Oxamniquine resistance alleles are widespread in Old WorldSchistosoma mansoniand predate drug deployment
Authors: Chevalier Frédéric D. , Clec’h Winka Le , McDew-White Marina , Menon Vinay , Guzman Meghan A. , Holloway Stephen P. , Cao Xiaohang , Taylor Alexander B. , Kinung’hi Safari , Gouvras Anouk N. , Webster Bonnie L. , Webster Joanne P. , Emery Aidan M. , Rollinson David , Djirmay Amadou Garba , Al Mashikhi Khalid M. , Yafae Salem Al , Idris Mohamed A. , Moné Hélène , Mouahid Gabriel , Hart P. John , LoVerde Philip T. , Anderson Timothy JC. 
Published: June 2019

ABSTRACTDo mutations required for adaptation occurde novo, or are they segregating within populations as standing genetic variation? This question is key to understanding adaptive change in nature, and has important practical consequences for the evolution of drug resistance. We provide evidence that alleles conferring resistance to oxamniquine (OXA), an antischistosomal drug, are widespread in natural parasite populations under minimal drug pressure and predate OXA deployment. OXA has been used since the 1970s to treatSchistosoma mansoniinfections in the New World whereS. mansoniestablished during the slave trade. Recessive loss-of-function mutations within a parasite sulfotransferase (SmSULT-OR) underlie resistance, and several verified resistance mutations, including a deletion (p.E142del), have been identified in the New World. Here we investigate sequence variation inSmSULT-ORinS. mansonifrom the Old World, where OXA has seen minimal usage. We sequenced exomes of 204S. mansoniparasites from West Africa, East Africa and the Middle East, and scored variants inSmSULT-ORand flanking regions. We identified 39 non-synonymous SNPs, 4 deletions, 1 duplication and 1 premature stop codon in theSmSULT-ORcoding sequence, including one confirmed resistance deletion (p.E142del). We expressed recombinant proteins and used anin vitroOXA activation assay to functionally validate the OXA-resistance phenotype for four predicted OXA-resistance mutations. Three aspects of the data are of particular interest: (i) segregating OXA-resistance alleles are widespread in Old World populations (4.29 – 14.91% frequency), despite minimal OXA usage, (ii) two OXA-resistance mutations (p.W120R, p.N171IfsX28) are particularly common (>5%) in East African and Middle-Eastern populations, (iii) the p.E142del allele has identical flanking SNPs in both West Africa and Puerto Rico, suggesting that parasites bearing this allele colonized the New World during the slave trade and therefore predate OXA deployment. We conclude that standing variation for OXA resistance is widespread inS. mansoni.AUTHOR SUMMARYIt has been argued that drug resistance is unlikely to spread rapidly in helminth parasites infecting humans. This is based, at least in part, on the premise that resistance mutations are rare or absent within populations prior to treatment, and take a long time to reach appreciable frequencies because helminth parasite generation time is long. This argument is critically dependent on the starting frequency of resistance alleles – if high levels of “standing variation” for resistance are present prior to deployment of treatment, resistance may spread rapidly. We examined frequencies of oxamniquine resistance alleles present inSchistosoma mansonifrom Africa and the Middle East where oxamniquine has seen minimal use. We found that oxamniquine resistance alleles are widespread in the Old World, ranging from 4.29% in the Middle East to 14.91% in East African parasite populations. Furthermore, we show that resistance alleles from West African and the Caribbean schistosomes share a common origin, suggesting that these alleles travelled to the New World withS. mansoniduring the transatlantic slave trade. Together, these results demonstrate extensive standing variation for oxamniquine resistance. Our results have important implications for both drug treatment policies and drug development efforts, and demonstrate the power of molecular surveillance approaches for guiding helminth control.