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Background  Genetic diversity in  Plasmodium falciparum  ( P. falciparum)  parasites is a major hurdle to the control of malaria. This study monitored changes in the genetic diversity and the multiplicity of  P. falciparum  parasite infection in asymptomatic children living in southern Ghana at 3 month intervals between April 2015 and January 2016.    Methods  Filter paper blood spots (DBS) were collected quarterly from children living in Obom, a community with perennial malaria transmission and Abura, a community with seasonal malaria transmission. Genomic DNA was extracted from the DBS and used in polymerase chain reaction (PCR)-based genotyping of the  merozoite surface protein  1 ( msp  1) and  merozoite surface protein  2 ( msp  2) genes.    Results  Out of a total of 787 samples that were collected from the two study sites, 59.2% (466/787) tested positive for  P. falciparum . The  msp  1 and  msp  2 genes were successfully amplified from 73.8% (344/466) and 82.5% (385/466) of the  P. falciparum  positive samples respectively. The geometric mean MOI in Abura ranged between 1.17 (95% CI: 1.08–1.28) and 1.48 (95% CI: 1.36–1.60) and was significantly lower ( p  < 0.01, Dunn’s multiple comparison test) than that determined in Obom, where the geometric mean MOI ranged between 1.82 (95% CI: 1.58–2.08) and 2.50 (95% CI: 2.33–2.678) over the study period. Whilst the  msp  1 R033:MAD20:KI allelic family ratio was dynamic, the  msp  2 3D7:FC27 allelic family ratio remained relatively stable across the changing seasons in both sites.    Conclusions  This study shows that seasonal variations in parasite diversity in these communities can be better estimated by  msp  1 rather than  msp  2 due to the constantly changing relative intra allelic frequencies observed in  msp  1 and the fact that the dominance of any  msp  2 allele was dependent on the transmission setting but not on the season as opposed to the dominance of any  msp  1 allele, which was dependent on both the season and the transmission setting.    Electronic supplementary material  The online version of this article (10.1186/s12879-018-3350-z) contains supplementary material, which is available to authorized users.

Seasonal variations in Plasmodium falciparum genetic diversity and multiplicity of infection in asymptomatic children living in southern Ghana