Pairwise diversity and tMRCA as potential markers for HIV infection recency.
Pairwise diversity and tMRCA as potential markers for HIV infection recency.
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DOI：
10.1097/md.0000000000006041
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发表时间：
2017-02
期刊：
影响因子：
1.6
通讯作者：
Novitsky V
中科院分区：
文献类型：
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作者：
Moyo S;Wilkinson E;Vandormael A;Wang R;Weng J;Kotokwe KP;Gaseitsiwe S;Musonda R;Makhema J;Essex M;Engelbrecht S;de Oliveira T;Novitsky V
宿主内人类免疫缺陷病毒（HIV）-1多样性随时间线性增加。我们评估了从宿主内HIV-1C env序列推断的平均成对距离和到最近共同祖先（tMRCA）的时间与估计的HIV感染时间的相关程度。本分析使用了博茨瓦纳一项主要HIV-1C感染研究的数据（N = 42）。 通过单基因组扩增和测序，共产生了2540个HIV-1包膜gp 120可变环区1至保守区5（V1 C5）的HIV-1包膜gp 120病毒序列，平均每个参与者61个病毒序列，每个参与者每个时间点11个序列。使用R软件中的ape包计算每个时间点和参与者的原始成对距离。使用贝叶斯进化分析（抽样树v1.8.2）中实施的系统发育推断估计tMRCA。配对距离和tMRCA与估计的HIV感染时间显著相关（均P <0.001）。 考虑到艾滋病毒感染的多样性，加强了这些联系。基于HIV-1C env的成对距离和tMRCA可用作HIV近度的潜在标记物。然而，tMRCA估计值与成对距离估计值相比没有优势。
Intrahost human immunodeficiency virus (HIV)-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intrahost HIV-1C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1C infection study in Botswana were used for this analysis (N = 42). A total of 2540 HIV-1C env gp120 variable loop region 1 to conserved region 5 (V1C5) of the HIV-1 envelope gp120 viral sequences were generated by single genome amplification and sequencing, with an average of 61 viral sequences per participant and 11 sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in Bayesian Evolutionary Analysis by Sampling Trees v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P < 0.001). Taking into account multiplicity of HIV infection strengthened these associations. HIV-1C env-based pairwise distances and tMRCA can be used as potential markers for HIV recency. However, the tMRCA estimates demonstrated no advantage over the pairwise distances estimates.