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

Esther Fearnhill*, Annabelle Gourlay, Ruslan Malyuta, Ruth Simmons, R. Bridget Ferns, Paul Grant, Eleni Nastouli, Iryna Karnets, Gary Murphy, Antonia Medoeva, Yuri Kruglov, Alexander Yurchenko, Kholoud Porter

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1127-1135
Number of pages9
JournalClinical Infectious Diseases
Issue number7
Publication statusPublished - 1 Oct 2017

Bibliographical note

Funding Information:
Financial support. This work was supported by the European Union Seventh Framework Programme (FP7/2007–2013) under EuroCoord (grant agreement number 260694). R. B. F. received funding related to this study from the National Institute for Health Research (NIHR) Biomedical Research Centre and the University College London Hospitals NHS Foundation Trust (UCLH)/University College London (UCL) Biomedical Research Centre (BRC)-funded NIHR Health Informatics Collaborative study.

Publisher Copyright:
© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved.


  • HIV
  • MSM
  • PWID
  • Ukraine
  • phylogenetic


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