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. 2016 Oct 4;6:34729. doi: 10.1038/srep34729

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Copyright © 2016, The Author(s)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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The phylogenetic tree was constructed using approximately-maximum-likelihood method based on pol region (HXB2: 2, 253 to 3, 306 nt) in FastTree 2.3. The nucleotide substitution mode was GTR + G + I. The bootstrap value ≥0.9 was identified as a lineage/sub-lineage and was indicated at all relevant nodes. HIV-1 subtype C was chosen as an out-group in the rooted tree. The various lineages/sub-lineages were color-coded.