Innovative genotyping in malaria research

Associate Professor Sarah Auburn, a molecular biologist based at Menzies School of Health Research, Northern Territory, combines her passion for genetics with a drive to address global health challenges. Growing up in Zambia, Sarah developed an appreciation for the natural world and a deep concern for the health issues affecting low- and middle-income countries. Inspired by her late mentor, Professor Dominic Kwiatkowski, she began on a journey to apply genetic approaches to the study of malaria.

“My parents fostered an early interest in the natural world and how things work,” Sarah shares. “I was particularly fascinated by natural selection and how a few simple concepts explained so many features in the biological world. This curiosity has fuelled my passion for medical research.”

Sarah’s current research focuses on the molecular surveillance of Plasmodium vivax, a major cause of malaria in the Asia-Pacific, Latin America, and the Horn of Africa. Her work leverages a unique network of global collaborators through the vivax Genomic Epidemiology Network (vivaxGEN). This network spans over 16 partner countries and has generated more than 1,000 global P. vivax genomes.

“In the same way genomic surveillance of SARS-CoV-2 informed public health responses for COVID-19, genetics surveillance of P. vivax can help malaria control programs make actionable decisions,” says Sarah. “It allows us to rapidly contain emerging biological threats, target critical reservoirs of infection, and monitor the efficacy of new or ongoing interventions.”

Key to Sarah’s research is the collaborative approach with AGRF, supporting her development of a targeted, multiplex P. vivax genotyping assay. This assay, designed for high-throughput genetic surveillance in malariaendemic countries, utilises the rhAmpSeq library preparation method and Illumina sequencing performed at AGRF. The assay and has been successfully applied to P. vivax samples from more than 10 countries and has been implemented in Indonesia, Thailand, Vietnam and Ethiopia. “

AGRF has provided critical support in developing this assay, which is essential for our work in malaria-endemic regions,” says Sarah. “Their expertise and technology enable us to gather and analyse genetic data efficiently, helping to drive our efforts towards the elimination of P. vivax.”

Genomics, for Sarah, is a powerful tool that offers unique insights into the hidden biology, epidemiology, and evolutionary history of organisms. “Genomics presents a critical detective tool to inform on how malaria-causing Plasmodium parasites are evolving and spreading within and across borders,” she says. “The declining costs of many genomics techniques are a welcome trend, increasing access for researchers globally, especially in low and middle-income countries.”

Sarah’s interests in investigating the genomes of P. vivax stems from the parasite’s complex biology and the challenges it presents. “P. vivax parasites are difficult to grow outside the human body, which limits laboratory experiments on features like antimalarial drug resistance,” she explains. “Additionally, the ability of P. vivax to form dormant liver stages (hypnozites), complicates detection of treatment failures and tracking infection spread. Genomics helps to untangle these challenges.”

The integration of molecular genetics into Sarah’s research informs public health decision-making by providing critical data for local malaria surveillance. “Our program aims to derive genetic information on transmission intensity, infection spread, importation, and treatment efficacy,” says Sarah. “This data helps national malaria control programs target interventions for maximum impact and adjust policies, such as antimalarial drug recommendations, as needed.”

Sarah’s partnership with AGRF is important to her research journey. “The AGRF team brought essential experience and skills to the development of the P. vivax rhAmpSeq library preparation protocol,” she says. “Their dedication and innovative approach ensured the protocol’s success, even in potentially low-resource settings.”

Through her work with AGRF and the vivaxGEN network, Associate Professor Sarah Auburn continues to push the boundaries of molecular biology and genomics, paving the way for innovative solutions to combat malaria and improve global health.