Table 1.
Mean number of named and genotyped partners by index case demographic characteristics.
Fig 1.
Genetic distance (Tamura-Nei 93; TN93) separating index cases and named partners.
Gray lines show the best-fitting mixture distribution. Additional tick marks indicating epidemiologically plausible thresholds between 0.01 and 0.02 substitutions/site are shown on x-axis. Blue denotes potential transmission partners (≤0.02 substitutions/site). Red denotes partners with “random” within or between subtype viral divergence.
Fig 2.
Number of genetic links and transmission clusters, as a function of the TN93 distance threshold.
The epidemiologically plausible range of thresholds between 0.01 and 0.02 substitutions/site is highlighted in gray.
Fig 3.
TN93 genetic distances between named partners ≤0.03 substitutions/site including and excluding codons associated with drug resistance.
Disagreement in classification (linked/unlinked) between distance models is shown in red. The line x = y is shown in solid gray. Dashed lines denote 1.75% genetic distance threshold.
Table 2.
Sensitivity to genetic distance thresholds ranging between 0.01 and 0.02 substitutions/site.
Fig 4.
Concordance between named partner and genetic networks.
(A) Genetic data mapped onto named partner network. Edges indicate partner naming. (B) Partner naming data mapped onto genetic network. Edges indicate genetic linkage (≤0.0175 substitutions/site).
Fig 5.
Proportion of partner namings and genetic links that agree, in relation to the TN93 genetic distance threshold.
The epidemiologically plausible range of thresholds between 0.01 and 0.02 substitutions/site is highlighted in gray.
Table 3.
Logistic regression analysis of index case being genetically-linked to at least one of their named partners.
Fig 6.
Genetic distance (TN93) separating index cases and named partners in select risk groups.
(A) Genetic distance between named heterosexual partners. (B) Genetic distance between named MSM partners. (C) Genetic distance between named partners where at least one partner reported injection drug use (IDU). (D) Genetic distance between named partners where at least one partner was diagnosed with acute or early HIV infection. Additional tick marks on the x-axis indicate epidemiologically plausible thresholds between 0.01 and 0.02 substitutions/site are shown on x-axis. Blue denotes potential transmission partners (≤0.02 substitutions/site). Red denotes partners with “random” within or between subtype viral divergence.
Table 4.
Index cases who were reciprocally named by their named partner (n = 189 partner pairs).