
BMC Infect Dis. 2016 Apr 18;16:163. doi: 10.1186/s12879-016-1488-0.
The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome.
Chronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software.
Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.
HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.
本研究的目的是基于丙型肝炎病毒（HCV）基因组核心区域的测序和系统发育分析，探索白沙瓦地区HCV 3a基因型的分子流行病学。
本横断面观察性研究纳入了在白沙瓦的三个三级医疗机构[白沙瓦开伯尔教学医院、白沙瓦丽晶医院、白沙瓦哈亚特阿巴德医疗中心]参加总理丙型肝炎控制项目的慢性丙型肝炎病毒感染患者。通过改良的逆转录聚合酶链反应（RT-PCR）和型特异性基因分型检测法对HCV进行定性检测和基因分型。对HCV 3a基因型的核心基因进行扩增、克隆和测序。使用MEGA 6软件对获得的序列进行系统发育分析。
在422份（82.75%）PCR阳性样本中，192份（45.5%）被鉴定为感染HCV 3a基因型。随机对HCV 3a进行核心基因测序以进行特征分析。基于部分HCV 3a核心基因序列与来自不同国家的参考序列对获得的病毒基因组序列进行核苷酸序列分析，结果显示我们的序列与一些本地和区域序列聚类，自展值较高。
HCV 3a在巴基斯坦白沙瓦地区高度流行，基于核心基因序列的系统发育分析表明白沙瓦地区存在不同谱系的HCV 3a，这可能对疾病管理策略产生影响，由于可能存在的抗病毒耐药性，会给贫困人口带来更大的经济压力。
