Viral heterogeneity and plasticity at the single-cell level – VITAL

Viruses are obligate intracellular parasites, often regarded as molecular automata with exceptional adaptability driven by a high mutation rate. While the adaptability of viruses has thoroughly been studied through the lens of genetics, it is unknown if viruses can adapt to their environment in a non-genetic fashion through single-cell heterogeneity and phenotypic plasticity, similarly to living cells. I recently showed that the infection of a homogeneous cell population with SARS-CoV-2 results in a highly heterogeneous viral RNA load across cells. However, it remains unclear whether individual viral gene expression is also heterogeneous, due to the inability up to now of common scRNA-seq techniques to detect most viral transcripts. Here, we will overcome these limitations by leveraging new scRNA-seq protocols and developing novel tools to detect viral transcriptome at the single-cell level. This will allow us to explore our main objective: test whether viruses are subject to non-genetic adaptation through heterogeneity and phenotypic plasticity. To do so, I will first assess whether the viral transcriptome is heterogenous across infected single-cells before testing the existence of viral phenotypic plasticity itself. Finally, I will determine whether viral heterogeneity is explained by an heterogenous cell state prior to infection. Overall, this project will significantly advance the field of virology by elucidating the contribution of non-genetic processes to viral adaptation, paving the way to novel therapeutic approaches that could highjack these newly identified viral adaption mechanisms.