Fig. 2.

Schematic representation of HIV-1 RNA population detected by ONT sequencing in infected T cells. Organization of HIV NL4-3 genome as well as position of SD and SA sites identified in Fig. 1 are indicated. Nomenclatures of introns and exons are according to [4, 5]. Only transcripts that were detected by ONT sequencing at least 5 times across infected CD4+ T cells are represented. Thick boxes correspond to retained exons and thin lines excised introns. Transcripts known or susceptible to encode the same viral proteins were grouped together and their ORF were color-coded (blue for Env/Vpu, green for Nef, yellow for Rev, pink for Tat, purple for Vif and red for Vpr). RNA species were named as indicated on the left side according to [4, 5, 10]. Putative new isoforms are indicated by black dots on the right side