Portable genomics for health monitoring of wild primates Parasitic nematode identification as a model for field-based disease surveillance

Monitoring the health of wildlife is increasingly critical in the face of biodiversity loss, zoonotic spillover risk, and conservation challenges. Yet, genetic tools for disease surveillance are often inaccessible in the remote or resource-limited settings where many vulnerable species live. Recent advances in portable molecular biology — including miniaturised PCR machines, gel electrophoresis systems, and the third-generation MinION DNA sequencer — have opened new opportunities to decentralise genetic diagnostics. This thesis presents a proof of concept for applying such low-cost, portable genomics technology to identify parasitic nematodes, using them as model organisms for non-invasive health monitoring in non-human primates (NHPs).
First, the accuracy of portable sequencing workflows was validated by comparing their outputs against Sanger sequencing, the gold standard for DNA barcoding. Reliable species identification across multiple nematode taxa was demonstrated using both conventional and fully portable equipment. The approach was subsequently tested in a real-world training setting in North Sumatra, Indonesia, where veterinary staff were trained to extract, amplify, and sequence DNA from orangutan parasites on site. The same protocols were successfully applied to preserved field samples from yellow baboons in Tanzania, demonstrating that archived material could also yield high-quality genomic data. Finally, the feasibility of metabarcoding nematode communities from faecal samples was explored, highlighting both the promise and limitations of in-field biodiversity assessments.
Together, these studies show that portable genomics can play a transformative role in primate health monitoring. This thesis contributes to the growing field of decentralised conservation science by demonstrating practical, scalable applications of genomics beyond the traditional laboratory.