Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus.
AIDS Clinic, Larnaca General Hospital, Larnaca, Cyprus.
Virulence. 2022 Dec;13(1):1331-1348. doi: 10.1080/21505594.2022.2106021.
Prospective molecular studies of HIV-1 region (2253-5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017-2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790-8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.
对塞浦路斯 269 名 HIV-1 感染者（2017-2021 年）的测序样本中 HIV-1 区（HXB2 基因组 2253-5250 位）的序列进行了前瞻性分子研究，结果发现了一个由 14 个未知 HIV-1 重组体组成的传播簇，这些重组体未被归类为先前建立的 CRF。最早的重组体于 2017 年 9 月采集，传播簇一直持续到 2020 年 11 月。成功获得了其中 11 个重组体的全长 HIV-1 基因组序列（HXB2 基因组 790-8795 位），并与 HIV-1 亚型和 CRF 的参考数据集进行了比对。我们使用 MEGAX 进行最大似然树构建（GTR 模型，1000 次 bootstrap 重复），使用 Cluster-Picker 进行系统发育聚类分析（遗传距离≤0.045，bootstrap 支持值≥70%），使用 REGA-3.0 进行亚型确定。使用 SimPlot-v3.5.1 进行 Bootscan 和相似性图谱分析（滑动窗口为 400 个核苷酸，重叠 40 个核苷酸），使用 MEGAX 进行亚区确认性邻接法树分析（Kimura 双参数模型，1000 次 bootstrap 重复，≥70%的 bootstrap 支持值）。HIV-1 重组体的独特聚类揭示了它们的独特性。重组分析显示了相同的独特镶嵌模式，有六个假定的亚间重组断点，七个 CRF02_AG、G、J 亚型和一个未分类片段的片段。我们通过洛斯阿拉莫斯 HIV 序列数据库，最终确定了新型 HIV-1 CRF（命名为 CRF91_cpx）的镶嵌结构。此外，我们还发现了一个带有两个额外重组位点的 CRF91_cpx URF，这是由 B 亚型和 CRF91_cpx 之间的重组事件产生的。自 CRF91_cpx 被发现以来，又有两个患者样本被归入 CRF91_cpx 传播簇，表明其仍在活跃增长。
