Koalas Use Ancient Viral DNA to Neutralize New Invaders

Some infections are worth remembering: Just ask your DNA.

About eight percent of the human genome is actually viral in origin—a fossil record of bygone illness. But the vast majority of these viral relics have degraded past the point of doing any damage: Somehow, over the course of millennia, former pathogens have decayed into permanent dormancy, leaving only genetic scars in their wake. Today, in the journal PNAS, scientists unveil some of the secrets behind this mysterious transition, with the help of one of Australia's most beloved marsupials.

Close encounters of the viral kind are usually temporary. Viruses enter bodies as tenants, not homeowners, intending to simply replicate and spread to other hosts. But for a certain class of viruses called retroviruses, a temporary lease can often turn into permanent cohabitation. When retroviruses invade cells, they insert their DNA into ours, allowing the new retroviral marching orders to be carried out alongside the cell’s workplace repertoire. If a retrovirus happens upon a sperm or egg, its genetic instructions may go on to infiltrate an embryo that will ferry viral stowaways in each of its cells. This allows the now “endogenous” retrovirus to be passed on, creating a genetic lineage that’s just a little bit more viral than before.

In early generations, the virus may remain intact enough to awaken out of dormancy and infect anew. But while retroviruses have breached the human genome at least 30 or 40 times, most of these viral vagabonds slipped into our genes at least 5 million years ago—and the mutations they’ve suffered since have rendered them innocuous.

Since it's been so long since we've dealt with a new retroviral invasion, there’s been no way for scientists to observe how our genomes reconcile with new onslaughts.

The key to unraveling part of the enigma, it turns out, is fuzzy, gray and sleeps up to 18 hours a day. All vertebrate genomes studied so far are riddled with retroviral remnants, and the koala is no exception. The only difference? Unlike most other animals, koalas are currently embroiled in a war with one of these trespassers—the aptly named koala retrovirus—giving scientists a rare opportunity to track retroviral assimiliation in real time.

“This is really our first and only opportunity to tackle this process… as a retrovirus is still [moving into] the host,” explains first author Ulrike Löber, a researcher at the Leibniz Institute for Zoo and Wildlife Research in Berlin.

Koala retrovirus appears to be a relatively young virus—something that entered the population within the last 50,000 years—and remains a significant adversary of these marsupials. Like its distant relative HIV, koala retrovirus appears to lower the ability of its host to fight off infections, potentially contributing to koalas’ extreme vulnerability to sexually transmitted diseases like chlamydia. To make matters worse, koala retrovirus has been linked to the development of several cancers, a relationship that may also be true of endogenous retroviruses in humans.

Despite these downsides, koalas have been living with this retrovirus for thousands of years. Something had to be neutralizing the attacks—but to understand this process, scientists needed to know where these viruses were landing, and how they were changing over time.

With the help of the scientists who published the full sequence of the koala genome this July, a team led by Alex Greenwood, a professor of wildlife diseases who supervises Löber’s work at the Leibniz Institute, and Alfred Roca, a professor of genetics and wildlife studies at the University of Illinois, was finally able to map out the koala retrovirus’ points of entry. The koala genome allowed the construction of a comprehensive retroviral cartography, giving researchers a point of reference with which to pinpoint koala retrovirus in the genome.

“Having the [full genome] sequence of the koala has given us a completely different picture of where [these retroviruses] are,” says Jenny Graves, a professor studying genetics, ecology and evolution at La Trobe University not affiliated with the work. “It’s not possible to do this any other way.”

The researchers first excavated the genomes of two unrelated koalas for evidence of viral vestiges—including still-active variants of koala retrovirus and copies that had already been domesticated into docility. They were surprised to find fragments of the koala retrovirus nestled in with pieces of another another retrovirus called PhER—a veteran resident of the koala genome that had put down roots long ago. PhER was likely once a retroviral interloper itself, but had long since fallen into a state of disrepair. When the team examined the PhER-koala retrovirus hybrid sequences—essentially broken versions of koala retrovirus—they realized that PhER had invaded and deactivated koala retrovirus by swapping koala retrovirus’ virulent genes for its own junky sequence, in a process called recombination.

While unrelated to koala retrovirus, PhER bore just enough of a resemblance to enable this phenomenon. The genetic switcheroo replaced crucial segments of koala retrovirus with inert body doubles, effectively neutralizing koala retrovirus’ arsenal and locking it in place. All recombination requires is two identical “flanks” on either side of a stretch of DNA: As long as the new segment has the correct bookends, a lethal instruction manual can be supplanted by a manifesto of nonsense.

In effect, PhER, an ancient retroviral element, was acting as a genomic sentinel against new invaders like koala retrovirus. When PhER itself had raided the koala genome millions of years ago, it had gotten stuck—which gave this now kept virus a vested interest in protecting its host from disease: If the koala died, so would PhER.

So, adopting an “if you can’t beat ‘em, join ‘em” attitude, PhER went from virulent villain to loyal footsoldier. “When a host genome and viral genome become a single entity, they have to learn to get along with each other,” explains Roca. “It’s as if these old viruses are saying to new viruses, ‘This is our territory, don’t mess with it.’”

But this great act of amnesty on PhER’s part may also have ulterior motives. Recombining with koala retrovirus isn’t just a way to stamp out the competition—it’s an opportunity for PhER to hijack some highly desirable machinery. When PhER replaces koala retrovirus’ weapons with its own harmless heirlooms, PhER has the chance to pocket the very tools that could break it out of genomic jail—and leave a damaged koala retrovirus to rot in its place.

“This process is bad for koala retrovirus because it becomes less of a virus, but it’s good for PhER, the original endogenous retrovirus, because it lets it proliferate,” says Greenwood.

It’s unlikely that PhER would emerge from the crossfire as a fully fledged infectious virus: It’s spent far too long languishing in the genome. Crippling a new retrovirus may give PhER a chance to shed its shackles—but the most severe consequences are sustained by koala retrovirus itself. Löber suspects that we are observing the slow taming of this pathogen.

In fact, recombination appears to be critical to koala retrovirus’ inactivation. When the researchers searched the genomes of 166 koalas distributed across Australia, they found that individual koalas harbored broken copies of koala retrovirus in many distinct locations in their genomes. Koala retrovirus was actively spreading through the koala population—but over and over again, PhER had raised its hackles until its opponent lost its legs. The sheer prevalence of koala retrovirus disarmament indicated that recombination with PhER has been a net positive for the koala species.

However, not all integrations are created equal. According to Maria Tokuyama, a postdoctoral researcher who studies endogenous retroviruses at Yale University, because koala retrovirus is stationed at so many outposts in the genome, some will likely be more advantageous than others. “Down the line, this may impact survival of certain groups over others,” explains Tokuyama, who was not involved in the research.

According to Greenwood and Roca, after hundreds of thousands of years, virulent versions of koala retrovirus will likely disappear from the population, until only mementos of its infectious past are left. When this happens, the battered hitchhikers that remain—those stationed in spots least detrimental to their hosts—will be the same across all koalas, like the ancient endogenous retroviruses in humans.

Of course, recombination can’t be the only way that retroviruses colonize a genome. The very first intrusions, for instance, couldn’t have relied on prior residents. A host’s cellular machinery may shut down viral DNA directly; or, if a virus makes a mistake during its own reproduction, it could accidentally shackle itself in place. Vertebrate genomes are flecked with dozens of these genomic graves, each commemorating a different ancient invasion of a once-virulent virus.

In their future work, the scientists will track how koala retrovirus continues to embed itself in the genome by sequencing the genomes of koala offspring that have inherited broken copies of the virus. Additionally, the team plans to continue to test the links between koala retrovirus, cancer and immune suppression in the hopes of preserving dwindling communities of the vulnerable koala.

Willa Huston, a professor of microbiology at the University of Technology Sydney who was not affiliated with the study, praised the work as “exciting” and “high quality”—the observation of a “really beautiful science experiment” naturally unfolding in the wild. Huston, who studies chlamydia in koalas, also emphasizes the importance of these findings for the future of koalas overall. “The next stage [in this research] is to understand what it means for conservation of this species,” she says.

While koala retrovirus has done quite a number on Australia’s eucalyptus-munching marsupials, there may still be a light at the end of the tunnel: The union of virus and vertebrate can sometimes yield unexpected benefits. When viruses dig their heels in, the host genome can occasionally take advantage of their enemies’ nifty tricks of the trade. For instance, in other mammals, the formation of the placenta co-opts a retroviral protein. Without this, humans as we know them today would simply not exist. Perhaps PhER’s defensive strategy is a harbinger of times to come, when koala retrovirus may, too, enjoy a less antagonistic (or even beneficial) relationship with its koala landlords. In future generations to come, koalas may yet turn the tables on one of their most formidable foes.

Katherine J. Wu | | READ MORE

Katherine J. Wu is a Boston-based science journalist and Story Collider senior producer whose work has appeared in National Geographic, Undark magazine, Popular Science and more. She holds a Ph.D. in Microbiology and Immunobiology from Harvard University, and was Smithsonian magazine's 2018 AAAS Mass Media Fellow.