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

• Published in: Clinical infectious diseases 2017-10, Vol.65 (7), p.1127-1135
• Main Authors: Fearnhill, Esther, Gourlay, Annabelle, Malyuta, Ruslan, Simmons, Ruth, Ferns, R. Bridget, Grant, Paul, Nastouli, Eleni, Karnets, Iryna, Murphy, Gary, Medoeva, Antonia, Kruglov, Yuri, Yurchenko, Alexander, Porter, Kholoud
• Format: Article
• Language: English
• Subjects: Adult; Age; and Commentaries; ARTICLES AND COMMENTARIES; Avidity; Cluster Analysis; Clustering; Confidence intervals; Demographics; Disease transmission; Drug resistance; Drug Resistance, Viral - genetics; Drugs; Enzyme immunoassay; Enzymes; Epidemics; Female; Females; Gene sequencing; Genetic distance; Heterosexuality - physiology; HIV; HIV Infections - epidemiology; HIV Infections - virology; HIV-1 - genetics; Homosexuality, Male - genetics; Human immunodeficiency virus; Humans; Immunoassay; Infections; Male; Males; Multivariate analysis; Mutation; Phylogenetics; Phylogeny; Risk analysis; Risk groups; RNA-directed DNA polymerase; Sequence Analysis, DNA - methods; Sexual and Gender Minorities; Transcription factors; Ukraine - epidemiology; Viruses
• ISSN: 1058-4838; 1537-6591
• DOI: 10.1093/cid/cix499

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 univeriate 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.