Fig. 8

Detailed analysis of the balance of IS and MS isoforms during early times of CD4+ T cell infection. Relative level of IS RNA Env/Vpu 1 (a) and MS RNA Nef 2 (b) at different times post-infection of CD4+ T cells from three different donors were monitored by qPCR using the ΔΔCq method and normalized to the level of total viral RNA. Relative level of viral isoforms expressed in donor 4 determined by ONT sequencing is indicated in orange. ONT quantifications were based on the number of reads mapping to a particular isoform normalized by the total number of viral reads. c Dynamic expression of Env/Vpu 1 and Nef 2 monitored by ONT sequencing and normalized to the total number of transcripts belonging to the D1A5 branch of the tree. d Relative level of transcripts resulting from splicing between D1 and A2 without inclusion of NCE 3 (Vpr 1 and Vpr 3) was monitored by qPCR and ONT sequencing as in a. e Total number of transcripts generated by D1A2 splicing was monitored as in a. f ONT quantification of IS or MS isoforms generated by D1A2 splicing with (w/) or without NCE 3. Relative levels were normalized to the total level of D1A2 transcripts. g Relative level of transcripts resulting from splicing between D1 and A1 without inclusion of NCE 2 (Vif 1 and Vif 2) was monitored by qPCR and ONT sequencing as in a. h Total number of transcripts generated by D1A1 splicing was monitored as in a. i ONT quantification of IS or MS isoforms generated by D1A1 splicing with (w/) or without NCE 2. Relative levels were normalized to the total level of D1A1 transcripts