Characterization of Two Novel Gammapapillomaviruses, HPV179 and HPV184, Isolated from Common Warts of a Renal-Transplant Recipient

Abstract

Gammapapillomavirus (Gamma-PV) is a diverse and rapidly expanding PV-genus, currently consisting of 76 fully characterized human papillomavirus (HPV) types. In this study, DNA genomes of two novel HPV types, HPV179 and HPV184, obtained from two distinct facial verrucae vulgares specimens of a 64 year-old renal-transplant recipient, were fully cloned, sequenced and characterized. HPV179 and HPV184 genomes comprise 7,228-bp and 7,324-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2); the non-coding region is typically positioned between L1 and E6 genes. Phylogenetic analysis of the L1 nucleotide sequence placed both novel types within the Gamma-PV genus: HPV179 was classified as a novel member of species Gamma-15, additionally containing HPV135 and HPV146, while HPV184 was classified as a single member of a novel species Gamma-25. HPV179 and HPV184 type-specific quantitative real-time PCRs were further developed and used in combination with human beta-globin gene quantitative real-time PCR to determine the prevalence and viral load of the novel types in the patient’s facial warts and several follow-up skin specimens, and in a representative collection, a total of 569 samples, of HPV-associated benign and malignant neoplasms, hair follicles and anal and oral mucosa specimens obtained from immunocompetent individuals. HPV179 and HPV184 viral loads in patients’ facial warts were estimated to be 2,463 and 3,200 genome copies per single cell, respectively, suggesting their active role in the development of common warts in organ-transplant recipients. In addition, in this particular patient, both novel types had established a persistent infection of the skin for more than four years. Among immunocompetent individuals, HPV179 was further detected in low-copy numbers in a few skin specimens, indicating its cutaneous tissue tropism, while HPV184 was further detected in low-copy numbers in one mucosal and a few skin specimens, suggesting its dual tissue tropism.

Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols

“…Our observations are not surprising since previous studies have demonstrated that typically cutaneous HPV types (Beta-and Gamma-PVs) were relatively common in the mucosal epithelia, suggesting a possible dual tissue tropism of the majority of HPV species [1,13,32,28,45,46]. In addition, two Gamma-PV types were identified in a surface swab of a genital wart and a cervical cancer biopsy sample, possible as part of the normal mucosal microbiota, as reported previously [23,26].…”

“…Samples of total DNA (n = 458), extracted from 249 swabs of the anal canal (226 initial and 23 follow-up samples), 94 cervical cancer formalin-fixed paraffinembedded (FFPE) tissue samples, 21 genital warts (11 swabs and 10 biopsies) from different anatomical sites [foreskin (n = 4), scrotum (n = 2), penile glans (n = 2), perianal area (n = 4) and pubis (n = 9)], and 94 oral swabs collected during routine paternity testing, were obtained from the archival collection of samples of the Instituto de Biología Molecular y Celular de Rosario (Rosario, Argentina) and the Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana (Ljubljana, Slovenia). Before subsequent analyses, all samples were collected, processed, and stored at − 80°C, as described previously [11,27,[29][30][31][32]. The adequacy of samples for downstream analyses was determined by PCR amplification of the human beta-globin gene, as previously described [33].…”

Molecular characterization, tissue tropism, and genetic variability of the novel Mupapillomavirus type HPV204 and phylogenetically related types HPV1 and HPV63

“…In 11/18 (61.1%) cutaneous warts with low viral load of Mu -PVs, we concomitantly detected cutaneous wart–associated Alpha -PVs (HPV2, HPV27, and HPV57), which were the most probable etiological agents of these warts [52, 54]. As shown in Table 3, we did not detect any additional cutaneous wart-associated HPV types in seven cutaneous warts, suggesting the involvement of rarer cutaneous wart-associated HPV types, such as HPV125, HPV179, and HPV184 [24, 44] or potentially novel HPV types. Second, the low viral load of Mu -PVs in these lesions could be a result of the dilution of Mu -PV–infected cells with heterogeneous, non-targeted cell populations.…”

Development of a novel multiplex type-specific quantitative real-time PCR for detection and differentiation of infections with human papillomavirus types HPV2, HPV27, and HPV57

“…Namely, in sporadic cases of common warts concurrent infections with two or more HPV types can be identified, including their well-known etiological agents, such as HPV1, HPV2, HPV4, HPV7, HPV27, HPV57, and HPV65 (3,7,10,26,32). Because one of the surrogate markers for determining the etiology of common warts is the estimation of the viral load of each HPV type present in the lesion of question (7,35,52), HPV2/27/57 multiplex RT-PCR can be used in combination with other quantitative HPV type-specific RT-PCRs to identify the HPV type with the highest HPV viral load and consequently the highest probability of being a "true" etiological agent of the investigated common wart.…”

“…genome sequences of targeted HPV types retrieved from the GenBank database (accession nos. X55964, EF117890, EF117891, EF362754, EF362755, X74473, AB211993, X55965, U37537, and AB361563) were aligned using the MAFFT v6.846 algorithm (34), as described previously (35). After evaluating the multiple alignment of complete HPV2, HPV27, and HPV57 genome sequences, the HPV L2 gene was selected as the most appropriate target region.…”