Genomic epidemiology of the current wave of artemisinin resistant malaria

Artemisinin resistant is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent mutations. In a large global survey, we find that mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African mutations have originated locally, and that shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.