Identification of a third human polyomavirus

Abstract

We have previously reported on a system for large-scale molecular virus screening of clinical samples. As part of an effort to systematically search for unrecognized human pathogens, the technology was applied for virus screening of human respiratory tract samples. This resulted in the identification of a previously unknown polyomavirus provisionally named KI polyomavirus. The virus is phylogenetically related to other primate polyomaviruses in the early region of the genome but has very little homology (<30% amino acid identity) to known polyomaviruses in the late region. The virus was found by PCR in 6 (1%) of 637 nasopharyngeal aspirates and in 1 (0.5%) of 192 fecal samples but was not detected in sets of urine and blood samples. Since polyomaviruses have oncogenic potential and may produce severe disease in immunosuppressed individuals, continued searching for the virus in different medical contexts is important. This finding further illustrates how unbiased screening of respiratory tract samples can be used for the discovery of diverse virus types.

FIG. 1.

Genome organization of KIPyV. Putative coding regions for VP1 to VP3, ST antigen, and LT antigen are marked by arrows.

FIG. 2.

Alignment of the origins of replication of nine polyomavirus species. Putative binding sites for LT antigen are boxed. MPtV, murine pneumotropic virus; BPV, bovine polyomavirus; LPV, lymphotropic papovavirus. This alignment is a modified form of that of Mayer and Dörries (26).

FIG. 3.

The noncoding regulatory region with putative binding sites for transcription factors indicated. Putative LT antigen binding sites are boxed, and other transcription factor binding sites and the A/T-rich domain are underlined.

FIG. 4.

Phylogenetic analysis of LT antigen amino acid sequences (a) and VP1 amino acid sequences (b). Bootstrap values are indicated at each branching point. Analysis of the ST antigen yielded a phylogenetic tree highly similar to that obtained by LT antigen analysis, and whole-genome analysis showed a similar pattern. Analysis of VP2 and VP3 yielded results highly similar to those obtained with VP1. GHPV, goose hemorrhagic polyomavirus; CPyV, crow polyomavirus; FPyV, finch polyomavirus; APV, avian polyomavirus; BPV, bovine polyomavirus; MPtV, murine pneumotropic virus; LPV, lymphotropic papovavirus; HaPyV, hamster polyomavirus.