Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal

Table 1 Summary of the genetic metrics used in this study and their expected relationship with transmission intensity

Genetic metric	Definition	Transmission reflected	Expectation
Polygenomic fraction	Proportion of infections that are polygenomic	Superinfection and cotransmission	Increase with transmission intensity
Complexity of infection (COI)	Number of strains per infection	Superinfection and cotransmission	Increase with transmission intensity
The fraction of non-unique monogenomic clones	Proportion of monogenomic infections carrying a clone that was sampled elsewhere in the population	Clonal transmission	Decrease with transmission intensity
R_H	Estimate of polygenomic inbreeding based on intra-host heterozygosity	Superinfection and cotransmission	Decrease with transmission intensity
Cotransmission fraction	Proportion of polygenomics resulting from cotransmission	Cotransmission	Decrease with transmission intensity

Clones are defined as a parasite whose barcode is observed more than once in the population and is calculated only for monogenomic infections. COI was calculated using THE REAL McCOIL

ISSN: 1475-2875