Background Chikungunya virus (CHIKV) is an arbovirus with a significant global public health burden. Delineating the specific contributions of individual behaviour, household structure and the natural and built environment to CHIKV transmission is important for mitigating risk but challenging in urban informal settlements due to their heterogeneous environments. The aim of this study was to quantify variation in CHIKV seroprevalence between and within four urban communities in a large Brazilian city, and identify the respective contributions of individual, household and environmental factors for seropositivity. Methodology/Principal Findings A cross-sectional serological survey was conducted in four low-income communities in Salvador, Brazil in 2018 to collect individual, household and CHIKV IgG serology data for 1217 participants. Fine-scale community mapping of high-risk environmental features and remotely sensed environmental data were used to improve characterisation of the microenvironment close to the household. We categorised risk factors into three dimensions - individual, household, and environmental and used binomial mixed-effect models to identify associations with CHIKV seropositivity. CHIKV seroprevalence was 4.8%, 6.1% and 4.3% in three communities and 22.6% in one community which had a distinct topographical profile. The only individual dimension variable associated with seropositivity was male sex (OR 1.67, 95% CI 1.11 - 2.36), but several environmental variables, including living in a house on a steep hillside, at medium to high elevations, and with surface water nearby, were associated with higher seropositivity. Conclusions/Significance Our findings indicate that CHIKV exposure risk can vary significantly between nearby communities and at fine spatial scales within communities, and is likely to be driven more strongly by the availability of mosquito breeding sites rather than human exposure patterns. They suggest that environmental deficiencies and topography, a proxy for several environmental processes including the degree of urbanisation and flooding risk, may play an important role in driving risk at both of these scales.

All authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: AIK has received funding from the National Institutes of Health for work related to Aedes aegypti in Brazil in A Cluster-Randomized Trial to Evaluate the Efficacy of Wolbachia-infected Aedes aegypti Mosquitoes in Reducing the Incidence of Arboviral Infection in Brazil (EVITA Dengue)- DMID 17-0111. No financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work.

The study was funded by the Medical Research Council (UK). Grant number: MR/P024084/1 to MB, Fundação de Amparo à Pesquisa do Estado da Bahia (BR) Grant number: 10206/2015, Wellcome Trust (UK) Grant number:102330/Z/13/Z and National Institutes of Health (US) Grant number:1 R01 TW009504 to FC. MTE was supported by a Reckitt Global Hygiene Institute (RGHI) fellowship. FC was supported by the National Institutes of Health NIH/AID grant numbers F31 AI114245, R01 AI052473, U01 AI088752, R01 TW009504 and R25 TW009338. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Ethical approval for this study was obtained from the Research Ethics Committee at the Collective Health Institute, Federal University of Bahia, Brazil (permit 041/17 2.245.914.17 2.245.914) and the National Commission for Research Ethics, Brazilian Ministry of Health (CAAE: 68887417.9.0000.5030). All participants involved in the study provided written informed consent before data collection.

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All data produced in the present study are available upon reasonable request to the authors.