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. 2017 Jun:506:45-54.
doi: 10.1016/j.virol.2017.03.007. Epub 2017 Mar 22.

Isolation and characterization of a novel putative human polyomavirus

Tarik Gheit  1 , Sankhadeep Dutta  1 , Javier Oliver  1 , Alexis Robitaille  1 , Shalaka Hampras  2 , Jean-Damien Combes  1 , Sandrine McKay-Chopin  1 , Florence Le Calvez-Kelm  1 , Neil Fenske  3 , Basil Cherpelis  3 , Anna R Giuliano  4 , Silvia Franceschi  1 , James McKay  1 , Dana E Rollison  2 , Massimo Tommasino  5
Affiliations

Isolation and characterization of a novel putative human polyomavirus

Tarik Gheit et al. Virology. 2017 Jun.

Abstract

The small double-stranded DNA polyomaviruses (PyVs) form a family of 73 species, whose natural hosts are primarily mammals and birds. So far, 13 PyVs have been isolated in humans, and some of them have clearly been associated with several diseases, including cancer. In this study, we describe the isolation of a novel PyV in human skin using a sensitive degenerate PCR protocol combined with next-generation sequencing. The new virus, named Lyon IARC PyV (LIPyV), has a circular genome of 5269 nucleotides. Phylogenetic analyses showed that LIPyV is related to the raccoon PyV identified in neuroglial tumours in free-ranging raccoons. Analysis of human specimens from cancer-free individuals showed that 9 skin swabs (9/445; 2.0%), 3 oral gargles (3/140; 2.1%), and one eyebrow hair sample (1/439; 0.2%) tested positive for LIPyV. Future biological and epidemiological studies are needed to confirm the human tropism and provide insights into its biological properties.

Keywords: Human; New polyomavirus; Skin.

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Figures

Fig. 1.
Fig. 1.
Genome organization of LIPyV. (A) The viral genome of 5269 bp comprises early and late coding regions that encode for two regulatory proteins (small T-antigen and large T-antigen), the 148 T-antigen, the putative alternate T antigen (ALTO), the major capsid protein VP1, and two minor capsid proteins, VP2 and VP3. These regions are separated by a non-coding control region (NCCR) of 401 bp. (B) Transcript mapping of small, large, and 148 T-antigens.
Fig. 2.
Fig. 2.
Structure of the large, small, and 148 T-antigens.
Fig. 3.
Fig. 3.
Maximum-likelihood phylogenetic unrooted trees produced from different regions of the LIPyV genome. The VP1 open reading frame (A), the large T-antigen (LT-Ag) open reading frame (B), and the amino acid sequence of LT-Ag (C) are compared separately. Scale bar shows substitution rate per site.
Fig. 3.
Fig. 3.
Maximum-likelihood phylogenetic unrooted trees produced from different regions of the LIPyV genome. The VP1 open reading frame (A), the large T-antigen (LT-Ag) open reading frame (B), and the amino acid sequence of LT-Ag (C) are compared separately. Scale bar shows substitution rate per site.
Fig. 3.
Fig. 3.
Maximum-likelihood phylogenetic unrooted trees produced from different regions of the LIPyV genome. The VP1 open reading frame (A), the large T-antigen (LT-Ag) open reading frame (B), and the amino acid sequence of LT-Ag (C) are compared separately. Scale bar shows substitution rate per site.
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