 about 64% of subtype C sequences from Kenya and 49% from Tanzania branched within the major clade C~EA~, while the remaining sequences were distributed in the multiple minor clades of southern African origin. Such geographical variation in the prevalence of different subtype C clades could be also observed at a more local scale in Tanzania ([Fig. 2b](#pone-0041904-g002){ref-type="fig"}). In the Kagera and Mwanza regions (north), most (\>70%) subtype C strains belong to the C~EA~ clade. In the Kilimanjaro region (northeast), sequences from both the C~EA~ and "southern African" clades reach a roughly similar prevalence. In the Mbeya region (southwest), only "southern African" clades were detected.

![Geographic distribution of HIV-1 subtype C clades in east Africa.\
a) Map of Africa showing the frequency of distinct HIV-1 subtype C clades across the five countries from the east region here studied (Burundi, Ethiopia, Kenya, Uganda and Tanzania). b) Map of Tanzania showing the frequency of distinct HIV-1 subtype C clades across different country regions where patients included in the present study resided (Kagera, Mwanza, Kilimanjaro and Mbeya). The legend for the colors on graphics is shown on the right.](pone.0041904.g002){#pone-0041904-g002}

Migration pattern of HIV-1 C~EA~ clade {#s3b}
--------------------------------------

A closer inspection of the HIV-1 C~EA~ clade showed that sequences from Burundi occupies the most basal position in the clade ([Figure S2](#pone.0041904.s002){ref-type="supplementary-material"}), thus suggesting that Burundi was the most probable epicenter of dissemination of this subtype C lineage. The migration pattern of the C~EA~ lineage was reconstructed using a Bayesian statistical framework that allows ancestral reconstruction of the locations at the interior nodes of Bayesian tree while accommodating phylogenetic uncertainty. Sequences with no information about sampling date (*n* = 2), sequences with unexpectedly long branches in the phylogenetic analysis (*n* = 10), and Et