Date Published: February 01, 2019
Publisher: Mary Ann Liebert, Inc., publishers
Author(s): Tetyana I. Vasylyeva, Mariia Liulchuk, Louis du Plessis, Esther Fearnhill, Victoriia Zadorozhna, Nataliia Babii, Alla Scherbinska, Vladimir Novitsky, Oliver G. Pybus, Nuno R. Faria.
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.
Ukraine has one of the worst HIV epidemics among European countries: in 2015, the country had the highest rate of new HIV infections in Europe (∼30 cases per 100,000 people).1 In the 1990s, people who inject drugs (PWID) were the transmission group that accounted for majority of new HIV infections in Ukraine.2,3 However, since the late 2000s, transmission among heterosexual nondrug-injecting populations has prevailed.4
Ukrainian HIV-1 subtype B sequences (n = 120) were obtained from patients belonging to four transmission groups: PWID (n = 26), MSM (n = 32), HET (non-PWID heterosexuals) (n = 54), and mother-to-child transmission (MTC, n = 8). Most of the Ukrainian sequences (75%, n = 90) were from male patients. Regarding their geographic distribution, 73 of the sequences (61%) came from Kyiv, 29 (24%) from Mykolaiv, and the remaining regions (N = 9) were represented by ≤5 sequences each (Table 1). The geographical distribution of the subtype B dataset used here is more representative than Ukrainian HIV-1 subtype B sequences available from the Los Alamos database (Fig. 1a), but is less extensive than that of the dominant HIV-1 subtype A in Ukraine (Fig. 1b).
HIV-1 subtype A has dominated the epidemic in Ukraine and other FSU countries since the mid-1990s.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. In this study, we characterize the current molecular epidemiology of HIV-1 subtype B in Ukraine, including its transmission group composition and virus transmission dynamics.
HIV drug resistance testing was performed at the L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine following all Ukrainian legal and ethical requirements. Fully anonymized genetic sequence data were transferred to Oxford through a Material Transfer Agreement for molecular evolutionary analyses.