Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns
Shetty AC., Jacob CG., Huang F., Li Y., Agrawal S., Saunders DL., Lon C., Fukuda MM., Ringwald P., Ashley EA., Han KT., Hlaing TM., Nyunt MM., Silva JC., Stewart KE., Plowe CV., O’Connor TD., Takala-Harrison S., Noedl H., Khan WA., Newton P., Kyaw MP., White NJ., Dondorp AM., Day NP., Woodrow CJ., Dhorda M., Faiz MA., Fairhurst RM., Lim P., Tripura R., Mayxay M., Htut Y., Nosten F., Phyo AP., Pukrittayakamee S., Hien TT., Nhien NTT., Mokuolu OA., Fanello CI., Onyamboko MA.
AbstractEstimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.