TY  - JOUR
A1  - Félez-Sánchez, Marta
A1  - Trösemeier, Jan-Hendrik
A1  - Bedhomme, Stéphanie
A1  - González-Bravo, Maria Isabel
A1  - Kamp, Christel
A1  - Bravo, Ignacio G.
T1  - Cancer, warts, or asymptomatic infections: clinical presentation matches codon usage preferences in human papillomaviruses
T2  - Genome biology and evolution
N2  - Viruses rely completely on the hosts' machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.
KW  - human viruses
KW  - codon usage preferences
KW  - mutation
KW  - translational selection
KW  - immune system
KW  - clinical presentation
KW  - genotype–phenotype
KW  - warts
KW  - cancer
KW  - chronic infection
KW  - acute infection
Y1  - 2015
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/41234
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-412341
SN  - 1759-6653
N1  - (c)The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits
non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
VL  - 7
IS  - 8
SP  - 2117
EP  - 2135
PB  - Oxford Univ. Press
CY  - Oxford
ER  -