High Frequency of Artemisinin Partial Resistance Mutations in the Great Lakes Region Revealed Through Rapid Pooled Deep Sequencing
Neeva Wernsman Young, Pierre Gashema, David Giesbrecht, Tharcisse Munyaneza, Felicien Maisha, Fred Mwebembezi, Rule Budodo, Alec Leonetti, Rebecca Crudale, Vincent Iradukunda, Ntwari Jean Bosco, Rebecca Kirby, Ross M. Boyce, Celine I. Mandara, Grace K. Kanyankole, Moses Ntaro, Lucy Okell, Oliver J. Watson, Edgar Mulogo, Deus S. Ishengoma, Stan Hangi, Corine Karema, Jean-Baptiste Mazarati, Jonathan J. Juliano, Jeffrey A. Bailey
Abstract
BACKGROUND: In Africa, the first Plasmodium falciparum artemisinin partial resistance mutation was Kelch13 (K13) 561H, detected and validated at appreciable frequency in Rwanda in 2014. Surveillance to better define the extent of the emergence in Rwanda and neighboring countries is critical. METHODS: We used novel liquid blood drop preservation with pooled sequencing to provide cost-effective rapid assessment of resistance mutation frequencies at multiple collection sites across Rwanda and neighboring regions in Uganda, Tanzania, and the Democratic Republic of the Congo. Malaria-positive samples (N = 5465) from 39 health facilities collected between May 2022 and March 2023 were sequenced in 199 pools. RESULTS: In Rwanda, K13 561H and 675V were detected in 90% and 65% of sites, with an average frequency of 19.0% (range, 0%-54.5%) and 5.0% (0%-35.5%), respectively. In Tanzania, 561H had high frequency in multiple sites. 561H appeared at 1.6% in Uganda. 561H was absent from the Democratic Republic of the Congo, although 675V was seen at low frequency. Concerningly, candidate mutations were observed: 441L, 449A, and 469F co-occurred with validated mutations, suggesting that they are arising under the same pressures. Other markers for decreased susceptibility to artemether-lumefantrine are common: P falciparum multidrug resistance protein 1 N86 at 98.0% (range, 63.3%-100%) and 184F at 47.0% (0%-94.3%) and P falciparum chloroquine resistance transporter 76T at 14.7% (0%-58.6%). Additionally, sulfadoxine-pyrimethamine-associated mutations show high frequencies. CONCLUSIONS: K13 mutations are rapidly expanding in the region, further endangering control efforts with the potential of engendering partner drug resistance.