Persistent childhood viruses are found in adult tissues, including internal organs, indicating the existence of a unique microbiome in our organs- the virome. doi.org/10.1093/nar/gk…
#microbiome
#virome
@lpyori @DgPratas @MariToppinen @Espoonklaussi @SajantilaAntti @MaFePerdomoC
Bacteriophages can be robustly detected in microbiome samples like feces or skin swabs. But identifying latent viruses remains a challenge, as they can slumber as episomes or integrated within cells and tissues without actively replicating.
As these viruses are intracellular they are not restricted to body's outer surfaces where most other microbiotas dwell.
Our study used advanced targeted-enrichment next-generation sequencing and virus species-specific qPCR techniques to identify persistent viruses in nine different human organs from 31 individuals.
Our analysis revealed that each individual harbored between 2 and 12 distinct viral species, with an average of 6.7 per person. Across the study population, we identified a total of 17 viral species. These results highlight the diverse range of viruses present in humans.
Our study revealed a diverse eukaryotic virome present within human tissues, with multiple viral species detected in each organ.
Interestingly, certain herpesviruses (Epstein-Barr virus, Human herpesvirus 6B, 7) were found more frequently in internal organs like the liver, kidney, and lung, while the skin and hair were found to harbor more polyomaviruses and papillomaviruses.
Torque Teno viruses were unique in a sense that they were the only ones found most frequently and abundantly in human blood.
Based on this study, human parvovirus B19 frequently inhabits all human tissues except for hair. The widespread persistence has been previously shown with multiple tissue types through (q)PCR. The virus has, however, remained undetected in most previous viral metagenomic research
Anecdotal data in this study show that some individuals with malignancies may exhibit significant differences in their organ-specific viromes. Viral transcripts have been previously detected in tumors by Zapatka et al. 2020 (doi.org/10.1038/s41588…) @DKFZ
We used two methods to look for viruses: targeted-enrichment high-throughput sequencing (HTS) and qPCR. NGS protocol optimized for viral DNA capture had a 92% positive agreement and 95% negative agreement with qPCR, which is considered the gold standard for viral DNA detection.
Our study also revealed a strong correlation between the coverage depth of viral genomes sequenced and viral quantity values obtained through qPCR. This means that samples with higher viral quantities showed better coverage with NGS.
With our custom pipeline TRACESPipe (doi.org/10.1093/gigasc…) we reconstructed 70 near-full viral genomes from sequencing data acquired directly from human tissues. The resulting phylogeny showed that person's own viruses from different parts of the body resemble each other.
Our study identified numerous DNA viruses in human tissues, but further research is needed to determine which members of this virome are actively transcribed and whether similar viromes exist for RNA viruses.
These viruses may remain hidden with minimal transcription. Research by Kumata et al. (2020) (doi.org/10.1186/s12915…)
have already demonstrated that some are actively transcribed in tissues, as evidenced by RNAseq data. @SystemsVirology
The future of virome research is promising as we continue to explore the tissue-resident virome and its impact on human health and disease. Stay tuned for exciting discoveries and insights into the complex interactions between viruses, other microbes and our bodies!
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