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A number of studies have analyzed the performance of malaria rapid diagnostic tests (RDTs) in Colombia with discrepancies in performance being attributed to a combination of factors such as parasite levels, interpretation of RDT results and/or the handling and storage of RDT kits. However, some of the inconsistencies observed with results from  Plasmodium falciparum  histidine-rich protein 2 (PfHRP2)-based RDTs could also be explained by the deletion of the gene that encodes the protein,  pfhrp2 , and its structural homolog,  pfhrp3 , in some parasite isolates. Given that  pfhrp2-  and  pfhrp3 -negative  P .  falciparum  isolates have been detected in the neighboring Peruvian and Brazilian Amazon regions, we hypothesized that parasites with deletions of  pfhrp2  and  pfhrp3  may also be present in Colombia. In this study we tested 100 historical samples collected between 1999 and 2009 from six Departments in Colombia for the presence of  pfhrp2 ,  pfhrp3  and their flanking genes. Seven neutral microsatellites were also used to determine the genetic background of these parasites. In total 18 of 100 parasite isolates were found to have deleted  pfhrp2 , a majority of which (14 of 18) were collected from Amazonas Department, which borders Peru and Brazil.  pfhrp3  deletions were found in 52 of the100 samples collected from all regions of the country.  pfhrp2  flanking genes PF3D7_0831900 and PF3D7_0831700 were deleted in 22 of 100 and in 1 of 100 samples, respectively.  pfhrp3  flanking genes PF3D7_1372100 and PF3D7_1372400 were missing in 55 of 100 and in 57 of 100 samples. Structure analysis of microsatellite data indicated that Colombian samples tested in this study belonged to four clusters and they segregated mostly based on their geographic region. Most of the  pfhrp2 -deleted parasites were assigned to a single cluster and originated from Amazonas Department although a few  pfhrp2 -negative parasites originated from the other three clusters. The presence of a high proportion of  pfhrp2 -negative isolates in the Colombian Amazon may have implications for the use of PfHRP2-based RDTs in the region and may explain inconsistencies observed when PfHRP2-based tests and assays are performed.

Deletion of Plasmodium falciparum Histidine-Rich Protein 2 (pfhrp2) and Histidine-Rich Protein 3 (pfhrp3) Genes in Colombian Parasites