Article Figures & Data
Figures
- FIG 1
Known taxa in skin swabs from healthy subjects, WHIM patients, and patients with other diseases. Donut graphs show the total numbers of reads of known taxa of interest detected in swab samples from individuals from various categories: healthy lab volunteers (TVMBS), lichen sclerosus (LS) patients, Merkel cell carcinoma (M) patients, EV patients, GATA2 (GA2), DOCK8, and WHIM patients (W or WG). For the WHIM patients, each graph shows the first collected sample of affected nongenital or genital (-Gen) skin for each patient.
- FIG 2
HPVs and HPyVs in wart biopsy samples/scrapings. (A and B) Warts from immunologically normal subjects (A) or immunodeficient patients (WILD, idiopathic CD4 lymphopenia [ICL], and WHIM [W] patients) (B) were assessed for the presence of distinct HPV types. Genera are depicted in different colors, with slices of the same color representing different types in the same genus. Blue numbers inside the donut represent the total number of viral types for the sample. In some cases, such as W03, some of the types represented a very small fraction of the whole, and wedges are not discernible. Black numbers on the donut correspond to the HPV type or isolate designation (letters are used to denote not-yet-assigned new HPV types), or human polyomavirus (HPyV) species number. For example, Wart I contained a single type, HPV1 from the Mupapillomavirus genus (Mu). For clarity, only the larger predominant graph segments are annotated with HPV type designations. Some patients had biopsy specimens of multiple warts, and each is shown individually.
- FIG 3
Phylogenetic analysis of reported HPV types. (A and B) Protein sequences from L1 (A) or E1 (B) were used to construct phylogenetic trees. At least one HPV type from each previously known species (black font) was analyzed along with each of the 83 complete HPV genomes catalogued in the current study. Asterisks were used to show known representative species that did not fit due to the figure’s space restrictions (counterclockwise, Beta 3-HPV49, Gamma 20-HPV163, Gamma 21-HPV167, and Gamma 2-HPV48). HPV genera are depicted by different colors as follows: orange, Alpha; red, Beta; blue, Gamma; pink, Mu; green, Nu. Dotted lines are not significant; they were used to indicate HPV type names. Arrows indicate potential new species.
- FIG 4
Comparison of viral diversity among skin swabs of patients. (A to D) Analysis of pooled swab samples from affected (warts, rashes, etc.) and healthy skin from the earliest single time point for MCC patients (A), EV patients (B), a GATA2, a DOCK8 and an ICL patient (originally classified as EV-like) (C), and WHIM patients (D). Blue numbers inside the donut represent the numbers of viral types. Black numbers on the donut represent predominant HPV types (letters are used to denote not-yet-assigned new HPV types).
- FIG 5
HPV typing for three individuals on plerixafor therapy. Analysis of samples from WHIM patients during long treatment. Each donut represents pooled samples from several anatomical locations. Samples from patient W06 are from the same time point, the first donut contains swabs from the following sites: right (R) 4th finger, R wrist, and an oral lesion; the second donut represents pooled swabs from the R 2nd finger, R forearm, and R palm. Samples from patient W20 are from different time points: (i) R calf, R ankle, left (L) top of foot, L thigh, and R sole of foot; (ii) normal skin of the abdomen; (iii) L palm and right foot, (iv) L eye cantus; (v) R leg follicular lesions; (vi) R leg open wound. Samples from patient W27 are from the following sites: (i) R toes, R dorsum of foot, R middle finger, R ankle, R jaw, L hand; (ii) R middle finger, L ring finger, L hand, R toes, R calf; (iii) R sole; (iv) L hand periungal. The first available time points for W20 and W27 were first shown in Fig. 4, and are also added here for comparison. Blue numbers inside the donut represent the numbers of viral types. Black numbers on the donut represent predominant HPV types (letters are used to denote not-yet-assigned new HPV types).
Tables
- TABLE 1
Characteristics of patients and samples in this study
↵a The age (in years) for one individual or age range (in years) for more than one individual is shown if known.
↵b The sex (female [F] or male [M]) of the patient or volunteer is shown if known. The number of individuals is shown in parentheses.
↵c One pool of swabs from 14 volunteers was processed as a single sample. The swabs from seven volunteers were processed individually. Vaginal washes from six individuals were pooled.
↵d Swabs from all 18 patients were pooled into a single sample.
TABLE S1
Sample description and sequencing data. Description of the samples used in this article, including anatomical site, date of collection, and number of reads per category. Download Table S1, XLSX file, 0.03 MB.
This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
FIG S1
HPV diversity in genital swabs of ICL or WHIM patients. Swabs shown are from a single time point for individual patients. Blue numbers inside the donuts represent the numbers of viral types. Black numbers on the donuts represent the numbers of predominant HPV types. Download FIG S1, TIF file, 0.2 MB.
This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
