Abstract
The rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the kelch13 C580Y mutation is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants’ genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites’ drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
↵* Contributed equally
The substance of the manuscript and its conclusions remains essentially the same as those of the first version, but we are presenting the evidence in a clearer and more contextualized fashion. Also, we have made some additions and improvements to the methods. We have changed some of the graphical presentation of results, to show more clearly that the patterns of identity by descent (IBD) between the C580Y mutants and the local populations are different from those between the C580Y mutants and the parasites in Papua Indonesia, and result from a different evolutionary process. We have conducted a new round of analyses of ancestry, using both IBD and fastSTRUCTURE, to provide more context to the ancestry patterns observed. In the process, we modified the hmmIBD analysis process, using pre-calculated allele frequencies for all population comparisons, rather than making the frequencies depend on the specific pair of populations being analyzed. This makes the results from different population pairs more directly comparable, and increases the method's sensitivity. As a result, predicted IBD levels are higher in the current version, and pair-against-pair comparisons are more meaningful. In spite of these differences, the patterns of genetic recombination in this dataset produce a very strong signal, and the earlier analysis was able to detect its most informative features in spite of lower sensitivity. As result, the headline results are essentially unchanged: the latest version shows them more clearly, and backs them up with additional evidence.