Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

中文翻译：

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系统发育学应用于人类1型免疫缺陷病毒（HIV-1）：从跨物种传播到接触网络推断

系统发育分析对于阐明大流行人类免疫缺陷病毒1型（HIV-1）M群病毒的起源和传播至关重要，无论是在人类隐密传播的流行前期还是在传播的流行阶段。系统发育和系统动力学方法的使用提供了重要的见识，以追踪创始人事件，这些事件导致HIV-1菌株在广大地理区域，特定国家和受地理限制的社区内传播。近年来，将系统进化分析与HIV序列的巨大可用性相结合已成为重建HIV传播网络并了解集中和普遍流行病传播动态的越来越重要的方法。