Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

• DOI: 10.1371/journal.pone.0032891
• Publication Date: 2012-02-29T17:53:06Z
• Authors: Sarah Auburn; Susana Campino; Olivo Miotto; Abdoulaye A. Djimde; Issaka Zongo; Magnus Manske; Gareth Maslen; Valentina Mangano; Daniel Alcock; Bronwyn MacInnis; Kirk A. Rockett; Taane G. Clark; Ogobara K. Doumbo; Jean Bosco Ouédraogo; Dominic P. Kwiatk...
• Keywords: Multiplicity of infection

Our understanding of the composition multi-clonal malarial infections and epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host has been defined in terms multiplicity infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be on genome-wide datasets facilitating development new statistical approaches describe diversity. In this class measures FWS metric characterizes its relationship population level Utilizing P. falciparum field isolates from patients West Africa we here explore between traditional MOI approaches. statistics were count data at 86,158 SNPs 64 samples sequenced Illumina GA platform. estimates PCR msp-1 -2 loci. Significant correlations observed two measures, particularly with locus (P = 5.92×10−5). The should more robust than approach owing reduced sensitivity potential locus-specific artifacts. Furthermore captures information a range parameters influence out-crossing risk including number clones (MOI), relative proportions genetic divergence. This provide novel insights into correlate with,