by Henri Christian Junior Tsoungui Obama, Kristan Alexander Schneider
The presence of multiple different pathogen variants within the same infection, referred to as multiplicity of infection (MOI), confounds molecular disease surveillance in diseases such as malaria. Specifically, if molecular/genetic assays yield unphased data, MOI causes ambiguity concerning pathogen haplotypes. Hence, statistical models are required to infer haplotype frequencies and MOI from ambiguous data. Such methods must apply to a general genetic architecture (i.e., multiple, multiallelic markers), when aiming to condition secondary analyses, e.g., population genetic measures such as heterozygosity or linkage disequilibrium, on the background of variants of interest, e.g., drug-resistance associated haplotypes.
This is a companion discussion topic for the original entry at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012955