Molecular epidemiology of continued Plasmodium falciparum 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 Plasmodium falciparum 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 P. falciparum encoded by the var multigene family. We used a high-resolution genotyping method, “ var coding”, involving targeted amplicon sequencing to fingerprint the DBLα encoding region of var genes to describe both antigenic var diversity and var repertoire similarity or relatedness in parasite isolates from clinical cases. We identified nine genetic var codes in 58 P. falciparum isolates causing clinical disease in 2013-2015. Network analyses revealed that four of the var codes were highly related to the outbreak var code, with identification of possible diversification of the outbreak parasites by recombination as seen in three of those var codes. The majority of clinical cases in Ecuador were associated with parasites with highly related or recombinant var 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 var codes to those sampled in South American var codes reflects historical parasite importation of some var codes, especially from Colombia and Peru. Our findings highlight the translational application of var 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.