Regularly assess to UNAIDS cascade 90-90-90 is important to check the progress and identify any obstacles to its implementation. For this we first studied efficacy of antiretroviral treatment (ART) in the blood of newly diagnosed HIV-positive in Bamako (Mali).In a second work we evaluated the feasibility of viral load and genotypic resistance tests from dried blood spot (DBS). The third part of our work is dedicated to pathophysiological aspects with evaluation of treatment on salivary and genital reservoirs (Bamako patients) and on the vaginal microbiota, as well as the study of the resistance profile of the strains archived in cellular DNA of rectal biopsies. We observed a high rate of lost to follow-up at one year in the Bamako cohort (45%). We also found a high rate of ART primary resistance in Bamako and Chad (> 15%). Reassuringly, the virological success after 1 year of treated follow was about 90% in these adherents. We also demonstrated the efficacy of ART in the salivary compartment and found a compartmentalization of the virus at the cervico-vaginal level in some women under ART. In addition, a dysbiosis was observed before ART, and a normal flora under effective ART. Similar profiles were observed on the main strain isolated in blood at the time of diagnosis and on the archived strain in the rectum after 1 to 5 years of ART.In conclusion, our work provides new information on the progress of the treatment stages of HIV infection in developing countries: low adherence to treatment which can constitute a major obstacle to achieve the plan 90/90/90; a high prevalence of primary resistance advocating accessibility and rational use of different classes of antiretrovirals drugs, widespread routine use of viral load tests and the development of ARVs resistance surveillance network in resource-limited countries; treatment efficacy data on mucosal reservoirs revealing the existence of genital dysbiosis and viral compartmentalization, which raises the problem of the residual risk of transmission in some people, even under ARVs.