How Do Acute Viral Infections Turn Chronic?

Infections caused by viruses, such as respiratory syncytial virus, or RSV, measles, parainfluenza and Ebola, are typically considered acute. These viruses cause disease quickly and live within a host for a limited time.

A team of researchers at the University of Pennsylvania became curious why certain, seemingly acute, viral infections can persist for extended periods of time. RSV, for example, can lead to chronic respiratory problems, measles can lead to encephalitis, and the Ebola virus can be transmitted by patients thought to be cured of the disease.

Now, new findings – published recently in Nature Communications in an article entitled “Replication Defective Viral Genomes Exploit a Cellular Pro-Survival Mechanism to Establish Paramyxovirus Persistence” – suggest a mechanism that may explain how viruses can linger.

The research team found that products of a viral infection called defective viral genomes (DVGs), which have been known to be involved in triggering an immune response, can also kick off a molecular pathway that keeps infected cells alive. In this new study, the investigators used a novel technique to examine the presence of DVGs on a cell-by-cell basis, showing that DVG-enriched cells have strategies to survive in the face of an immune-system attack.

“One of the things the field has known for a long time is that DVGs promote persistent infections in tissue culture,” explained senior study investigator Carolina López, Ph.D., associate professor of microbiology and immunology at the University of Pennsylvania, School of Veterinary Medicine. “But the question was, how do you reconcile that with the fact that they’re also very immunostimulatory? How can they help clear virus at the same time as they promote persistence? Our work helps explain this apparent paradox.”

DVGs are partial viral genomes produced in infected cells when a virus begins to replicate rapidly, leading to defective versions of itself that contain large deletions. Once thought not to have any biological function, DVGs are increasingly believed to be important components of viral infections.

Previous studies from the Penn team found that DVGs were critical in stimulating an immune response to respiratory viruses in mice—when DVGs were depleted from a virus, mice had more severe infections. Moreover, in 2015, the researchers reported that DVGs were critical for stimulating an immune response to the human virus RSV, also demonstrating for the first time that the presence of DVGs in human respiratory samples from infected patients correlates with enhanced antiviral immune responses.

In the current study, Dr. López and her colleagues’ sophisticated technique allowed them to differentiate full-length genomes from the partial genomes of DVGs at the single-cell level. They studied cells in culture infected with the Sendai virus or with RSV, a virus that often affects infants and can lead to chronic respiratory problems.

Labeling the full-length genomes in red and the partial DVGs in green, the researchers found differences from cell to cell. Some cells had hardly any DVGs, while others were highly enriched with DVGs, with only a small number of full-length genomes.

“We saw this in many different cell lines and even in infected lungs in mice,” López said. “We hadn’t appreciated before that there is a lot of heterogeneity in what is going on with these DVGs.”

To dig deeper into how the DVGs were influencing the course of infection, the researchers infected cells either with a version of the Sendai virus that lacked DVGs or one enriched in DVGs. The cells infected with the virus high in DVGs survived more than twice as long as those infected with virus lacking DVGs. Adding purified DVGs boosted the cells’ survival time, indicating a direct role for the DVGs in promoting cell survival. Comparable results were seen with RSV, suggesting that the pro-survival role of DVGs held across viral types.

A final set of experiments elucidated the mechanism by which a subset of DVG-enriched cells persisted during viral infection. The scientists found that signaling through the mitochondrial antiviral-signaling protein (MAVS) and tumor necrosis factor (TNF) receptor 2 protects infected cells from apoptosis that is otherwise triggered by TNFα.

“We found this dual role for TNF during these infections,” Dr. López remarked. “If TNF binds to a cell that doesn’t have the MAVS pathway engaged but is infected, the cell is killed; but, if the cell does have this pathway engaged, then it is protected. MAVS is engaged during the antiviral response, and only cells that have a lot of DVGs activate this pathway. These data show that our cells are wired to survive if they are engaged in an antiviral response, explaining the paradoxical functions of DVGs. It seems that in order to persist, the virus is taking advantage of these host pathways that are there to promote the survival of cells working to eliminate the virus.”

The results, though limited to in vitro studies in the current report, point to a way that DVGs could enable “acute” viral infections to linger. Dr. López hopes to build on these findings to be sure they hold in vivo. She’s also curious to learn more about the dual roles of TNF, which may help explain why the use of TNF-targeted therapies hasn’t always turned out as expected.

“I want to see if there’s a way we can harness this pathway to minimize and avoid the persistence of these viruses, which is really relevant if we think about the chronic diseases associated with some of these respiratory viruses,” Dr. López concluded.