Publications

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

Dr Vito Baraka

Tanzania

EDCTP portfolio: Career Development Fellowships

Dr Vito Baraka uses high-throughput next-generation sequencing to determine genetic profiles of drug resistance and population structure of Plasmodium falciparum.

Molecular markers of resistance to artemisinin and partner drugs 

The emergence and spread of Plasmodium falciparum resistance present major challenges for malaria control and elimination. Thus, molecular monitoring of drug resistance is considered important for the detection and tracking of drug-resistant parasites. The recent advancement in next-generation sequencing (NGS) facilitates cost-effective high-throughput detection of resistance and the origin of parasite populations with different genetic backgrounds. This is relevant for monitoring antimalarial drug resistance and tracking the geographic spread of parasite populations.

The challenge

Dr Baraka will use NGS-based approaches to determine molecular markers of resistance to both artemisinin and partner drugs, parasite genetic diversity and population structure in African settings. In addition, the study will also generate evidence on the ex vivo susceptibility of antimalarial drugs.

Samples will be collected from sentinel sites of the national malaria control programmes (NMCPs) in Burkina Faso, the Democratic Republic of the Congo, and Tanzania. The detection of molecular markers of drug resistance will be carried out using a high-throughput NGS platform (Illumina®-based technology) for targeted amplicon sequencing. Following multiplexing PCR amplification of the targeted sequences and indexing, pooled gene fragments will be sequenced using the Illumina Miseq® platform.

To determine the geographical origin and spread of P. falciparum population to other regions, we will use polymorphisms (SNPs barcode) in the organellar genome. Photo-induced electron transfer real-time PCR (PET-PCR) assay will be used to detect plasmepsin 2-3 and pfmdr1 copy number of P. falciparum. Ex vivo tests will be performed using the HRP-2 assay.

The project

The study is expected to generate P. falciparum temporal genotyping data of molecular markers of resistance to artemisinin (Pfkelch 13), parasite background mutation (mdr2, fd, arps10, pfap2mu and pfubp1) and resistance to partner drugs (Pfmdr1, Pfcrt and Plasmepsin 2-3 copy numbers). The molecular evidence is critical to inform NMCPs, WHO and others on the efficacy of ACTs as well as drugs used in chemoprevention strategies in the region.

Data on the geographical origin and spread of parasite populations is crucial to signal the dispersal of artemisinin-resistant strains to African settings. Furthermore, data generated on ex vivo sensitivity of antimalarial partner drugs is highly relevant as resistance against long-acting partner drugs is likely to accumulate due to post-treatment selection.

Furthermore, the capacity building in next-generation sequencing and bioinformatics will enhance local capacity and further interaction with partner institutions in addressing global health challenges.

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 emergence and spread of Plasmodium falciparum resistance present major challenges for malaria control and elimination. Thus, molecular monitoring of drug resistance is considered important for the detection and tracking of drug-resistant parasites. The recent advancement in next-generation sequencing (NGS) facilitates cost-effective high-throughput detection of resistance and the origin of parasite populations with different genetic backgrounds. This is relevant for monitoring antimalarial drug resistance and tracking the geographic spread of parasite populations.

Dr Baraka will use NGS-based approaches to determine molecular markers of resistance to both artemisinin and partner drugs, parasite genetic diversity and population structure in African settings. In addition, the study will also generate evidence on the ex vivo susceptibility of antimalarial drugs.

Samples will be collected from sentinel sites of the national malaria control programmes (NMCPs) in Burkina Faso, the Democratic Republic of the Congo, and Tanzania. The detection of molecular markers of drug resistance will be carried out using a high-throughput NGS platform (Illumina®-based technology) for targeted amplicon sequencing. Following multiplexing PCR amplification of the targeted sequences and indexing, pooled gene fragments will be sequenced using the Illumina Miseq® platform.

To determine the geographical origin and spread of P. falciparum population to other regions, we will use polymorphisms (SNPs barcode) in the organellar genome. Photo-induced electron transfer real-time PCR (PET-PCR) assay will be used to detect plasmepsin 2-3 and pfmdr1 copy number of P. falciparum. Ex vivo tests will be performed using the HRP-2 assay.

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.

The study is expected to generate P. falciparum temporal genotyping data of molecular markers of resistance to artemisinin (Pfkelch 13), parasite background mutation (mdr2, fd, arps10, pfap2mu and pfubp1) and resistance to partner drugs (Pfmdr1, Pfcrt and Plasmepsin 2-3 copy numbers). The molecular evidence is critical to inform NMCPs, WHO and others on the efficacy of ACTs as well as drugs used in chemoprevention strategies in the region.

Data on the geographical origin and spread of parasite populations is crucial to signal the dispersal of artemisinin-resistant strains to African settings. Furthermore, data generated on ex vivo sensitivity of antimalarial partner drugs is highly relevant as resistance against long-acting partner drugs is likely to accumulate due to post-treatment selection.

Furthermore, the capacity building in next-generation sequencing and bioinformatics will enhance local capacity and further interaction with partner institutions in addressing global health challenges.

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