Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon

Author:

Cabrera-Sosa Luis1,Nolasco Oscar1,Kattenberg Johanna H.2,Fernandez-Miñope Carlos3,Valdivia Hugo O.4,Barazorda Keare4,Rios Silvia Arévalo de los5,Rodriguez-Ferrucci Hugo6,Vinetz Joseph M.7,Rosanas-Urgell Anna2,geertruyden Jean-Pierre Van3,Gamboa Dionicia1,Delgado-Ratto Christopher3

Affiliation:

1. Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia

2. Department of Biomedical Sciences, Institute of Tropical Medicine

3. Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp

4. Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)

5. Laboratorio de Salud Pública de Loreto, Gerencia Regional de Salud de Loreto

6. Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana

7. Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine

Abstract

Abstract

Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 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 = 0.07–0.52 & 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, pfhrp2/3 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.

Publisher

Springer Science and Business Media LLC

Reference68 articles.

1. Ministerio de Salud. Documento Técnico: Plan hacia la Eliminación de la Malaria 2022–2030, (2022).

2. Ministerio de Salud. Número de casos de malaria, Perú 2020–2023, (2022).

3. World Health Organization. Strategy to respond to antimalarial drug resistance in Africa, (2022).

4. Use cases for genetic epidemiology in malaria elimination;Dalmat R;Malar J,2019

5. Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon;Villena FE;Sci Rep,2022

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