Clinic of Infectious Diseases, University of Bari, Bari, Italy.
J Clin Virol. 2012 Dec;55(4):370-3. doi: 10.1016/j.jcv.2012.08.014. Epub 2012 Sep 13.
In Western Europe, a previously subtype B HIV-1 restricted area, BC recombinants have been rarely reported.
To describe an outbreak of HIV-1 BC recombinants in southern Italy.
We analyzed pol (protease/reverse transcriptase) sequences from 135 newly diagnosed HIV-1-infected patients during the years 2009-2011. For phylogenetic relationships, sequences were aligned to the most recent reference data set from the Los Alamos database using BioEdit (version 7.1.3). The resulting alignment was analyzed with the Phylip package (version 3.67) building a neighbor-joining tree based on the Kimura two-parameter substitution model. The reliability of the tree topology was assessed through bootstrapping using 1000 replicates. The recombination pattern was characterized using SimPlot 3.5.1 and SplitsTree 4.
At phylogenetic analysis, 22 (16.2%) isolates whose sequences were not unequivocally assigned to a pure subtype or known CRF, formed a distinct monophyletic clade (100% of bootstrap value). For these isolates, the recombination analysis identified a BC mosaic pattern with two breakpoints at positions 2778±5 and 3162±8 (HXB2 numbering) which differed from those of known BC CRFs. All patients from whom these sequences were derived were highly educated youth Italians, 91% males and 82% MSM. Sequences of pol integrase, gp120 and gp41 from these same patients were classified as C subtype.
This outbreak which further reflects the increasing heterogeneity of HIV epidemic in our country is the first report of an Italian outbreak of a BC recombinant, possibly a novel candidate CRF.
在西欧这个先前局限于 B 亚型 HIV-1 的地区，很少有报道称存在 BC 重组体。
描述意大利南部 HIV-1 BC 重组体的暴发情况。
我们分析了 2009-2011 年期间新诊断的 135 例 HIV-1 感染患者的 pol（蛋白酶/逆转录酶）序列。为了进行系统发育关系分析，使用 BioEdit（版本 7.1.3）将序列与最近的 Los Alamos 数据库参考数据集进行比对。使用 Phylip 包（版本 3.67）基于 Kimura 双参数取代模型构建邻接树来分析得到的比对结果。通过 1000 次重复的自举检验评估树拓扑结构的可靠性。使用 SimPlot 3.5.1 和 SplitsTree 4 来描述重组模式。
在系统发育分析中，22 个（16.2%）序列无法明确分配到单一亚型或已知的 CRF 的分离株，形成了一个独特的单系分支（自举值 100%）。对于这些分离株，重组分析确定了一种 BC 嵌合体模式，有两个断点位于位置 2778±5 和 3162±8（HXB2 编号），与已知的 BC CRF 不同。从这些分离株中获得序列的所有患者均为高学历的意大利青年，91%为男性，82%为男男性行为者。来自这些患者的 pol 整合酶、gp120 和 gp41 序列被归类为 C 亚型。
此次暴发进一步反映了我国 HIV 流行的异质性不断增加，这是意大利首例报道的 BC 重组体暴发，可能是一种新的候选 CRF。
