Deployment of Amplicon-Based Sequencing Platforms Using Oxford Nanopore Technologies for the Detection and Surveillance of Trypanosomatids

This chapter delves into the transformative potential of Amplicon-based sequencing (ABS) by Oxford Nanopore Technologies (ONT) for detecting and surveilling Trypanosomatids, a family of challenging protozoan parasites in medical and veterinary domains. Our focus centers on T. cruzi and Leishmania. Leveraging ONT’s real-time sequencing and full-length reads, ABS-ONT underscores the importance of precise genomic target selection, evidence-based primer design, and robust PCR standardization for reliable results. We emphasize the significance of high-fidelity, long-read polymerases in ABS, crucial for capturing subtle genetic variations essential for precise genotyping. In remote areas, the field implementation of ABS-ONT could proves invaluable, facilitating on-site diagnostics and surveillance with high resolution and sensitivity. The method’s accuracy offers real-time insights into the prevalence and diversity of Trypanosomatids. We discuss challenges in large-scale ABS implementation, including logistical and ethical considerations, emphasizing the need for collaborative efforts, standardized protocols, and stringent ethical practices. Envisioning ABS as the gold standard for diagnostics and genotyping, we contribute to a comprehensive understanding of Trypanosomatids, guiding data-driven public health decisions. Here, we provide a holistic perspective on advancements in detection and surveillance, showcasing the potential of ONT-ABS platform to revolutionize understanding and pave the way for personalized medicine in a one-health approach in parasitology.