Supplementary Methods, Figures, and Tables.

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Observed and expected age distribution.

(A) Age distributions of the reported case numbers during the epidemic periods (red, blue, green, yellow circles correspond to the serotype 1, 2, 3, 4, respectively). (B) The seroprevalence of antibodies against DENV obtained from the serological survey (red dashed lines with error bars). In both (A) and (B), black solid lines give model predictions, with 95%-CI represented by the grey shaded areas (95%-CI).</p

Epidemiology of dengue in French Polynesia (directly obtained from data).

(A) Spatial distribution of the number of cases reported between 1979 and 2014, in the different islands of French Polynesia. Each circle represents the size of the population, where the radius is defined as 0.2log10P with the population size P. The colours of the circles represent the number of reported cases. (B) Monthly number of cases reported for DENV-1 to DENV-4. (C) Age distribution of cases, averaged over the period between 1979 and 2014. (D) The results of serological surveys (seroprevalence of antibodies against DENV) conducted in 2014 and 2015. Error bars indicate 95%-CI.</p

Estimated FOI and immunity (obtained from our model).

(A) The observed (dots) and expected (line) number of cases reported annually. Shaded area represents 95%-CI. (B) Fitted FOI for the four serotypes. (C) Average immunity profile of the population. The grey area shows the fraction of the population that were never infected, averaged over age groups. Red, blue, green, and yellow areas represent the fraction of the population who have been infected once by a serotype i (before the time we consider), where i = 1,2,3,4 correspond to red, blue, green, yellow, respectively. Black area represents the fraction of the population who have been infected more than once (before the time we consider).</p

Estimated reporting probabilities (obtained from our model).

(A) Reporting probability of primary infections by DENV-1 as a function of time. The grey shaded area shows 95%-CI. (B) Relative strength of the reporting probabilities of secondary infections (DENV-1) compared with primary infections (DENV-1). (C) Comparison of the reporting probabilities for different serotypes, for primary (black circle) and secondary (red circle) infections. The reference group is primary Serotype 1 infection for primary infections and secondary Serotype 1 infection for secondary infections. (D) Variations of the reporting probability with the age group, considering individuals aged 5–9 year old as the reference group. See Section B in S1 Text for the mathematical definitions of the relative risks plotted in these panels.</p

Spatial and temporal distribution of confirmed cases of DENV-1 and DENV-4 infections between January and December 2009.

<p>Spatial and temporal distribution of confirmed cases of DENV-1 and DENV-4 infections between January and December 2009.</p

Relevant amino acid substitutions on the E protein based on the consensus sequence of 142 DENV-4 strains.

<p>*non conservative aa substitution; strains of interest are in bold characters.</p

Monthly recorded dengue suspected and confirmed cases from January 2009 to December 2010.

<p>Monthly recorded dengue suspected and confirmed cases from January 2009 to December 2010.</p

Evolutionary relationships of DENV-4 E gene sequences.

<p>ML original tree derived from 110 DENV-4 E gene sequences. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown for values over 80. The number of strains with identical E gene sequence is indicated in parenthesis (these additional strains could have been collected in a different district or island and at a different date than the strain that appears in the tree).</p

Significant nucleotide substitutions on the E gene (1485 bp) within the DENV-4 clade IIa Oceania group.

<p>- Identical to Solomon.</p