HIV-1 subtype D infections among Caucasians from Northwestern Poland--phylogenetic and clinical analysis

Abstract

Background: HIV-1 subtype D infections, which are associated with a faster rate of progression and lymphocyte CD4 decline, cognitive deficit and higher mortality, have rarely been found in native Europeans. In Northwestern Poland, however, infections with this subtype had been identified. This study aimed to analyze the sequence and clinical data for patients with subtype D using molecular phylogeography and identify transmission clusters and ancestry, as well as drug resistance, baseline HIV tropism and antiretroviral treatment efficacy.

Methods: Phylogenetic analyses of local HIV-1 subtype D sequences were performed, with time to the most recent common ancestor inferred using bayesian modeling. Sequence and drug resistance data were linked with the clinical and epidemiological information.

Results: Subtype D was found in 24 non-immigrant Caucasian, heterosexually infected patients (75% of females, median age at diagnosis of 49.5 years; IQR: 29-56 years). Partial pol sequences clustered monophyletically with the clades of Ugandan origin and no evidence of transmission from other European countries was found. Time to the most common recent ancestor was 1989.24 (95% HPD: 1968.83-1994.46). Baseline drug resistance to nucleoside reverse transcriptase inhibitors was observed in 54.5% of cases (mutations: M41L, K103N, T215S/D) with evidence of clustering, no baseline integrase or protease resistance and infrequent non-R5 tropism (13.6%). Virologic failure was observed in 60% of cases and was associated with poor adherence (p<0.001) and subsequent development of drug resistance (p = 0.008, OR: 20 (95%CI: 1.7-290).

Conclusions: Local subtype D represented an independently transmitted network with probably single index case, high frequency of primary drug resistance and evidence of transmission clusters.

Figure 1. Relationships between the subtype D sequences inferred using maximum likelihood phylogeny (GenBank deposited pol sequences).

Country-specific sequences are marked with the same color: red – Poland, blue – Uganda, green – Tanzania, yellow – Europe (except Poland), brown – Cameroon, magenta - Senegal, cyan- Sudan, dark green – other African countries, violet – South America, grey – Asia, orange – North America.

Figure 2. Phylogenetic trees of the subtype D sequences from Northwestern Poland.

Figure a - maximum likelihood tree with bootstrap values for 1000 replicates drawn at the branches. Figure b – time scaled Bayesian MCMC tree. On the tree branches estimated time to the most recent common ancestor (tMRCA) and posterior probabilities expressed as percentage are shown. For both figures clustered sequences are marked in red and four identified clusters indicated as blue boxes and numbered are drawn on the right. Drug resistance mutations are marked at the tip nodes after the sequence identifier. *source patient for the transmission of the drug resistance within the cluster.

Figure 3. Bayesian skyline plot for estimation of the number of subtype D HIV-1 cases in the local population.

95% CI are marked in blue. Y-axis: predicted number of cases (log scale), X-axis: timescale (years).

Figure 4. Frequency of baseline drug resistance mutations among treatment-naive patients.

Figure 5. Frequency of secondary drug resistance mutations in patients failing antiretroviral therapy.