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Rarely Seen Giant Viruses Have Been Caught Using CRISPR as a Weapon

DAVID NIELD
3 APR 2019

We've seen plenty of ways that the precise genetic cutting tool CRISPR could be used to improve health outcomes or reduce the risk of disease, but it seems we're not the only ones taking advantage of its potential power.

 

Scientists have discovered hundreds of new giant viruses that use CRISPR techniques to attack both the bacteria they prey on and rival viruses – and they're living inside our guts as well as many other environments.

Known as bacteria viruses (or bacteriophages) because they infect bacteria, viruses of this super size have only recently become known to science, as they don't usually show up on traditional tests.

They're so odd, their very existence is challenging our definition of a 'virus'. But in recent years we've become better at detecting them and realised they may not be as rare as we once thought.

This recent stash was found thanks to a comprehensive DNA collection technique known as metagenomics. That's where the DNA of microbial communities can be sequenced straight after being taken from their natural environment, removing the need for lab cultivation.

Now that we know that these massive, gene-packed bacteriophages are out there, and weaponising CRISPR, it could help our own attempts to fight off bacteria and viruses in the human body.

"The potential impact on health and disease is huge," one of the team, Joanne Santini from University College London in the UK, told Michael Le Page at New Scientist.

 

Even just a drop of seawater can be packed with millions of bacteriophages, and up until now it was thought that large phages – ones with more than tens of thousands of DNA letters in their genomes – were very rare.

Apparently not: earlier this year the same team of scientists discovered more than a dozen huge phages, and now they've identified hundreds more, including many that have a mastery of CRISPR techniques.

The longest bacteriophage the researchers have found yet, and the longest ever discovered, has a genome 716,000 letters long. Considering some normal viruses can get away with just two genes, that's a lot of extra material.

Right now we don't know what these viruses look like, or how they use all the extra genes they're carrying.

But we do know that they've found a unique way to weaponise CRISPR.

The CRISPR sequence itself actually comes originally from bacteria, where it's used as a way of self-defence against invading viruses.

We have also seen giant viruses use CRISPR before – but never on a scale like this.

 

It seems the giant phages found in this study use it in new and sophisticated ways: turning bits of bacterial CRISPR on the bacteria itself, or isolating genes to destroy other viruses. That may help them infect a broader range of bacteria, the researchers suggest.

The study of these giant viruses is still at its early stages, and it's worth pointing out that this study has yet to be peer-reviewed - for now it's been uploaded for scrutiny among the scientific community on the preprint server bioRxiv.

But it's worth paying attention, because further down the line we could use some of the ninja CRISPR skills these megaphages have to wipe out unhealthy bacteria from our gut microbiome.

That could mean substantial health benefits for humans and animals.

More broadly the discovery should teach us more about the fundamentals and the evolution of biology.

The scientists say these giant viruses are "blurring the distinctions between life and non-life", and may have a lot of new information to give us about how life first got started on our planet.

"We wonder if they are ancient and arose simultaneously with cells and other phage from a pre-life (protogenote) state rather than appearing more recently via episodes of genome expansion," write the researchers.

The research has yet to be published but is available on the preprint server bioRxiv.