Metagenomic Discovery of 83 New Human Papillomavirus Types in Patients with Immunodeficiency

Abstract

Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samples from 48 patients with rare genetic immunodeficiencies, including patients with warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, or epidermodysplasia verruciformis (EV). Their profiles were compared with the profiles of swabs from 14 healthy adults and warts from 6 immunologically normal children. Individual patients were typically infected with multiple HPV types; up to 26 different types were isolated from a single patient (multiple anatomical sites, one time point). Among these, we identified the complete genomes of 83 previously unknown HPV types and 35 incomplete genomes representing possible additional new types. HPV types in the genusGammapapillomaviruswere common in WHIM patients, whereas EV patients mainly shed HPVs from the genusBetapapillomavirus.Preliminary evidence based on three WHIM patients treated with plerixafor, a leukocyte mobilizing agent, suggest that longer-term therapy may correlate with decreased HPV diversity and increased predominance of HPV types associated with childhood skin warts.IMPORTANCEAlthough some members of the viral familyPapillomaviridaecause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shedGammapapillomavirus(Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of knownGammaHPV types and suggest that WHIM syndrome patients are uniquely susceptible toGammaHPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusualGammaHPV skin warts observed in WHIM patients.

Mash Screen: High-throughput sequence containment estimation for genome discovery

“…The SRA project SRP064400 was downloaded using fastq-dump from the SRA Toolkit [4], and assembled using metaspades [31] with default parameters. Assembled contigs were screened using blastx and a custom blast database containing a select set of conserved proteins from DNA viruses [32]. Contigs containing likely viral protein sequences were further screened all known viruses using blastn.…”

“…Contigs with less than 90% nucleotide identity to any known viral genome were then manually annotated and analyzed for completeness, which revealed a nearly complete genome for a new polyomavirus related to HPyV6 and HPyV7. The viral genome was completed using methods previously described by Pastrana and colleagues [32].…”

PuMA: a papillomavirus genome annotation tool

“…We are currently developing a homology-based approach to improve the identification 108 of initiation codons. Finally, we used PuMA to annotate 168 newly isolated papillomaviruses 109 (Tirosh et al, 2018;Pastrana et al, 2018), and successfully annotated 1424 novel viral features 110 (Fig 1 D) with high accuracy compared to manual annotation. 111…”

Human papillomavirus type 7‐associated anal condyloma after renal transplantation in a child

“…This is exemplified by detection of many HPV sequences of various genotypes in metagenomes generated from samples collected at various body sites from healthy or diseased people in diverse clinical settings. 1,2 We describe here HPV7-related anal condyloma as an uncommon renal transplantation complication. The case-patient, an 11year-old boy, was transplanted at 10 years of age due to congenital anomalies of the kidney and urinary tract.…”

“…Nonetheless, the prevalence, clinical significance, and spectrum of many HPV genotypes are currently largely untapped. This is exemplified by detection of many HPV sequences of various genotypes in metagenomes generated from samples collected at various body sites from healthy or diseased people in diverse clinical settings …”