Abstract
The DNA genome of a novel HPV genotype, HPV-125, isolated from a hand wart of an immuno-competent 19-year old male was fully cloned, sequenced and characterized. The full genome of HPV-125 is 7,809-bp in length with a GC content of 46.4%. By comparing the nucleotide sequence of the complete L1 gene, HPV-125 is phylogenetically placed within cutaneotrophic species 2 of Alphapapillomaviruses, and is most closely related to HPV-3 and HPV-28. HPV-125 has a typical genomic organization of Alphapapillomaviruses and contains genes coding for five early proteins, E6, E7, E1, E2 and E4 and two late capsid proteins, L1 and L2. The genome contains two non-coding regions: the first located between the L1 and E6 genes (nucleotide positions 7,137–7,809, length 673-bp) and the second between genes E2 and L2 (nucleotide positions 3,757–4,216, length 460-bp). The E6 protein of HPV-125 contains two regular zinc-binding domains at amino acid positions 29 and 102, whereas the E7 protein exhibits one such domain at position 50. HPV-125 lacks the regular pRb-binding core sequence within its E7 protein. In order to assess the tissue predilection and clinical significance of HPV-125, a quantitative type-specific real-time PCR was developed. The 95% limit-of-detection of the assay was 2.5 copies per reaction (range 1.7–5.7) and the intra- and inter-assay coefficients of variation were 0.47 and 2.00 for 100 copies per reaction, and 1.15 and 2.15 for 10 copies per reaction, respectively. Testing of a representative collection of HPV-associated mucosal and cutaneous benign and malignant neoplasms and hair follicles (a total of 601 samples) showed that HPV-125 is a relatively rare HPV genotype, with cutaneous tropism etiologically linked with sporadic cases of common warts.
Highlights
Papillomaviruses (PV) are small non-enveloped viruses with a double stranded circular DNA genome, approximately 8-kb in size
In order to be recognized as a distinct genotype, the entire L1 open reading frame (ORF) of a candidate human papillomaviruses (HPV) isolate must differ by at least 10% from all other officially recognized HPV genotypes [1,2] and the entire genome of the novel genotype must be deposited, in the form of one or more clones, in the Reference Centre for Papillomaviruses in Heidelberg, Germany, so that the full genomic sequence can be independently confirmed
It was initially identified as a putative novel HPV genotype by the use of HVP2/B5 primers [13,14], designed to detect various cutaneous HPVs, with which a 474-bp sequence of the L1 gene was amplified and sequenced
Summary
Papillomaviruses (PV) are small non-enveloped viruses with a double stranded circular DNA genome, approximately 8-kb in size. A quantitative type-specific real-time PCR (RT-PCR) was developed and a representative collection of HPV-associated benign and malignant neoplasms and hair follicles was tested in order to assess the tissue predilection and clinical significance of HPV-125.
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