Building capacity for an innovative amplicon deep sequencing tool to genotype Plasmodium infections for improved surveillance

Achieving the goal of malaria elimination in the Asia-Pacific region by 2030 will require novel, highly sensitive, and reproducible genotyping tools for improved surveillance strategies. Despite major advances in reducing the incidence and prevalence of Plasmodium spp regionally, this decrease is often geographically heterogeneous resulting in residual transmission foci that are difficult to detect with current surveillance methods. Furthermore, a challenge for countries approaching elimination is the increasing prevalence of low-density, asymptomatic infections that contribute to sustain transmission but are difficult to detect with routine surveillance strategies. It is thus necessary to utilise molecular tools that are suitable for large scale epidemiological studies (i.e., high-throughput), sensitive enough to detect low-density infections, and allow assessment of individual clone density over time during natural infections. A novel amplicon deep sequencing (AmpSeq) protocol to genotype genetically distinct Plasmodium clones within infections with high discriminatory power has recently been developed in the field based on two genetic markers, csp and cpmp. Currently, this methodology has been validated on archival samples from Papua New Guinea demonstrating a higher sensitivity compared to standard genotyping tools (i.e. msp2 genotyping) and highlighting its utility for investigating infection dynamics with high resolution at the individual clone level. To date it has not been determined whether the genetic markers provide sufficient resolution in other geographic areas besides PNG and/or if AmpSeq will be suitable for low-density infections and in the context of different surveillance methods employed in the Asia-Pacific region.

Capacity Building
Enabling Technologies & Assays
Surveillance

May 2019 — Oct 2023

$15,000

Australia

Australian Centre for Research Excellence in Malaria Elimination (ACREME)

Malaria Molecular Surveillance (MMS)