Popkin-Hall Zachary R, Niaré Karamoko, Crudale Rebecca, Simkin Alfred, Fola Abebe A, Sanchez Juan F, Pannebaker Danielle L, Giesbrecht David J, Kim Isaac E, Aydemir Özkan, Bailey Jeffrey A, Valdivia Hugo O, Juliano Jonathan J
medRxiv. 2024 Jun 28:2024.06.27.24309599. doi: 10.1101/2024.06.27.24309599.
transmission occurs throughout the tropics and is an emerging threat in areas of decline, causing relapse infections that complicate treatment and control. Targeted sequencing for has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for . Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD>0.99), copy number variation in and multiple , fixation of putative antimalarial resistance, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of transmission.
传播发生在整个热带地区，并且在疟疾发病率下降的地区正成为一种新出现的威胁，导致复发感染，使治疗和控制变得复杂。针对疟原虫的靶向测序已被广泛应用于检测种群结构以及抗疟和诊断抗性的地理传播。然而，针对间日疟原虫的此类工具较少。利用全球变异数据，我们设计了四个分子倒置探针（MIP）基因分型面板，分别针对地理上有差异的单核苷酸多态性（SNP）、中性SNP、假定的抗疟抗性基因和疫苗候选基因。我们将这些MIP面板应用于来自秘鲁亚马逊地区的866份感染样本，识别出具有克隆性（IBD>0.99）的传播网络、间日疟原虫的拷贝数变异以及多个单倍型、假定抗疟抗性的固定以及13个疫苗候选基因中的平衡选择。我们的MIP面板是目前可用的最广泛的基因分型面板，有望在间日疟原虫传播的其他地区成功应用。
