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Molecular Epidemiology of HIV Infection in Eastern Europe and Central...
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Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 10867

Special Issue Editor

Dr. Marina Bobkova

E-Mail Website
Guest Editor
Ivanovsky Institute of Virology, Gamaleya National Research Center for Epidemiology and Microbiology, Russian Ministry of health, 123098 Moscow, Russia
Interests: HIV-infection; epidemiology; drug resustance; human genetics

Special Issue Information

Dear Colleagues,

The HIV epidemic began in Eastern Europe and Central Asia (EECA) somewhat later than in Western countries, but the spread of infection was much faster. The incidence rate in the region continues to be the highest in the world today. This is largely explained by the features of the epidemic, which was determined by the virus transmission among intravenous drug users in the first decade of the epidemic.

Over the years of the epidemic, many studies have been carried out regarding the spread of HIV subtypes in Russia and other countries. Over time, the tendency towards the dominance of the A6 sub-subtype gradually changed, and at present there is an increase in the prevalence of other genetic variants of HIV, including recombinant forms, as well as a tendency to the formation of double recombinants. These data are very important for the strategies of HIV infection diagnosis and treatment both in the EECA countries and worldwide.

This Special Issue will focus on the molecular epidemiology of HIV infection in the EECA region, and highlight current trends in HIV diversity in these countries. We welcome original research and reviews related to the prevalence of HIV genetic variants in the EECA region, with emphasis on HIV recombinants, drug resistance, transmission networks and virus evolution. Consideration of the role of HIV genome polymorphism in antiretroviral therapy effectiveness is also of high interest.

Dr. Marina Bobkova
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (6 papers)

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Research

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13 pages, 2067 KiB  
Article
Reconstructing the Temporal Origin and the Transmission Dynamics of the HIV Subtype B Epidemic in St. Petersburg, Russia
by Marina Siljic, Valentina Cirkovic, Luka Jovanovic, Anastasiia Antonova, Aleksey Lebedev, Ekaterina Ozhmegova, Anna Kuznetsova, Tatiyana Vinogradova, Aleksei Ermakov, Nikita Monakhov, Marina Bobkova and Maja Stanojevic
Viruses 2022, 14(12), 2748; https://doi.org/10.3390/v14122748 - 9 Dec 2022
Cited by 1 | Viewed by 1268
Abstract
The HIV/AIDS epidemic in Russia is among the fastest growing in the world. HIV epidemic burden is non-uniform in different Russian regions and diverse key populations. An explosive epidemic has been documented among people who inject drugs (PWID) starting from the mid-1990s, whereas [...] Read more.
The HIV/AIDS epidemic in Russia is among the fastest growing in the world. HIV epidemic burden is non-uniform in different Russian regions and diverse key populations. An explosive epidemic has been documented among people who inject drugs (PWID) starting from the mid-1990s, whereas presently, the majority of new infections are linked to sexual transmission. Nationwide, HIV sub-subtype A6 (previously called AFSU) predominates, with the increasing presence of other subtypes, namely subtype B and CRF063_02A. This study explores HIV subtype B sequences from St. Petersburg, collected from 2006 to 2020, in order to phylogenetically investigate and characterize transmission clusters, focusing on their evolutionary dynamics and potential for further growth, along with a socio-demographic analysis of the available metadata. In total, 54% (107/198) of analyzed subtype B sequences were found grouped in 17 clusters, with four transmission clusters with the number of sequences above 10. Using Bayesian MCMC inference, tMRCA of HIV-1 subtype B was estimated to be around 1986 (95% HPD 1984–1991), whereas the estimated temporal origin for the four large clusters was found to be more recent, between 2001 and 2005. The results of our study imply a complex pattern of the epidemic spread of HIV subtype B in St. Petersburg, Russia, still in the exponential growth phase, and in connection to the men who have sex with men (MSM) transmission, providing a useful insight needed for the design of public health priorities and interventions. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
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14 pages, 2188 KiB  
Article
Prevalence of Pretreatment HIV-1 Drug Resistance in Armenia in 2017–2018 and 2020–2021 following a WHO Survey
by Alina Kirichenko, Dmitry Kireev, Ilya Lapovok, Anastasia Shlykova, Alexey Lopatukhin, Anastasia Pokrovskaya, Natalya Ladnaya, Trdat Grigoryan, Arshak Petrosyan, Tatevik Sarhatyan, Narina Sargsyants, Tamara Hovsepyan, Hovsep Ghazaryan, Hermine Hovakimyan, Siranush Martoyan and Vadim Pokrovsky
Viruses 2022, 14(11), 2320; https://doi.org/10.3390/v14112320 - 22 Oct 2022
Cited by 2 | Viewed by 1447
Abstract
The increased antiretroviral therapy (ART) coverage of patients in the absence of routine genotyping tests and in the context of active labor migration highlight the importance of HIV-1 drug resistance (DR) surveillance in Armenia. We conducted a two-phase pretreatment DR (PDR) study in [...] Read more.
The increased antiretroviral therapy (ART) coverage of patients in the absence of routine genotyping tests and in the context of active labor migration highlight the importance of HIV-1 drug resistance (DR) surveillance in Armenia. We conducted a two-phase pretreatment DR (PDR) study in 2017–2018 (phase I; 120 patients) and 2020–2021 (phase II; 133 patients) according to the WHO-approved protocol. The analysis of HIV-1 genetic variants showed high degrees of viral diversity, with the predominance of A6. The prevalence of any PDR was 9.2% in phase I and 7.5% in phase II. PDR to protease inhibitors was found only in 0.8% in phase II. PDR to efavirenz and nevirapine was found among 5.0% and 6.7% of patients in phase I, and 6.0% and 6.8% of patients in phase II, respectively. The prevalence of PDR to nucleoside reverse-transcriptase inhibitors decreased from 5.0% in phase I to 0.8% in phase II. In addition, we identified risk factors associated with the emergence of DR—male, MSM, subtype B, and residence in or around the capital of Armenia—and showed the active spread of HIV-1 among MSM in transmission clusters, i.e., harboring DR, which requires the immediate attention of public health policymakers for the prevention of HIV-1 DR spread in the country. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
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8 pages, 227 KiB  
Article
Prevalence and Spectrum of HIV-1 Resistance Mutations in the Siberian Federal District
by Sergey Shtrek, Lidiya Levakhina, Aleksey Blokh, Oksana Pasechnik and Nataliya Pen’evskaya
Viruses 2022, 14(10), 2117; https://doi.org/10.3390/v14102117 - 25 Sep 2022
Cited by 1 | Viewed by 1348
Abstract
The Siberian Federal District is among the most affected regions with a high prevalence of HIV-infection and is characterized by high HIV-infection incidence rate and high mortality among the HIV-infected population. HIV drug resistance poses a major threat to public health and is [...] Read more.
The Siberian Federal District is among the most affected regions with a high prevalence of HIV-infection and is characterized by high HIV-infection incidence rate and high mortality among the HIV-infected population. HIV drug resistance poses a major threat to public health and is associated with increased mortality, HIV incidence, and cost of epidemic control programs. A total of 1281 samples from HIV-infected patients were sequenced and analyzed with the DEONA and HIVdb Program to assess the prevalence of drug resistance mutations in patients in the Siberian Federal District in 2016–2018. The federal surveillance data obtained from 0.5% of HIV-infected patients during the long-term follow-up care in 2021 were also used. The incidence rate of HIV infection in the Siberian Federal District has declined since 2016: from 135.8 per 100 thousand population to 81.1 per 100 thousand population in 2021. Mutations associated with resistance to NRTI and NNRTI were found in 10.3% of the samples in 2016–2018 and in 28.4% of the samples in 2020. The rising prevalence of drug resistance in HIV-infected patients indicates that it is increasingly important to continuously monitor and improve the approaches to the use of effective treatment regimens. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
19 pages, 3499 KiB  
Article
Prevalence and Structure of HIV-1 Drug Resistance to Antiretrovirals in the Volga Federal District in 2008–2019
by Olga Peksheva, Elena Kuzovatova, Olga Parfenova and Natalia Zaytseva
Viruses 2022, 14(9), 1898; https://doi.org/10.3390/v14091898 - 27 Aug 2022
Viewed by 1282
Abstract
The increasing number of HIV-infected people who are receiving ART, including those with low adherence, is causing the spread of HIV drug resistance (DR). A total of 1396 plasma samples obtained from treatment-experienced patients from the Volga federal district (VFD), Russia, were examined [...] Read more.
The increasing number of HIV-infected people who are receiving ART, including those with low adherence, is causing the spread of HIV drug resistance (DR). A total of 1396 plasma samples obtained from treatment-experienced patients from the Volga federal district (VFD), Russia, were examined to investigate HIV DR occurrence. The time periods 2008–2015 and 2016–2019 were compared. Fragmentary Sanger sequencing was employed to identify HIV resistance to reverse transcriptase inhibitors (RTIs) and protease inhibitors (PIs) using an ABI 3500XL genetic analyzer, a ViroSeq™ HIV-1 genotyping system (Alameda, CA, USA) and AmpliSense HIV-Resist-Seq reagent kits (Moscow, Russia). In 2016–2019, HIV DR was detected significantly more often than in 2008–2015 (p < 0.01). Mutations to RTIs retained leading positions in the structure of DR. Frequencies of resistance mutations to nucleoside and non-nucleoside RTIs (NRTIs and NNRTIs) in the spectra of detected mutations show no significant differences. Resistance to NRTIs after 2016 began to be registered more often as a part of multidrug resistance (MDR), as opposed to resistance to a single class of antiretrovirals. The frequency of DR mutations to PIs was low, both before and after 2016 (7.9% and 6.1% in the spectrum, respectively, p > 0.05). MDR registration rate became significantly higher from 2008 to 2019 (17.1% to 72.7% of patients, respectively, p < 0.01). M184V was the dominant replacement in all the years of study. A significant increase in the frequency of K65R replacement was revealed. The prevalence of integrase strand transfer inhibitor (INSTI) resistance mutations remains to be investigated. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
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15 pages, 4502 KiB  
Article
Identifying HIV-1 Transmission Clusters in Uzbekistan through Analysis of Molecular Surveillance Data
by Aleksey Lebedev, Anna Kuznetsova, Kristina Kim, Ekaterina Ozhmegova, Anastasiia Antonova, Elena Kazennova, Aleksandr Tumanov, Adkhamjon Mamatkulov, Evgeniya Kazakova, Nargiz Ibadullaeva, Krestina Brigida, Erkin Musabaev, Dildora Mustafaeva, Visola Rakhimova and Marina Bobkova
Viruses 2022, 14(8), 1675; https://doi.org/10.3390/v14081675 - 29 Jul 2022
Cited by 1 | Viewed by 2594
Abstract
The CRF02_AG and sub-subtype A6 are currently the predominant HIV-1 variants in the Republic of Uzbekistan, but little is known about their time-spatial clustering patterns in high-risk populations. We have applied molecular evolution methods and network analyses to better understand the transmission patterns [...] Read more.
The CRF02_AG and sub-subtype A6 are currently the predominant HIV-1 variants in the Republic of Uzbekistan, but little is known about their time-spatial clustering patterns in high-risk populations. We have applied molecular evolution methods and network analyses to better understand the transmission patterns of these subtypes by analyzing 316 pol sequences obtained during the surveillance study of HIV drug resistance. Network analysis showed that about one third of the HIV infected persons were organized into clusters, including large clusters with more than 35 members. These clusters were composed mostly of injecting drug users and/or heterosexuals, with women having mainly high centrality within networks identified in both subtypes. Phylogenetic analyses of the ‘Uzbek’ sequences, including those publicly available, show that Russia and Ukraine played a role as the main sources of the current subtype A6 epidemic in the Republic. At the same time, Uzbekistan has been a local center of the CRF02_AG epidemic spread in the former USSR since the early 2000s. Both of these HIV-1 variants continue to spread in Uzbekistan, highlighting the importance of identifying transmission networks and transmission clusters to prevent further HIV spread, and the need for HIV prevention and education campaigns in high-risk groups. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
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Review

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9 pages, 892 KiB  
Review
Romania, a Harbour of HIV-1 Subtype F1: Where Are We after 33 Years of HIV-1 Infection?
by Mădălina Preda and Loredana Cornelia Sabina Manolescu
Viruses 2022, 14(9), 2081; https://doi.org/10.3390/v14092081 - 19 Sep 2022
Cited by 4 | Viewed by 1958
Abstract
Infection with the human immunodeficiency virus (HIV) has been a major public health concern worldwide for more than 30 years, including in Romania. The F1 HIV-1 subtype was exported from Angola to Romania most probably because of the two countries’ close political connections. [...] Read more.
Infection with the human immunodeficiency virus (HIV) has been a major public health concern worldwide for more than 30 years, including in Romania. The F1 HIV-1 subtype was exported from Angola to Romania most probably because of the two countries’ close political connections. Patients infected with HIV-1 via re-used and improperly sterilized injection equipment and through transfusions of unscreened blood, also known as the “Romanian cohort”, were the most common type of HIV-1 infection in Romania in the early 1990s, when the virus’s presence was recognized. Recently, subtype B started to increase in our country, mostly diagnosed in people using intravenous drugs or in men having sex with men. The evolution of the HIV-1 infection in Romania has been unique, with a dominance of the subtype F1, making it different from other countries in Europe. Full article
(This article belongs to the Special Issue Molecular Epidemiology of HIV Infection in Eastern Europe and Central Asia)
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