Recombination Between High-Risk Human Papillomaviruses and Non-Human Primate Papillomaviruses: Evidence of Ancient Host Switching Among Alphapapillomaviruses

Abstract

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.

A Comprehensive Study of Cutaneous Fibropapillomatosis in Free-Ranging Roe Deer (Capreolus capreolus) and Red Deer (Cervus elaphus): from Clinical Manifestations to Whole-Genome Sequencing of Papillomaviruses

“…PVs exhibit a slow but astonishing evolutionary success, and traditional assumptions about the mechanisms of PV evolution include that they have very low mutation rates, co-diverge with their hosts and are host-specific [3,[39][40][41]. However, various alternative mechanisms that drive PV evolution have recently been proposed, such as cross-species transmission, recombination and incongruence in the phylogenetic trees of viruses and their hosts [3,40,[42][43][44]. The general conclusions about PV evolution may still be unclear and speculative, as knowledge about nonhuman PV diversity is particularly unbalanced and limited [3,42,45].…”

“…The bovine BPV-1 and BPV-2 types that infect cattle provide an example of cross-species transmission, not only between closely related hosts but also between more distantly related species, as they also infect buffaloes, bison, yaks, giraffes, tapirs, sable antelope, horses, donkeys and red deer [11,12,14,46]. The assumption that virus-host co-divergence alone was the driving force for current PV diversity has also been opposed by several studies describing distantly related PVs infecting the same host species, leading to incongruence in the phylogenetic trees of the viruses and their hosts [3,[42][43][44]. In this study, very low variability between the CcaPV1-type genomes (99.95% identity at the complete genome level compared to the sequences deposited in GenBank) and the CePV1v-type variant genomes (99.96-99.99% identity at the complete genome level compared to the sequences deposited in GenBank) was observed, with five out of six CcaPV1 genomes being 100% identical.…”

Analysis of the improvement path of English listening and speaking ability based on big data technology

“…Therefore, it is necessary to focus on the cultivation of students' listening and speaking skills in English teaching, to enhance students' ability to use the language and to use it flexibly in practice [8][9]. And in this process, we realize the change of teaching philosophy and teaching methods, so that students can break through the shackles of exam-oriented education in learning and become innovative and practical comprehensive talents, and then better realize English communication [10][11]. When students learn English, they also tend to transition from listening to reading and writing, but in the actual English teaching, the proportion of listening teaching content is much lower compared with vocabulary, grammar and reading.…”

HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis

“…Although DNA viruses are considered to recombine with significantly lower frequency than RNA viruses [24], nevertheless, there have been reports of homologous [25,26] and even non-homologous [27] recombination among distant lineages of animal papillomaviruses. Recombination has also been reported among members of alpha-HPVs [28][29][30] and even among HPV16 lineages [31,32]. These reports indicated that HPV16 inter-lineage recombination may occur during infection, however the prevalence of recombinant HPV16 strains or the impact of these recombination events on viral pathogenicity remains unclear.…”