Table 3.
Results of the systematic review of 105 articles employing different strategies to define HIV-1 transmission clusters.
| Categories of cluster definition | Number of articles | Mediana number of sequences (IQRb) | Median study period in years (IQRb) | Median sequence length (IQRb) | Most analysed genetic region (proportion of articles)c | Tree building model used (proportion of articles)c,d | Substitution model used (proportion of articles)c,e | Branch support approach (proportion of articles)c,d | Median cut-off for determining clusters (IQRb) |
| Phylogenetic | 53 | 219 (96–562) | 6 (2–12) | 1100 (895–1497) | pol (88%) | ML (60%) | GTR (73%) | Bootstrap (71%) | 90% (75–90%) |
| Distance-based | 7 | 2747 (179–40950) | 11 (6–16) | 900 (500–1800) | pol (100%) | NA | TN (100%) | NA | 0.015 Substitutions/site (0.014–0.019) |
| Distance-based & phylogenetic | 45 | 534 (131–1413) | 7 (2–12) | 1150 (915–1308) | pol (98%) | ML (76%) | GTR (74%) | Bootstrap (86%) | 90% (90–98%), 0.015 Substitutions/site (0.015–0.038) |
aPairwise comparisons using the Mann–Whitney U test: phylogenetic vs. distance-based, P = 0.036; phylogenetic vs. distance-based & phylogenetic, P = 0.030; distance-based vs. distance-based & phylogenetic, P = 0.13.
bInterquartile range.
cThe most commonly used methodology are presented with the proportion of articles in which this methodology was used.
dML, maximum likelihood; NA, not applicable.
eGTR, general time reversible; TN, Tamura–Nei.