Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within and among its various subtypes. Two complementary hypotheses are suggested to explain the sequence variability among HIV-1 subtypes. The first suggests that the functional constraints at each site remain the same across all subtypes, and the differences among subtypes are a direct reflection of random substitutions, which have occurred during the time elapsed since their divergence. The alternative hypothesis suggests that the functional constraints themselves have evolved, and thus sequence differences among subtypes in some sites reflect shifts in function. To determine the contribution of each of these two alternatives to HIV-1 subtype evolution, we have developed a novel Bayesian method for testing and detecting site-specific rate shifts. The RAte Shift EstimatoR (RASER) method determines whether or not site-specific functional shifts characterize the evolution of a protein and, if so, points to the specific sites and lineages in which these shifts have most likely occurred. Applying RASER to a dataset composed of large samples of HIV-1 sequences from different group M subtypes, we reveal rampant evolutionary shifts throughout the HIV-1 proteome. Most of these rate shifts have occurred during the divergence of the major subtypes, establishing that subtype divergence occurred together with functional diversification. We report further evidence for the emergence of a new sub-subtype, characterized by abundant rate-shifting sites. When focusing on the rate-shifting sites detected, we find that many are associated with known function relating to viral life cycle and drug resistance. Finally, we discuss mechanisms of covariation of rate-shifting sites.

人类免疫缺陷病毒1型（HIV-1）的标志性特征之一，是其在各亚型内部及亚型之间演化速率极快。目前存在两个互补假说，用于解释HIV-1亚型间的序列变异：其一认为，各亚型在每个位点的功能约束始终保持一致，亚型间的差异直接反映了亚型分化以来所经历时间内发生的随机碱基替换；其二则提出，功能约束本身发生了演化，因此部分位点的亚型间序列差异反映了功能的转变。为明确这两种假说各自对HIV-1亚型演化的贡献，我们开发了一种全新的贝叶斯方法，用于检验并检测位点特异性演化速率偏移。速率偏移估算器（RAte Shift EstimatoR，RASER）可用于判断位点特异性的功能偏移是否为蛋白质演化的特征，若存在此类偏移，则可精准定位最有可能发生该类变化的特定位点与演化支系。将RASER应用于由不同M组亚型的大量HIV-1序列样本构成的数据集后，我们发现HIV-1全蛋白质组中普遍存在演化速率偏移。此类速率偏移大多发生在主要亚型的分化过程中，这证实了亚型分化与功能多样化同步发生。我们还进一步发现了新型亚亚型出现的证据，该亚亚型以存在大量速率偏移位点为特征。当聚焦于检测到的速率偏移位点时，我们发现其中许多位点与病毒生命周期及耐药性相关的已知功能存在关联。最后，我们讨论了速率偏移位点的协同演化机制。