How mutant viral swarms spread disease

Sometime in late 2013, a mosquito-borne virus called chikungunya appeared for the first time in the Western Hemisphere. Chikungunya, or “chik,” as it’s called, rarely kills its human hosts. But it can cause fever, rash and debilitating joint pain. In the two years since it first arrived in the Caribbean, chik has spread wildly across the Americas. It is now suspected of having infected over 1 million people in 44 countries and territories, creating a hemisphere-wide horde of mosquito-borne suffering.

The same biological quirks that have contributed to chik’s success are showing researchers how to fight it — and other viruses like it. Chik is an RNA virus, just like influenza, West Nile virus, hepatitis and Ebola, among others. Unlike DNA viruses, which contain two copies of their genetic information, RNA viruses are single-stranded. When they replicate, any errors in the single strand get passed on. As a result, copying is sloppy, and so each new generation of RNA viruses tends to have lots of errors. In only a few generations, a single virus can become a mutant swarm of closely related viruses.

This viral genetic jumble has given Marco Vignuzzi, a virologist at the Pasteur Institute in Paris, a way to predict the future evolution of RNA viruses like chik. Vignuzzi has re-created a single mutation in chik that occurred early in the virus’s around-the-world adventure, work that illuminated how the virus was able to spread so widely in such a short amount of time. Now Vignuzzi is trying to predict chik’s future. This past June, at the annual meeting of the American Society for Microbiology in New Orleans, Vignuzzi showcased the two mutations in chik that are most likely to develop next.

Viruses are tricky and complex beasts; no one can predict exactly what they will do. But if researchers are ever to get a step ahead of the rapidly shifting world of viruses around us, they will need to deconstruct the viral swarm.

A Viral Potluck

For almost 40 years, scientists have worked to understand how RNA viruses can have so many mutations and still be so successful.

In the late 1970s, the virologist Esteban Domingo of the Autonomous University of Madrid was trying to measure the sloppiness of replication using an RNA virus that infects bacteria. He found that one mutation occurred every time the virus copied its genome, on average. As a result, a single virus produces an array of daughter viruses that are almost, but not quite, identical. Every generation spawns another array of viruses, leading to what Domingo called a “mutant cloud” of viruses.

However, most of the mutations in viral clouds create problems for the virus. Researchers assumed that any single mutated version of a healthy virus was likely destined for extinction. But then in 2006, scientists published an account of a thriving dengue virus in Myanmar with what should have been a catastrophic error in the middle of a vital gene.

When a virus infects a cell, it begins to copy the cell’s genome, incurring mutations as it does so. When daughter viruses assemble themselves in the cytoplasmic soup of genes and proteins, the overall virus that results is often a mash-up of these mutated copies. If one mutation creates a dud protein, as happened with dengue, the virus can survive because of other viruses in the swarm that have a good copy. Think of it as a potluck, Domingo said. The host asks people to bring many types of dishes. That way, if any one person arrives late or burns a pie, a single missing item won’t ruin the dinner.

For a virus, a variety of options allows it not only to infect different hosts, as chik and dengue do with humans and mosquitoes, but also to infect different tissues within the same host. “This cloud of mutations makes it easier for viruses to explore new tissues and new hosts,” Domingo said.

In 2005, Vignuzzi was studying polio, another RNA virus, as a researcher in the lab of the virologist Raul Andino at the University of California, San Francisco. Polio infections tend to start in the gut and move to the brain; Vignuzzi wanted to study the role that viral diversity plays in the leap. He started by engineering a polio virus that copied its genome with fewer errors than usual. The virus could infect the brain just fine — as long as it was directly injected and didn’t have to travel to get there. But without a swarm of diversity, the virus couldn’t move from the gut to the brain.

Next, Vignuzzi and his colleagues used chemicals to induce mutations in this polio virus, enlarging the size of the mutant cloud. The polio traveled from the gut and into the brain, which it then infected quite well. The virus needed a large swarm in order to do its job.

“This was the first time we could control the number of mutations and see whether the mutant swarm was biologically relevant or just an accident,” Vignuzzi said. “And we found that when you have a more restricted swarm, you can’t adapt as well.”

On the flip side, too many mutants aren’t good for a viral swarm either. Domingo and Vignuzzi pointed out that the popular antiviral medication ribavirin pushes viruses to develop a swarm that is so big and so full of mutations that the resulting viral potluck is missing vital components. “Viruses have to optimize the size of the swarm to have enough mutants that you can adapt to new conditions, but not making too many mistakes, which would then kill your population,” Vignuzzi said.

Viral variants also let viruses evolve and spread themselves to new species. In 2009, a rabies outbreak in gray foxes in Humboldt County, north of San Francisco, was traced back to skunk virus that had jumped to foxes. To see when this jump may have occurred, Monica Borucki, a virologist at the Lawrence Livermore National Laboratory in California, used advanced next-generation genetic sequencing to examine the viral swarms of rabies-infected animals going all the way back to 1995. This type of deep sequencing lets researchers search for minor variants in a virus that can acquire mutations and ultimately take over. And indeed, Borucki found genetic traces of the outbreak virus even in the earliest samples.

The results, published in PLOS Neglected Tropical Diseases in 2013, showed that rare viral variants in an individual provide crucial reservoirs of genetic diversity that can help a virus jump species and evolve. It also offered some of the first clues that could help scientists begin to predict what might happen in the future, if they could only deconstruct the viral swarm.

One Mutation, and a Huge Jump

Half a world away from Borucki’s California lab, Vignuzzi had turned his attention to chikungunya, which had gained popular and scientific interest after an outbreak on Reunion, a French island off the east coast of Madagascar, sickened more than one-third of the population. Chikungunya is frequently found on the east coast of Africa, where it is transmitted by Aedes aegypti mosquitoes, but Reunion had very few of those mosquitoes. Instead, the island had a closely related species known as the Asian tiger mosquito (Aedes albopictus). Chik didn’t typically fare very well in Asian tiger mosquitoes, but on Reunion, the virus seemed to be thriving. Researchers eventually realized that a single mutation in one of the proteins that coat the virus allowed chik to pick the lock of the Asian tiger mosquito cells and enter much more easily.

When researchers compared the original strain, from Kenya, to the Reunion one, they found that the Reunion strain was 40 to 100 times better suited to the Asian tiger mosquito — an amazing jump for just one mutation. Subsequent work revealed that similar mutations had happened at least three more times as the chik outbreak spread throughout countries along the Indian Ocean.

Since this mutation was so simple and so advantageous, Vignuzzi decided to see if it would happen again in the lab while he watched. If it did, it would provide some of the first evidence that researchers could watch a viral swarm as it adapted, and maybe even predict its future. He took the original chikungunya strain circulating in Kenya and infected a group of Asian tiger mosquitoes with it.

Like polio, chik moves from one place to another in the body. It starts replicating in the mosquito’s midgut before making its way to the salivary glands and then into the saliva, a process that takes around a week.

On the seventh day of this process, Vignuzzi and his postdoc Kenneth Stapleford dissected the mosquitoes, extracting virus from the midgut, salivary glands and saliva, and sequencing the viruses found in each sample. In the midgut, they found many random mutations, but no single mutation appeared in more than one mosquito. The saliva, however, told a different story. The saliva in three of four mosquitos contained the Reunion mutant. In one of these, the Reunion mutant made up 99 percent of the total virus population.

“We were able to create, within seven days, the emergence in the swarm of an epidemic strain that took at least several years to occur in nature,” Vignuzzi said.

The virus didn’t stop evolving in Reunion. A continuing outbreak meant ongoing opportunities to evolve further. The first mutation had popped up so quickly in the lab that Vignuzzi and Stapleford began to wonder if they could predict further changes to the virus. So they repeated their experiments, but this time they started by infecting the mosquitoes with the Reunion strain. They let the virus percolate in the mosquitoes for 10 days, to give it more time to acquire new mutations. Again they sequenced the viruses they found in the various mosquito tissues, and they identified two new mutants, both with mutations in the same lock-picking coat protein as the original Reunion mutant, results they published last year in Cell Host and Microbe. Ongoing work, which Vignuzzi presented at the microbiology meeting in June, has involved tracking how these mutations were selected in mice, a stand-in for chik-infected humans.

A New Measure of Fitness

The swarm concept is forcing some scientists to rethink some of the basic tenets of population genetics. Typically, the fitness of a virus is measured by how many copies of itself it can make compared to another virus, according to Andino. But, he said, that doesn’t capture the full picture. Virologists like Andino and Domingo argue that the evolutionary fitness of a virus should include its ability to mutate. “If an infection is a process of adaptation, a fitter virus is better able to adapt,” Andino said.

Furthermore, you can’t measure the fitness of a single virus. Since individual virus variants can cooperate and interact, readily swapping proteins in their final product, the smallest unit evolution can select for is the swarm itself. Only by considering the whole mutant cloud of viruses can scientists hope to understand how they behave and what they might do in the future.

“If you look back at all the viruses in historical samples, you can see how it changed to get where it is today, which you can also use to, say, predict a new host,” Borucki said.

As Vignuzzi continues to work on identifying chik’s next mutations, the inherent unpredictability of viral behavior has become clear. No one was surprised when chik reached the Americas. What was unexpected was the viral strain that arrived. “Everyone thought that it was going to be the Reunion strain that reached the Americas,” said Scott Weaver, a virologist at the University of Texas Medical Branch.

Instead, it was an Asian strain of chik that had been circulating at low levels for decades, producing its own mutant swarms. The Reunion strain continues to circulate, but with a million infected in the Americas and millions more at risk, the urgency to understand chik has shifted to the Asian strain. Vignuzzi and Stapleford have begun their mosquito experiments anew to try and predict what chik might do in Central and South America, as the swarm continues its inexorable evolution.