Table 1 Temporal distribution of P. falciparum sample clusters

		Proportion of samples in each year						Resistance
Cluster	Previous names	2017	2018	2019	2020	2021	2022	ART	PPQ	MQ	CQ	SX	PM	Main kelch13	KEL1/PLA1
KLV01		5%	8%	21%	16%	4%	0%	100%	89%	0%	100%	100%	100%	C580Y	Yes
KLV02		1%	12%	18%	4%	0%	0%	100%	98%	0%	100%	100%	100%	C580Y	Yes
KLV03		0%	1%	13%	10%	16%	33%	100%	54%	0%	100%	100%	100%	C580Y	Yes
KLV04	LAA1^a	0%	0%	0%	18%	15%	4%	100%	0%	13%	100%	100%	100%	R539T
KLV05		4%	4%	3%	3%	0%	0%	100%	78%	0%	100%	100%	100%	C580Y	Yes
KLV06		5%	3%	1%	1%	0%	0%	6%	1%	0%	100%	0%	100%	WT
KLV07	LAA2^a; KH2^b	1%	1%	0%	3%	10%	9%	100%	1%	0%	100%	100%	100%	C580Y
KLV08		5%	2%	0%	0%	0%	0%	100%	84%	0%	100%	100%	100%	C580Y	Yes
KLV09		1%	1%	3%	4%	0%	0%	100%	100%	0%	100%	100%	100%	C580Y	Yes
KLV10		3%	2%	0%	0%	0%	0%	1%	0%	0%	100%	0%	100%	WT
KLV11		0%	0%	0%	0%	14%	0%	0%	0%	0%	0%	0%	100%	WT
KLV12		0%	0%	0%	0%	1%	16%	100%	0%	0%	100%	100%	100%	Y493H
KLV13		2%	1%	1%	0%	0%	0%	0%	2%	0%	100%	100%	100%	WT
KLV14		0%	1%	2%	1%	0%	0%	100%	85%	0%	100%	100%	100%	C580Y	Yes
KLV15		0%	2%	0%	0%	0%	0%	0%	0%	0%	100%	100%	100%	WT
KLV16		1%	1%	0%	0%	0%	0%	8%	0%	0%	100%	0%	100%	WT
KLV17		0%	1%	0%	3%	0%	0%	0%	0%	0%	100%	0%	100%	WT
KLV18		2%	1%	0%	0%	0%	0%	100%	97%	0%	100%	100%	100%	C580Y	Yes
KLV19		0%	1%	0%	0%	0%	0%	0%	0%	0%	100%	0%	100%	WT
KLV20		0%	1%	0%	0%	0%	0%	0%	0%	0%	100%	0%	100%	WT
KLV21		0%	1%	0%	0%	0%	0%	0%	0%	0%	100%	100%	100%	WT
KLV22		1%	0%	1%	0%	0%	0%	0%	0%	0%	100%	100%	100%	WT
KLV23		0%	0%	0%	1%	4%	1%	100%	0%	0%	100%	100%	100%	C580Y
KLV24		1%	1%	0%	0%	0%	0%	100%	100%	0%	100%	100%	100%	C580Y	Yes
KLV25		1%	1%	0%	0%	0%	0%	75%	0%	0%	100%	100%	100%	C580Y
KLV26		0%	0%	1%	1%	0%	0%	100%	94%	0%	100%	100%	100%	C580Y	Yes
KLV27		1%	0%	0%	0%	0%	0%	0%	7%	0%	100%	100%	100%	WT
Not clustered	55%	43%	30%	26%	26%	36%
Total samples	1291	1894	1447	608	413	329

For each cluster, we show: the cluster label; the name by which the cluster was identified in previous studies, if any; in each year of collection, the proportion of samples that belong to the cluster; the proportion of samples predicted resistant to artemisinin (ART), piperaquine (PPQ), and mefloquine (MQ), chloroquine (CQ), sulfadoxine (SX) and pyrimethamine (PM); the majority kelch13 variant carried by parasites in the cluster; and whether the cluster carries a KEL1/PLA1 haplotype. Only clusters with ≥20 members are shown; the full list of clusters can be found at Supplementary Table 5. Samples that were not assigned to a cluster with these parameters were labeled as ‘not clustered’.
^aWasakul et al.³².
^bMiotto et al.³⁴.

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