Site 4 - Santa Rita 2021-2022

<b>Study name:</b> Dynamics of residual and re-emerging malaria transmission in the amazon: Defining pathways to malaria elimination.

<br><br><br><b>Background:</b>
Malaria elimination is now a priority for the Ministries of Health in the region. In Peru, the department of Loreto in the Amazon Region, with only 4% of Peru's total population, concentrates 95% of the country's total malaria cases and since 2011, this number has increased. In 2011, 9,306 cases of P. vivax and 2,473 cases of P. falciparum were reported, and in 2015 there were 46,924 and 12,425 cases, respectively. The endemicity of malaria in Peru is low to moderate, with permanent and seasonal transmission and high spatial and temporal heterogeneity (Rosas et al 2017; Carrasco-Escobar et al 2017). More than 80% of the detected cases of CPD are concentrated in ~20-30% of the total communities in the region, mostly peri-urban and rural, scattered along the different watersheds that flow into the Amazon River. A large proportion are asymptomatic, with low or submicroscopic parasite densities. Entomological studies have shown a large variation in the entomological inoculation rate (EIR) of the highly anthropophilic vector, An. darlingi, at the micro-geographical level in the different riverine communities (Mazán district) and in communities along the Iquitos-Nauta highway (Moreno et al 2015). The data from this project will be used to identify, and further predict, the occurrence and location of these malaria transmission "hotspots," outbreaks, and seasonality, which will allow for the will allow for the planning of targeted intervention strategies.

<br><br>Changes in malaria incidence and prevalence are key indicators for any control program. However, these measurements are the result of complex processes that include human migration. While epidemiological data provide critical information on the determinants and patterns of the spatiotemporal dynamics of transmission, they are often limited to reporting where and when infection took place, but cannot distinguish between autochthonous and imported cases. This has serious implications for the planning of control measures aimed at elimination. In this project we will focus on this problem using molecular epidemiology tools. We will measure parasite diversity factors at the basal level to evaluate the effect of current intervention measures, such as reduction in parasite diversity would be an indicator of a closed system in which human migration would not have an important role in maintaining transmission; but the replacement of parasite populations would imply the introduction of different parasites, brought in by migrants, which would be maintaining these residual transmission foci or "hot spots".

<br><br><br><b>Objectives: </b>
<br>1. Determine, longitudinally, the malaria transmission dynamics in residual malaria "hot spots" in Peru.
<br>2. Identify and quantify changes in P. vivax and P. falciparum populations to detect parasite re-introduction and estimate the complexity of parasite populations at baseline and after potential interventions.
<br>3. Determine whether consecutive episodes of malaria diagnosed at the population cohort level are due to parasite lineages that persist in human populations or are new, genetically unrelated parasites introduced by migration of symptomatic and asymptomatic carriers.

<br><br><b>Methodology:</b>

<br><b>Study sites</b>: Project 1 visited during the years 2021 and 2022 the community of Santa Rita in the district of Mazán, province of Maynas, in the region of Loreto, Peru.

<br><br><b>Dates of data collection</b>: Santa Rita was visited during the months of February to December during the year 2021 until January 2022. This community was visited for 12 consecutive months.

<br><br><b>Study design:</b> The study design is a population-based cohort study. It consists of several methods of community-based malaria assessment: 1) census, 2) monthly population screening, 3) weekly active case detection (ACD) of symptomatic individuals, 4) mobile population ACD, and 5) routine passive case detection (PCD).

<br><br><b>Eligibility criteria:</b>
Adults and children will contribute data for the aims of the study. The inclusion of children is essential for the study goals, since - as our previous studies in Amazonia show - different age groups may differ in acquired immunity and, therefore, in the risk of having symptoms when carrying malaria parasites (Barbosa et al. 2014, Nicolete et al. 2016).
<br>Inclusion criteria are:
<br>• Age ≥ 3 months of age.
<br>• Resident in the communities selected for the study.
<br>• Participant willing to provide written informed consent, or with written informed parental consent and assent according to age.
<br>Exclusion criteria are:
<br>• Children under three months of age will be excluded from the study because heel or finger prick procedures to draw blood may be perceived by parents as inappropriate for this age group.
<br>• Participant not willing to comply with all procedures requested by the study.
<br>• Parents or guardians not willing to provide informed consent.
<br>• Any chronic or acute condition that, in the opinion of the field physician or nurse, may affect the results of the study or the ability to provide informed consent.

<br><br><b>Data collection:</b>
<br><b>House-to-house visits:</b>
<br>Each household will be visited and its members will hear a summary of the study objectives by a member of the field team, in the local language (Spanish mostly). Interested parties will meet with the field team to review the consent form. Literate participants will be invited to sign the consent form in the local language. After the study has been fully explained and informed consent obtained from each subject or their parents/guardians, a subject identification number (SID) will be assigned to each participant. Standardized questionnaires will be administered to all study participants, or their parents when relevant, to collect demographic, health and socioeconomic data. Information on selected households' assets, land ownership and housing characteristics will be collected to obtain a wealth index, from which socioeconomic status will be estimated (Filmer & Pritchett 2001).
<br><b>Blood collection and sample labeling:</b>
<br>All laboratory procedures will be in accordance with current World Health Organization (WHO) biosafety guidelines. We obtained 100-300 μL of capillary blood at enrollment (baseline survey) and during follow-up for microscopy, DNA extraction, and plasma separation. Cryoresistant labels were used to label all samples with the NID, date of sample collection, and sample type. During clinical and laboratory surveillance to identify clinical episodes of malaria, between monthly visits, finger stick blood samples (100-300 μL of capillary blood) will be obtained from each study participant who reports fever at the time of sampling or recent fever, headache, or any other malaria-related symptoms. Laboratory diagnosis for malaria will be based on rapid on-site diagnostic (RDD) tests or thick blood drop microscopic examinations, subsequently supplemented with quantitative real-time PCR (qPCR).
<br><br><b>Geospatial information:</b>
<br>Geographic coordinates of all houses were collected to facilitate assessment of the spatial pattern of residual malaria. Acquiring satellite imagery and collecting high resolution imagery with drones to extract information on the local environment (both natural and anthropogenic). The images have high spatial resolution (≤ 1m), less than 10% cloud cover, and correspond to the same years as the household survey data, if feasible. Although the imagery reflects only one point in time during the year, it provides crucial information on land cover and land use, allows the calculation of vegetation and soil indices commonly used in vector-borne disease studies, and facilitates the validation of terrain features such as roads, rivers, large water ponds, and buildings.

<br><br><b>Acknowledgments:</b>
<br>We would like to thank all inhabitants and local authorities from San Jose de Lupuna, Santa Rita, San Pedro, Cahuide, 12 de Abril, La Habana, Lago Yuracyacu, Salvador, and Urco Miraño in Loreto, Peru for their enthusiastic participation in the study as well as all field workers and laboratory technicians for their dedication during the study.

<br><br><b>Financial support:</b>
<br>This work was supported by National Institutes of Health, National Institute of Allergy and Infectious Diseases (grant numbers U19AI089681).

<br><br><b>Ethics statement:</b>
<br>The samples tested for this study were selected from the Universidad Peruana Cayetano Heredia projects which was approved by the Institutional Ethical Review Board of the Universidad Peruana Cayetano Heredia (protocols SIDISI 101645/2017 and SIDISI 101518/2018). Informed consent was obtained from all participants and/or their legal guardians. All methods were performed in accordance with the relevant guidelines and regulations.

<br><br><b>Principal investigator and collaborators:</b>
<br><b>Principal Investigators:</b>
<br>• Joseph Vinetz (YSM/UPCH).
<br>• Dionicia Gamboa Vilela (IMTAvH/FCF/UPCH)
<br><b>Co-investigators:</b>
<br>• Alejandro Llanos-Cuentas (FASPA/UPCH).
<br>• Ángel Rosas (UPCH)
<br>• Mitchel Guzmán Guzmán (UPCH)
<br>• Joaquín Gómez Pauca (UPCH)
<br>• Caroline Abanto (UPCH)
<br>• Danielle Pannebaker (NAMRU-6)
<br>• Juan F. Sanchez (NAMRU-6)
<br>• Hugo Valdivia (NAMRU-6)
<br><b>Coordinator in Iquitos:</b>
<br>• Roberson Ramirez (UPCH)
<br><b>Coordinator in Lima:</b>
<br>• Pamela Rodríguez (UPCH)

<br><b>Institutions:</b>
<br>• Universidad Peruana Cayetano Heredia (UPCH).
<br>• School of Medicine, Yale University (YSM)
<br>• Regional Health Directorate of Loreto (DIRESA)
<br>• U.S. Navy Tropical Disease Research Center - NAMRU-6.