About

The Challenge

The COVID-19 pandemic led to an unprecedented expansion in global genomic sequencing capacity, including on the African continent. However, to realise the full potential of this newly created sequencing capacity, genomic data needs to be integrated with epidemiological data to better inform public health decision making. The improved ability to link genomic sequencing data to clinical and epidemiological data will create better surveillance systems for the monitoring of infectious diseases in sub-Saharan Africa.

The Solution

EDCTP3 and the Bill & Melinda Gates Foundation joined forces to initiate a network of projects that would strengthen genomic epidemiology in Africa and foster the translation of data to inform public health decision making.  Building on the lessons learnt in responding to SARS-CoV-2 and applying them to the diagnosis, monitoring and clinical management of other pathogens, this will not only enable African countries to better respond to current infectious diseases, but also prepare them better for future pandemics.

The main objectives to help achieve these overarching goals are:

  • Creation of successful case studies: Implementing selected projects of translational research to establish proof of principle and best practice.

  • Building the environment in which such approaches can be rolled out further: Increase capacities of genomic epidemiology approaches on the continent by establishing sustainable networks and communities of practice to strengthen expertise in the principles and methods of epidemiology.

Our Approach

The overall goal of the proposed Genomic Surveillance to Control Pathogen Infections in Africa Project is to build on the lessons learnt in responding to SARS-CoV-2 and apply them to the diagnosis, monitoring and clinical management of other pathogens to be able to better respond to our current epidemics but at the same time be better prepared for future pandemics. The project will address the following objectives:

  1.  Expand the use of genomic epidemiology in South Africa, Kenya and Mozambique to respond to current epidemics.

  2. Develop, implement, and assess NGS-driven approaches to combat drug resistant TB and resistance to ARVs through precision medicine and precision public health.

  3. Conduct early warning surveillance in wastewater and animals (One Health) in South Africa and Kenya.

  4. Contribute to the creation of data platforms that seamlessly integrate epidemiologic, clinical, and genomic data in South Africa, Kenya, and Mozambique.

  5. Conduct capacity strengthening training to inform decision making and policy development in support of robust genomics surveillance in Mozambique and other LMICs.

  6.  Help streamline African efforts through our active participation in the African Genomic Epidemiology Network in close collaboration with Africa PGI, PHA2GE and other international consortia.

Research Highlights

  • South Africa has one of the highest global burdens of rifampicin-resistant tuberculosis (RR-TB). Approximately 5% of all TB cases in South Africa are RR-TB with the highest notification rates in the Western Cape (WC), Eastern Cape and KwaZulu-Natal provinces. Though cases of RR-TB tuberculosis cases have seemingly dropped since 2019, it is not clear if the reduction is due to service disruption and lower testing rates during the COVID-19 pandemic. In 2023, the South African National Department of Health (DoH) plans to implement the novel BPaLM (bedaquiline, pretomanid, linezolid and moxifloxacin) injection-free regimen for the treatment of all RR-TB patients. However, routine drug susceptibility testing (DST) remains limited to isoniazid, rifampicin, second-line injectable drugs and fluoroquinolones. Only when requested, is extended DST performed with associated time delays, meaning individual patients may receive ineffective treatment and the disease can spread further. To combat this issue, the GenPath Africa project will use next-generation sequencing (NGS) in real-time to detect drug resistance, design effective individualized treatment regimens and perform targeted contact and source investigation aimed at halting the acquisition and spread of drug resistant TB.

  • Increasing genomic surveillance to other pathogens in Africa is important to be able to quickly detect new emergent epidemics as well as monitor ongoing pathogens. In Kenya, Rift Valley Fever (RVF) virus is a dangerous zoonotic pathogen that has the capacity to harm millions of animals and humans in sub-Saharan Africa where the pathogen is endemic. RVF has been identified and listed by the WHO as likely to cause future epidemics in a new emergency plan developed after the Ebola epidemics of 2018. Recently, the frequency of RVF outbreaks has increased in the eastern Africa region due to the changing climate patterns and indiscriminate livestock movements. Kenya, Uganda, Rwanda and Burundi have each reported at least one outbreak in the last two years. In some of these cases, the outbreaks have affected new geographical locations where the local governments and communities do not have adequate capacity to respond. Genomic surveillance of the virus evolution is crucial in developing intervention strategies. ILRI (Kenya) and CERI (SU) have generated vast knowledge on the occurrence patterns and modern detection technologies of the disease in the region that can be applied in implementing the project.

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