Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa

Abstract

Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.

High prevalence and risk of malaria among asymptomatic individuals from villages with high rates of artemisinin partial resistance in Kyerwa district, North-western Tanzania

“…This CSS was conducted as part of a larger project on MSMT which aims at establishing the capacity and implementing malaria molecular surveillance (MMS) in Tanzania [36]. The MSMT project has been implemented in 13 regions of Tanzania from 2021 and it has now been extended to cover integrated malaria molecular surveillance (iMMS) in all 26 regions of Mainland Tanzania, from January 2023 (Ishengoma et al Unpublished data).…”

Advances in the application of molecular diagnostic techniques for the detection of infectious disease pathogens (Review)

“…NGS can read billions of nucleotide sequences in a single assay, it does not rely on cell culture and it retrieves all DNA ( Fig. 8A ); it can also comprehensively detect microbial species and sequences ( 96 ), which makes it suitable as a complementary means of pathogen detection when no clear etiological evidence is available from routine laboratory testing ( Table II ). For the identification and genotyping of known pathogens, NGS is significantly more sensitive than traditional methods.…”

Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination

“…Several similar efforts are currently ongoing in other sub-Saharan countries such as Tanzania. 154,155 Such longitudinal studies provide valuable insights for further understanding the role of molecular surveillance and its complementarity to existing routine epidemiological surveillance in guiding malaria control programs.…”