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Antonova A, Kazennova E, Lebedev A, Ozhmegova E, Kuznetsova A, Tumanov A, Bobkova M. Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses 2023; 15:2312. [PMID: 38140553 PMCID: PMC10748268 DOI: 10.3390/v15122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.
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Affiliation(s)
- Anastasiia Antonova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Elena Kazennova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksey Lebedev
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Ekaterina Ozhmegova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Anna Kuznetsova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksandr Tumanov
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia;
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Ogarkova D, Antonova A, Kuznetsova A, Adgamov R, Pochtovyi A, Kleimenov D, Tsyganova E, Gushchin V, Gintsburg A, Mazus A. Current Trends of HIV Infection in the Russian Federation. Viruses 2023; 15:2156. [PMID: 38005834 PMCID: PMC10674383 DOI: 10.3390/v15112156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Russia remains one of the areas most affected by HIV in Eastern Europe and Central Asia. The aim of this study was to analyze HIV infection indicators and study trends in Russia using data from the Federal Statistic Form No. 61 "Information about HIV infection". HIV incidence, prevalence, HIV testing and mortality rates (from 2011 to 2022), and treatment success rates (from 2016 to 2022) were analyzed. These indicators were compared across different federal districts (FDs) of Russia. The findings revealed a significant downward trend in HIV incidence, while a significant upward trend was observed for HIV prevalence. The mortality rate has stabilized since 2018. The coverage of HIV testing and antiretroviral therapy increased over time. The number of people living with HIV-1 (PLWH) with a suppressed viral load in Russia as a whole varied between 72% and 77% during the years under observation. The Siberian and Ural federal districts recorded the highest HIV incidence, while the North Caucasian FD reported the lowest. An increase in HIV testing coverage was observed across all FDs. This comprehensive evaluation of HIV infection indicators within the regional context contributes to the timely implementation of measures aimed at preventing the spread of HIV.
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Affiliation(s)
- Daria Ogarkova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Anastasiia Antonova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Anna Kuznetsova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Ruslan Adgamov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Andrei Pochtovyi
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Denis Kleimenov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
| | - Elena Tsyganova
- Moscow City Center for AIDS Prevention and Control, 105275 Moscow, Russia; (E.T.); (A.M.)
| | - Vladimir Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
- Department of Virology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Aleksandr Gintsburg
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya”, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.O.); (A.A.); (R.A.); (A.P.); (D.K.); (A.G.)
- Department of Infectiology and Virology, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
| | - Aleksei Mazus
- Moscow City Center for AIDS Prevention and Control, 105275 Moscow, Russia; (E.T.); (A.M.)
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Kirichenko A, Kireev D, Lapovok I, Shlykova A, Lopatukhin A, Pokrovskaya A, Bobkova M, Antonova A, Kuznetsova A, Ozhmegova E, Shtrek S, Sannikov A, Zaytseva N, Peksheva O, Piterskiy M, Semenov A, Turbina G, Filoniuk N, Shemshura A, Kulagin V, Kolpakov D, Suladze A, Kotova V, Balakhontseva L, Pokrovsky V, Akimkin V. HIV-1 Drug Resistance among Treatment-Naïve Patients in Russia: Analysis of the National Database, 2006-2022. Viruses 2023; 15:v15040991. [PMID: 37112971 PMCID: PMC10141655 DOI: 10.3390/v15040991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
In Russia, antiretroviral therapy (ART) coverage has significantly increased, which, in the absence of routine genotyping testing, could lead to an increase in HIV drug resistance (DR). The aim of this study was to investigate the patterns and temporal trends in HIV DR as well as the prevalence of genetic variants in treatment-naïve patients from 2006 to 2022, using data from the Russian database (4481 protease and reverse transcriptase and 844 integrase gene sequences). HIV genetic variants, and DR and DR mutations (DRMs) were determined using the Stanford Database. The analysis showed high viral diversity, with the predominance of A6 (78.4%), which was the most common in all transmission risk groups. The overall prevalence of surveillance DRMs (SDRMs) was 5.4%, and it reached 10.0% in 2022. Most patients harbored NNRTI SDRMs (3.3%). The prevalence of SDRMs was highest in the Ural (7.9%). Male gender and the CRF63_02A6 variant were association factors with SDRMs. The overall prevalence of DR was 12.7% and increased over time, primarily due to NNRTIs. Because baseline HIV genotyping is unavailable in Russia, it is necessary to conduct surveillance of HIV DR due to the increased ART coverage and DR prevalence. Centralized collection and unified analysis of all received genotypes in the national database can help in understanding the patterns and trends in DR to improve treatment protocols and increase the effectiveness of ART. Moreover, using the national database can help identify regions or transmission risk groups with a high prevalence of HIV DR for epidemiological measures to prevent the spread of HIV DR in the country.
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Affiliation(s)
- Alina Kirichenko
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Ilya Lapovok
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | | | | | - Anastasia Pokrovskaya
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
- Department of Infectious Diseases with Courses of Epidemiology and Phthisiology, Medical Institute, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Marina Bobkova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Sergey Shtrek
- Omsk Research Institute of Natural Focal Infections, 644080 Omsk, Russia
- Department of Microbiology, Virology and Immunology, Omsk State Medical University, 644099 Omsk, Russia
| | - Aleksej Sannikov
- Omsk Research Institute of Natural Focal Infections, 644080 Omsk, Russia
- Department of Microbiology, Virology and Immunology, Omsk State Medical University, 644099 Omsk, Russia
| | - Natalia Zaytseva
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor, 603022 Nizhny Novgorod, Russia
| | - Olga Peksheva
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor, 603022 Nizhny Novgorod, Russia
| | - Michael Piterskiy
- Federal Scientific Research Institute of Viral Infections «Virome» Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Ekaterinburg, Russia
| | - Aleksandr Semenov
- Federal Scientific Research Institute of Viral Infections «Virome» Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 620030 Ekaterinburg, Russia
| | - Galina Turbina
- Lipetsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, 398043 Lipetsk, Russia
| | - Natalia Filoniuk
- Lipetsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, 398043 Lipetsk, Russia
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS Treatment and Prevention of the Ministry of Health of Krasnodar Region, 350000 Krasnodar, Russia
- Department of Infectious Diseases and Epidemiology, The Faculty of Advanced Training and Professional Retraining of Specialists, Kuban State Medical University of the Ministry of Health of the Russian Federation, 350063 Krasnodar, Russia
| | - Valeriy Kulagin
- Clinical Center of HIV/AIDS Treatment and Prevention of the Ministry of Health of Krasnodar Region, 350000 Krasnodar, Russia
- Department of Infectious Diseases and Epidemiology, The Faculty of Advanced Training and Professional Retraining of Specialists, Kuban State Medical University of the Ministry of Health of the Russian Federation, 350063 Krasnodar, Russia
| | - Dmitry Kolpakov
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia
| | - Aleksandr Suladze
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia
| | - Valeriya Kotova
- Khabarovsk Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor, 680610 Khabarovsk, Russia
| | - Lyudmila Balakhontseva
- Khabarovsk Research Institute of Epidemiology and Microbiology of the Rospotrebnadzor, 680610 Khabarovsk, Russia
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
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Kuznetsova AI, Munchak IM, Lebedev AV, Tumanov AS, Kim KV, Antonova AA, Ozhmegova EN, Pronin AY, Drobyshevskaya EV, Kazennova EV, Bobkova MR. [Genetic diversity of capsid protein (p24) in human immunodeficiency virus type-1 (HIV-1) variants circulating in the Russian Federation]. Vopr Virusol 2023; 68:66-78. [PMID: 36961237 DOI: 10.36233/0507-4088-161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Indexed: 04/22/2023]
Abstract
INTRODUCTION The human immunodeficiency virus (HIV) protein p24 plays an important role in the life cycle of the virus, and also is a target for diagnostic tests and for new antiretroviral drugs and therapeutic vaccines. The most studied variant of HIV-1 in the world is subtype B. In Russia, the most common variant is A6, the spread of recombinant forms (CRF63_02A6, CRF03_A6B) is observed as well as circulation of G and CRF02_AG variants. However, a detailed study of the p24 protein in these variants has not yet been conducted. The aim was to study the features of the p24 protein in HIV-1 variants circulating in Russia and estimate the frequency of occurrence of pre-existing mutations associated with resistance to lenacapavir, the first antiretroviral drug in the class of capsid inhibitors. MATERIALS AND METHODS The objects of the study were the nucleotide sequences obtained from the Los Alamos international database and clinical samples from HIV infected patients. RESULTS AND DISCUSSION The features of HIV-1 variants circulating in Russia have been determined. V86A, H87Q, I91F are characteristic substitutions in A6 genome. It is shown that the presence of preexisting mutations associated with resistance to lenacapavir is unlikely. CONCLUSION Features of the p24 protein in HIV-1 variants circulating in Russia allow them to be distinguished from others variants and among themselves. The prognosis for the use of lenacapavir in Russia is generally favorable. The results obtained could be taken into account in developing and using antiretroviral drugs and therapeutic vaccines.
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Affiliation(s)
- A I Kuznetsova
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - I M Munchak
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - A V Lebedev
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - A S Tumanov
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - K V Kim
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - A A Antonova
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - E N Ozhmegova
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - A Y Pronin
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases
| | - E V Drobyshevskaya
- Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases
| | - E V Kazennova
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology of FSBI "National Reseach Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya"
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van de Klundert MAA, Antonova A, Di Teodoro G, Ceña Diez R, Chkhartishvili N, Heger E, Kuznetsova A, Lebedev A, Narayanan A, Ozhmegova E, Pronin A, Shemshura A, Tumanov A, Pfeifer N, Kaiser R, Saladini F, Zazzi M, Incardona F, Bobkova M, Sönnerborg A. Molecular Epidemiology of HIV-1 in Eastern Europe and Russia. Viruses 2022; 14:v14102099. [PMID: 36298654 PMCID: PMC9609922 DOI: 10.3390/v14102099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 12/04/2022] Open
Abstract
The HIV epidemic in Eastern Europe and Russia is large and not well-controlled. To describe the more recent molecular epidemiology of HIV-1, transmitted drug resistance, and the relationship between the epidemics in this region, we sequenced the protease and reverse transcriptase genes of HIV-1 from 812 people living with HIV from Ukraine (n = 191), Georgia (n = 201), and Russia (n = 420) before the initiation of antiretroviral therapy. In 190 Ukrainian patients, the integrase gene sequence was also determined. The most reported route of transmission was heterosexual contact, followed by intravenous drug use, and men having sex with men (MSM). Several pre-existing drug resistance mutations were found against non-nucleoside reverse transcriptase inhibitors (RTIs) (n = 103), protease inhibitors (n = 11), and nucleoside analogue RTIs (n = 12), mostly polymorphic mutations or revertants. In the integrase gene, four strains with accessory integrase strand transfer inhibitor mutations were identified. Sub-subtype A6 caused most of the infections (713/812; 87.8%) in all three countries, including in MSM. In contrast to earlier studies, no clear clusters related to the route of transmission were identified, indicating that, within the region, the exchange of viruses among the different risk groups may occur more often than earlier reported.
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Affiliation(s)
| | - Anastasiia Antonova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Giulia Di Teodoro
- EuResist Network, 00152 Rome, Italy
- Department of Computer Control and Management Engineering Antonio Ruberti, Sapienza University of Rome, 00185 Rome, Italy
| | - Rafael Ceña Diez
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
| | - Nikoloz Chkhartishvili
- Infectious Diseases, AIDS and Clinical Immunology Research Center (IDACIRC), 0160 Tbilisi, Georgia
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Anna Kuznetsova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Aleksey Lebedev
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Aswathy Narayanan
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
| | - Ekaterina Ozhmegova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Alexander Pronin
- Moscow Regional Center for Control and Prevention of AIDS and Infectious Diseases, 123098 Moscow, Russia
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia
| | - Alexandr Tumanov
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Nico Pfeifer
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Francesco Saladini
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | | | - Marina Bobkova
- T-Lymphotropic Viruses Laboratory, Gamaleya Centre of Epidemiology and Microbiology, 123098 Moscow, Russia
- Correspondence: (M.B.); (A.S.)
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, 14152 Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
- Correspondence: (M.B.); (A.S.)
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Sivay MV, Maksimenko LV, Osipova IP, Nefedova AA, Gashnikova MP, Zyryanova DP, Ekushov VE, Totmenin AV, Nalimova TM, Ivlev VV, Kapustin DV, Pozdnyakova LL, Skudarnov SE, Ostapova TS, Yaschenko SV, Nazarova OI, Chernov AS, Ismailova TN, Maksutov RA, Gashnikova NM. Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic. Front Microbiol 2022; 13:946787. [PMID: 36118194 PMCID: PMC9470837 DOI: 10.3389/fmicb.2022.946787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
HIV-1 epidemic in Russia is one of the fastest growing in the world reaching 1.14 million people living with HIV-1 (PLWH) in 2021. Since mid-1990s, the HIV-1 epidemic in Russia has started to grow substantially due to the multiple HIV-1 outbreaks among persons who inject drugs (PWID) leading to expansion of the HIV-1 sub-subtype A6 (former Soviet Union (FSU) subtype A). In 2006, a local HIV-1 sub-epidemic caused by the distribution of novel genetic lineage CRF63_02A6 was identified in Siberia. In this study, we used a comprehensive dataset of CRF63_02A6 pol gene sequences to investigate the spatiotemporal dynamic of the HIV-1 CRF63_02A6 sub-epidemic. This study includes all the available CRF63_02A6 HIV-1 pol gene sequences from Los Alamos National Laboratory (LANL) HIV Sequence Database. The HIV-1 subtypes of those sequences were conferred using phylogenetic analysis, and two automated HIV-1 subtyping tools Stanford HIVdb Program and COMET. Ancestral state reconstruction and origin date were estimated using Nextstrain. Evolutionary rate and phylodynamic analysis were estimated using BEAST v 1.10.4. CRF63_02A6 was assigned for 872 pol gene sequences using phylogenetic analysis approach. Predominant number (n = 832; 95.4%) of those sequences were from Russia; the remaining 40 (4.6%) sequences were from countries of Central Asia. Out of 872 CRF63_02A6 sequences, the corresponding genetic variant was assigned for 75.7 and 79.8% of sequences by Stanford and COMET subtyping tools, respectively. Dated phylogenetic analysis of the CRF63_02A6 sequences showed that the virus most likely originated in Novosibirsk, Russia, in 2005. Over the last two decades CRF63_02A6 has been widely distributed across Russia and has been sporadically detected in countries of Central Asia. Introduction of new genetic variant into mature sub-subtype A6 and CRF02_AGFSU epidemics could promote the increase of viral genetic diversity and emergence of new recombinant forms. Further HIV-1 studies are needed due to a continuing rapid virus distribution. Also, the implementation of HIV-1 prevention programs is required to reduce HIV-1 transmission. This study also highlights the discrepancies in HIV-1 subtyping approaches. The reference lists of HIV-1 sequences implemented in widely used HIV-1 automated subtyping tools need to be updated to provide reliable results.
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Affiliation(s)
- Mariya V. Sivay
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
- *Correspondence: Mariya V. Sivay, ;
| | - Lada V. Maksimenko
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Irina P. Osipova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Anastasiya A. Nefedova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Mariya P. Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Dariya P. Zyryanova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Vasiliy E. Ekushov
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Alexei V. Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Tatyana M. Nalimova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Vladimir V. Ivlev
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | | | | | - Sergey E. Skudarnov
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk, Russia
| | - Tatyana S. Ostapova
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk, Russia
| | | | - Olga I. Nazarova
- Omsk City Center of Prevention and Control of AIDS and Other Infectious Diseases, Omsk, Russia
| | - Aleksander S. Chernov
- Tomsk Regional Center for Prevention and Control of AIDS and Other Infectious Diseases, Tomsk, Russia
| | - Tatyana N. Ismailova
- Tomsk Regional Center for Prevention and Control of AIDS and Other Infectious Diseases, Tomsk, Russia
| | - Rinat A. Maksutov
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Natalya M. Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
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Safina KR, Sidorina Y, Efendieva N, Belonosova E, Saleeva D, Kirichenko A, Kireev D, Pokrovsky V, Bazykin GA. Molecular Epidemiology of HIV-1 in Oryol Oblast, Russia. Virus Evol 2022; 8:veac044. [PMID: 35775027 PMCID: PMC9239399 DOI: 10.1093/ve/veac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight into the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data are only available for <1 per cent of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its known HIV-positive population (768 out of 2,157 patients). We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in eighty-two transmission lineages that together comprise 66 per cent of the samples. Most introductions are of subtype A (315/332), the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number Re for subtype A at 2.8 [1.7–4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median Re of 11.8 [4.6–28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to a smaller extent, people who inject drugs transmission. Samples attributed to men who have sex with men (MSM) transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of the MSM transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic, and rapid displacement of subtype A with the recombinant CRF63 variant.
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Affiliation(s)
- Ksenia R Safina
- The Institute for Information Transmission Problems of Russian Academy of Sciences , Moscow, Russian Federation
- Skolkovo Institute of Science and Technology , Moscow, Russian Federation
| | - Yulia Sidorina
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Natalya Efendieva
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Elena Belonosova
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Darya Saleeva
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Alina Kirichenko
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Dmitry Kireev
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Georgii A Bazykin
- The Institute for Information Transmission Problems of Russian Academy of Sciences , Moscow, Russian Federation
- Skolkovo Institute of Science and Technology , Moscow, Russian Federation
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8
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Construction and Characterization of HIV-1 env-Pseudoviruses of the Recombinant Form CRF63_02A and Subtype A6. Bull Exp Biol Med 2022; 172:729-733. [PMID: 35501651 DOI: 10.1007/s10517-022-05466-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 10/18/2022]
Abstract
HIV-1 env-pseudoviruses are a useful tool in the search for antiviral drugs (entry inhibitors) and evaluation of the efficacy of HIV-1 vaccines. Given the high genetic variability of HIV-1, it is necessary to regularly update the panels of pseudoviruses in accordance with the emergence of new strains. Based on genetic variants of HIV-1 circulating in the regions of the Siberian Federal District, 13 HIV-1 env-pseudoviruses of recombinant form CRF63_02A and subtype A6 were obtained. Most pseudoviruses have been shown to be sensitive to neutralization by bnAbs VRC01, PGT126, and 10E8, moderately sensitive to bnAbs PG9 and 4E10, and resistant to bnAbs 2G12, PG16, and 2F5. All obtained variants of pseudoviruses are CCR5-tropic.
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Mamatkulov A, Kazakova E, Ibadullaeva N, Joldasova E, Bayjanov A, Musabaev E, Kan N, Mustafaeva D, Lebedev A, Bobkova M, Kazennova E, Zohrabyan L. Prevalence of Antiretroviral Drug Resistance Mutations Among Pretreatment and Antiretroviral Therapy-Failure HIV Patients in Uzbekistan. AIDS Res Hum Retroviruses 2021; 37:38-43. [PMID: 32873061 DOI: 10.1089/aid.2020.0096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To evaluate the national prevalence of antiretroviral therapy (ART)-resistant HIV-1 viruses among both ART-initiators (pretreatment drug resistance, PDR) and ART-failure HIV patients in Uzbekistan. A nation-wide, cross-sectional active HIV-1 PDR surveillance was conducted in Uzbekistan from 2015 to 2016. In total, 713 blood plasma samples from adults were collected, including samples from ART-naive patients initiating ART and ART-failure HIV patients. HIV-1 genome polregion viral sequences were obtained from 309 patients, of those 106 on ART and 203 on ART-initiators. Analysis of HIV-1 subtypes and drug resistance mutations (DRMs) to HIV protease and reverse transcriptase inhibitors was performed. Among all the viruses studied, HIV-1 CRF 02_AG recombinant was the most common-57% (176/309). The second major group was represented by A1-40.5% (125/309). Two viruses were found to be recombinants formed by subtypes A1 and CRF02_AG sequences. ART-naive cohort I (PDR) included six samples that contained at least one surveillance drug resistance mutation (SDRM) (2.96%), with the most common being K103N mutation (4/6). In ART-experienced patients, cohort II, 77.4% (82/106) of viruses contained at least one mutation against PIs, NRTIs, or NNRTIs, with the most common mutations of M184V/I (49.1%; 52/106), K65R (18.9%; 20/106), K103N (23.6%; 25/106), and G190S (22.6%; 24/106). The significant difference in frequency of mutations was found between two dominant subtypes, A1 and CRF02_AG. The molecular epidemiological profile of HIV infection in Uzbekistan has changed toward a predominance of CRF02_AG viruses. In the first national-scale study of the PDR prevalence, it was found to be relatively low (2.96%). The DR mutations in failure patients correspond to the main therapy regimens (NRTI/NNRTI) adopted in the country. The observations provide new evidence for differences in ART efficacy and resistance profiles for different subtypes.
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Affiliation(s)
| | | | | | | | | | | | - Nataliya Kan
- Research Institute of Virology, Tashkent, Uzbekistan
| | | | - Aleksey Lebedev
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, T-Lymphotropic Viruses Laboratory Russian MoH, Moscow, Russia
| | - Marina Bobkova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, T-Lymphotropic Viruses Laboratory Russian MoH, Moscow, Russia
| | - Elena Kazennova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, T-Lymphotropic Viruses Laboratory Russian MoH, Moscow, Russia
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10
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Lebedev A, Pasechnik O, Ozhmegova E, Antonova A, Blokh A, Grezina L, Sandyreva T, Dementeva N, Kazennova E, Bobkova M. Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries. PLoS One 2020; 15:e0241269. [PMID: 33095842 PMCID: PMC7584246 DOI: 10.1371/journal.pone.0241269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
- * E-mail:
| | - Oksana Pasechnik
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksey Blokh
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Liliya Grezina
- Clinical Diagnostic Laboratory, Yamalo-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Noyabr'sk, Russia
| | - Tatiana Sandyreva
- Clinical Diagnostic Laboratory, Sverdlovsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Ekaterinburg, Russia
| | - Natalia Dementeva
- Clinical Diagnostic Laboratory, Saint-Petersburg Center for Prevention and Control of AIDS and Infectious Disease, Saint-Petersburg, Russia
| | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
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11
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Maksimenko LV, Totmenin AV, Gashnikova MP, Astakhova EM, Skudarnov SE, Ostapova TS, Yaschenko SV, Meshkov IO, Bocharov EF, Maksyutov RА, Gashnikova NM. Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9057541. [PMID: 32964045 PMCID: PMC7501552 DOI: 10.1155/2020/9057541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/28/2019] [Indexed: 12/31/2022]
Abstract
More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75-85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.
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Affiliation(s)
- Lada V. Maksimenko
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Aleksey V. Totmenin
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Mariya P. Gashnikova
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | | | - Sergey E. Skudarnov
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Tatyana S. Ostapova
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Svetlana V. Yaschenko
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Ivan O. Meshkov
- Novosibirsk Tuberculosis Research Institute, Novosibirsk 630040, Russia
| | - Evgeniy F. Bocharov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Rinat А. Maksyutov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
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12
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Zyryanova DP, Totmenin AV, Bogacheva NV, Gashnikova NM. Construction and Characterization of Infectious Molecular Clones of HIV-1 CRF63_02A6. AIDS Res Hum Retroviruses 2020; 36:227-233. [PMID: 31482716 DOI: 10.1089/aid.2019.0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Currently, HIV-1 CRF63_02A6 is the prevalent genetic variant of the HIV-infected subjects in the major part of the Siberian Federal District (Russia). The HIV-1 CRF63_02A6 R5-tropic pT11.17 and X4-tropic pMtBs.18 infectious molecular clones (IMCs) were constructed using the virus isolates recovered in 2015 and 2017 of male HIV-infected Russian residents (from Tomsk and Novosibirsk, respectively). Near full-length proviral HIV-1 sequences (9,644 and 9,748 bp) were subcloned in pBluescript II KS(-). The CRF63_02A6 IMC virions were obtained by transfecting HEK293T cells with the constructed plasmids and demonstrated a stable growth in peripheral blood mononuclear cell culture (p24 concentration increased >1,000-fold and the virus protein accumulation in culture liquid exceeded 100,000 pg/mL). The tropism of CRF63_02A6 IMCs was determined genotypically (using Geno2pheno) and phenotypically by cultivating the IMC virions in MT-2, U87-CD4-CCR5, and U87-CD4-CXCR4 cell cultures. The obtained HIV-1 CRF63_02A6 IMCs may be useful in basic and applied research.
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Affiliation(s)
- Daria P Zyryanova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Alexei V Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Natalia V Bogacheva
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Natalya M Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
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13
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Abstract
PURPOSE OF REVIEW To explore the consequences of policies implemented in the Russian Federation in response to syndemic of HIV-1 and opioid use disorder and compare the responses to the concomitant syndemic in rural America. RECENT FINDINGS The syndemic spread has not been reduced by policies implemented by the Russian government, which continues to underfund harm reduction efforts to reduce HIV transmission, refuses to approve evidence-based opioid agonist treatments for opioid use disorder, and relies on criminal justice and abstinence approaches to control illicit opioids. When effective measures have been undertaken locally, the lessons learned have not been transferred to other parts of the country and local programs have been allowed to wither. As in many parts of rural America, Russia has experienced intertwined epidemics of opioid misuse and HIV-1 that continue to expand. The expansion has been facilitated by adoption of policies that run contrary to medical and public health evidence.
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Affiliation(s)
- Robert Heimer
- Department of Epidemiology of Microbial Diseases and Center for Interdisciplinary Research on AIDS, Yale University School of Public Health, New Haven, CT, 06520-8034, USA.
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14
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Ulyanova YS, Gashnikova NM, Ivlev VV, Krasnova EI, Khokhlova NI, Totmenin AV, Melnikova OV, Vorotova MV, Glushko IR, Ulyanov VV. Clinical and laboratory characterictic of acute HIV-infection in adult residents of Novosibirsk region. JOURNAL INFECTOLOGY 2019. [DOI: 10.22625/2072-6732-2019-11-2-40-44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Purpose of the study. To study the characteristics of acute HIV infection in adults in the Novosibirsk region in 2017– 2018.Materials and methods. 200 patients with acute HIV infection, residents of the Novosibirsk region, aged 15 to 74 years, hospitalized in 2017–2018, 104 men and 96 women were examined. The diagnosis was verified by detecting antibodies to HIV in ELISA with a negative or doubtful result of the immunoblot, as well as by determining the quantitative content of HIV RNA in the blood by PCR. The hemogram, the content of CD4 + lymphocytes in the blood were determined. In addition, HIV-1 was studied in 71 patients for belonging to a genetic group.Results. Patients of 20–40 years old prevailed – 70.5%. The sexual way was dominant in women (69.0%), injecting psychoactive substances was more often in men (32.2%). Frequent symptoms were fever (99%), exanthema (65.5%), polylimfoadenopathy (54.0%). Less common were diarrhea (36.0%), pharyngotonsillitis (23.0%), aphthous stomatitis (6.5%), hepatomegaly or hepatosplenomegaly (8.5%). Secondary diseases were revealed in 26.5% of patients. Leukopenia was recorded in 63.0%, thrombocytopenia in 62.5%, lymphocytosis and atypical cells of the lymphoid series in 14.0%. All patients had a high “viral load” – from 23,000 to 10,000,000 or more copies / ml, a decrease in the number of CD4 + less than 350 cells – in 38.0%. From among 71 patients, 19.7% had HIV-1 subtype A, and 76.0% had recombinant HIV-1 CRF63_02A. In the latter, “viral load” of more than 10,000,000 copies / ml was more often recorded (67.8% vs. 33.4%, p = 0.004).Conclusion. A significant number of cases of acute HIV infection were reported in the Novosibirsk region in 2017– 2018. Its detection is possible by examination of all febrile patients who apply to medical institutions. Early initiation of antiretroviral therapy with the appointment of well-tolerated regimens contributes to the formation of a high commitment to therapy.
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Affiliation(s)
| | | | - V. V. Ivlev
- State Research Center of Virology and Biotechnology “Vector”
| | | | | | - A. V. Totmenin
- State Research Center of Virology and Biotechnology “Vector”
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15
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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16
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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17
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Agapkina YY, Pustovarova MA, Korolev SP, Zyryanova DP, Ivlev VV, Totmenin AV, Gashnikova NM, Gottikh MB. Consensus Integrase of a New HIV-1 Genetic Variant CRF63_02A1. Acta Naturae 2019; 11:14-22. [PMID: 31024744 PMCID: PMC6475865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
The high genetic variability of the human immunodeficiency virus (HIV-1) leads to a constant emergence of new genetic variants, including the recombinant virus CRF63_02A1, which is widespread in the Siberian Federal District of Russia. We studied HIV-1 CRF63_02A1 integrase (IN_CRF) catalyzing the incorporation of viral DNA into the genome of an infected cell. The consensus sequence was designed, recombinant integrase was obtained, and its DNA-binding and catalytic activities were characterized. The stability of the IN_CRF complex with the DNA substrate did not differ from the complex stability for subtype A and B integrases; however, the rate of complex formation was significantly higher. The rates and efficiencies of 3'-processing and strand transfer reactions catalyzed by IN_CRF were found to be higher, too. Apparently, all these distinctive features of IN_CRF may result from specific amino acid substitutions in its N-terminal domain, which plays an important role in enzyme multimerization and binding to the DNA substrate. It was also found that the drug resistance mutations Q148K/G140S and G118R/E138K significantly reduce the catalytic activity of IN_CRF and its sensitivity to the strand transfer inhibitor raltegravir. Reduction in sensitivity to raltegravir was found to be much stronger in the case of double-mutation Q148K/G140S.
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Affiliation(s)
- Y. Y. Agapkina
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - M. A. Pustovarova
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - S. P. Korolev
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - D. P. Zyryanova
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - V. V. Ivlev
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - A. V. Totmenin
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - N. M. Gashnikova
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - M. B. Gottikh
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
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18
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Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
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Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
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19
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Karamov E, Epremyan K, Siniavin A, Zhernov Y, Cuevas MT, Delgado E, Sánchez-Martínez M, Carrera C, Kornilaeva G, Turgiev A, Bacqué J, Pérez-Álvarez L, Thomson MM. HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of A FSU, Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant. AIDS Res Hum Retroviruses 2018; 34:629-634. [PMID: 29587492 DOI: 10.1089/aid.2018.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (AFSU) variant was the predominant clade (62.9%), followed by subtype B (22.6%), unique recombinants (6.5%), subtype G (6.5%), and CRF01_AE (1.6%). AFSU predominated among people who inject drugs (88.9%) and heterosexually acquired infections (77.8%), while subtype B was the most prevalent genetic form among men who have sex with men (44%), although AFSU was also frequent in this population (36%). Forty-eight (77.4%) viruses branched within intrasubtype clusters, three of which, of subtype B, had a majority of viruses collected outside of FSU. The four subtype G viruses identified in this study belonged to the Portuguese-Spanish (Iberian) variant and, together with three from databases, formed a Russian cluster closely related to viruses from Denmark. This is the first report of the circulation of the Iberian subtype G variant in Russia.
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Affiliation(s)
- Eduard Karamov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Khoren Epremyan
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Andrei Siniavin
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Yury Zhernov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Galina Kornilaeva
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Ali Turgiev
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
- Immunomica LLC, Moscow, Russia
| | - Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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20
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Lapovok IA, Lopatukhin AE, Kireev DE, Kazennova EV, Lebedev AV, Bobkova MR, Kolomeets AN, Turbina GI, Shipulin GA, Ladnaya NN, Pokrovsky VV. [Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015]. TERAPEVT ARKH 2018; 89:44-49. [PMID: 29260745 DOI: 10.17116/terarkh2017891144-49] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. SUBJECTS AND METHODS The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. RESULTS The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. CONCLUSION The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.
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Affiliation(s)
- I A Lapovok
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - A E Lopatukhin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - D E Kireev
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - E V Kazennova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A V Lebedev
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A N Kolomeets
- Omsk Research Institute of Natural Focal Infections, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G I Turbina
- Lipetsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Lipetsk, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - N N Ladnaya
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V V Pokrovsky
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
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21
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Predominance of CRF63_02A1 and multiple patterns of unique recombinant forms of CRF63_A1 among individuals with newly diagnosed HIV-1 infection in Kemerovo Oblast, Russia. Arch Virol 2016; 162:379-390. [PMID: 27761744 DOI: 10.1007/s00705-016-3120-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/18/2022]
Abstract
Kemerovo Oblast (KO) has had the highest rate of HIV spread in Russia since 2011. The aim of this work was to study the genetic variation of HIV-1 in Kemerovo Oblast. Blood was sampled from a total of 91 HIV-positive antiretroviral-therapy-naïve individuals in 2013 (38) and 2015 (53). HIV-1 subtypes, pol gene drug resistance mutations, and viral tropism were analyzed. In 2013-2015, the prevalence of HIV-1 subtype A decreased in KO from 60.5 to 7.5 %. The samples collected in 2015 from the patients with newly diagnosed HIV demonstrate the current dominance of HIV-1 CRF63_02A1 (71.7 %) and HIV-1 URF63_A1 (20.8 %), their parental viruses being CRF63_02A1 and subtype A. The initially predominant genetic variant, HIV-1 subtype A, was replaced in KO. An unusually high incidence of HIV-1 unique recombinant forms is probably the result of HIV-1 CRF63_02A1 introduction in the group of injection drug users with the initial HIV-1 subtype A infection and the practice of risky behavior that promotes reinfection. HIV-1 CRF63_02A1, which recently emerged in Siberia, and its recombinant forms have an ever-increasing impact on the current HIV epidemic in Russia, making urgent the need for in-depth study of this HIV-1 genetic variant.
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22
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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23
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Gashnikova NM, Bogachev VV, Baryshev PB, Totmenin AV, Gashnikova MP, Kazachinskaya AG, Ismailova TN, Stepanova SA, Chernov AS, Mikheev VN. A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia. AIDS Res Hum Retroviruses 2015; 31:456-60. [PMID: 25738513 DOI: 10.1089/aid.2014.0375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of HIV infection in different Russian regions is nonuniform. In the Tomsk region (TR), 2020 HIV new infection cases were recorded in 2013, the morbidity having increased 5.9-fold as compared to 2012. In total, 64 blood plasma samples from primary HIV cases have been examined. HIV-specific fragments of the pol gene have been obtained for 61 samples (of protease for 58 and of integrase for 23) and of the env gene V3 region for 40 samples. Phylogenetic analysis of the determined HIV-1 sequences has detected CRF63_02A1 in 55 (90.2%) cases, whereas HIV subtype A1, characteristic of Russia, has been observed in only three (4.9%) patients. Three (4.9%) cases contain CRF63_02A1/A recombinant variants. This article demonstrates that a drastic activation of the epidemic in the Tomsk region is accompanied by a rapid spreading of the recently described HIV-1 CRF63_02A1, which we detected in the Novosibirsk region outbreak of 2008.
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Affiliation(s)
- Natalya M Gashnikova
- 1 Department of Retroviruses, State Research Center of Virology and Biotechnology Vector , Koltsovo, Russia
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24
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A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS 2014; 28:F1-8. [PMID: 25259833 DOI: 10.1097/qad.0000000000000485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The subtype A variant in the Former Soviet Union (A(FSU)) causes most of Russia's HIV-1 infections. However, the spectrum of drug-resistance mutations (DRMs) in antiretroviral experienced patients with this variant has not been studied. METHODS Between 2010 and 2013, genotypic resistance testing was performed on plasma samples from 366 antiretroviral-experienced patients in Siberia. RESULTS Three-hundred patients (82%) had subtype A(FSU) and 55 (15%) had CRF02_AG viruses. The pattern of DRMs was consistent with patient antiretroviral history with one exception. G190S was the most common nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, occurring in 55 (33%) subtype A(FSU) viruses from 167 NNRTI-experienced patients compared with none of 37 CRF02_AG viruses from NNRTI-experienced patients (P < 0.001). The next most common subtype A(FSU) NNRTI-resistance mutation, K103N, occurred in 25 (15%) viruses. Wild-type glycine (G) at position 190 is encoded by GGC in more than 99% of published A(FSU) strains. By contrast, G190 is encoded by GGA or GGG in 97% of other subtypes and in subtype A strains outside of the FSU. Therefore, G190S results from a single G→A transition: G (GGC) → S (AGC) almost exclusively in subtype A(FSU) viruses. CONCLUSION The predisposition of subtype A(FSU) to G190S is concerning because G→A is the most common HIV-1 mutation and because G190S causes higher levels of nevirapine and efavirenz resistance than K103N. This study exemplifies the need for characterizing the genetic mechanisms of resistance in diverse populations and warrants studies to verify that NRTI/NNRTI regimens are as efficacious in treating subtype A(FSU) as viruses belonging to other subtypes.
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25
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Shcherbakova NS, Shalamova LA, Delgado E, Fernández-García A, Vega Y, Karpenko LI, Ilyichev AA, Sokolov YV, Shcherbakov DN, Pérez-Álvarez L, Thomson MM. Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:912-9. [PMID: 25050828 DOI: 10.1089/aid.2014.0075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.
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Affiliation(s)
- Nadezhda S. Shcherbakova
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Lyudmila A. Shalamova
- Department of Zoonotic Infections and Influenza, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Larissa I. Karpenko
- Laboratory of Recombinant Vaccine, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Alexander A. Ilyichev
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Yuri V. Sokolov
- Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk, Russia
| | | | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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