Proviral and viral sequencing of SIVmac251 in a non human primate model of post treatment control
Near-full-length SIV genome sequencing was conducted with the nanopore technology in samples from 5 post treatment controllers(3 treated at 4 weeks post infection (pi), 2 treated at W24 pi) and 5 non controllers (2 treated at W4 pi, 3 treated at W24 pi). SIV proviruses were sequenced from PBMCs and various tissues at the end of the study, including thymus, spleen, cervical and mesenteric LN, ileum, colon, rectum, lungs, kidney, depending on their availability in sufficient quantities. If plasma was available, circulating SIV RNA were sequenced at primary infection, W4 pi and at W24 pi (for macaques treated at W24 pi). For NCs, plasma SIV RNA was also sequenced at the time of viral rebound and at the end of the study. The inoculum that served for initial infection was sequenced to track genetic evolution.