Molecular epidemiology of continued disease transmission after an outbreak in Ecuador.

To better understand the factors underlying the continued incidence of clinical episodes of falciparum malaria in E-2025 countries targeting elimination, we characterized the molecular epidemiology of disease transmission after a clonal outbreak in Ecuador. Here we study disease transmission by documenting the diversity and population structure of the major variant surface antigen of the blood stages of encoded by the multigene family. We used a high-resolution genotyping method, "coding", involving targeted amplicon sequencing to fingerprint the DBLα encoding region of genes to describe both antigenic diversity and repertoire similarity or relatedness in parasite isolates from clinical cases. We identified nine genetic codes in 58 isolates causing clinical disease in 2013-2015. Network analyses revealed that four of the codes were highly related to the outbreak code, with identification of possible diversification of the outbreak parasites by recombination as seen in three of those codes. The majority of clinical cases in Ecuador were associated with parasites with highly related or recombinant codes to the outbreak clone and due to local transmission rather than recent importation of parasites from other endemic countries. Sharing of types in Ecuadorian codes to those sampled in South American codes reflects historical parasite importation of some codes, especially from Colombia and Peru. Our findings highlight the translational application of coding for outbreak surveillance in epidemic/unstable malaria transmission, such as in E-2025 countries, and point to the need for surveillance of local reservoirs of infection in Ecuador to achieve the malaria elimination goal by 2025.