Human immunodeficiency virus 1 Raw sequence reads

We study epitranscriptomic modifications of viral RNA genomes and their role in viral replication. In the context of the study of HIV-1, it has been shown that certain modifications of the viral RNA genome allow the virus to escape detection by innate immune sensors. However, we want to know if these epitranscriptomic marks modify the fidelity of the HIV polymerase to the reverse transcription step. To do so, we perform an in vitro primer elongation experiment with HIV polymerase on a 100mer RNA (modified or not on a single site) corresponding to an HIV-1 genome sequence and a DNA primer. We test different reverse transcription conditions, mimicking different cell types infected by the virus (activated or quiescent cells with more or less dNTP for example).