Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada.
Department of Decision Sciences, HEC Montréal, Montreal, Québec, Canada.
PLoS One. 2019 Mar 6;14(3):e0213366. doi: 10.1371/journal.pone.0213366. eCollection 2019.
Phylogenetics has been used to investigate HIV transmission among men who have sex with men. This study compares several methodologies to elucidate the role of transmission chains in the dynamics of HIV spread in Quebec, Canada.
The Quebec Human Immunodeficiency Virus (HIV) genotyping program database now includes viral sequences from close to 4,000 HIV-positive individuals classified as Men who have Sex with Men (MSMs), collected between 1996 and early 2016. Assessment of chain expansion may depend on the partitioning scheme used, and so, we produce estimates from several methods: the conventional Bayesian and maximum likelihood-bootstrap methods, in combination with a variety of schemes for applying a maximum distance criterion, and two other algorithms, DM-PhyClus, a Bayesian algorithm that produces a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast non-phylogenetic approach. Sequences obtained from individuals in the Primary HIV Infection (PHI) stage serve to identify incident cases. We focus on the period ranging from January 1st 2012 to February 1st 2016.
The analyses reveal considerable overlap between chain estimates obtained from conventional methods, thus leading to similar estimates of recent temporal expansion. The Gap Procedure and DM-PhyClus suggest however moderately different chains. Nevertheless, all estimates stress that longer older chains are responsible for a sizeable proportion of the sampled incident cases among MSMs. Curbing the HIV epidemic will require strategies aimed specifically at preventing such growth.
系统发生学已被用于研究男男性行为者中的 HIV 传播。本研究比较了几种方法，以阐明传播链在加拿大魁北克 HIV 传播动态中的作用。
魁北克人类免疫缺陷病毒（HIV）基因分型计划数据库现在包含了近 4000 名 HIV 阳性个体的病毒序列，这些个体被归类为男男性接触者（MSM），收集于 1996 年至 2016 年初。对链扩展的评估可能取决于所使用的分区方案，因此，我们使用几种方法生成估计值：传统的贝叶斯和最大似然-bootstrap 方法，结合各种应用最大距离标准的方案，以及另外两种算法，DM-PhyClus，这是一种产生提议分区不确定性度量的贝叶斯算法，以及 Gap 程序，一种快速的非系统发生方法。从原发性 HIV 感染（PHI）阶段的个体获得的序列用于识别新发病例。我们关注的时间段为 2012 年 1 月 1 日至 2016 年 2 月 1 日。
分析结果表明，传统方法获得的链估计值之间存在相当大的重叠，从而导致最近时间扩展的估计值相似。然而，Gap 程序和 DM-PhyClus 建议的链略有不同。尽管如此，所有的估计值都强调，较长的旧链是 MSM 中相当一部分抽样新发病例的原因。遏制 HIV 流行需要专门针对预防这种增长的策略。
