Principal Investigator: Natasha Onalenna Moraka

Study Objectives:

General Aim

This study aims to study the viral dynamics of recently diagnosed people living with HIV in the era of “Treat all” in Botswana.

Specific Objectives

  1. To determine recency of HIV infection among individuals initiating cART in Botswana
  2. To determine transmitted and pre-treatment HIV-1 drug resistance patterns in individuals initiating cART in Botswana: TDR in recently infected and PDR in patients initiating cART
  3. Determining impact of baseline HIVDR on clinical outcomes of recently diagnosed individuals initiating cART in Botswana
  4. To determine virologic characteristics of HIV-1 strains from recently infected individuals:

- HIV full genome sequencing of early founder viruses

- Clustering of early founder virus HIV-1 strains

- Determining presence and effect of bNab escape mutations

Study Design:

This will be a longitudinal study utilizing samples from the Botswana national ART program. Whole blood EDTA samples (7mL) will be collected using a consecutive census approach; where all participants diagnosed with HIV will be included in the analysis.

Data from MoHW shows monthly newly initiations onto cART average 200 in the Gaborone area. We target to enroll 50% of these participants (100) monthly for a total of 1200 participants in a year into the study.

Plasma samples (n = 106) from recently diagnosed individuals from the BCPP/”Ya Tsie” study will also be used to generate HIV-1 near-full length sequences using a long-range HIV genotyping protocol from viral RNA by Illumina MISeq and HISeq by BioPolimers Facility in collaboration with the PANGEA HIV consortium at Welcome Trust Sanger Institute (Cambridge, UK;

Study Population and Size:

  • All recently HIV diagnosed individuals within the Gaborone area. All participants will be consenting adults (age >18 years).
  • Stored left over samples for Participants from the Botswana Combination Prevention Project (BCPP) / Ya Tsie Study with documented HIV seroconversion during the study period.
  • This will be a longitudinal cohort of individuals recently diagnosed with HIV. We will use a consecutive census approach, where participants will be recruited according to HIV status for the 1 year sampling period. We target to enroll a maximum of 1200 participants (100 monthly for a year) from all recruitment sites.
  • A total of 106 participants in the BCPP study had documented serocoversion and their residual samples and sequence data will be included in this study.

Study duration: 3 years

Study Results: Study is on-going and no results yet.


  1. The Ministry of Communications, Knowledge and Technology-Botswana - Department of Research, Science and Technology (DRST)
  2. Sub-Saharan Network for TB and HIV research excellence- SANTHE)
  3. Botswana Harvard Health Partnership


Contact Details