Unmasking the tissue-resident eukaryotic DNA virome in humans

Abstract

Little is known on the landscape of viruses that reside within our cells, nor on the interplay with the host imperative for their persistence. Yet, a lifetime of interactions conceivably have an imprint on our physiology and immune phenotype. In this work, we revealed the genetic make-up and unique composition of the known eukaryotic human DNA virome in nine organs (colon, liver, lung, heart, brain, kidney, skin, blood, hair) of 31 Finnish individuals. By integration of quantitative (qPCR) and qualitative (hybrid-capture sequencing) analysis, we identified the DNAs of 17 species, primarily herpes-, parvo-, papilloma- and anello-viruses (>80% prevalence), typically persisting in low copies (mean 540 copies/ million cells). We assembled in total 70 viral genomes (>90% breadth coverage), distinct in each of the individuals, and identified high sequence homology across the organs. Moreover, we detected variations in virome composition in two individuals with underlying malignant conditions. Our findings reveal unprecedented prevalences of viral DNAs in human organs and provide a fundamental ground for the investigation of disease correlates. Our results from post-mortem tissues call for investigation of the crosstalk between human DNA viruses, the host, and other microbes, as it predictably has a significant impact on our health.

Figure 1.

Flow diagram of the study design. Figure created with BioRender.com.

Figure 2.

The human DNA virome. Prevalences (%) of viral DNAs in the body (≥1 tissue positive for a virus) and in different organs as determined by qPCR or NGS. *HPV prevalence was determined only via NGS from 10 individuals. Figure created with BioRender.com.

Figure 3.

Viral distributions and quantities by qPCR. The y-axis indicates the organs and the x-axis indicates all the individuals of the cohort. Each bubble represents a positive finding, and the bubble size illustrates the viral copies/million cells (log₁₀ values).

Figure 4.

The number of viruses within an individual. The number of viruses detected with qPCR and NGS in the body (≥1 tissue positive for a virus) of the study population (mean as dashed line). On the x-axis are individuals of the cohort.

Figure 5.

Heatmap of breadth coverages of assembled viral sequences. The y-axis indicates the samples sequenced (individual number and organ) and the x-axis indicates the respective viruses. The color intensity reflects the breadth (0–100%) of the viral genomes assembled. The table presents the number of genomes assembled with >50% and >90% breadth. *10 skin refers to the sample taken from the face.

Figure 6.

Representative coverage profiles of reconstructed viral genomes. The x-axis indicates genome position and y-axis indicates the depth of the reads (different scales). The percentage of breadth coverage of each genome is shown in the upper right corner. Correspondingly are HSV-1-blood; VZV-skin; EBV-skin; HCMV-lung; HHV-6B-liver; HHV-7-colon; B19V-skin; TTV-liver; BKPyV-heart; JCPyV-kidney; MCPyV-hair; HPyV6-hair; HPyV7-hair; HPV-hair and HBV-skin.

Figure 7.

Phylogenetic tree including all the B19V genomes (>70% breadth) assembled in this study and previously published full genome sequences (including hairpins). The tree was built using Bayesian inference with Tamura-Nei (TN93) substitution model. Only posterior probabilities >0.9 are shown. Colors illustrate the sequences from each individual. Bolded sequences clustered together with sequences in this study are derived from bone (39) or bone marrow (46) of the same individuals.

Figure 8.

Within- and between- sample diversity. (A) Alpha diversity (within sample diversity) estimation by the number of viral species detected (richness) with qPCR and NGS in different sample types (mean in bar column). (B) Alpha diversity estimation of different organ viromes by mean Shannon index. Statistical significance was calculated by one-way ANOVA (P< 0.001). Post-hoc pairwise comparison of groups was done by Ryan–Einot–Gabriel–Welsh F (REGWF) stepwise procedure and divided into four categories (a,b,c,d) with p-value < 0.05 between categories (i.e. If two groups do not share a same letter, their mean Shannon index difference was statistically significant). (C) Beta diversity (between-sample diversity) was estimated using Bray-Curtis dissimilarity and plotted with t-distributed stochastic neighbor embedding (t-SNE) for visualization. Ellipses show 75% confidence interval of four observed clusters, being the solid circles the mean value of each cluster. The blue cluster consists of all colon, kidney, liver and lung samples, and the yellow of hair samples. The red cluster represents 69% of blood samples, and the green 51% of brain, heart and skin samples.