Figure 1.
Map of Brazil showing the five country regions.
An expanded map of the South region with the states (Paraná, Santa Catarina and Rio Grande do Sul) and state capitals (Curitiba, Florianópolis and Porto Alegre) is shown to the right. The number and sampling dates of sequences from the three southern state capitals included in the present study are indicated.
Figure 2.
ML phylogenetic tree for HIV-1 subtype C pol (PR/RT) sequences circulating in Brazil.
The color of a branch represents the geographic region from where the subtype C strain was sampled, according to the legend given in the figure. Brackets indicate the monophyletic clade formed by Brazilian subtype C sequences and the position of subtype C reference sequences of African origin. The box highlights the position of the sub-cluster circulating in Porto Alegre (BR-PA). The aLRT support values are indicated only at key nodes. Horizontal branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site. The tree was rooted using HIV-1 subtype A1 and F1 reference sequences.
Figure 3.
Bayesian MCC tree for HIV-1 subtype C pol (PR/RT) sequences circulating in Brazil.
Branches are colored according to the most probable location state of their descendent nodes. The legend for the colors is shown on the left. Brackets indicate the monophyletic clade formed by subtype C sequences sampled from Brazil, and the position of subtype C reference sequences of African origin used to root the tree. The box highlights the position of the sub-cluster BR-PA. The state posterior probability is indicated only at key nodes. Horizontal branch lengths are drawn to scale with the bar at the bottom indicating years.
Table 1.
Bayesian MCMC test of phylogenetic isolation of Brazilian HIV-1 subtype C sequences by geographic region.
Figure 4.
HIV-1 subtype C migration rates and routine traffic of people amongst the three states of the South Brazilian region.
Capitals are represented by blue circles proportional to the incidence of AIDS cases per 100,000 inhabitants in each city in 2009 [1]. The arrows are colored according to the routine traffic between states [41], from green (less) to red (more) passing through yellow, and their thickness is proportional to HIV-1 subtype C migration rate between state capitals as measured by BayesTraits. HIV-1 subtype C migration rate from Porto Alegre to Curitiba was more than 100 fold smaller than any of the others and is not represented in this picture.
Table 2.
Viral migration rates and routine traffic of people within the South Brazilian region.