Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers

Characterizing the circulation of Mayaro virus (MAYV), an emerging arbovirus threat, is essential for risk assessment but challenging due to cross-reactivity with other alphaviruses such as chikungunya virus (CHIKV). Here, we develop an analytical framework to jointly assess MAYV epidemiology and the extent of cross-reactivity with CHIKV from serological data collected throughout French Guiana (N = 2697). We find strong evidence of an important sylvatic cycle for MAYV with most infections occurring near the natural reservoir in rural areas and in individuals more likely to go to the forest (i.e., adult males) and with seroprevalences of up to 18% in some areas. These findings highlight the need to strengthen MAYV surveillance in the region and showcase how modeling can improve interpretation of cross-reacting assays.

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Simon Cauchemez
Apr 23, 2020 No software was used for data collection.
Custom code was developed in R (version 3.3.2). MCMC algorithm was performed using the R package rstan (version 2.19.2). The code was uploaded to a public repository https://github.com/nathoze/Mayaro The following data is available in a format that maintains anonymity of survey participants. For each individual: age group (10-year classes), MAYV RFI, CHIKV RFI, region (Maroni, Coast, Interior and High Oyapock), sex, income (high or low), environment (urban or rural), and sampling weight. The data was uploaded to a public repository https://github.com/nathoze/Mayaro nature research | reporting summary

October 2018
Behavioural & social sciences study design All studies must disclose on these points even when the disclosure is negative. We estimated the sample size for this survey at 2,500 persons distributed in the French Guiana territory based on a 50% seroprevalence, 95% confidence, 90% power and a cluster effect. To reach the desired sample size, a total of 1,600 households were randomly selected for possible participation in the study from household databases maintained by the Geographic information and knowledge dissemination unit of the Regional environment, planning and housing agency and the National Institute of Economic and Statistical Information (INSEE). A stratified simple random sampling was adopted to select households allowing an over-representation of the isolated and small municipalities. The global sampling fraction of the households was 1:49 varying from 1:103 to 1:5 according to the municipality. We employ the following notation to describe the study design: -i: one of the 22 strata (municipalities); -Mi: number of primary sampling units (households) in the ith stratum, i=1, …, 22; -Si: number of primary sampling units (households) selected from the ith stratum, i=1, …, 22; -mi: number of primary sampling units (households) actually enrolled in the study from the ith stratum, i=1, …, 22; -Pi: number of individuals living within the ith stratum, i=1, …, 22 (census data); -pi: number of individuals actually enrolled in the study from the ith stratum, i=1, …, 22; We considered that, in each municipality i, the probability of selecting a particular subject was equal to the probability of selecting his household and was (mi/Mi), corresponding to a statistical weight equal to (1/ mi/Mi) = (Mi/mi). This statistical weight indicates the number of people in the population represented by each subject in the sample. We applied a post-stratification adjustment to each of these weights to arrive at the final statistical weight for each subject. This adjustment helped us to weight the age-sex groups within each municipality to match the distribution in the French Guiana total population. Ten age groups ([2-5 years [, [5-10[, [10-15[, [15-20[, [20-25[, [25-35[, [35-45[, [45-55[, [55-65[, and !65 years) were defined within male and female groups, and for each age-sex subgroup, we applied an adjustment factor cijk to obtain a final statistical weight wijk = (Mi/mi)*cijk, where i, j, k are the indices of municipalities, sex groups, and age groups, respectively Data were collected through a standardized questionnaire installed on tablets to register demographics, socioeconomics, and household characteristics. A venous blood sample of 10 mL was collected from each participant, in accordance with current biosafety standards. The researcher was not blind to sampling procedure.
between June and October 2017.