Viral metagenomics reveals a novel human papillomavirus in anogenital wart tissues

Abstract Background: Viral metagenomics is widely employed to identify novel virus in biological samples. Recently, although numerous novel HPV strains have been identified in clinical samples including anogenital warts (AGWs), many unknown HPV sequences remain to be discovered. Methods: 110 tissue samples of wart were collected from AGW patients, including 34 female and 76 male. Viral metagenomics was used to detect the viral nucleic acid and obtain the virus genomes from samples. Phylogenetic analysis was performed to infer the evolutionary relationships of novel HPV found here among predicted ORFs on the basis of the closest related HPVs and the most representative strain of α, β and γ genus. Epidemiological survey of novel HPV was performed by using the nested PCR method. Results: A novel HPV designated as HPV-JDFY01 was discovered from a library. The complete genomic sequence of HPV-JDFY01 was a 7,186 bp full-length double-stranded DNA with 7 open reading frames (ORFs). Phylogenetic analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and was clustered into the genus Gammapapillomavirus. Epidemiological investigation showed that one positive sample was screened out by specific screening PCR primers among 413 tissue samples from AGWs. Conclusions: This is the first time to report a novel Gammapapillomavirus identified by viral metagenomics from AGW in China. However, functional, biophysical and carcinogenic properties of HPV-JDFY01 are needed in the future research.