Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.
PATH, Lusaka, Zambia.
Nat Commun. 2024 Feb 15;15(1):1413. doi: 10.1038/s41467-024-45688-z.
Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
疟原虫基因组监测可以提供与抗疟药物耐药性、诊断测试失败以及疫苗靶标进化相关的政策信息。然而，疟原虫庞大而低复杂度的基因组增加了基因组方法的开发难度，而疟疾流行地区的资源限制可能会限制其应用。在这里，我们展示了一种针对干燥血斑（DBS）中疟原虫的靶向纳米孔测序方法，该方法可在资源有限的环境中实现经济高效的疟疾基因组监测。我们发布了一款软件，该软件可灵活设计扩增子测序面板，并使用该软件设计了两个针对疟原虫的目标面板。这两个面板分别生成 3-4kbp 的 8 个和 16 个目标的读长，覆盖关键的耐药相关基因、诊断测试抗原、多态性标记和疫苗靶标 csp。我们在模拟和现场样本中验证了我们的方法，证明了其具有强大的测序覆盖能力、在编码序列内进行准确的变异调用的能力、探索样本内疟原虫多样性的能力以及检测导致快速诊断测试失败的缺失。
