A Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Sequences in Kiev: Findings Among Key Populations

Abstract

Background: The human immunodeficiency virus (HIV) epidemic in Ukraine has been driven by a rapid rise among people who inject drugs, but recent studies have shown an increase through sexual transmission.

Methods: Protease and reverse transcriptase sequences from 876 new HIV diagnoses (April 2013-March 2015) in Kiev were linked to demographic data. We constructed phylogenetic trees for 794 subtype A1 and 64 subtype B sequences and identified factors associated with transmission clustering. Clusters were defined as ≥2 sequences, ≥80% local branch support, and maximum genetic distance of all sequence pairs in the cluster ≤2.5%. Recent infection was determined through the limiting antigen avidity enzyme immunoassay. Sequences were analyzed for transmitted drug resistance mutations.

Results: Thirty percent of subtype A1 and 66% of subtype B sequences clustered. Large clusters (maximum 11 sequences) contained mixed risk groups. In univariate analysis, clustering was significantly associated with subtype B compared to A1 (odds ratio [OR], 4.38 [95% confidence interval {CI}, 2.56-7.50]); risk group (OR, 5.65 [95% CI, 3.27-9.75]) for men who have sex with men compared to heterosexual males; recent, compared to long-standing, infection (OR, 2.72 [95% CI, 1.64-4.52]); reported sex work contact (OR, 1.93 [95% CI, 1.07-3.47]); and younger age groups compared with age ≥36 years (OR, 1.83 [95% CI, 1.10-3.05] for age ≤25 years). Females were associated with lower odds of clustering than heterosexual males (OR, 0.49 [95% CI, .31-.77]). In multivariate analysis, risk group, subtype, and age group were independently associated with clustering (P < .001, P = .007, and P = .033, respectively). Eighteen sequences (2.1%) indicated evidence of transmitted drug resistance.

Conclusions: Our findings suggest high levels of transmission and bridging between risk groups.

Figure 1.

Subtype A1 phylogeny (clusters of size 4 and above), human immunodeficiency type 1 (HIV-1) pol sequences collected in Kiev, April 2013–March 2015. Subtype A1 clusters sizes 4 and above only. Individual clusters are highlighted and colored according to the risk group of >60% of samples in the cluster (see Figure 3). Abbreviations: MSM, men who have sex with men; PWID, people who inject drugs. Scale bar = nucleotide substitutions per site.

Figure 2.

Subtype B phylogeny (all clusters), human immunodeficiency type 1 (HIV-1) pol sequences collected in Kiev, April 2013–March 2015. Subtype B clusters all sizes. Individual clusters are highlighted and colored according to the risk group of >60% of samples in the cluster (see Figure 3). Abbreviations: MSM, men who have sex with men; PWID, people who inject drugs. Scale bar = nucleotide substitutions per site.

Figure 3.

Clusters by risk group. Subtype A1 and B human immunodeficiency type 1 (HIV-1) pol sequences collected in Kiev, April 2013–March 2015. Groups based on >60% of samples in the cluster. Abbreviations: Het, heterosexual sexual contact (male and female); HetM/MSM, heterosexual males (sexual contact and PWID) and men who have sex with men; Het/PWID, heterosexual sexual contact (male and female) and people who inject drugs (male and female); MSM, men who have sex with men; PWID, people who inject drugs (male and female).

Figure 4.

Scatterplot of association of risk groups within clusters. Subtype A1 and B human immunodeficiency type 1 (HIV-1) pol sequences collected in Kiev, April 2013–March 2015. On each graph, points represent every cluster, with the marker scaled to cluster size. The x- and y-axes denote risk groups, and the location of the marker shows the proportion of sequences in the cluster belonging to each of the risk groups. Abbreviations: MSM, men who have sex with men; PWID, people who inject drugs.