Publications

Funding for clinical research |drugs, vaccines, microbicides, diagnostics | HIV/AIDS, tuberculosis, malaria, other infectious diseases |sub-Saharan Africa

EDCTP portfolio: Career Development Fellowships

Dr Deogratius Ssemwanga

Uganda

Dr Deogratius Ssemwanga investigates the role of immune responses among individuals with established HIV infection who acquire new HIV strains.

Immunological selection of recombinants following HIV-1 superinfection

The challenge is to understand the role of immune responses among individuals with established HIV infection who subsequently acquire new HIV strains, a phenomenon known as HIV superinfection (SI), and delineate the evolutionary pathways of mosaic recombinant viruses between initial and SI strains.

The hypothesis is that HIV-1 recombination has a high rate immediately after superinfection; is not random but due to immune selection; facilitates immune escape; and accelerates disease progression.

The challenge

The objective of the study is to determine the recombination rate following superinfection, its causes, and its consequences for the virus (i.e. persistence by immune escape) and for the host (i.e. accelerated disease progression).

Initially, 15 individuals will be included in the study. These participants are previously confirmed SI (n=8) and multiple infected (n=7) cases among female sex workers. Other SI cases identified during an on-going screening from three cohorts will also be included in the study. These cohorts are the female sex worker cohort in Kampala, the fisherfolk communities along the shores of Lake Victoria, and the General Population Cohort in rural South-western Uganda.

Participants with superinfection are defined as having phylogenetically distinct HIV-1 strains using next-generation sequencing (NGS) of partial p24 and gp41 genomic regions. The SI cases will be confirmed by full envelope Single-Genome Sequencing. In SI cases, near full-length genome NGS will be performed on longitudinal plasma samples taken after SI and analysed for recombination using the Iterative Virus Assembler pipeline, REGA subtyping tool, jumping profile Hidden Markov Model, and Simplot software.

In SI cases, the team will generate pseudotyped virus stocks from autologous viral envelope genes representing the initial infecting virus, the SI virus and their recombinant strains. These pseudoviruses will be tested against autologous longitudinal serum (pre- and post-SI). The NAb assays will be done using autologous pseudoviruses and TZM/bl cells expressing the reporter gene luciferase. CTL epitopes will be evaluated by comparing full HIV proteomes from SI cases and controls to analyse and identify predicted Human Leucocyte Antigen (HLA)-restricted CTL epitopes with a special interest in epitopes mapped to recombination sites. High-resolution HLA typing on SI cases and controls will be done to evaluate if there is genetic predisposition to HIV-1 superinfection and emergence of recombinants.

The project

Dr Ssemwanga had the opportunity to train and develop biomedical clinical research skills. Moreover, a panel of envelope pseudoviruses representing pre-SI, SI and recombinant strains will be made freely available for future evaluation of vaccine candidates.

Impact


test the safety and efficacy of this new formulation in young children

Bringing antiretroviral drugs to children

The CHAPAS trials have ensured that many more children with HIV have benefited
from life-saving antiretrovirals.

EDCTP portfolio: HIV & HIV-associated infections

The challenge

The challenge is to understand the role of immune responses among individuals with established HIV infection who subsequently acquire new HIV strains, a phenomenon known as HIV superinfection (SI), and delineate the evolutionary pathways of mosaic recombinant viruses between initial and SI strains.

The hypothesis is that HIV-1 recombination has a high rate immediately after superinfection; is not random but due to immune selection; facilitates immune escape; and accelerates disease progression.

The objective of the study is to determine the recombination rate following superinfection, its causes, and its consequences for the virus (i.e. persistence by immune escape) and for the host (i.e. accelerated disease progression).

Initially, 15 individuals will be included in the study. These participants are previously confirmed SI (n=8) and multiple infected (n=7) cases among female sex workers. Other SI cases identified during an on-going screening from three cohorts will also be included in the study. These cohorts are the female sex worker cohort in Kampala, the fisherfolk communities along the shores of Lake Victoria, and the General Population Cohort in rural South-western Uganda.

Participants with superinfection are defined as having phylogenetically distinct HIV-1 strains using next-generation sequencing (NGS) of partial p24 and gp41 genomic regions. The SI cases will be confirmed by full envelope Single-Genome Sequencing. In SI cases, near full-length genome NGS will be performed on longitudinal plasma samples taken after SI and analysed for recombination using the Iterative Virus Assembler pipeline, REGA subtyping tool, jumping profile Hidden Markov Model, and Simplot software.

In SI cases, the team will generate pseudotyped virus stocks from autologous viral envelope genes representing the initial infecting virus, the SI virus and their recombinant strains. These pseudoviruses will be tested against autologous longitudinal serum (pre- and post-SI). The NAb assays will be done using autologous pseudoviruses and TZM/bl cells expressing the reporter gene luciferase. CTL epitopes will be evaluated by comparing full HIV proteomes from SI cases and controls to analyse and identify predicted Human Leucocyte Antigen (HLA)-restricted CTL epitopes with a special interest in epitopes mapped to recombination sites. High-resolution HLA typing on SI cases and controls will be done to evaluate if there is genetic predisposition to HIV-1 superinfection and emergence of recombinants.

The project

The later CHAPAS-3 trial compared the efficacy and safety of three fixed-dose combinations including two without stavudine (found to have some long-term side effects in adults, leading to a recommendation that its use be discontinued in children). The trial the first of its kind in Africa studied nearly 500 children at four sites in two African countries.

Dr Ssemwanga had the opportunity to train and develop biomedical clinical research skills. Moreover, a panel of envelope pseudoviruses representing pre-SI, SI and recombinant strains will be made freely available for future evaluation of vaccine candidates.

ratios forfixed-dose combinations and on appropriatedosage according to weight. 

The CHAPAS-3 trial confirmed the effectiveness of fixed-dose combinations, providing further impetus to the rollout of antiretrovirals to children. Its evidence on abacavir informed the WHO recommendation of abacavir-containing combinations for first-line therapy in children. Trial data have also been used to support applications for regulatory approval for new scored efavirenz tablets.

Impact

L’homme RF et al. Nevirapine, stavudine and lamivudine pharmacokinetics in African children on paediatric fixed-dose combination tablets. AIDS. 2008;22(5):557–65.

Mulenga V et al. Abacavir, zidovudine, or stavudine as paediatric tablets for African HIVinfected children (CHAPAS-3): an open-label, parallel-group, randomised controlled trial. Lancet Infect Dis. 2016;16(2):169–79.

WHO. Guidelines on the use of antiretroviral drugs for treating and preventing HIV infection: recommendations for a public health approach. 2010.

WHO. Consolidated guidelines on the use of antiretroviral drugs
for treating and preventing

HIV infection: Recommendations for a public health approach
(second edition). 2016

Projects: Children with HIV in Africa Pharmacokinetics and Adherence of Simple Antiretroviral Regimens (CHAPAS): CHAPAS-1 and -3

Project lead: Professor Chifumbe Chintu, University Teaching Hospital, Zambia (CHAPAS-1); Dr Veronica Mulenga, University Teaching Hospital, Zambia (CHAPAS-3)

Target population(s): Children with HIV

Sample size: 71 (CHAPAS-1); 480 (CHAPAS-3)

Countries involved: Ireland, the Netherlands, the UK, the USA, Zambia (CHAPAS-1); Uganda, Zambia (CHAPAS-3)

Project duration: 2005–2009 (CHAPAS-1); 2010 –2011 (CHAPAS-3)

EDCTP funding: €1.2M (CHAPAS-1); €4.6M (CHAPAS-3)

Total project funding: €1.2M (CHAPAS-1); €5.0M