评价用于推断人类免疫缺陷病毒（HIV）传播方向的系统发育方法：HIV 预防试验网络（HPTN）052。
Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.
机构信息
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
出版信息
Clin Infect Dis. 2021 Jan 23;72(1):30-37. doi: 10.1093/cid/ciz1247.
BACKGROUND
Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction.
METHODS
Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env).
RESULTS
Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction.
CONCLUSIONS
We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.
背景
系统发育分析可用于评估人群中的人类免疫缺陷病毒（HIV）传播。我们使用来自具有已知关联感染和已知传播方向的夫妇的全基因组 HIV 序列推断 HIV 传播的方向。
方法
从参加 HIV 预防试验网络（HPTN）052 研究的 32 对夫妇中获得了 105 对独特的索引伙伴样本对的完整下一代测序（NGS）数据（每个个体最多 2 个样本）。索引样本是在伴侣感染前最多 5.5 年获得的；伴侣样本是在血清转换时获得的。使用 phyloscanner 生物信息学方法推断传播方向。使用来自个体样本对的样本、来自所有夫妇的样本（每个个体 1 个样本；组分析）以及所有可用样本（多样本组分析）进行分析。还使用 HIV 基因组（gag、pol、env）定义区域的 NGS 数据进行了分析。
结果
使用全基因组 NGS 数据，在 105 对个体样本对中的 98 对（93.3%）、105 对样本对中的 99 对（94.3%）使用组分析、32 对夫妇中的 31 对（96.9%）使用多样本组分析中正确推断了传播方向（从索引到伴侣）。没有推断出错误的传播方向（伴侣到索引）的情况。在索引和伴侣样本采集之间时间间隔较大时，该方法的准确性更高。与 env 或 gag 序列相比，pol 区域序列在推断传播方向方面表现更好。
结论
我们证明了使用全基因组和 pol NGS 数据通过系统发育方法推断两个个体之间 HIV 传播方向的潜力。
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