90 per cent skin-based viruses represent viral 'dark matter'

Most DNA viruses on healthy human skin are viral 'dark matter' that have never been described before, according to researchers who used state-of-the-art techniques to survey the skin's virus population, or 'virome'.
The research also includes the development of a set of virome analysis tools that are now available to researchers for further investigations.
Researchers and the public are increasingly aware that microbes living on and inside us - our "microbiomes" - can be crucial in maintaining good health, or in causing disease. Skin-resident bacteria are no exception.
Ideally they help ward off harmful infections, and maintain proper skin immunity and wound-healing, but under certain circumstances they can do the opposite.

"There has been a real need for a better understanding of these viruses, given their potential effects on our skin cells as well as on our resident bacteria," said senior author Elizabeth A Grice, an assistant professor of Dermatology at University of Pennsylvania School of Medicine.
"Until now, relatively little work has been done in this area, in part because of the technical challenges involved. For example, a skin swab taken for analysis will contain mostly human and bacterial DNA, and only a tiny amount of viral genetic material - the proverbial needles in the haystack," said Grice.

Previous mapping attempts used databases of known viral genes to recognise some of this viral genetic material amid all of the bacteria and human DNA. But such an approach tends to overlook the many viruses not already catalogued in databases.

Using optimised techniques for isolating virus-like particles (VLPs) from skin swabs, and for analysing very small amounts of genetic material, the research team was able to focus their sequencing and analysis on viral DNA without entirely depending on databases.
Their analysis of samples from 16 healthy individuals revealed some results that were expected. The most abundant skin-cell infecting virus was human papilloma virus, which causes common warts and has been linked to skin cancers.
However, most of the detected DNA from the VLPs did not match viral genes in existing databases.
"More than 90 per cent was what we call viral dark matter - it had features of viral genetic material but no taxonomic classification," Grice said.

That came as a surprise, although of course it highlighted the importance of mapping this unexplored territory.
The findings also clearly linked the skin virome to the skin microbiome. Most of the detected viral DNA appeared to belong to phage viruses, which infect and often take up long-term residence within bacteria.
When Grice and colleagues sequenced skin bacterial DNA from the same 16 subjects, they found that it often contained tell-tale marks - called CRISPR spacers - of prior invasion by the same phage viruses.
The study was published in the journal mBio.