The HIV-1 TRACE (TRAnsmission Cluster Engine) is a new computational tool to identify molecular transmission clusters in large databases. This approach is based on viral genetic relatedness to a reference sequence in order to construct and visualize the connections among clusters. Our objective was to identify transmission clusters in CoRIS cohort (2018 update) by using HIV-1 TRACE computational tool focusing on subtype B patients and to compare TRACE identified clusters with phylogenetic approaches.
We used the RT available regions from newly HIV diagnoses in 2018 in CoRIS. HIV-1 TRACE (http://hivtrace.datamonkey.org/hivtrace) was used to estimate transmission clusters in 484 subtype B antiretroviral-naïve patients enrolled in the CoRIS cohort. Phylogenetic analysis was conducted by maximum likelihood method (ML) with bootstrap using the GTR+G as nucleotide substitution model. Sequences were phylogenetically analysed along with all the most similar sequences as identified by a BLAST search. Local transmission networks (LTNs) were defined as phylogenetic clusters including sequences from Spain at proportions >70%, receiving bootstrap value >70%.
HIV-1 TRACE results showed that 354 patients (73.1%, n=354/484) were not involved in any cluster and 130 patients (26.9%, n=130/484) were grouped in 54 clusters: 39 clusters with 2 nodes, 11 clusters with 3 nodes, 2 clusters with 4 nodes, 1 cluster with 5 nodes and 1 cluster with 6 nodes (range 2-6). Phylogenetic analysis revealed that 330 (68.2%, n=330/484) and 154 patients (31.8%, n=154/484) were involved in 63 clusters: 48 clusters with 2 nodes, 7 clusters with 3 nodes, 4 clusters with 4 nodes and 4 clusters with 5 nodes (range 2-5). Overall, the concordance between phylogenetic approaches and HIV-1 TRACE tool was 84.4%. The discrepancies were not observed only in the number of clusters, as previously described, but also in the distribution, since phylogenetic tools identified 8 clusters with more than 3 nodes and HIV-1 TRACE identified only 4 of these clusters.
The implementation of HIV-1 TRACE is an easy to use tool and it allows identification of transmission clusters. Our results revealed that HIV-1 TRACE identified fewer clusters among B-subtype patients than traditional phylogenetic approaches. Those discrepancies were due to the non-use of a threshold in the patristic distances in phylogenetic analysis.