Figure 1. Adjudication criteria used in assigning transmission linkages.

For each pair, adjudicators evaluated monophyly (yes/no), genetic distance, and Bayesian posterior probability (≥0.5 or <0.5) and classified the pair as ‘linked’, ‘unlinked’, or ‘indeterminate’. Further evaluation of ‘unlinked’ or ‘indeterminate’ pairs involved gathering additional data, including sequencing of consensus gag and/or clonal, single molecule or pyrosequencing of env, as well as obtaining sequences from non-transmitting HIV-1 infected participants from the same study site. New trees, distance distributions and Bayesian priors were generated and each pair was re-adjudicated to make final linkage assignments.