Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues

Abstract

Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01.

Keywords: Gammapapillomavirus; anogenital warts; putative novel human papillomavirus; viral metagenomics.

Figure 1

Genomic organization of HPV-JDFY01 isolated from AGW. Early proteins: E6 (nt 1–420, 420 bp); E7 (nt 417–701, 285 bp); E1 (nt 688–2514, 1827 bp); E2 (nt 2447–3604, 1158 bp) and E4 (nt 3048–3374, 327 bp). Late proteins: L2 (nt 3606–5135, 1530 bp) and L1 (nt 5146–6699, 1554 bp), and a 487 bp long control region (LCR) located at 6700 to 7186 of the genome between L1 and E6. The sizes of overlapping fragments are 4 bp between E6 and E7, 14 bp between E7 and E1, and 68 bp between E1 and E2. Even the entire E4 lies fully inside the E2 ORF.

Figure 2

Phylogenetic analysis based on the amino acid sequence of HPV-JDFY01 L1 protein. HPV-JDFY01 is labeled in red.

Figure 3

Clinical and pathological manifestations of AGW with HPV-JDFY01 positive by epidemiological screening. (A) Genital warts present as multiple, flat papules on the inguinal skin. (B) Representative pathological findings with HE staining in 100-fold magnification indicate hyperkeratosis, parakeratosis, acanthosis, papillomatosis, and characteristic vacuolated parakeratotic and granular cells (koilocytes).