Sub-Saharan region in Africa still holds the highest burden of HIV/AIDS globally. HIV-1 requires coreceptor to gain entry into permissive cells to initiate infection. Molecular analysis of the chemokine coreceptor usage is important clinically and in the effective management of AIDS virus. This study aims to determine the coreceptor usage among HIV-1 drug-naive patients residing in the rural Eastern cape, South Africa. We collected blood samples from 55 HIV-infected patients into an anticoagulant vacutainer. RNA was extracted from separated plasma, and reverse transcription-polymerase chain reaction (RT-PCR) was performed followed by nested polymerase chain reaction to amplify the partial envelope fragment spanning the C2–C3 region. Sanger sequencing was done on the amplicons using the BigDye Terminator V3.1 sequencing kit (Applied Biosystems, Foster City, CA) while sequences were manually edited using BioEdit and Geneious 10.2.6 tools. The WebPSSM and Geno2pheno online tools were also utilized to predict coreceptor tropism while the phylogenetic analysis of the isolates was determined using MEGA 7. Of the 55 blood samples collected for the study, 50 (91%) were successfully amplified and sequenced. The mean age of the patients was 32 (18–56) years while the ratio of men to women was 35% and 65% correspondingly. Phylogenetic analysis revealed that all 50 sequences clustered with HIV-1 subtype C reference strains. Viral tropism of the V3 loop revealed 47 sequences to be R5 strains, while three sequences (T1E, T10E, and T11E,) were classified as X4 strains based on the WebPSSM and the Geno2pheno algorithm. HIV-1 R5 tropic strains were the most dominant virus obtained from this study, while HIV-1 subtype C still drives the epidemic in South Africa suggesting greater in vivo and host pathogen fitness. Documented data on mapping out cellular tropism based on viral tropism are important as maraviroc and the other CCR5 antagonist could be introduced as part of the treatment regimen in South Africa.

中文翻译：

---

居住在南非东开普省农村地区的未接受过HIV-1药物治疗的患者中趋化因子共受体的使用。

非洲撒哈拉以南地区仍然是全球艾滋病毒/艾滋病负担最大的国家。HIV-1需要共感受器进入允许性细胞才能开始感染。趋化因子共受体使用的分子分析在临床上和对艾滋病病毒的有效管理中具有重要意义。这项研究旨在确定居住在南非东部开普敦农村地区的未接受过HIV-1药物治疗的患者中的共受体使用情况。我们将55名HIV感染患者的血液样本收集到抗凝真空器中。从分离的血浆中提取RNA，然后进行逆转录聚合酶链反应（RT-PCR），然后进行嵌套聚合酶链反应，以扩增跨越C2-C3区域的部分包膜片段。使用BigDye Terminator V3.1测序试剂盒（Applied Biosystems，使用BioEdit和Geneious 10.2.6工具手动编辑序列。WebPSSM和Geno2pheno在线工具也被用来预测共感受器的向性，而分离株的系统发育分析则使用MEGA 7进行了确定。在用于研究的55个血液样本中，有50个（91％）被成功扩增和测序。患者的平均年龄为32（18-56）岁，男女比例分别为35％和65％。系统发育分析表明，所有50个序列均与HIV-1亚型C参考菌株聚集在一起。V3环的病毒向性显示47个序列为R5菌株，而三个序列（T1E，T10E和T11E）根据WebPSSM和Geno2pheno算法被分类为X4菌株。HIV-1 R5热带毒株是本研究获得的最主要的病毒，体内和宿主病原体适应性。由于马拉维罗克和另一种CCR5拮抗剂可以作为南非治疗方案的一部分，因此有关基于病毒嗜性确定细胞嗜性的文献资料很重要。