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Eritrea was the first African country to complete a nationwide switch in 2016 away from HRP2-based RDTs due to high rates of false-negative RDT results caused by  Plasmodium falciparum  parasites lacking  hrp2/hrp3  genes. A cross-sectional survey was conducted during 2019 enrolling symptomatic malaria patients from nine health facilities across three zones consecutively to investigate the epidemiology of  P. falciparum  lacking  hrp2/3  after the RDT switch. Molecular analyses of 715 samples revealed the overall prevalence of  hrp2-, hrp3 -, and dual  hrp2/3 -deleted parasites as 9.4% (95%CI 7.4–11.7%), 41.7% (95% CI 38.1–45.3%) and 7.6% (95% CI 5.8–9.7%), respectively. The prevalence of  hrp2-  and  hrp3- deletion is heterogeneous within and between zones: highest in Anseba (27.1% and 57.9%), followed by Gash Barka (6.4% and 37.9%) and Debub zone (5.2% and 43.8%).  hrp2/3 -deleted parasites have multiple diverse haplotypes, with many shared or connected among parasites of different  hrp2/3  status, indicating mutant parasites have likely evolved from multiple and local parasite genetic backgrounds. The findings show although prevalence of  hrp2/3 -deleted parasites is lower 2 years after RDT switching, HRP2-based RDTs remain unsuitable for malaria diagnosis in Eritrea. Continued surveillance of  hrp2/3 -deleted parasites in Eritrea and neighbouring countries is required to monitor the trend.

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Epidemiology of mutant Plasmodium falciparum parasites lacking histidine-rich protein 2/3 genes in Eritrea 2 years after switching from HRP2-based RDTs