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首页> 外文期刊>AIDS Research and Human Retroviruses >A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses
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A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses

机译：使用封套序列的系统发育分析对新诊断的个体中新生儿HIV-1透射簇进行短期评估

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The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of <= 10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (kappa) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.
机译：使用系统发育分析的HIV-1的透射簇（TCS）的鉴定可以为病毒传输网络提供见解，并有助于改善预防策略。我们将部分HIV-1包络片段与其回路3（108bp）的使用部分HIV-1包络片段进行了比较，以确定其在推断HIV-1传输聚类方面的实用性。最近（n = 106）和长期（n = 156）HIV-1感染患者的血清样品进行了测序。 HIV-1包膜基于核苷酸的系统发育分析用于推断HIV-1 TCS。考虑到阈值的成对遗传距离，使用Clusterpickergui_1.2.3构建。逻辑回归分析用于检查可能与HIV-1聚类相关的人口因子之间的关系。对98个不同的共有封装序列进行系统发育分析。使用局部包络片段序列，将42个序列分组成15个不同的小TCS，而V3环再现10个簇。部分包络和v3环片段之间的协议随着0.59，P <.00001的COHEN的Kappa（Kappa）系数而显着温和。平均年龄（<38.8岁）和HIV-1b亚型是鉴定的两个因素，其与群组中的HIV-1传播聚类有显着相关，在群组中，差异比（或）= 0.25,95％置信区间（CI，0.04-0.66 ），p = .002和或：0.17,95％CI（0.10-0.61），P = .011分别。本研究证实HIV-1包络序列的部分片段是变速器聚类的更好预测因子。然而，循环3段可以用于筛选目的，并且可以更符合在监控程序中的集成。

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