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Background  Malaria is still one of the serious public health problems in Grande Comore Island, although the number of annual cases has been greatly reduced in recent years. A better understanding of malaria parasite population diversity and transmission dynamics is critical for assessing the effectiveness of malaria control measures. The objective of this study is to investigate temporal changes in genetic diversity of  Plasmodium falciparum  populations and multiplicity of infection (MOI) in Grande Comore 10 years after introduction of ACT.    Methods  A total of 232  P. falciparum  clinical isolates were collected from the Grande Comore Island during two sampling periods (118 for 2006‒2007 group, and 114 for 2013‒2016 group). Parasite isolates were characterized for genetic diversity and complexity of infection by genotyping polymorphic regions in merozoite surface protein gene 1 ( msp - 1 ),  msp - 2 , and  msp - 3  using nested PCR and DNA sequencing.    Results  Three  msp - 1  alleles (K1, MAD20, and RO33), two  msp - 2  alleles (FC27 and 3D7), and two  msp - 3  alleles (K1 and 3D7) were detected in parasites of both sampling periods. The RO33 allele of  msp - 1  (84.8%), 3D7 allele of  msp - 2  (90.8%), and K1 allele of  msp - 3  (66.7%) were the predominant allelic types in isolates from 2006–2007 group. In contrast, the RO33 allele of  msp - 1  (63.4%), FC27 allele of  msp - 2  (91.1%), and 3D7 allele of  msp - 3  (53.5%) were the most prevalent among isolates from the 2013–2016 group. Compared with the 2006‒2007 group, polyclonal infection rates of  msp - 1  (from 76.7 to 29.1%,  P  < 0.01) and  msp - 2  (from 62.4 to 28.3%,  P  < 0.01) allelic types were significantly decreased in those from 2013‒2016 group. Similarly, the MOIs for both  msp - 1  and  msp - 2  were higher in  P. falciparum  isolates in the 2006 – 2007 group than those in 2013 – 2016 group (MOI = 3.11 vs 1.63 for  msp - 1 ; MOI = 2.75 vs 1.35 for  msp - 2 ). DNA sequencing analyses also revealed reduced numbers of distinct sequence variants in the three genes from 2006‒2007 to 2013‒2016:  msp - 1 , from 32 to 23 (about 28% decline);  msp - 2  from 29 to 21 (about 28% decline), and  msp - 3  from 11 to 3 (about 72% decline).    Conclusions  The present data showed dramatic reduction in genetic diversity and MOI among Grande Comore  P. falciparum  populations over the course of the study, suggesting a trend of decreasing malaria transmission intensity and genetic diversity in Grande Comore Island. These data provide valuable information for surveillance of  P. falciparum  infection and for assessing the appropriateness of the current malarial control strategies in the endemic area.

Temporal changes in genetic diversity of msp-1, msp-2, and msp-3 in Plasmodium falciparum isolates from Grande Comore Island after introduction of ACT