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Background  Malaria is a leading cause of mortality and morbidity in tropical countries, especially in sub-Saharan Africa. In Senegal, a control plan implemented in the beginning of the 2000s has enabled a substantial reduction of mortality and morbidity due to malaria. However, eradication of malaria requires a vaccine that protects against  Plasmodium falciparum  the deadliest species of the parasite that causes this disease.  Plasmodium falciparum  is characterized by an extensive genetic diversity that makes vaccine development challenging. In this study, the diversity of  P. falciparum  isolates was analysed from asymptomatic children residing in the district of Toubacouta, Senegal.    Methods  A nested PCR approach was used to perform genotyping of the  msp - 1  and  msp - 2  loci in samples from 87 asymptomatic children infected with  P. falciparum , collected during a cross sectional survey in November and December 2010. Parasite densities in blood samples were determined by microscopic examination and statistical analyses were used to identify association of parasite genotype and parasitaemia.    Results  Genotyping was successful in 84/87 and 82/87 samples for  msp - 1  and  msp - 2 , respectively. A strong genetic diversity was found with a total of 15 and 21 different alleles identified for  msp - 1  and  msp - 2 , respectively. RO33 was the most frequent allelic family of  msp - 1  followed by MAD20, then by K1. Regarding  msp - 2  allelic families, 3D7 was more common than FC27. Multiple infections were predominant, since 69% and 89% of the samples genotyped for  msp - 1  and  msp - 2  showed more than one clone of  P. falciparum  with complexity of infection (COI) of 2.5 and 4.7, respectively. Expected heterozygosity (H E ) was 0.57 and 0.55 for  msp - 1  and  msp - 2 , respectively. Interestingly, polyclonal infections were significantly associated with higher parasitaemia.    Conclusions  The strong genetic diversity of  P. falciparum  clones and the association of polyclonal infection with high parasitaemia call for a multi-allelic approach in the design of vaccine candidates for efficient malaria eradication.    Electronic supplementary material  The online version of this article (10.1186/s12936-019-2684-3) contains supplementary material, which is available to authorized users.

Association of high Plasmodium falciparum parasite densities with polyclonal microscopic infections in asymptomatic children from Toubacouta, Senegal