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. 2021 Aug 19;13(8):1643. doi: 10.3390/v13081643

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© 2021 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Phylogenetic resolution of patterns of HIV spread using HIV-TRACE and Microbe TRACE compared to MEGA10 phylogeny. (A) The number and size of individual clusters assigned by HIV-TRACE at different genetic distances (GDs). (B) MicrobeTrace topology (2.5% GD) of singleton transmissions assigned based on MEGA10 phylogeny. 5 (C) MicrobeTrace topology (2.5% GD) of small clusters assigned using MEGA10. (D,E) MicrobeTrace (1.5% and 2.5% GD) shows singleton/small cluster outliers at 1.5% failing to associate with MEGA10-defined large clusters. (F) MicrobeTrace (2.5% GD) depicts years of infection of large cluster members.