Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia

Abstract

Molecular epidemiology of HIV-1 infection in treatment-naive HIV-1 infected persons from Croatia was investigated. We included 403 persons, representing 92.4% of all HIV-positive individuals entering clinical care in Croatia in 2014-2017. Overall prevalence of transmitted drug resistance (TDR) was estimated at 16.4%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTI (NNRTIs) and protease inhibitors (PIs) was found in 11.4%, 6.7% and 2.5% of persons, respectively. Triple-class resistance was determined in 2.2% of individuals. In addition, a single case (1.0%) of resistance to integrase strand-transfer inhibitors (InSTIs) was found. Deep sequencing was performed on 48 randomly selected samples and detected additional TDR mutations in 6 cases. Phylogenetic inference showed that 347/403 sequences (86.1%) were part of transmission clusters and identified forward transmission of resistance in Croatia, even that of triple-class resistance. The largest TDR cluster of 53 persons with T215S was estimated to originate in the year 1992. Our data show a continuing need for pre-treatment HIV resistance testing in Croatia. Even though a low prevalence of resistance to InSTI was observed, surveillance of TDR to InSTI should be continued.

Figure 1

Maximum likelihood phylogenetic analysis of the Croatian HIV-1 subtype B sequences from the old (2006–2008), the new (2014–2017) datasets and background sequences. Branches of Croatian sequences from the new dataset are coloured according to transmission risk: red, men who have sex with men (MSM); green, other. Branches of sequences from the old dataset are coloured blue, while branches of all background sequences are coloured black. All identified surveillance drug resistance mutations (SDRMs) are positioned on the tree along with the corresponding sequences. For SDRMs T215S; T215S + L210W; K101E; M41L + T215L; V32I + I47V + T215D/E + K103N + L100I (TRIPLE_CLASS_RES) that form local transmission clusters (TCs), above each cluster corresponding SDRMs were noted, meaning that all sequences inside TCs harbour SDRMs. TCs with >75% of Croatian sequences (local clusters) are highlighted blue, while TCs with <75% of Croatian sequences (mixed clusters) are highlighted yellow.

Figure 2

Bayesian maximum clade-credibility tree of the Croatian HIV-1 subtype B sequences from the new dataset (2014–2017) and corresponding background sequences. Branches are coloured according to the geographic origin, as presented on the legend of Fig. 2, with the exception of less frequent background sequences, which are coloured black. TCs with >75% of Croatian sequences (local clusters) are highlighted blue, while TCs with <75% of Croatian sequences (mixed clusters) are highlighted yellow. TCs with ≥5 Croatian sequences (Table 3) are marked on the sideward by ordinal numbers. The scale is set at 5-year intervals starting at the sampling time of the latest sequence (2017.91).