Human polyomavirus related to African green monkey lymphotropic polyomavirus

Abstract

While studying the virome of the skin surface of a patient with a Merkel cell carcinoma (MCC) by using unbiased, high-throughput sequencing, we identified a human polyomavirus nearly identical to human polyomavirus 9, a virus recently reported in blood and urine of renal transplantion patients and closely related to the African green monkey lymphotropic polyomavirus. Specific PCR analysis further identified this virus in 2/8 patients with MCC but in only 1/111 controls without MCC. This virus was shed for ≥20 months by the MCC index patient and was on the skin of the spouse of the index patient. These results provide information on the viral ecology of human skin and raise new questions regarding the pathology of virus-associated skin disorders.

Figure 1

Genomic map of the circular genome of the Institut Pasteur polyomavirus (IPPyV) strain of human polyomavirus 9. Arrows indicate open reading frames. Small T, small T antigen; VP, viral protein; Large T, large T antigen.

Figure 2

A) Viral protein 1 (VP1) and B) large T antigen (LT) nucleotide-based phylogenetic reconstructions of polyomaviruises inferred by using a Bayesian method. Taxa annotations include reference number, name of the virus, host taxonomic order (in parentheses), host genus whenever available, and reported collection date. Human viruses are indicated in blue, and monkey viruses are indicated in green. Red vertical bars highlight groups for which VP1 and LT signals are incongruent. Posterior probabilities are indicated at each node. GenBank identification numbers are indicated directly on trees for each sequence. Scale bars indicate nucleotide substitutions per site.

Figure 3

Identification of viral protein 1 (VP1) residues differing between human polyomavirus 9 (HPyV9) and lymphotropic polyomavirus (LPV). The DE, HI, and BC loops that extend outward from VP1 are indicated. The crystal structure of simian virus VP1, derived from strain 3BWQ, was used as a template. The red region in the center indicates part of a β strand, which is mostly hidden. Residues differing between HPyV9 and LPV are indicated by pink squares.