Urban census tracts.

<p>Urban census tracts (<i>i.e.</i>, continuous and homogeneous areas comprising 300 buildings on average, IBGE 2002) according to socioeconomic levels (quartile) and dengue cases with molecular analysis according to strains from January 2006 to June 2006 (A); urban census tracts according to incidence coefficients of dengue cases (quartile) reported to the Surveillance System from September 2005 to August 2006 (B).</p

São José do Rio Preto map.

<p>São José do Rio Preto map with urban census tracts, irregular development areas and autochthonous dengue cases reported and confirmed by the Surveillance System from September to November (A), December (B), January (C) and February (D). The areas outside the urban perimeter are irregular development areas with urban characteristics, but with inadequate sanitation infrastructure and lowest socioeconomic conditions in comparison to urban census tracts. There is a cluster of cases in one of these irregular areas in the North Zone of the city (Santa Clara) in September 2005 and a spread of the transmission to the rest of the urban perimeter (A).</p

Logistic fitting of the Bayesian skyline plot and force of infection.

<p>A) the normalized median of the Bayesian estimates from the sequences analyzed, <i>y(t)</i>, fitted to a continuous logistic curve according to equation (1). Diamonds represent the data and the continuous line the fitted function. The period of time entails the epidemics during the fat growing phase during January and February of 2006. B) Force of infection calculated from the fitted model in A) using equation (2).</p

Bayesian skyline (BSL) plot and number of dengue reported cases.

<p>A) Bayesian skyline (BSL) plot of the virus genealogy-based estimate of the number of new infections (presented as <i>Ne.g</i>) indicated as the median for 82 DENV-3 isolates showing the increase from 180 to 120 days before the last sampling (from present day 0 or day of the last sample taken to the past), which matches with uncanny precision the rise in number of reported cases per 100,000 inhabitants from December of 2005. Apparent differences in overall population sizes are due to both the fact that the BSL shows accumulated number of new infections and to scaling problems or misreport. B) Number of Dengue reported cases in SJRP during the seasons of 2001–2002 (01_02), 2003 (02_03), 2004 (03_04), 2005 (04_05) and 2006 (05_06). It is noticeable that the maximum number of reported cases in 2006 happened in April, when the zenith of the epidemics, determined by the Bayesian skyline plot, was around February.</p

Relation among the socioeconomic level of the census tracts and the incidence coefficients.

*<p>Qui-squared test for non-significant adherence: χ² = 0.778; p = 0,8548.</p>**<p>Qui-squared test for significant independence: χ² = 101.679; p<0.0001.</p

Maximum clade credibility (MCC) tree for 131 Dengue 3 isolates.

<p>MCC tree for 131 Dengue 3 isolates from several places in World, indicating that the origin of the 60 lineage 1 samples (with 90% posterior probability support) from viruses from the lineage 2 (with 77% posterior probability support). The close-related BR47886 sampled in 2002 in Brazil and the H IMTSSA sampled in 2000 in Martinique had a basal position in relation to the SJRP lineages (with 100% posterior probability support).</p

Estimated routes of dispersion of dengue as obtained by the “Nepotistic algorithm”.

<p>The basis of the three dimensional graphic represents the geographic coordinates of the positions where the sample were collected, while the vertical axis represents the months of the sampling. Each independent lineage starts with a “star” (oldest sample of the lineage) and the connections to the other samples (names are displayed as close to point as possible) are done with lines, whose width is proportional to the genetic relatedness between the samples. The three lineages represented are: (<i>i</i>) green the more recent, with only one sample, the 122-145, (<i>ii</i>) red or “South-eastern” lineage (starting with 22-18, that turns to yellow with more recent “ancestry” samples) and (<i>iii</i>) blue, or North-western” lineage 1 (starting at 01-00, and that gets lighter as for the previous one).</p

Symmetrical matrices.

<p>Symmetrical matrices representing: A) temporal, B) genetic and C) spatial distances among the 46 samples. For easy visual comparison, numbers were substituted by a scale of colours that ranges from white (lower value) to black (higher value). The samples were organized temporally as indicated by the gradual pattern observed in matrix A), and the colours of the names of the samples are meant to facilitate the comparison with the results.</p

Route of viral dispersion - I.

<p>Estimated route of dispersion of the “North-western”, departing from the putative ancestor (blue dot and dispersing to other places where dengue cases were recorded - lines with more recent nodes tends to the lighter tones) projected on the aerial image of the city of São José do Rio Preto (SJRP). The sample of the third viral introduction is also shown in a green dot. (Background image obtained from Google Earth 4.2.0181.2634 – download date: September 16th 2007).</p