Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study. Virus Evolution
Kusejko et al. aimed to study the age difference at infection in HIV transmission pairs using phylogenetic methods. The authors used HIV-1 pol-sequences of 11’922 Swiss HIV Cohort Study (SHCS) patients and approximately 240’000 Los Alamos background sequences to build a phylogenetic tree.
Considering the tree with all 11’922 SHCS patients, 2’991 pairs could be extracted, with 31.9% men who have sex with men (MSM) pairs, 21.2% heterosexual (HET) pairs, 13.8% intravenous drug user (IDU) pairs, and 11.8% HET/IDU pairs. For all transmission groups, the age difference at infection was significantly (P<0.001) smaller for pairs in the tree compared with randomly assigned pairs, meaning that patients of similar age are more likely to be pairs. The mean age difference in the phylogenetic analysis was 9.2, 9.0, 7.3 and 5.6 years for MSM-, HET-, HET/IDU-, and IDU-pairs, respectively. Decreasing the cophenetic distance threshold from 0.05 to 0.01 significantly decreased the mean age difference. Similarly, repeated sampling of 100% down to 1% of the tips revealed an increased age difference at lower sample proportions.
In summary, the study-results suggest that HIV-transmission is age-assortative, but the age difference of transmission pairs detected by phylogenetic analyses depends on both sampling proportion and distance criterion. The mean age difference decreases when using more conservative distance thresholds, implying an underestimation of age-assortativity when using liberal distance criteria. Similarly, overestimation of the mean age difference occurs for pairs from sparsely sampled trees, as it is often the case in sub-Saharan Africa.