BKV activates the interferon-β response in primary and immortalized microvascular endothelial cells late in the infectious cycle, resulting in persistence.

UNLABELLED: Our previous studies have shown that inoculation of primary endothelial cells with BKV results in a long-term persistent infection, with inoculated cultures surviving up to 60 days while producing low levels of infectious viral progeny. Unlike the permissive renal proximal tubule cells, infected endothelial cells activate innate immunity pathways in response to BKV infection. We hypothesized that the innate immune response limits BKV infection, resulting in persistence. In this report, we show that activation of innate immune pathways is not triggered by incoming virus particles but rather occurs at a late stage of the infectious cycle, when viral DNA replication, high levels of late viral transcription, and progeny virion assembly are occurring. Single-cell transcriptomic data indicate that this response varies across the infected cell population, with some cells showing little or no innate immune response, while others appear to be highly activated. Bulk RNA-seq experiments show that the addition of interferon-β to endothelial cells results in the upregulation of a subset of known interferon-stimulated genes (ISGs), as well as many other genes not known to be associated with the interferon response. Finally, we show that the addition of interferon-β blocks BKV infection, so long as it is added prior to or soon after inoculation. These results lead to a model in which BKV infection of endothelial cells results in interferon production and ISG induction that restrict subsequent rounds of infection and lead to a persistent state. IMPORTANCE: BKV infects nearly every human on Earth, and the infection persists throughout life. The cell types where the virus persists remain a mystery, as do the state of the viral genome during persistence, as well as the mechanisms that limit productive infection and maintain persistence. While BKV is known to replicate robustly in renal proximal tubule cells during disease, it is not clear whether the virus persists in these cells. The proximal tubules are located in close proximity to endothelial cells, raising the possibility that BKV persistence occurs in the endothelia, and virus particles from infected endothelia potentially seed infections in the neighboring tubular epithelia during times of cellular stress or immunosuppression. The development of cell culture systems to study the interactions between innate immunity, virus production, and persistence is needed to advance the development of anti-viral strategies.