School of Medicine, Nankai University, Tianjin, China.
State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Front Cell Infect Microbiol. 2023 Oct 30;13:1284815. doi: 10.3389/fcimb.2023.1284815. eCollection 2023.
Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into and regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into , , and regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks.
不同人类免疫缺陷病毒 1 型（HIV-1）亚型在感染人群中的共同循环可能导致新重组体的产生。在巴基斯坦，亚型 A1 和 CRF02_AG 是主要流行人群中的优势株。关键人群中新感染 HIV 的高流行率突出了优势株之间发生重组的可能性，这可能导致新重组体的产生。在这里，我们在拉卡纳感染 HIV 的儿童中发现了一个由 CRF02_AG、亚亚型 A3 和亚型 G 组成的重组簇。在这项研究中，使用了 10 个在基因中具有重组信号的回顾性收集样本进行全长近基因组（NFLG）测序。在这 10 个样本中，有 7 个成功地进行了 NFLG 测序。对这 7 个 NFLG 的系统发育分析表明，所有重组体形成了一个独特的单系聚类，与已知的 HIV-1 循环重组形式（CRFs）不同。重组分析表明，所有七个 NFLG 都具有相似的重组结构，由 CRF02_AG、亚亚型 A3 和亚型 G 组成，亚亚型 A3 片段插入到 和 区域，跨越（HXB2：4218-5518），而亚型 G 片段插入到 、 、 和 区域跨越（HXB2：5957-8250）的 CRF02_AG 骨架。独特重组形式的鉴定可能表明在拉卡纳存在和传播几种共同循环的谱系，导致新的 CRFs。这项研究还强调了持续进行分子监测的重要性，以充分了解巴基斯坦，特别是 HIV 爆发的中心拉卡纳的 HIV-1 遗传多样性。
