Transmission patterns of HIV-1 non-R5 strains in Poland

Abstract

HIV-1 env sequencing enables predictions of viral coreceptor tropism and phylogenetic investigations of transmission events. The aim of the study was to estimate the contribution of non-R5 strains to the viral spread in Poland. Partial proviral env sequences were retrieved from baseline blood samples of patients with newly diagnosed HIV-1 infection between 2008-2014, including 46 patients with recent HIV-1 infection (RHI), and 246 individuals with long-term infection (LTHI). These sequences were subjected to the genotypic coreceptor tropism predictions and phylogenetic analyses to identify transmission clusters. Overall, 27 clusters with 57 sequences (19.5%) were detected, including 15 sequences (26.3%) from patients with RHI. The proportion of non-R5 strains among all study participants was 23.3% (68/292), and was comparable between patients with RHI and LTHI (11/46, 23.9% vs 57/246, 23.2%; p = 1.000). All 11 patients with non-R5 strains and RHI were men having sex with men (MSM). Among these patients, 4 had viral sequences grouped within phylogenetic cluster with another sequence of non-R5 strain obtained from patient with LTHI, indicating potential acquisition of non-R5 HIV-1 for at least 4/46 (8.7%) patients with RHI. We were unable to confirm the contribution of patients with RHI to the forward transmission of non-R5 strains, but a relatively high proportion of non-R5 strains among them deserves attention due to the limited susceptibility to CCR5 antagonists.

Figure 1

MCMC phylogenetic tree of env sequences obtained from 292 patients diagnosed in Poland in the years 2008–2014. Transmission clusters identified with the maximum likelihood aLRT value of >90%, maximum intracluster pairwise genetic distance <3%, and posterior probability of 1 in Bayesian inference are highlighted. Clusters highlighted in green contain sequences obtained from patients with long-term and recent HIV-1 infection. Clusters highlighted in grey and light blue contain sequences obtained from patients with long-term HIV-1 infection only and recent HIV-1 infection only, respectively. Squares indicate the presence of non-R5 strains. Self-reported transmission routes for patients with clustered HIV-1 sequences are specified with MSM (for sex between men), MSM/HET (for sex between men or women and men), IDU (for injecting drug use), O/Unk (for other/unknown). Majority of sequences represented subtype B, thus only non-B subtypes are indicated.

Figure 2

HIV-1 transmission clusters inferred from the analysis of env sequences obtained from 292 study participants diagnosed in the years 2008–2014. Clusters were identified with the maximum likelihood aLRT value of >90%, maximum intracluster pairwise genetic distance <3%, and posterior probability of 1 in Bayesian inference. Viral tropism is indicated with shapes: squares and circles represent sequences of non-R5 and R5 strains, respectively. For all patients with clustering viral sequences shapes are colored according to: city of HIV-1 diagnosis (a), self-reported transmission route (MSM - sex between men, MSM/HET - sex between men or women and men, IDU - injecting drug use, O/Unk - other/unknown) (b), and duration of HIV-1 infection (c).