Molecular epidemiology of continued Plasmodium falciparum disease transmission after an outbreak in Ecuador

Resumen

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