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. 2018 Dec 6;9:2799. doi: 10.3389/fmicb.2018.02799

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Copyright © 2018 Dalai, Junqueira, Wilkinson, Mehra, Kosakovsky Pond, Levy, Israelski, de Oliveira and Katzenstein.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Maximum likelihood HIV-1 pol transmission clusters in San Mateo County, California. Colored semi-circles indicate HIV subtypes. Black branches represent sequences obtained from 316 HIV-positive adults receiving antiretroviral treatment as part of the publicly funded San Mateo County AIDS Program. Gray branches denote reference sequences. Clades highlighted in blue indicate transmission clusters identified in Cluster Picker (TBE ≥ 90 and genetic distance threshold of 8%). Asterisks indicate transmission pairs mutually identified as transmission links in Cluster Picker and HIV-TRACE. The scale bar at the bottom represents the number of substitutions per site along branches in the tree topology.