ike phylogenetic signals, respectively.

(PPT)

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**Close view of the HIV-1 C~EA~ lineage despited in** [**Figure 1**](#pone-0041904-g001){ref-type="fig"} **.** The color of branches represents the country from where the sequence originated, according to the legend shown on the left. The boxes highlight the position of the major country-specific sub-clades detected in our study. The aLRT support values are indicated only at key nodes.

(PPTX)

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**Time-scaled Bayesian MCC tree of HIV-1 subtype C** ***pol*** **sequences from Ethiopia.** Branches are colored according to the initial clade assignment of each sequence based on ML analysis: C~ET~ (blue), C′~ET~ (red), other clades (green). The *PP* support is indicated only at key nodes. Positions of the putative interclade C/C′ recombinant sequences are marked with asterisks. Horizontal branch lengths are drawn to scale with the scale at the bottom indicating years. The tree was automatically rooted under the assumption of a relaxed molecular clock. Representative bootscanning plots of some putative C/C′ intrasubtype recombinant sequences are depicted on the right. Query sequences were compared to reference sequences of HIV-1 clades A1 (AB253429), D (AY371157), C~ET~ (AY242589), and C′~ET~ (AY242581).

(PPTX)

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We wish to thank Dr. Vera Bongertz for critical review of the manuscript and anonymous reviewers for comments.

[^1]: **Competing Interests:**The authors have declared that no competing interests exist.

[^2]: Conceived and designed the experiments: GB. Performed the experiments: GB EOD. Analyzed the data: GB EOD. Contributed reagents/materials/analysis tools: GB EOD. Wrote the paper: GB EOD.


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