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Background   Plasmodium falciparum  delayed clearance with the use of artemisinin-based combination therapy (ACTs) has been reported in some African countries. Single nucleotide polymorphisms (SNPs) in two genes,  P. falciparum  adaptor protein complex 2 mu subunit ( pfap2mu ) and ubiquitin specific protease 1 ( pfubp1 ), have been linked to delayed clearance with ACT use in Kenya and recurrent imported malaria in Britain. With over 12 years of ACT use in Ghana, this study investigated the prevalence of SNPs in the  pfap2mu  and  pfubp1  in Ghanaian clinical  P. falciparum  isolates to provide baseline data for antimalarial drug resistance surveillance in the country.    Methods  Filter paper blood blots collected in 2015–2016 from children aged below 9 years presenting with uncomplicated malaria at hospitals in three sentinel sites Begoro, Cape Coast and Navrongo were used. Parasite DNA was extracted from 120 samples followed by nested polymerase chain reaction (nPCR). Sanger sequencing was performed to detect and identify SNPs in  pfap2mu  and  pfubp1  genes.    Results  In all, 11.1% (9/81) of the isolates carried the wildtype genotypes for both genes. A total of 164  pfap2mu  mutations were detected in 67 isolates whilst 271  pfubp1  mutations were observed in 72 isolates. The majority of the mutations were non-synonymous (NS): 78% (128/164) for  pfap2mu  and 92.3% (250/271) for  pfubp1 . Five unique samples had a total of 215  pfap2mu  SNPs, ranging between 15 and 63 SNPs per sample. Genotypes reportedly associated with ART resistance detected in this study included  pfap2mu  S160N (7.4%, 6/81) and  pfubp1  E1528D (7.4%, 6/81) as well as D1525E (4.9%, 4/81). There was no significant difference in the prevalence of the SNPs between the three ecologically distinct study sites ( pfap2mu: χ  2  = 6.905,  df  = 2,  P  = 0.546;  pfubp1 :  χ  2  = 4.883,  df  = 2,  P  = 0.769).    Conclusions  The detection of  pfap2mu  and  pfubp1  genotypes associated with ACT delayed parasite clearance is evidence of gradual nascent emergence of resistance in Ghana. The results will serve as baseline data for surveillance and the selection of the genotypes with drug pressure over time. The  pfap2mu  S160N,  pfubp1  E1528D and D1525E must be monitored in Ghanaian isolates in ACT susceptibility studies, especially when cure rates of ACTs, particularly AL, is less than 100%.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2762-3) contains supplementary material, which is available to authorized users.

parasites and vectors

Prevalence of Plasmodium falciparum delayed clearance associated polymorphisms in adaptor protein complex 2 mu subunit (pfap2mu) and ubiquitin specific protease 1 (pfubp1) genes in Ghanaian isolates