Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania.
PLoS One. 2013 Aug 5;8(8):e71131. doi: 10.1371/journal.pone.0071131. Print 2013.
The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR) of 38 (28-50) sequences per subject). Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84%) subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60%) subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69%) to 36 (82%) over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.
本研究估计了坦桑尼亚女性酒吧和酒店工作者中 HIV-1 亚型内重组变异体的流行情况。虽然 HIV-1 中会发生亚型内重组，但通常被低估。对 45 名研究对象的 HIV-1 env gp120 V1-C5 准种进行了单基因组扩增和测序（每个研究对象的中位数（IQR）为 38（28-50）条序列）。使用重组检测程序版本 3 中的七种方法（重组检测程序版本 3 中的七种方法）进行重组分析，RDP3。如果至少有三种方法检测到重组信号，且经 Bonferroni 校正多重比较后的 p 值≤0.05，则认为 HIV-1 序列为重组序列。38 名（84%）研究对象的 HIV-1 显示出亚型内重组的证据，包括 22 名 HIV-1 亚型 A1、13 名 HIV-1 亚型 C 和 3 名 HIV-1 亚型 D。患者内重组断点的分布表明正在发生重组，并在 23 名（60%）研究对象中选择性富集重组变异体。在一年的随访中，有证据表明发生亚型内重组的研究对象数量从 29 名（69%）增加到 36 名（82%），尽管增加没有达到统计学意义。对亚型内重组进行调整对于分析 HIV 感染的多重性非常重要。这是在坦桑尼亚 HIV/AIDS 流行地区首次报告 HIV-1 亚型内重组的高流行率，该地区多种 HIV-1 亚型同时流行。HIV-1 亚型内重组增加了病毒多样性，并为 HIV-1 疫苗设计带来了额外的挑战。
