Ana S. Gonzalez-Reiche, PhD

During the coronavirus disease 2019 (COVID-19) pandemic we have seen continued appearance of new variants of the SARS-CoV-2 virus, which causes COVID-19. People with weakened immune systems due to underlying conditions such as cancer can develop prolonged viral infections lasting for months to over a year. Under these conditions, the virus can diversify faster, which is thought to give rise to new viral variants that evade existing immunity, such as Omicron. We will study how the virus evolves during long-term infections and becomes able to evade immunity. By examining these changes over time, we can see evolution happening at higher resolution compared to typical infections. This detailed view will give us a better idea of how viral variants arise. Because the virus evolves faster due to unrestricted growth in long-term infections, tracking these genetic changes could help us predict SARS-CoV-2 evolution in the population and inform vaccine development.

Update: Over the past year, our research has focused on long-term SARS-CoV-2 infections in immuno-compromised patients. We identified several new cases of long-term infection and analyzed the virus’s genetic makeup in each, including newer variants like JN.1, KP.2, and KP.3.1.1. We found that these variants also continued mutating during these prolonged infections. During the past year, we have focused on developing an efficient system to characterize the impact of mutated variants. To ensure accuracy, we developed a system to confirm that lab-grown virus samples match those from the original patients. We are also building tools to visualize better how these variants may change over time and escape immunity, despite prior vaccination or infection. This work helps us understand how this now endemic virus continues to adapt in the human population, supporting efforts to prepare for future outbreaks.