The second seminar in our series on “Emergent Pathogens, with a Special Focus on Flaviviruses” featured Dr. Julien Pompon, head of the Interhost Arbovirus Transmission (iHAT) team at the French Institute of Research and Development. Dr. Pompon is also the project coordinator of  Flavivaccine, an EU research project that aims to combat mosquito-borne diseases.

How Flaviviruses Use SF RNA to Evade Immune Detection

In his presentation, Dr. Pompon focused on the role of subgenomic flavivirus RNA (SF RNA), a non-coding RNA produced by the virus during infection. Differently to viral components that help replicate the genome or build new virus particles, SF RNA plays another role: it helps the virus avoid early detection by the host’s immune system.

“SF RNA suppresses the interferon response, which is a key part of our body’s first line of defense,” Dr. Pompon said. “That gives the virus a head start, allowing it to replicate more efficiently in skin cells, where infection usually begins after a mosquito bite.”

Dr. Pompon also highlighted how mosquitoes deliver SF RNA into the host. Rather than being released freely, the RNA is enclosed in tiny extracellular vesicles within mosquito saliva. These microscopic packages protect the RNA from degradation and help it reach its target.

“Mosquitoes don’t just inject the virus—they inject these vesicles carrying SF RNA,” he explained. “It’s a clever delivery system that ensures the RNA interferes with immune signalling right where the virus needs it most.”

A Direct Link Between SF RNA and Infection Severity

Pompon also shared recent findings from his team, showing that the amount of SF RNA in mosquito saliva directly impacts infection severity. In both human cell cultures and mouse models, they found higher SF RNA levels led to more aggressive viral replication and severe symptoms.

This evidence suggests that SF RNA is not a passive byproduct of infection, but a strategic tool the virus uses to strengthen its grip on the host.

Implications for Vaccines and Future Treatments

These findings come at a crucial time, as public health experts face ongoing challenges with mosquito-borne diseases. While vaccines for yellow fever and Japanese encephalitis are effective, others, like dengue, remain difficult to tackle.

Dr. Pompon’s research opens up the possibility of targeting SF RNA directly—either to weaken the virus or to boost the immune system’s response. Blocking SF RNA activity could become a promising new strategy in the fight against flaviviruses, potentially making existing vaccines more effective or reducing reliance on them altogether.