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

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

doi:10.1093/cid/cix499

Cited by 11 publications

(8 citation statements)

References 29 publications

(30 reference statements)

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“…38 The molecular epidemiology of subtype A in Ukraine has been well described in the late 1990s, when this HIV subtype was discovered in the country, 10,13 and in recent years. 8,11,17 However, very few studies were published between 2000 and 2015 even though the number of new HIV cases continued to grow rapidly in the early to late 2000s. 3,39,40 The molecular epidemiology of HIV-1 subtype B in Ukraine has been mostly neglected, primarily due to its lower prevalence.…”

Section: Discussionmentioning

confidence: 99%

“…However, the geographic distribution of HIV-1 subtype B sequences in our study is quite different: the majority of HIV-1 subtype B sequences come from Kyiv (61% of the Ukrainian dataset) or other regions (15%). This could be explained by a potential selection bias in the CASCADE data, 17 sampled exclusively in Kyiv. Among the available 46 HIV-1 subtype B sequences in the Ukrainian HIV Drug Resistance database, 24 (52%) originate from Mykolaiv, followed by small numbers of sequences from 9 other regions across Ukraine.…”

Section: Discussionmentioning

confidence: 99%

“…Second, we used 73 HIV-1 subtype B pol sequences collected as part of the CASCADE (Concerted Action on SeroConversion to AIDS and Death in Europe) cohort study in Kyiv in 2013–2015. 17 These data were collected anonymously in four infectious disease clinics that are part of the Kyiv AIDS Centre 18 and were sequenced at University College London Hospital laboratories on Sanger or Illumina MiSeq platforms. Third, we accessed the Los Alamos HIV database 9 and retrieved all available HIV-1 subtype B sequences ( N = 9) collected in Ukraine that spanned the same genomic region (HXB2 positions: 2,568–3,256) and which had available sampling dates and transmission group information.…”

Section: Methodsmentioning

confidence: 99%

“…15,16 A recent study demonstrated high levels of phylogenetic clustering (66%) among men who have sex with men (MSM) and heterosexual men infected with HIV-1 subtype B in Kyiv, the capital of Ukraine. 17…”

Section: Introductionmentioning

confidence: 99%

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The Changing Epidemiological Profile of HIV-1 Subtype B Epidemic in Ukraine

Vasylyeva

Liulchuk

Plessis

et al. 2019

AIDS Research and Human Retroviruses

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While HIV-1 subtype B has caused a large epidemic in the Western world, its transmission in Ukraine remains poorly understood. We assessed the genetic diversity of HIV-1 subtype B viruses circulating in Ukraine, characterized the transmission group structure, and estimated key evolutionary and epidemiological parameters. We analyzed 120 HIV-1 subtype B pol sequences (including 46 newly generated) sampled from patients residing in 11 regions of Ukraine between 2002 and 2017. Phylogenies were estimated using maximum likelihood and Bayesian phylogenetic methods. A Bayesian molecular clock coalescent analysis was used to estimate effective population size dynamics and date the most recent common ancestors of identified clades. A phylodynamic birth–death model was used to estimate the effective reproductive number (Re) of these clades. We identified two phylogenetically distinct predominantly Ukrainian (≥75%) clades of HIV-1 subtype B. We found no significant transmission group structure for either clade, suggesting frequent mixing among transmission groups. The estimated dates of origin of both subtype B clades were around early 1970s, similar to the introduction of HIV-1 subtype A into Ukraine. Re was estimated to be 1.42 [95% highest posterior density (HPD) 1.26–1.56] for Clade 1 and 1.69 (95% HPD 1.49–1.84) for Clade 2. Evidently, the subtype B epidemic in the country is no longer concentrated in specific geographical regions or transmission groups. The study results highlight the necessity for strengthening preventive and monitoring efforts to reduce the further spread of HIV-1 subtype B.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Changing Epidemiological Profile of HIV-1 Subtype B Epidemic in Ukraine

Vasylyeva

Liulchuk

Plessis

et al. 2019

AIDS Research and Human Retroviruses

Self Cite

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“…In addition, these samples could be used to conduct phylogenetic analyses of potential HIV transmission clusters to enhance the focus of targeted testing and index testing implementation. 53 …”

Section: Pooled Pcr To Facilitate Detection Of and Intervention Durinmentioning

confidence: 99%