Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon.
Luis Cabrera-Sosa, Oscar Nolasco, Johanna H Kattenberg, Carlos Fernandez-Miñope, Hugo O Valdivia, Keare Barazorda, Silvia Arévalo de Los Rios, Hugo Rodriguez-Ferrucci, Joseph M Vinetz, Anna Rosanas-Urgell, Jean-Pierre Van Geertruyden, Dionicia Gamboa, Christopher Delgado-Ratto
Author Information
Luis Cabrera-Sosa: Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia.
Oscar Nolasco: Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia.
Johanna H Kattenberg: Department of Biomedical Sciences, Institute of Tropical Medicine.
Carlos Fernandez-Miñope: Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp.
Hugo O Valdivia: Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH).
Keare Barazorda: Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH).
Silvia Arévalo de Los Rios: Laboratorio de Salud Pública de Loreto, Gerencia Regional de Salud de Loreto.
Hugo Rodriguez-Ferrucci: Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana.
Joseph M Vinetz: Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine.
Anna Rosanas-Urgell: Department of Biomedical Sciences, Institute of Tropical Medicine.
Jean-Pierre Van Geertruyden: Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp.
Dionicia Gamboa: Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia.
Christopher Delgado-Ratto: Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp.
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed (Pv) and (Pf) transmission dynamics, resistance markers, and Pf deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = -0.52 & Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
