We use all the currently known 405 Papillomavirus (PV) sequences, 343 curated PV sequences from both humans and animals from the PAVE data base, to analyse the recombination dynamics of these viruses at the whole genome levels. After showing some evidence of human and non-human primate PV recombination, we report a comprehensive recombination analysis of all currently known 82 Alphapapillomaviruses (Alpha-PVs). We carried out an exploratory study and found novel recombination events between High-Risk HPV Types and Macaca fascicularis PV1 (MfPV1), Macaca Fuscata PV2 (MfuPV2) and Pan Paniscus PV1 (PpPV1) Papillomaviruses. This is the first evidence of interactions between PVs from different hosts and hence postulates the likelihood of ancient host switching among Alpha-PVs. Notwithstanding these results should be interpreted with caution because the major and minor parents indicated by RDP4 program are simply the sequences in the alignment that most closely resemble the actual parents. We found statistically significant differences between the phylogenies of the PV sequences with recombination regions and PV sequences without recombination regions using the Shimodaira–Hasegawa phylogenetic incongruence testing. We show that not more than 76MYA Alpha-PVs were in the same biological niche, a pre-requisite for recombination, and as the hosts evolved and diversified, the viruses adapted to specific host niches which eventually led to coevolution with specific hosts before speciation of primate species. Thus providing evidence that in ancient times no earlier than the Cretaceous period of the Mesozoic age, Alpha-PVs recombined and switched hosts, but whether this host switching is occurring currently is unknown. However, a clearer picture of the PVs evolutionary landscape can only be achieved with the incremental discovery of PV sequences, especially from the animal kingdom.

我们使用所有目前已知的 405 个乳头瘤病毒(PV) 序列、来自 PAVE 数据库的人类和动物的 343 个精选 PV 序列，在全基因组水平上分析这些病毒的重组动态。在展示了人类和非人类灵长类动物 PV 重组的一些证据后，我们报告了对所有目前已知的 82 种Alphapapillomavirus ( Alpha-PV )的综合重组分析。我们进行了一项探索性研究，发现了高危 HPV 类型与食蟹猴PV1 (MfPV1)、富斯卡猕猴PV2 (MfuPV2) 和Pan Paniscus PV1 (PpPV1)乳头瘤病毒之间的新型重组事件。这是来自不同宿主的 PV 之间相互作用的第一个证据，因此假设古代宿主在 Alpha-PV 之间切换的可能性。尽管如此，应谨慎解释这些结果，因为 RDP4 程序指示的主要和次要亲本只是比对中与实际亲本最相似的序列。我们使用 Shimodaira-Hasegawa 系统发育不一致测试发现具有重组区域的 PV 序列和没有重组区域的 PV 序列的系统发育之间存在统计学上的显着差异。我们表明不超过 76MYA Alpha-PV 处于相同的生物生态位，这是重组的先决条件，并且随着宿主的进化和多样化，病毒适应了特定的宿主生态位，最终导致在灵长类物种形成之前与特定宿主共同进化。从而提供证据表明，在不早于中生代白垩纪的远古时代，Alpha-PVs 重组并转换了宿主，但目前尚不清楚这种宿主转换是否发生。然而，只有通过逐步发现 PV 序列，尤其是来自动物界的 PV 序列，才能更清楚地了解 PV 的进化格局。