Population genomics of bulk malaria infections is unable to examine intrahost evolution; therefore, most work has focused on the role of recombination in generating genetic variation. We used single-cell sequencing protocol for low-parasitaemia infections to generate 406 near-complete single Plasmodium vivax genomes from 11 patients sampled during sequential febrile episodes. Parasite genomes contain hundreds of de novo mutations, showing strong signatures of selection, which are enriched in the ApiAP2 family of transcription factors, known targets of adaptation. Comparing 315 P. falciparum single-cell genomes from 15 patients with our P. vivax data, we find broad complementary patterns of de novo mutation at the gene and pathway level, revealing the importance of within-host evolution during malaria infections.

大量疟疾感染的群体基因组学无法检查宿主内的进化；因此，大多数工作都集中在重组在产生遗传变异中的作用。我们对低寄生虫血症感染使用单细胞测序方案，从连续发热发作期间采样的 11 名患者中生成 406 个近乎完整的单个间日疟原虫基因组。寄生虫基因组包含数百个从头突变，显示出强烈的选择特征，它们富含 ApiAP2 转录因子家族，已知的适应目标。将来自 15 名患者的315个恶性疟原虫单细胞基因组与我们的间日疟原虫数据进行比较，我们发现了广泛的从头互补模式基因和通路水平的突变，揭示了疟疾感染期间宿主内进化的重要性。