Журнал «Актуальная инфектология» Том 9, №4, 2021
Вернуться к номеру
Chronic viral infections in internally displaced people who inject drugs in Оdessa, Ukraine
Авторы: T. Vasylyeva (1), A. Yakovleva (2), G. Kovalenko (3), L. Meredith (3), L. Kotlyk (4), G. Kolodyazeva (4), G. Podolina (4), S. Chernyavskaya (4)
(1) — Division of Infectious Diseases and Global Public Health, University of California San Diego, CA, USA
(2) — Medical Sciences Division, University of Oxford, Oxford, UK
(3) — Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
(4) — Odessa Regional Virology Laboratory, Odessa, Ukraine
Рубрики: Инфекционные заболевания
Разделы: Медицинские форумы
Версия для печати
Internally displaced people (IDPs) often have higher burden of otherwise preventable and controllable infectious diseases. As of 2021, over 1.4 million people in Ukraine have been internally displaced due to the military conflict in the Donbass region. At the same time, Ukraine has a high prevalence of injection drug use (IDU) that is leading Ukraine to be one of the 5 countries that accounts for 80 % of total global HCV infections. We assessed the feasibility of HCV genetic sequencing with the portable technology MinION from Nanopore and subsequent phylodynamic analysis to estimate timing of viral transmission events relative to the time of IDPs migration. We generated the first partial and near full length genome (NFLG) HCV sequences from Ukraine and described HCV transmission dynamics in internally-displaced people who inject drugs (IDPWID) currently residing in Odessa, Ukraine.
Materials and methods. We used respondent-driven sampling (RDS) techniques to recruit IDPWID in Odessa, Ukraine, in June — September 2020. All participants were interviewed about their socio-demographic characteristics and their migration experience and screened for HIV and HCV by rapid tests. Whole blood samples were collected from all participants; serum was isolated at the Odessa Regional Virology Laboratory and stored at –80 °C. We used the ARTIC Network nCoV-2019 Sequencing Protocol V3 LoCost that employs MinION from Nanopore technology to sequence HCV. For each identified HCV subtype, all resulting consensus genome HCV sequences were aligned using the Muscle algorithm in AL iView. RaxML was then used to reconstruct maximum likelihood (ML) phylogenetic trees for each subtype under a general time-reversible nucleotide substitution model with gamma-distributed rate-variation among sites (GTR + G). We used Cluster Picker to identify possible transmission clusters defined as clades with > 90 % bootstrap support and within-clades genetic distance < 3 %. We used Beast 1.10.4 to perform molecular clock analyses and reconstruct population growth history for each of the identified HCV subtypes and transmission clusters.
Results. 164 IDPWID were recruited: 81 % male, 73 % completed secondary or higher education, 47 % were single, and 54 % arrived in Odessa between 2014–2015. Rapid testing identified prevalence of HIV, HCV and HIV/HCV coinfection of 39; 67.7, and 31.1 %, respectively. Of those testing HIV-positive in our study, 43.8 % were newly diagnosed. We obtained 57 partial or NFLG HCV sequences across genotypes 1a (n = 14), 1b (n = 23), and 3a (n = 20) from our 164 samples (34.8 %). We identified three, four, and one potential transmission clusters (5 clusters of 2 sequences, and 2 clusters of 3 sequences) on the subtype 1a, 1b, and 3a phylogenetic trees, respectively. Phylodynamic analysis showed that the time of most recent common ancestor (TMRCA) was in 1958 (95 Highest Posterior Density (HPD) 1915–1990), 1949 (1897–1983), and 1955 (1907–1992) for subtypes 1a, 1b, and 3a, respectively. The TMRCAs for all subtype 1a clusters, subtype 1b cluster 3, and the 3a cluster dated pre-conflict and were estimated to be between 1987 and 2013, unlikely indicating a recent transmission event. Three of the subtype 1b clusters were more recent: TMRCAs for cluster 1, 2, and 4 were estimated to be in November 2011 (May 2005 — April 2016), May 2018 (August 2016 — October 2019), and December 2017 (October 2015 — May 2019), respectively.
Conclusions. We demonstrate that HCV genetic sequencing with the portable technology MinION from Nanopore is feasible and that molecular clock analysis allows us to estimate timing of viral transmission events in a population of IDPWID relative to the time of their migration. We show evidence that HCV transmission events are likely to occur soon after arrival to the host region. We also show evidence of HCV infection with 1a (25 %), 1b (40 %), and 3a (35 %) genotypes within IDPWID in Odessa, Ukraine, which is similar to what has been reported in the general population in Ukraine. Increased monitoring and understanding of the dynamics of infectious disease transmission networks, is a crucial step in the development of effective interventions for IDPWID.