Heterogeneity in viral replication dynamics shapes the antiviral response

Abstract

In response to virus infection, host cells can activate antiviral signaling to restrict virus replication and communicate viral infection to neighboring cells. For poorly understood reasons, antiviral response activation is highly heterogeneous among infected cells; both quantitatively (level of pathway activation) and qualitatively (transcribed antiviral gene set). Here, we used live-cell single-molecule imaging to simultaneously visualize viral infection and antiviral signaling, providing quantitative insights into antiviral response activation in single cells; first, the probability of activating an antiviral response varies throughout infection, with most efficient activation occurring several hours after the first viral replication. Second, cell-to-cell heterogeneity in viral replication rates early in infection determine the efficiency of antiviral response activation. Finally, variation in signaling strength of the viral sensing pathway result in qualitatively distinct antiviral responses. Together, this works identifies key parameters that shape the antiviral response and provides quantitative insights into the origin of heterogeneity in the antiviral response.

Pharmacological modulators of epithelial immunity uncovered by synthetic genetic tracing of SARS-CoV-2 infection responses

“…Here, we report the COVGT sLCRs, and the validation of the approach to design such reporters, as a useful resource for investigating mechanisms of cellular response to SARS-CoV-2 entry and replication as well as a phenotypic platform for high-throughput screening of therapeutics. Efforts to combine reporters for viral entry and replication with those measuring cellular transcriptional responses are timely 22 . The flexibility to use such systems in any chosen model, potentially including preclinical models in vivo , is a unique feature of our system.…”

“…Additionally, the adaptability of our system to establish in vitro infection models allows the rapid testing of wild-type and evolving pathogens stains. Whereas heterogeneous responses to viral infection are likely rooted in biology 22 , future experiments with this and other reporters will likely benefit from using cellular models that are physiologically more accurate than cell lines. Incidentally, our experiments uncovered 293T cells as a better responsive model to triggers of innate immunity and viral infection.…”

Single-molecule visualization of mRNA circularization during translation

“…The smFI methods will help answer these questions. Since the development of NCT or SINAPS, the sm study of translational kinetics/dynamics in living cells has focused on various subjects [77][78][79][80][81] . Nevertheless, it is still difficult to track single or multiple translation regulators at the same time owing to the high intracellular concentration of the targets 74,75 , although one example has been reported 50 .…”

Zika virus NS3 and NS5 proteins determine strain-dependent differences in dsRNA accumulation in a host cell type-dependent manner

“…It is well established that ZIKV nonstructural proteins, including both NS3 and NS5, interfere with both the induction of type I IFN responses and IFN signalling [15][16][17][18][19][20][21]. Furthermore, there is growing evidence that despite variability in the antiviral response, viral factors shape the host response to infection [7,[22][23][24][25]. We previously identified ZIKV isolates with differing levels of dsRNA accumulation, ZIKV PR (high dsRNA per infected cell) and ZIKV CDN (low dsRNA per infected cell) [26].…”