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.