Nanopore whole genome sequencing Plasmodium falciparum

For SWGA Project: see PRJEB90489. Imported malaria cases, driven by human migration and travel, pose a significant challenge to malaria elimination efforts. Genomic approaches have become essential for distinguishing between local transmission and imported infections. The state of Sarawak, Malaysia, provides a pertinent example of a malaria-eliminating setting under continuous pressure from malaria importation, particularly through labour migration and returning travellers. In this study, we investigated 21 Plasmodium falciparum cases using isolates obtained from archived whole blood samples collected between 2008 and 2011. By applying nanopore sequencing and population genomic analyses, we found that the majority of cases likely originated from endemic regions outside Malaysia, supported by patient travel histories and high multiplicity of infection levels. These findings are consistent with the historical epidemiology of the suspected source regions. Notably, two cases showed genomic evidence of origins inconsistent with the patients' reported travel histories, underscoring the limitations of traditional epidemiological methods. Ancestry clustering was identified in only two cases, suggesting that most infections were isolated introductions rather than sustained local transmission. Our results highlight the power of malaria genomics in discerning imported from locally acquired cases and emphasise its critical role in maintaining malaria elimination, particularly in regions situated along major migration corridors.