Nature News Article: Machine learning spots treasure trove of elusive viruses

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Many viruses are difficult to study because they cannot be grown in the lab. Credit: Sebastian Kaulitzki/SPL/Getty for Nature.

An interesting news article was just published in Nature about how the emerging tool of artificial intelligence (AI) is making it easier for scientists to study viruses. The article,  written by science journalist Amy Maxmen, focuses on the difficulty of identifying the vast number of viruses within our bodies, as they are difficult to isolate or culture, and because we know so little about them that we don’t know what to even look for. To overcome this challenge, several computational scientists have applied artificial intelligence (AI) or machine learning approaches to sequencing the bulk of the microbiome (bacteria and viruses) that inhabits human tissues.  Given the complexity of this vast microbial ecosystem, AI approaches are showing great promise in decoding or identifying novel viruses among the sea of other sequences, most of which will be bacterial or host in origin. This could be an important direction in revealing important relationships or dynamics between viruses, bacteria, and human cells.

Viruses overall play a major role in human health and disease, from causing known conditions like the flu or HIV to potentially having an effect on the human microbiome and maybe even ME/CFS disease. Indeed, a recent review article in Clinical Science on the state of ME/CFS microbiome research pointed out that viruses that infect bacteria could alter the microbiome by transferring genes to these bacteria or by outright killing them, and that this could have a direct or indirect effect on human health. This makes the human virome an interesting topic in the context of ME/CFS, and an area that needs more study. Derya was quoted in the Nature article, and he speculated on the potential impact: “Biomedical researchers have long wondered whether viruses contribute to the symptoms of several elusive conditions, such as [ME/CFS] and inflammatory bowel disease. Derya Unutmaz, an immunologist at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut, speculates that viruses might trigger a destructive inflammatory reaction — or they might modify the behaviour of bacteria in a person’s microbiome, which in turn could destabilize metabolism and the immune system.”

To read the full Nature article, click here. 

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