The high burden of dengue and chikungunya in southern coastal Ecuador: Epidemiology, clinical presentation, and phylogenetics from a prospective study in Machala in 2014 and 2015

Background: Dengue (DENV), chikugunya (CHIKV) and zika (ZIKV) viruses are arboviruses transmitted by the Ae. aegypti mosquito, that cause febrile illness and present a major public health challenge in tropical low- and middle-income countries such as Ecuador. Here we report the methods and findings from the first two years (January 1, 2014 to December 31, 2015) of an active and passive surveillance study conducted in the southern coastal city of Machala, Ecuador. Methods: Individuals whom presented at one of four sentinel clinics or the central hospital of the Ministry of Health with suspected DENV (index cases) were recruited into the study (n = 324). Index cases with confirmed acute DENV infection triggered a cluster investigation (n = 44) of DENV infections in the index household and four neighboring households (associates) within 200 meters, (n = 397). We conducted genomic sequencing and phylogenetic analysis of select DENV positive samples from 2014. Results: In 2014, 72.5% of index patients and 35.6% of associates had evidence of acute or recent DENV infections. In 2015, 28.3% and 12.85% of index patients and associates, respectively, had acute or recent infections. The first cases of CHIKV were detected in an associate on epidemiological week 12 in 2015. There were a total of 54 cases of acute CHIKV infections, including seven DENV/CHIKV co-infections. No cases of ZIKV were detected. DENV symptoms varied significantly by age and by primary versus secondary infections. Symptoms that were associated with DENV and CHIKV infections are presented. Phylogenetic analyses of isolates revealed genetic relatedness and shared ancestry of DENV1, DENV2 and DENV4 genomes from Ecuador with those from Venezuela and Colombia, as well as more than one introduction of the same serotype into Ecuador, indicating presence of viral flow between Ecuador and the surrounding countries. Discussion: Findings from this study highlight the importance of (1) implementing rapid active surveillance protocols and (2) strengthening local molecular diagnostic capacities in resource-limited settings where DENV, CHIKV, and ZIKV co-circulate.