The Burden of Dengue Fever and Chikungunya in Southern Coastal Ecuador: Epidemiology, Clinical Presentation, and Phylogenetics from the First Two Years of a Prospective Study

Abstract. Here, we report the findings from the first 2 years (2014–2015) of an arbovirus surveillance study conducted in Machala, Ecuador, a dengue-endemic region. Patients with suspected dengue virus (DENV) infections (index cases, N = 324) were referred from five Ministry of Health clinical sites. A subset of DENV-positive index cases (N = 44) were selected, and individuals from the index household and four neighboring homes within 200 m were recruited (N = 400). Individuals who entered the study, other than the index cases, are referred to as associates. In 2014, 70.9% of index cases and 35.6% of associates had acute or recent DENV infections. In 2015, 28.3% of index cases and 12.8% of associates had acute or recent DENV infections. For every DENV infection captured by passive surveillance, we detected an additional three acute or recent DENV infections in associates. Of associates with acute DENV infections, 68% reported dengue-like symptoms, with the highest prevalence of symptomatic acute infections in children aged less than 10 years. The first chikungunya virus (CHIKV) infections were detected on epidemiological week 12 in 2015; 43.1% of index cases and 3.5% of associates had acute CHIKV infections. No Zika virus infections were detected. Phylogenetic analyses of isolates of DENV from 2014 revealed genetic relatedness and shared ancestry of DENV1, DENV2, and DENV4 genomes from Ecuador with those from Venezuela and Colombia, indicating the presence of viral flow between Ecuador and surrounding countries. Enhanced surveillance studies, such as this, provide high-resolution data on symptomatic and inapparent infections across the population.


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The region of the Americas is facing an unprecedented public health crisis of co- . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint 1 6 this study (Table 1). A total of 72 index cases were positive by NS1 rapid test, and from these we  DENV transmission was highly seasonal in 2014 and 2015, with a peak in May (Fig 3). CHIKV was first identified in our study on epidemiological week 12 in 2015, and transmission 3 2 8 followed a similar seasonal curve as DENV (Fig 3). No ZIKV infections were detected ( Table   3 2 9 1).
3 3 0 Table 1 shows the diagnostic results from 2014 and 2015. There were some individuals 3 3 1 who did not have enough information to categorize as DENV positive or negative, for example, 3 3 2 an individual who was negative for an NS1 rapid test and PCR, but did not have any ELISA or 3 3 3 serology test results. To account for these discrepancies, prevalence estimates include people for 3 3 4 whom test results were available, as indicated by the denominators in the diagnostic results   . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint (Table 4). The majority reported a fever within the last seven days (97.3%), 21.3% had fever 3 4 5 (>38°C) upon entering the study, and 16.0% were hospitalized.

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We estimated the prevalence of symptomatic acute (SA) infections for DENV and  generally declined with increasing age, with the exception of individuals 50 to 59 years of age 3 6 4 (7/21, 33.3%). Interestingly, the proportion of primary DENV infections decreased from 0 to 49 3 6 5 years, and increased from 50 to 79 years (as determined by index cases with serology and acute 3 6 6 or recent DENV infections). In contrast, the prevalence of SA CHIKV infections, as a proportion . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint 1 8 of all individuals recruited into the study, was greatest in index cases 60 to 79 years of age (7/9, 3 6 8 77.8%), and prevalence increased with increasing age.

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We compared the demographics and symptoms of index cases with acute DENV versus 3 7 0 CHIKV infections. Index cases with acute DENV infections were significantly younger 3 7 1 (mean=20.2 years, SD=15.0) and more likely to report anorexia and nausea, vomiting and 3 7 2 abdominal pain (p<0.05). Index cases with CHIKV were more likely to be female, were older 26.5%; p=0.06); however, these differences were not statistically significant. We also compared the demographics and symptoms of primary versus secondary DENV  Table 5). Individuals with secondary DENV infections were significantly older infections were more likely to report vomiting, and hospitalized individuals were more likely to were more likely to report fever (p<0.05). We did not find significant differences in symptoms  CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint (Table 2). A similar proportion of primary (46.9%) and secondary infections (53.0%) were 3 9 8 detected (as determined by associates with serology and acute or recent DENV infections) ( Table   3  9  9 3). In 2015, as with index cases, the prevalence of DENV infections decreased as a proportion of 4 0 0 all associates recruited (11/86, 12.9%), and primary DENV infections were more common (4/6, 4 0 1 66.7% of associates with serology and acute or recent DENV infections, Table 3). Only one   Table 1). The most 4 0 9 commonly reported symptoms were headache (32%), drowsiness/lethargy (24%), fever (22%), 4 1 0 muscle/joint pain (22%), and retro-orbital pain (22%). Only two associates with symptomatic 4 1 1 acute DENV infections had sought medical care within the last seven days (2/34, 5.9%), and no 4 1 2 associates were hospitalized due to a DENV infection (Table 4). There were no significant 4 1 3 . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint The burden of dengue and chikungunya in Ecuador  Table 4).

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In associates, we determined the prevalence of SA DENV infections by age class as a 4 1 6 proportion of the total number of associates recruited per age class (Fig 4, Supplementary Table   4  1  7 3). Children 0 to 9 years of age had the highest prevalence of SA DENV infections (5/22, infections similarly decreased with increasing age. We calculated the prevalence of symptomatic  At the cluster level, prevalence rates varied by the DENV serotype of the initiate index 44.3%) (p=0.02) had an acute or recent DENV infections, with a range of 12.5% to 87.5%. . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint The burden of dengue and chikungunya in Ecuador 2 4 emergence of CHIKV. We temper this with caution, however, as our cluster sample size was 5 0 6 smaller in 2015 (n=12) than 2014 (n=32).

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In Latin America, enhanced surveillance studies that have reported DENV infection rates traits of the local population (e.g., past exposure to DENV serotypes). In a pediatric cohort in One of the limitations of this study was that we surveyed the nearest neighbors of the within 200 meters. We did not collect information on those who were not willing to participate in 5 2 5 the study. Also, people may have been more willing to participate in the study if they or someone  We did not detect ZIKV during the study period, consistent with MoH reports, which  Another explanation is that our definition of symptomatic DENV infections included mildly Phylogenetic analyses of DENV1 showed Ecuadorian samples falling into two distinct 5 9 5 clusters, sharing a common ancestor with viruses from Colombia in one cluster and a common 5 9 6 . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint The burden of dengue and chikungunya in Ecuador  could not be determined due to low node support. Nevertheless, the results suggested a close 6 1 4 relationship between DENV4 in Ecuador, Venezuela, Colombia and Brazil. It is important to 6 1 5 note that samples from Peru were missing here as well, and that there is a possibility this country   . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint the name of the clade. Colored taxa represent known genotype references.  . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018. ; https://doi.org/10.1101/102004 doi: bioRxiv preprint Table 1. Demographic data and infection status of index cases and associates. The  . CC-BY-NC-ND 4.0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted January 26, 2018.