Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study

Abstract

Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for genomic epidemiology of infectious disease. AmpSeq data for infectious microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ( 4CAST ) composed of highly diverse antigens, and a 129-locus panel ( AMPLseq ) composed of drug resistance markers, highly diverse loci for measuring relatedness, and a locus to detect Plasmodium vivax co-infections. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. We find that the smaller 4CAST panel performs reliably across a wide range of parasitemia levels without DNA pre-amplification, and could be highly informative for evaluating the number of distinct parasite strains within samples (complexity of infection) and distinguishing recrudescent infections from new infections in therapeutic efficacy studies. The AMPLseq panel performs similarly to two existing panels of comparable size for relatedness measurement, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates design and comparative evaluation of AmpSeq panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for genomic epidemiology of infectious disease.