Last Updated: 17/02/2023
Methodological comparison of P. vivax genotyping approaches for molecular surveillance within the ACREME network
Objectives
This project will involve an integrated comparative analysis of different genotyping panels to harmonise and potentially standardise the application of such markers for use in future genomic surveillance within the ACREME network. Furthermore, we propose a proof-of principle application of different targeted amplicon 7 sequencing and genotyping approaches in a unique P. vivax sample set from the Solomon Islands.
Walter and Eliza Hall Institute of Medical Research (WEHI), Australia
P. vivax is a relapsing form of malaria where the major reservoir for blood-stage infections comes from re-emergence of latent parasites in an individual’s liver. Determining if an individual is suffering from a new infectious mosquito bite or from the re-emergence of a dormant liver infection has been a long-standing challenge for the field. Likewise, establishing an understanding of the population structure of P. vivax in terms of routes of transmission and parasite diversity has been challenging. Both are important for identifying new strategies for disrupting transmission. Novel molecular surveillance tools provide a valuable resource for answering these questions and several P. vivax genotyping panels are currently in development within the ACREME network, as well as elsewhere.
The Solomon Islands, despite recent resurgence of malaria, is significantly understudied in terms of parasite genetic diversity and population structure. Here, we aim to leverage and extend existing research programs within the ACREME network by applying the various genotyping methods in development within ACREME to this P. vivax sample set. With this proof-of-principle application of different genotyping approaches, we will compare the utility of the different assays for analyses of within-host parasite relatedness, transmission dynamics and identify events of drug failure to clear infection.
This study will have important implications within ACREME and partner institutions by informing on the most practical, cost-effective, and reliable P. vivax molecular surveillance tool for inference of parasite genetics to answer the intended biological question with the appropriate resolution.
We aim to evaluate and provide a comparison of a variety of marker panels based on WGS and other in-house or publicly available P. vivax genomes. We propose to bioinformatically estimate how well these markers perform across different regions, and particularly amongst samples from regions that were not used in assay development (i.e., Solomon Islands).
We next aim to perform a proof-of-principle set of experiments generating new genotyping data for samples from a clinical trial conducted in the Solomon Islands. This cohort has already been genotyped using one AmpSeq panel and we are currently in the process of generating WGS as part of an already funded program of research.
Leveraging the availability of WGS and paired P. vivax genotyping, we will perform an integrated analysis to compare the applicability of each tool to the same set of Solomon Islands samples; describing the genomic resolution obtained with each assay. Our analyses will include an empirical comparison of estimates of relatedness, estimates of multiplicity of infection, within-host clone dynamics, parasite diversity, drug susceptibility and assess relatedness of paired infections over time; notably discriminating between potential relapse, reinfection or recrudescence due to treatment failure.
Nov 2021 — Oct 2023
$15,000
