Amplicon deep sequencing (Amp-Seq) of malaria parasite genomes towards understanding forest transmission systems

摘要 森林疟疾传播知之甚少，对东南部消除疟疾的努力构成挑战 亚洲和拉丁美洲。引起季节性传播的寄生虫的来源尚不清楚， 以及这些感染是如何传播的利用更大规模的家长研究，该项目旨在推动 柬埔寨蒙多基里省利用寄生虫进行森林疟疾季节性传播的证据基础 基因分型和全球定位系统跟踪，以绘制疟疾季节寄生虫株的运输图。 目标1：确定蒙多基里三个风险群体中基线疟原虫种群结构的特征 省，柬埔寨.我们将使用扩增子深度测序（Amp-Seq）来进行基线表征， 遵循具有不同旅行模式和行为的森林游客群体中的寄生虫单倍型：季节性 来自当地村庄的林业工人、永久森林居民和护林员。我们假设每一个 一个组将具有不同的Pf和Pv单倍型群体（密度和多样性），其中一个组 主要负责启动季节性森林疟疾传播。 目的2：绘制疟原虫单倍型在一个基本清除的原发性恶性疟原虫感染队列中的移动图。 在柬埔寨蒙多基里省的三个森林风险群体和附近村庄，我们将 确定新的疟疾感染及其寄生虫基因型、感染时间和地点。我们 假设每一组森林活动者都有特定危险因素促成持续传播， 这可能包括他们的行为和睡眠条件在森林中，干预使用，地点， 频率和相应的按蚊媒介的丰度，以及它们的移动程度。 目标3：估计乡村林业工人、森林游客和森林居民的相对贡献 柬埔寨蒙多基里省的疟疾传播。我们将研究寄生虫的运动 基因型跨越时间和空间沿着与风险因素和驱动因素的传播。我们假设 对传播的贡献最大的将是当地按蚊的水库，其次是 森林游客，与一个较小的传播水库之间的村民。 这项研究的结果将为未来的3期干预研究提供基础，该研究针对的是 启动森林疟疾传播，将寄生虫运送到其他地点，并大大有助于 柬埔寨蒙多基里省的传播水库。

ABSTRACT Forest malaria transmission is poorly understood, and is challenging malaria elimination efforts in Southeast Asia and Latin America. There is a lack of clarity on the source of parasites that initiate seasonal transmission, and how these infections propagate. Leveraging a larger parent study, this project seeks to advance the evidence base on the seasonal transmission of forest malaria in Mondulkiri Province, Cambodia using parasite genotyping and GPS tracking to map the transportation of parasite strains across a malaria season. Aim 1: To characterize baseline Plasmodium population structure in three risk-groups in Mondulkiri province, Cambodia. We will use Amplicon deep sequencing (Amp-Seq) to both baseline characterize and follow parasite haplotypes in groups of forest goers that have different travel patterns and behaviors: seasonal forest workers from local villages, permanent forest dwellers, and forest rangers. We hypothesize that each group will have different populations (density and diversity) of Pf and Pv haplotypes, with one of these groups primarily responsible for initiating seasonal forest malaria transmission. Aim 2: To map the movement of Plasmodium haplotypes in a radically cleared cohort of the primary three forest-risk groups and in nearby villages across a year in Mondulkiri province, Cambodia. We will identify new malaria infections and their parasite genotypes, the time of infection, and their locations. We hypothesize that each group of forest goer have specific risk factors that contribute to ongoing transmission, which may include their behaviors and sleeping conditions in the forest, intervention use, the locations they frequent and its corresponding abundance of Anopheles vectors, and their degree of mobility. Aim 3: To estimate the relative contribution of village forest workers, forest goers, and forest dwellers to malaria transmission in Mondulkiri province, Cambodia. We will investigate the movement of parasite genotypes across time and space along with risk factors and drivers of transmission. We hypothesize that contributions to transmission will be highest among a reservoir of local Anopheles mosquitos, followed by forest goers, with a smaller transmission reservoir among villagers. Results from this study will provide a basis for a future phase 3 intervention study that targets the sources that initiate forest malaria transmission, transport parasites to other locations, and substantially contribute to the reservoir of transmission in Mondulkiri Province, Cambodia.