Clonal spread of Plasmodium falciparum candidate artemisinin partial resistance Kelch13 622I mutation and co-occurrence with pfhrp2/3 deletions in Ethiopia

The emergence and spread of drug- and diagnostic-resistant Plasmodium falciparum are major impediments to malaria control and elimination. We deep sequenced known drug resistance mutations and other informative loci across the genome of 609 samples collected during a study across three regions of Ethiopia. We found that 8.0% (95% CI 7.0-9.0) of malaria cases were caused by P. falciparum carrying the candidate artemisinin partial-resistance K13 622I mutation, which occurred less commonly in diagnostic-resistant pfhrp2/3- deleted than normal non-deleted parasites ( p =0.03). Identity-by-descent analysis showed that 622I parasites were significantly more related than wild-type (p<0.001), consistent with recent expansion and spread. Pfhrp2/3- deleted parasites were also highly related, with evidence of clonal transmissions at the district level. Parasites carrying both pfhrp2/3 deletion and 622I mutation were observed in some sites. These findings raise concern for future spread of combined drug- and diagnostic-resistant parasites and warrant close monitoring. ### Competing Interest Statement JBP reports research support from Gilead Sciences, non-financial support from Abbott Diagnostics, and consulting from Zymeron Corporation, all outside the scope of the current work. Other authors do not have a relevant conflict of interest to report. ### Funding Statement This project was funded in part by the US NIH (R01AI132547 and K24AI134990 to J.J.J). The parent study was funded by the Global Fund to Fight AIDS, Tuberculosis, and Malaria through the Ministry of Health-Ethiopia (EPHI5405 to S.M.F.) and by the Bill and Melinda Gates Foundation through the World Health Organization (OPP1209843 to J.C., J.B.P.), with partial support from MSF Holland which supported fieldwork in the Gambella region. Under the grant conditions of the Bill and Melinda Gates Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The parent study was approved by the Ethiopian Public Health Institute (Addis Ababa, Ethiopia; protocol EPHI-IRB-033-2017) and the World Health Organization Research Ethics Review Committee (Geneva, Switzerland; protocol ERC.0003174 001). Parasite sequencing and analysis of de-identified samples was deemed nonhuman subjects research by the University of North Carolina at Chapel Hill (NC, USA; study 17-0155). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.