Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye. She had been using tap water to dilute the cleaning solution for her contact lenses, and even though they were meant to be replaced every month, she would wear them for three. As a result, the fluid in her contact lens case had become contaminated with three species of bacteria, an amoeba called Acanthamoeba polyphaga that can caused inflamed eyes.

The mystery of the woman’s inflamed eyes was solved, but Bernard La Scola and Christelle Desnues looked inside the amoeba, they found more surprises.

It was carrying two species of bacteria, and a giant virus that no one had seen before—they called it Lentille virus. Inside that, they found a virophage—an virus that can only reproduce in cells infected by other viruses—which they called Sputnik 2. And in both Lentille virus and Sputnik 2, they found even smaller genetic parasites – tiny chunks of DNA that can hop around the genomes of the virus, and stow away inside the virophage. They called these transpovirons.

So, the poor red eyes of the French patient were carrying an entire world of parasites, nested within one another like Russian Matryoshka nesting dolls. The transpovirons were hidden in the virophage, which infected the giant virus, which infected the amoeba, which infected the woman’s eyes.

Rise of the virophages

The same team found the first virophage – Sputnik – back in 2008, under similar circumstances. In dirty water from a Parisian cooling tower, they had isolated an amoeba that contained a new giant virus – mamavirus – which was hijacked by Sputnik (named after the Russian for “fellow traveller”). Mamavirus – a virus as big as some bacteria – creates large viral factories inside the amoeba, where it makes new copies of itself. Sputnik hijacks these factories to replicate itself at mamavirus’ expense. It was a groundbreaking discovery—proof that viruses themselves can “get sick”.

The world of virophages continued to grow. Last year, Matthias Fischer and Curtis Suttle discovered a second one – Mavirus – inside another giant virus called CroV. Weeks later, Sheree Yau announced a third virophage – OLV – infecting the giant viruses of Antarctica’s Organic Lake. Yau also searched through genetic databases for sequences that looked like OLV, and found matches from the Galapagos Islands, Panama, the USA and elsewhere in Antarctica. An entire world of virophages lay waiting to be found.

In Sputnik 2, La Scola and Desnues have discovered the fourth virophage. More importantly, they found its DNA inside that of its Lentille virus host. This proves that, just as other viruses such as HIV and herpes can insert their DNA into animal genomes, Sputnik 2 can insert its DNA into viral ones. This could explain why distantly related giant viruses often carry similar genes. By hopping in and out of their genomes, virophages could be acting as vehicles that transfer genes from one giant virus to another.

Transpovirons

Next, the team did scoured the DNA they recovered from Lentille virus for fragments that didn’t belong into either Lentille’s or Sputnik 2’s genomes. It’s a process that team leader Didier Raoult describes as “looking in the trash”. He says, “If you want to see something really bizarre, you have to look where you didn’t know to look in the first place.” And he was right.

The team found an stretch of DNA that lived inside Lentille virus, and outnumbered its own genome by 3 to 14 times. This fragment can either exist independently within the virus, or insert itself into Lentille’s genome, stowing away within its very DNA. It looked like a transposon – a jumping gene that hops in and out of the genomes of living cells – and different to the other types of mobile DNA that have been found inside giant viruses. Raoult called it a transpoviron.

Just as the discovery of Sputnik hinted at a previously unseen world of virophages, Raoult’s new study tells us that viruses contain many transpovirons, just waiting to be found. “Very few people work on giant viruses and [transpovirons] may have been neglected as they are unexpected,” says Raoult. His team have already found some in the genomes of three other giant viruses.

It’s still unclear where the transpovirons came from, or how exactly they copy themselves, but we do know a few tantalising pieces about their biology. They depend on the giant viruses to copy themselves, and they are incredibly good at reproducing. When Lentille virus first infects the amoeba, the transpoviron jumps to the head of the copying queue. “It’s produced like mad,” says Raoult, to a far greater extent than either the virophage or virus.

They can stow away inside Sputnik 2, and Raoult thinks that they may use virophages as vehicles for getting from one giant virus to another. And they seem to be a mish-mash of DNA from many sources. All of them contain between six to eight genes. Some look like giant virus genes, one or two are extremely similar to virophage genes, and one looks like it came from bacteria. The transpoviron is a genetic chimera, which has pilfered genes from various sources.

The same is true for virophages themselves. Sputnik’s tiny genome contains genes that look like they came from giant viruses, bacteria or more complex cells. Mavirus has genes that look like jumping genes called ‘Maverick transposons’, which are found in many complex cells, including our own. It’s possible that these Maverick sequences evolved from virophages. Virophages hijack the reproductive factories of giant viruses and stop them from making copies of themselves. By adding virophage DNA into their own genomes, early cells might have effectively domesticated these sequences to defend them from giant viruses.

Cells like bacteria, and those that make up our bodies, are plagued by viruses and mobile bits of parasitic DNA. And now, we know that viruses themselves face the same problems, in the form of virophages and transpovirons. For Raoult, it’s further support for the idea that giant viruses could be a fourth domain of life (a long-running and complicated story; see Carl Zimmer and this excellent Nature feature for more).

Raoult suspects that more virophages, more transpovirons, and entirely new classes of mobile DNA will be found in the future, nestled within other giant viruses. Suttle agrees. “The natural viral world encompasses the greatest genetic and biological diversity on Earth,” he says. “Its continued exploration will undoubtedly unlock many more secrets that fundamentally change our understanding of the evolution and diversity of life on our planet.”

Can virophages infect humans?

There is one more twist to the virophage story. In 2010, a French couple fell ill with fever, dizziness and nausea. Both of them were born in Laos, and had recently travelled there to visit friends and family. Five days after they got back, their symptoms started. Both carried traces of infections by parasitic worms, which they probably picked up from the raw fish they ate on their travels. Whatever the specific cause, anti-parasitic treatments curtailed their illness.

But in their blood, Raoult found something stranger: antibodies that recognised the Sputnik virophage.

Until the recent example of Sputnik 2, no virophage had ever been associated with a human before. Even more confusingly, Raoult couldn’t find any antibodies that recognised giant viruses. It’s possible that the couple were exposed to virophages which live in unknown giant viruses that our current tools cannot detect. Alternatively, they were exposed to free virophages found in contaminated water – after all, Yau’s study from last year found traces of virophage DNA in samples from a New Jersey estuary and a Panamanian lake. Could some virophages infect humans too? Raoult suspect that’s possible, but it remains to be seen.

Reference: Desnues, La Scola, Yutin, Fournous, Robert, Azza, Jardot, Monteil, Campocasso, Koonin & Raoult. 2012. Provirophages and transpovirons as the diverse mobilome of giant viruses. http://dx.doi.org/10.1073/pnas.1208835109