Synonymous nucleotide changes drive papillomavirus evolution

King, Kelly M.; Rajadhyaksha, Esha Vikram; Tobey, Isabelle G.; Doorslaer, Koenraad Van

doi:10.1016/j.tvr.2022.200248

Cited by 9 publications

(5 citation statements)

References 128 publications

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“…These results are most consistent with a non-random mutation burden associated with genetic drift [88,89]. Given the rarity of positive Darwinian selection [26] and recombination, new HPV variants emerge containing different combinations of non-coding elements as we describe from our analysis of 13 higher-order nucleotide motifs. Surprisingly, even nucleotide composition alone discriminated closely related types, e.g., alpha-9 types (compare Figure 3A/B and Figure 5).…”

Section: Discussionsupporting

confidence: 74%

“…Thus, current evidence for selection or its counterpart genetic drift are hampered by few analytical methods. Whole genome analyses of various HPV types do not support the notion that pathogenicity is more strongly connected to nonsynonymous substitutions [26] than perhaps to a lack thereof [27][28][29] or to other kinds of substitution in papillomavirus genomes [29,30]. Indeed, elevated oncogenic risk from large epidemiological studies is also associated with variation in noncoding regions and with silent substitutions that are non-randomly distributed across the ~8000 bp genome [30][31][32][33].…”

Section: Introductionmentioning

confidence: 96%

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Genetic Drift and <em>Alphapapillomavirus</em> Evolution

Burk¹,

Mirabello²,

DeSalle³

2023

Preprint

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Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history. Whereas the role of selection on, and drift of, non-coding DNA elements on HPV diversification is poorly understood. More than a thousand complete genomes representing Alphapapillomavirus types, lineages and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the 4 nucleotides (A,C,G,T), codon usage, trimer usage and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages

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Section: Discussionsupporting

confidence: 74%

Section: Introductionmentioning

confidence: 96%

Genetic Drift and <em>Alphapapillomavirus</em> Evolution

Burk¹,

Mirabello²,

DeSalle³

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…These results are most consistent with directional mutation pressure and neutral evolution (i.e., genetic drift as described by Sueoka [ 97 , 98 ]). Given the rarity of positive Darwinian selection [ 26 ] and recombination, new HPV variants emerge containing different combinations of non-coding motifs as we describe from our analysis of 13 higher-order nucleotide motifs. Surprisingly, even nucleotide composition alone discriminated closely related types, e.g., alpha-9 types (compare Figure 3 and Figure 5 ).…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 91%

“…Thus, current evidence for selection or its alternative, genetic drift, are hampered by few analytical methods. Whole genome analyses of various HPV types do not support the notion that pathogenicity is more strongly connected to nonsynonymous substitutions [ 26 ] than, perhaps, to a lack thereof [ 27 , 28 , 29 ] or to other kinds of substitution in papillomavirus genomes [ 29 , 30 ]. Indeed, elevated oncogenic risk from large epidemiological studies is also associated with variations in non-coding regions and with silent substitutions that are non-randomly distributed across the ~8000 bp genome [ 30 , 31 , 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

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Distinguishing Genetic Drift from Selection in Papillomavirus Evolution

Burk

Mirabello

DeSalle

2023

Viruses

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Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.

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Progression Pathways of Human Papillomavirus-Associated Cancer

Velázquez-Márquez,

Velez-Haro

2024

Pathogens Associated With the Development of Cancer in Humans

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Synonymous nucleotide changes drive papillomavirus evolution

Cited by 9 publications

References 128 publications

Genetic Drift and <em>Alphapapillomavirus</em> Evolution

Genetic Drift and <em>Alphapapillomavirus</em> Evolution

Distinguishing Genetic Drift from Selection in Papillomavirus Evolution

Progression Pathways of Human Papillomavirus-Associated Cancer

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