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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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Siljic M, Cirkovic V, Jovanovic L, Antonova A, Lebedev A, Ozhmegova E, Kuznetsova A, Vinogradova T, Ermakov A, Monakhov N, Bobkova M, Stanojevic M. Reconstructing the Temporal Origin and the Transmission Dynamics of the HIV Subtype B Epidemic in St. Petersburg, Russia. Viruses 2022; 14:v14122748. [PMID: 36560752 PMCID: PMC9783597 DOI: 10.3390/v14122748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
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 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.
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Affiliation(s)
- Marina Siljic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Valentina Cirkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Luka Jovanovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Institute for Oncology and Radiology of Serbia, 11000 Belgrade, Serbia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Anna Kuznetsova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | | | - Aleksei Ermakov
- St. Petersburg City AIDS Center, 190103 St. Petersburg, Russia
| | - Nikita Monakhov
- St. Petersburg City AIDS Center, 190103 St. Petersburg, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Correspondence:
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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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Hendricks CM, Cash MN, Tagliamonte MS, Riva A, Brander C, Llano A, Salemi M, Stevenson M, Mavian C. Discordance between HIV-1 Population in Plasma at Rebound after Structured Treatment Interruption and Archived Provirus Population in Peripheral Blood Mononuclear Cells. Microbiol Spectr 2022; 10:e0135322. [PMID: 35699458 PMCID: PMC9431602 DOI: 10.1128/spectrum.01353-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/07/2022] [Indexed: 11/20/2022] Open
Abstract
Antiretroviral therapy (ART) can sustain the suppression of plasma viremia to below detection levels. Infected individuals undergoing a treatment interruption exhibit rapid viral rebound in plasma viremia which is fueled by cellular reservoirs such as CD4+ T cells, myeloid cells, and potentially uncharacterized cellular sources. Interrogating the populations of viruses found during analytical treatment interruption (ATI) can give insights into the biologically competent reservoirs that persist under effective ART as well as the nature of the cellular reservoirs that enable viral persistence under ART. We interrogated plasma viremia from four rare cases of individuals undergoing sequential ATIs. We performed next-generation sequencing (NGS) on cell-associated viral DNA and cell-free virus to understand the interrelationship between sequential ATIs as well as the relationship between viral genomes in circulating peripheral blood mononuclear cells (PBMCs) and RNA from rebound plasma. We observed population differences between viral populations recrudescing at sequential ATIs as well as divergence between viral sequences in plasma and those in PBMCs. This indicated that viruses in PBMCs were not a major source of post-ATI viremia and highlights the role of anatomic reservoirs in post-ATI viremia and viral persistence. IMPORTANCE Even with effective ART, HIV-1 persists at undetectable levels and rebounds in individuals who stop treatment. Cellular and anatomical reservoirs ignite viral rebound upon treatment interruption, remaining one of the key obstacles for HIV-1 cure. To further examine HIV-1 persistence, a better understanding of the distinct populations that fuel viral rebound is necessary to identify and target reservoirs and the eradication of HIV-1. This study investigates the populations of viruses found from proviral genomes from PBMCs and plasma at rebound from a unique cohort of individuals who underwent multiple rounds of treatment interruption. Using NGS, we characterized the subtypes of viral sequences and found divergence in viral populations between plasma and PBMCs at each rebound, suggesting that distinct viral populations appear at each treatment interruption.
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Affiliation(s)
- Chynna M. Hendricks
- Department of Microbiology and Immunology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Melanie N. Cash
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Massimiliano S. Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | | | - Anuska Llano
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
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Kuznetsova AI, Gromov KB, Kireev DE, Shlykova AV, Lopatukhin AE, Kazennova EV, Lebedev AV, Tumanov AS, Kim KV, Bobkova MR. [Analysis of Tat protein characteristics in human immunodeficiency virus type 1 sub-subtype A6 (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1)]. Vopr Virusol 2022; 66:452-464. [PMID: 35019252 DOI: 10.36233/0507-4088-83] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tat protein is a major factor of HIV (human immunodeficiency virus) transcription regulation and has other activities. Tat is characterized by high variability, with some amino acid substitutions, including subtypespecific ones, being able to influence on its functionality. HIV type 1 (HIV-1) sub-subtype A6 is the most widespread in Russia. Previous studies of the polymorphisms in structural regions of the A6 variant have shown numerous characteristic features; however, Tat polymorphism in A6 has not been studied.Goals and tasks. The main goal of the work was to analyze the characteristics of Tat protein in HIV-1 A6 variant, that is, to identify substitutions characteristic for A6 and A1 variants, as well as to compare the frequency of mutations in functionally significant domains in sub-subtype A6 and subtype B. MATERIAL AND METHODS The nucleotide sequences of HIV-1 sub-subtypes A6, A1, A2, A3, A4, subtype B and the reference nucleotide sequence were obtained from the Los Alamos international database. RESULTS AND DISCUSSION Q54H and Q60H were identified as characteristic substitutions. Essential differences in natural polymorphisms between sub-subtypes A6 and A1 have been demonstrated. In the CPP-region, there were detected mutations (R53K, Q54H, Q54P, R57G) which were more common in sub-subtype A6 than in subtype B. CONCLUSION Tat protein of sub-subtype A6 have some characteristics that make it possible to reliably distinguish it from other HIV-1 variants. Mutations identified in the CPP region could potentially alter the activity of Tat. The data obtained could form the basis for the drugs and vaccines development.
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Affiliation(s)
- A I Kuznetsova
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - K B Gromov
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia; FSBI «Central Research Institute for Epidemiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - D E Kireev
- FSBI «Central Research Institute for Epidemiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A V Shlykova
- FSBI «Central Research Institute for Epidemiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A E Lopatukhin
- FSBI «Central Research Institute for Epidemiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - E V Kazennova
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A V Lebedev
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A S Tumanov
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - K V Kim
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
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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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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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Zhou M, Humbert M, Mukhtar MM, Scinto HB, Vyas HK, Lakhashe SK, Byrareddy SN, Maurer G, Thorat S, Owuor J, Lai Z, Chen Y, Griffiths A, Chenine AL, Gumber S, Villinger F, Montefiori D, Ruprecht RM. Adaptation of an R5 Simian-Human Immunodeficiency Virus Encoding an HIV Clade A Envelope with or without Ablation of Adaptive Host Immunity: Differential Selection of Viral Mutants. J Virol 2019; 93:e02267-18. [PMID: 30760566 PMCID: PMC6475780 DOI: 10.1128/jvi.02267-18] [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: 12/19/2018] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
Simian-human immunodeficiency virus (SHIV) infection in rhesus macaques (RMs) resembles human immunodeficiency virus type 1 (HIV-1) infection in humans and serves as a tool to evaluate candidate AIDS vaccines. HIV-1 clade A (HIV-A) predominates in parts of Africa. We constructed an R5 clade A SHIV (SHIV-A; strain SHIV-KNH1144) carrying env from a Kenyan HIV-A. SHIV-A underwent rapid serial passage through six RMs. To allow unbridled replication without adaptive immunity, we simultaneously ablated CD8+ and B cells with cytotoxic monoclonal antibodies in the next RM, resulting in extremely high viremia and CD4+ T-cell loss. Infected blood was then transferred into two non-immune-depleted RMs, where progeny SHIV-A showed increased replicative capacity and caused AIDS. We reisolated SHIV-KNH1144p4, which was replication competent in peripheral blood mononuclear cells (PBMC) of all RMs tested. Next-generation sequencing of early- and late-passage SHIV-A strains identified mutations that arose due to "fitness" virus optimization in the former and mutations exhibiting signatures typical for adaptive host immunity in the latter. "Fitness" mutations are best described as mutations that allow for better fit of the HIV-A Env with SIV-derived virion building blocks or host proteins and mutations in noncoding regions that accelerate virus replication, all of which result in the outgrowth of virus variants in the absence of adaptive T-cell and antibody-mediated host immunity.IMPORTANCE In this study, we constructed a simian-human immunodeficiency virus carrying an R5 Kenyan HIV-1 clade A env (SHIV-A). To bypass host immunity, SHIV-A was rapidly passaged in naive macaques or animals depleted of both CD8+ and B cells. Next-generation sequencing identified different mutations that resulted from optimization of viral replicative fitness either in the absence of adaptive immunity or due to pressure from adaptive immune responses.
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Affiliation(s)
- Mingkui Zhou
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Humbert
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Muhammad M Mukhtar
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanna B Scinto
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Hemant K Vyas
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Samir K Lakhashe
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Siddappa N Byrareddy
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregor Maurer
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- VetCore, Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Swati Thorat
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua Owuor
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | - Agnès-Laurence Chenine
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Henry M. Jackson Foundation, Bethesda, Maryland, USA
- Military HIV Research Program, Silver Spring, Maryland, USA
| | - Sanjeev Gumber
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - François Villinger
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ruth M Ruprecht
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Southwest National Primate Research Center, San Antonio, Texas, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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9
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Lebedev A, Lebedeva N, Moskaleychik F, Pronin A, Kazennova E, Bobkova M. Human Immunodeficiency Virus-1 Diversity in the Moscow Region, Russia: Phylodynamics of the Most Common Subtypes. Front Microbiol 2019; 10:320. [PMID: 30863382 PMCID: PMC6399469 DOI: 10.3389/fmicb.2019.00320] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/06/2019] [Indexed: 01/12/2023] Open
Abstract
This study analyzes the HIV-1 subtype diversity and its phylodynamics in Moscow region, which is the most densely populated area of Russia characterized by high rates of internal and external migration. The demographic and viral data from 896 HIV-infected individuals collected during 2011–2016 were analyzed. The study revealed broad diversity in the HIV-1 subtypes found in Moscow, which included A6 (85.1%), B (7.6%), CRF02_AG (1.2%) and URF_A6/B recombinants (4.2%). Other HIV-1 subtypes were detected as single cases. While A6 was most prevalent (>86.0%) among heterosexuals, injecting drug users and cases of mother-to-child transmission of HIV, subtype B (76.3%) was more common in men who have sex with men. Phylogenetic reconstruction revealed that the A6 sequences were introduced into the epidemic cluster that arose approximately around 1998. Within the subtype B, six major epidemic clusters were identified, each of which contained strains associated with only one or two dominant transmission routes. The date of origin of these clusters varied between 1980 and 1993, indicating that the HIV-1 B epidemic began much earlier than the HIV-1 A6 epidemic. Reconstruction of the demographic history of subtypes A6 and B identified at least two epidemic growth phases, which included an initial phase of exponential growth followed by a decline in the mid/late 2010s. Thus, our results indicate an increase in HIV-1 genetic diversity in Moscow region. They also help in understanding the HIV-1 temporal dynamics as well as the genetic relationships between its circulating strains.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | | | - Fedor Moskaleychik
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | | | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
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10
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Vasylyeva TI, Liulchuk M, du Plessis L, Fearnhill E, Zadorozhna V, Babii N, Scherbinska A, Novitsky V, Pybus OG, Faria NR. The Changing Epidemiological Profile of HIV-1 Subtype B Epidemic in Ukraine. AIDS Res Hum Retroviruses 2019; 35:155-163. [PMID: 30430838 PMCID: PMC6360399 DOI: 10.1089/aid.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
While HIV-1 subtype B has caused a large epidemic in the Western world, its transmission in Ukraine remains poorly understood. We assessed the genetic diversity of HIV-1 subtype B viruses circulating in Ukraine, characterized the transmission group structure, and estimated key evolutionary and epidemiological parameters. We analyzed 120 HIV-1 subtype B pol sequences (including 46 newly generated) sampled from patients residing in 11 regions of Ukraine between 2002 and 2017. Phylogenies were estimated using maximum likelihood and Bayesian phylogenetic methods. A Bayesian molecular clock coalescent analysis was used to estimate effective population size dynamics and date the most recent common ancestors of identified clades. A phylodynamic birth-death model was used to estimate the effective reproductive number (Re) of these clades. We identified two phylogenetically distinct predominantly Ukrainian (≥75%) clades of HIV-1 subtype B. We found no significant transmission group structure for either clade, suggesting frequent mixing among transmission groups. The estimated dates of origin of both subtype B clades were around early 1970s, similar to the introduction of HIV-1 subtype A into Ukraine. Re was estimated to be 1.42 [95% highest posterior density (HPD) 1.26-1.56] for Clade 1 and 1.69 (95% HPD 1.49-1.84) for Clade 2. Evidently, the subtype B epidemic in the country is no longer concentrated in specific geographical regions or transmission groups. The study results highlight the necessity for strengthening preventive and monitoring efforts to reduce the further spread of HIV-1 subtype B.
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Affiliation(s)
| | - Mariia Liulchuk
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Esther Fearnhill
- Institute for Global Health, University College London, United Kingdom
| | - Victoriia Zadorozhna
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Nataliia Babii
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla Scherbinska
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vladimir Novitsky
- Department of Immunology and Infectious diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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11
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Kazennova EV, Laga VY, Gromov KB, Sankov MN, Popova ES, Lgumnova EG, Oparina EN, Sorokina TA, Bobkova MR. [Molecular epidemiological analysis of hiv infection in northern seaports of Russia]. Vopr Virusol 2018; 62:154-161. [PMID: 29733164 DOI: 10.18821/0507-4088-2017-62-4-154-161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/13/2016] [Indexed: 11/17/2022]
Abstract
The results of the molecular-epidemiological analysis of HIV-1 variants circulating in Arkhangelsk and Murmansk - northern seaports of Russia - were presented. In these seaports the HIV-1 variants belonging to subtype A1 were predominant (93% in Murmansk, 83% in Arkhangelsk). In addition to these variants, viruses of other subtypes such as B, C, D and recombinant forms CRF02_AG and CRF03_AB were identifed. The heterogeneity of circulating HIV-1 variants was higher in Arkhangelsk than in Murmansk. According to the results of phylogenetic analysis, subtype A1 sequences formed the common branch with nucleotide sequences of IDU-A strains found in other regions of Russia. HIV-1 variants of subtype B sub-clustered with sequences of East European B-variants. The recombinant strains CRF02_AG formed the common branch with HIV-1 sequences from Central Asia republics of the former USSR. Among 124 therapy-naive patients from Arkhangelsk and Murmansk (n = 124) the transmitted resistance was less than 5%.
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Affiliation(s)
- E V Kazennova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - V Yu Laga
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - K B Gromov
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - M N Sankov
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - E S Popova
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - E G Lgumnova
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - E N Oparina
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - T A Sorokina
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
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12
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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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13
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Kazennova E, Laga V, Gromov K, Lebedeva N, Zhukova E, Pronin A, Grezina L, Dement'eva N, Shemshura A, Bobkova M. Genetic Variants of HIV Type 1 in Men Who Have Sex with Men in Russia. AIDS Res Hum Retroviruses 2017; 33:1061-1064. [PMID: 28443684 DOI: 10.1089/aid.2017.0078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The men who have sex with men (MSM) population infected with HIV is poorly studied in Russia because of stigma and discrimination. In the first years of the HIV epidemic, the only HIV genetic variant that circulated among MSM was subtype B, usually acquired abroad. Meanwhile, the massive epidemic of HIV in Russia was caused by a highly homogenic subtype A variant, AFSU (A6), and spread mainly among drug users. In this study, 155 HIV pol sequences from MSM collected during the 2006-2016 period were analyzed. Phylogenetic analysis found that 19.4% of the viral sequences from MSM clustered with HIV genetic variants A6 and BFSU, which were previously identified only among drug users and their heterosexual partners. These data show that the MSM population in Russia is gradually becoming less isolated from the general epidemic process. Urgent measures should be taken to prevent the spread of HIV among the MSM population.
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Affiliation(s)
- Elena Kazennova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Vita Laga
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Konstantin Gromov
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | | | | | | | | | | | | | - Marina Bobkova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
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14
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Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:169-179. [PMID: 27262355 PMCID: PMC5157885 DOI: 10.1016/j.meegid.2016.05.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their spread around the world over the last 50years and describe significant spread patterns. We show that subtype B travelled from North America to Western Europe in different occasions, while Central/Eastern Europe remained isolated for the most part of the early epidemic. Looking with more detail in European countries we see that the United Kingdom, France and Switzerland exchanged viral isolates with non-European countries than with European ones. The observed pattern is likely to mirror geopolitical landmarks in the post-World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. In conclusion, HIV-1 spread through specific migration routes which are consistent with geopolitical factors that affected human activities during the last 50years, such as migration, tourism and trade. Our findings support the argument that epidemic control policies should be global and incorporate political and socioeconomic factors.
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Affiliation(s)
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Glenn Lawyer
- Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Daniel Struck
- Centre de Recherche Public de la Sante, Luxembourg, Luxembourg
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Annemarie Wensing
- Department of Virology, University Medical Center, Utrecht, The Netherlands
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Perpétua Gomes
- Molecular Biology Lab, LMCBM, SPC, HEM, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Snjezana J Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases "Dr. F. Mihaljevic", Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals", Bucharest, Romania
| | | | - Mario Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | - Maja Stanojevic
- University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | | | | | - Georgios Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Samuel R Friedman
- Institute of Infectious Diseases Research, National Development and Research Institutes, Inc., New York, USA
| | - David van de Vijver
- Eijkman Winkler Institute, Department of Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Andrea de Luca
- Institute of Clinical Infectious Diseases, Catholic university, Rome, Italy
| | - Klaus Korn
- University of Erlangen, Erlangen, Germany
| | - Clive Loveday
- International Clinical Virology Centre, Buckinghamshire, England, United Kingdom
| | | | | | | | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece.
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15
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Ksobiech K, Somlai AM, Kelly JA, Benotsch E, Gore-Felton C, McAuliffe T, Ostrovski D, Kozlov AP. Characteristics and HIV Risk Behaviors among Injection Drug Users in St. Petersburg, Russia: A Comparison of Needle Exchange Program Attenders and Nonattenders. JOURNAL OF DRUG ISSUES 2016. [DOI: 10.1177/002204260403400404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The purpose of this descriptive study was to compare young Russian NEP attenders (N = 209) and nonattenders (N = 207) on a multitude of dependent variables related to drug and sexual knowledge, attitudes, and behaviors. Questionnaire data found NEP attenders were more likely to be female, inject more frequently, use heroin heavily, be in long-term relationships, use clean needles, have more unprotected vaginal sex acts, and have drug-using friends with positive safer sex attitudes. Comparisons were also made between male and female NEP attenders, male NEP attenders and nonattenders, female NEP attenders and nonattenders, and male and female NEP nonattenders. Significant differences between those subgroups were found. A logistic regression was run to determine which variables served to predict NEP attendance. Four variables accounted for 17% of the variance and predicted NEP attendance in two thirds of the cases: safer sex attitudes of drug-using friends, heroin use, using new needles to inject, and relationship status.
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16
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Beloukas A, Psarris A, Giannelou P, Kostaki E, Hatzakis A, Paraskevis D. Molecular epidemiology of HIV-1 infection in Europe: An overview. INFECTION GENETICS AND EVOLUTION 2016; 46:180-189. [PMID: 27321440 DOI: 10.1016/j.meegid.2016.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.
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Affiliation(s)
- Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alexandros Psarris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polina Giannelou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- 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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Junqueira DM, Almeida SEDM. HIV-1 subtype B: Traces of a pandemic. Virology 2016; 495:173-84. [PMID: 27228177 DOI: 10.1016/j.virol.2016.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/18/2022]
Abstract
Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Centro Universitário Ritter dos Reis - UniRitter, Departamento de Ciências da Saúde, Avenida Orfanotrófio, 555 - Teresópolis, Porto Alegre, RS, Brazil.
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Instituto de Ciências da Saúde, Universidade FEEVALE, Rodovia RS 239, 2755 - Vila Nova, Novo Hamburgo, RS, Brazil.
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Heimer R, Levina OS, Osipenko V, Ruiz MS, Sergeyev B, Sirotkin AV, Vyshemirskaya I. Impact of incarceration experiences on reported HIV status and associated risk behaviours and disease comorbidities. Eur J Public Health 2015; 25:1089-94. [PMID: 26381650 DOI: 10.1093/eurpub/ckv157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The Russian human immunodeficiency virus (HIV) epidemic among people who inject drugs (PWID) originated in Kaliningrad, but research into risk behaviours among PWID has been lacking. The potential for heterosexual spread has not been analysed. METHODS A sample of PWID was accrued using two methods. A questionnaire was administered to assess HIV-related risk behaviours for parenteral and sexual transmission, sociodemographic factors, HIV knowledge and attitudes about sexual risks. Data were analysed focusing on the role of imprisonment, factors associated with awareness of being HIV infected and condom use. RESULTS More than a quarter of the sample reported having been diagnosed with HIV infection, with higher prevalence among women and those with a history of incarceration. More than half reported having been diagnosed with hepatitis C virus infection. Those reporting being HIV positive were less likely to distribute used syringes to other PWID and more likely to have used a condom the last time they had sex. A history of incarceration was associated with higher rates of receptive syringe sharing among those not having ever received an HIV-positive diagnosis and a lower likelihood of believing that condoms are needed when having sex with a casual partner. CONCLUSION Although extensive HIV testing has alerted many PWID to their HIV-positive status, which is associated with less distributive syringe sharing and higher likelihood of condom use, substantial risk for parenteral and especially sexual HIV transmission remains. More active prevention programs will be required to control the heterosexual spread of HIV.
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Affiliation(s)
- Robert Heimer
- 1 Department of Epidemiology of Microbial Diseases and the Center for Interdisciplinary Research on AIDS, Yale University School of Public Health, New Haven, CT 06520, USA
| | | | | | - Monica S Ruiz
- 4 Department of Prevention and Community Health, Milkin Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Boris Sergeyev
- 5 Office of the Nordic Council of Ministers, Kaliningrad, RF
| | - Aleksander V Sirotkin
- 6 International Laboratory for Applied Network Research, National Research University Higher School of Economics, St. Petersburg, RF
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Soodla P, Rajasaar H, Avi R, Zilmer K, Kink K, Novikova L, Huik K, Maimets M, Lutsar I. Design and structure of the Estonian HIV Cohort Study (E-HIV). Infect Dis (Lond) 2015; 47:768-75. [PMID: 26153824 DOI: 10.3109/23744235.2015.1061203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Estonia is experiencing the new Eastern Europe human immunodeficiency virus (HIV) epidemic, with the highest incidence of new infections in the EU. We describe demographic changes, HIV-related laboratory parameters and co-infections during the concentrated HIV epidemic using the Estonian HIV Cohort Study (E-HIV) database, founded in 2009. METHODS All 3750 subjects in the E-HIV database on December 31, 2013 were included. Subjects were divided into risk groups: people who inject drugs (PWIDs), sexual transmission (heterosexual/homosexual), and other (perinatal) or unknown risk group. Subjects diagnosed before 2009 (first period) and after (second period) were analyzed separately. RESULTS The mean age at diagnosis has increased from 22.8 years (interquartile range (IQR) = 19.5-27.2) to 29.7 years (IQR = 25.3-36.2) (p < 0.001) between the first and second periods. PWIDs were younger than other transmission groups (23.2 vs 27.1; p < 0.001). There is a statistical difference in the route of transmission among genders, with overall increasing sexual transmission. The most common AIDS-defining illness was tuberculosis (0.5%). HIV/hepatitis C (HCV) co-infection was diagnosed in 42% of cases. The population median CD4 + cell count at diagnosis has declined over the years; in total 53% have been late presenters. Half of the patients are receiving antiretroviral treatment (cART). The most common combinations are nucleoside reverse transcriptase inhibitor (NRTI) backbone plus protease inhibitors (PIs) (57%) or NRTI backbone + non-NRTIs (42%). CONCLUSION The E-HIV enables us to fill the gap in the lack of data on the course of the new Eastern European HIV epidemic. These data demonstrate that the HIV epidemic in Estonia is moving from PWIDs to the general population, suggesting that prevention measures and testing guidelines should be revised.
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Affiliation(s)
- Pilleriin Soodla
- From the Institute of Microbiology, Faculty of Medicine, University of Tartu , Tartu , Estonia
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Kazennova E, Laga V, Lapovok I, Glushchenko N, Neshumaev D, Vasilyev A, Bobkova M. HIV-1 genetic variants in the Russian Far East. AIDS Res Hum Retroviruses 2014; 30:742-52. [PMID: 24773167 DOI: 10.1089/aid.2013.0194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A molecular analysis of HIV-1 subtypes and recombinants circulating in cities in the Russian Far East was performed. The study included samples from 201 outpatients from Vladivostok, Khabarovsk, and Blagoveshchensk. In most parts of Russia, patients are infected with HIV-1 subtype A, known as the IDU-A variant. Subtype B, including the IDU-B variant, is rare in Russia but widespread in the Ukraine, and the CRF02_AG is prevalent in Central Asian countries and Siberia, Russia. One of the challenges of this study in the Far East was to determine whether the molecular landscape of HIV infection in this region is influenced by the bordering countries, including China and Japan, where a distinct set of HIV subtypes is circulating, such as B', C, and CRF01_AE. The distribution of HIV-1 genetic variants in the cities studied was as follows: subtype A (IDU-A), 55.7%; subtype B, 25.3% (IDU-B variant-24.3%); subtype C, 10.0%; CRF02_AG, 1.5%; and CRF63_02A1, 7.5%. A phylogenetic analysis confirmed the relationship of subtype A viruses with the IDU-A variant predominating in Ukraine, Russia and other former Soviet Union (FSU) countries, of subtype B viruses with IDU-B in the Ukraine and of CRF02_AG variants with variants in Uzbekistan, Russia, and other former USSR countries. Subtype C sequences were not uniform, and most clustered between each other and HIV-1 sequences originating from Africa; there was only one sample possibly related to Chinese variants. Thus, despite close cultural and commercial relationships among Russia, China, and Japan, the distribution of HIV-1 subtypes in the Russian Far East is still primarily influenced by contacts with the countries of the former USSR.
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Affiliation(s)
| | - Vita Laga
- Ivanovsky Institute of Virology, Moscow, Russia
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21
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Lapovok I, Kazennova E, Laga V, Vasilyev A, Utegenova A, Abishev A, Dzissyuk N, Tukeev M, Bobkova M. Short communication: molecular epidemiology of HIV type 1 infection in Kazakhstan: CRF02_AG prevalence is increasing in the southeastern provinces. AIDS Res Hum Retroviruses 2014; 30:769-74. [PMID: 24873898 DOI: 10.1089/aid.2013.0291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To analyze HIV-1 genetic variants in Kazakhstan, HIV-1 sequences were obtained from 205 antiretroviral-treated (ART) and naive patients in 2009-2013. Samples were collected in the most populous cities and provinces of Kazakhstan. On the basis of phylogenetic analyses of partial pol sequences, subtype A variant intravenous drug user (IDU)-A (which is dominant in the former Soviet Union) was found in 60.0% of the individuals, followed by CRF02_AG (34.6%); the rest of the samples were subtype B, CRF03_AB, CRF63_02A1, and CRF07_BC. The proportion of CRF02_AG has increased significantly since 2001-2003, when it was less than 5%. The majority of the CRF02_AG cases were found in Almaty, the former capital and the most populous city in Kazakhstan. The IDU-A variant dominated in the industrial regions of northern and central Kazakhstan and some other regions. Both dominant HIV-1 genetic variants were almost equally represented in the two main transmission groups: IDUs and heterosexuals. The analysis of drug-resistant mutations found a low prevalence of drug resistance in 165 therapy-naive individuals (3.0%). Thus, in the beginning of the second decade of the 2000s, the HIV epidemic in Kazakhstan is driven by two main genetic variants: IDU-A and CRF02_AG.
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Affiliation(s)
| | | | - Vita Laga
- Ivanovsky Institute of Virology, Moscow, Russia
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Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013; 194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [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: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.
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Affiliation(s)
- Raj Shankarappa
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, United States
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Frentz D, Wensing AMJ, Albert J, Paraskevis D, Abecasis AB, Hamouda O, Jørgensen LB, Kücherer C, Struck D, Schmit JC, Åsjö B, Balotta C, Beshkov D, Camacho RJ, Clotet B, Coughlan S, De Wit S, Griskevicius A, Grossman Z, Horban A, Kolupajeva T, Korn K, Kostrikis LG, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher CAB, Van de Vijver DAMC. Limited cross-border infections in patients newly diagnosed with HIV in Europe. Retrovirology 2013; 10:36. [PMID: 23551870 PMCID: PMC3626648 DOI: 10.1186/1742-4690-10-36] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND International travel plays a role in the spread of HIV-1 across Europe. It is, however, not known whether international travel is more important for spread of the epidemic as compared to endogenous infections within single countries. In this study, phylogenetic associations among HIV of newly diagnosed patients were determined across Europe. RESULTS Data came from the SPREAD programme which collects samples of newly diagnosed patients that are representative for national HIV epidemics. 4260 pol sequences from 25 European countries and Israel collected in 2002-2007 were included.We identified 457 clusters including 1330 persons (31.2% of all patients). The cluster size ranged between 2 and 28. A number of 987 patients (74.2%) were part of a cluster that consisted only of patients originating from the same country. In addition, 135 patients (10.2%) were in a cluster including only individuals from neighboring countries. Finally, 208 patients (15.6%) clustered with individuals from countries without a common border. Clustering with patients from the same country was less prevalent in patients being infected with B subtype (P-value <0.0001), in men who have sex with men (P-value <0.0001), and in recently infected patients (P-value =0.045). CONCLUSIONS Our findings indicate that the transmission of HIV-1 in Europe is predominantly occurring between patients from the same country. This could have implications for HIV-1 transmission prevention programmes. Because infections through travelling between countries is not frequently observed it is important to have good surveillance of the national HIV-1 epidemics.
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Affiliation(s)
- Dineke Frentz
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
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A decline in the prevalence of injecting drug users in Estonia, 2005-2009. THE INTERNATIONAL JOURNAL OF DRUG POLICY 2013; 24:312-8. [PMID: 23290632 DOI: 10.1016/j.drugpo.2012.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 11/20/2022]
Abstract
AIMS Here we report a study aimed at estimating trends in the prevalence of injection drug use between 2005 and 2009 in Estonia. BACKGROUND Descriptions of behavioural epidemics have received little attention compared with infectious disease epidemics in Eastern Europe. METHODS The number of injection drug users (IDUs) aged 15-44 each year between 2005 and 2009 was estimated using capture-recapture methodology based on 4 data sources (2 treatment data bases: drug use and non-fatal overdose treatment; criminal justice (drug related offences) and mortality (injection drug use related deaths) data). Poisson log-linear regression models were applied to the matched data, with interactions between data sources fitted to replicate the dependencies between the data sources. Linear regression was used to estimate average change over time. RESULTS There were 24305, 12,292, 238, 545 records and 8100, 1655, 155, 545 individual IDUs identified in the four capture sources (police, drug treatment, overdose, and death registry, accordingly) over the period 2005-2009. The estimated prevalence of IDUs among the population aged 15-44 declined from 2.7% (1.8-7.9%) in 2005 to 2.0% (1.4-5.0%) in 2008, and 0.9% (0.7-1.7%) in 2009. Regression analysis indicated an average reduction of about 1600 injectors per year. CONCLUSION While the capture-recapture method has known limitations, the results are consistent with other data from Estonia. Identifying the drivers of change in the prevalence of injection drug use warrants further research.
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Eremin VF, Gasich EL, Sasinovich SV. A new unique recombinant HIV type 1 isolated from a child born to an HIV-infected mother. AIDS Res Hum Retroviruses 2011; 27:1323-6. [PMID: 21534848 DOI: 10.1089/aid.2011.0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The new HIV-1 recombinant, with a B(gag) A(pol)A(env) structure, is described. This recombinant virus differs from the classical "Kaliningrad" (AF193276.1) virus with an A(gag) B(pol)B(env) structure. The number of new HIV cases in Belarus has been increasing in the past few years. Within the 12 months of 2010, 1069 new cases of HIV infection were registered. Molecular epidemiological investigations have shown that though HIV-1 subtype A (84.5%) still dominates in HIV/AIDS patients, the quantity of CRFs has also increased to 7.1%. Although cases with the CRF03_AB virus were previously described in patients from Belarus, CRF06_cpx and CRF02_AG are described in Belarus for the first time.
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Affiliation(s)
- Vladimir F. Eremin
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Elena L. Gasich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Sviataslau V. Sasinovich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
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Skar H, Hedskog C, Albert J. HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Ann N Y Acad Sci 2011; 1230:108-18. [PMID: 21824168 DOI: 10.1111/j.1749-6632.2011.06128.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HIV/AIDS has become one of the most important infectious diseases with a cumulative number of almost 60 million infections worldwide. The prevalence and epidemiological patterns are unevenly distributed across the globe and also within countries. HIV is one of the fastest evolving organisms known. Several genetically distinct subtypes are present and new circulating recombinant forms are continuously emerging. This review discusses HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Factors and concepts that influence global spread and within-patient evolution of HIV-1 are discussed as well as future perspectives on the use of phylodynamics in HIV epidemiology.
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Affiliation(s)
- Helena Skar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
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Avi R, Huik K, Sadam M, Karki T, Krispin T, Ainsalu K, Paap P, Schmidt J, Nikitina N, Lutsar I. Characterization of integrase region polymorphisms in HIV type 1 CRF06_cpx viruses in treatment-naive patients in Estonia. AIDS Res Hum Retroviruses 2010; 26:1109-13. [PMID: 20849300 DOI: 10.1089/aid.2010.0097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Natural polymorphisms of HIV-1, often associated with drug resistance, are widely described in protease and reverse transcriptase regions but data on their presence in the integrase region, especially in non-B subtypes, are still very limited. We aimed to characterize naturally occurring polymorphisms in the integrase region in 104 treatment-naive and 10 treatment-experienced patients infected predominantly with HIV-1 CRF06_cpx and its recombinant with subtype A1 and/or CRF03_AB viruses. No primary drug resistance mutations against integrase inhibitors were found, but resistance-associated polymorphisms such as V72I, L74I, V201I, and T206S were seen in more than 90% of viruses. Substitutions E157Q and E157K, associated with raltegravir resistance, were found in only two CRF06_cpx strains. We conclude that similar to other HIV-1 non-B subtypes, the CRF06_cpx and its recombinants with subtype A1 and CRF03_AB are rich in integrase region natural polymorphisms, which may impact the development of resistance against integrase inhibitors.
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Affiliation(s)
- Radko Avi
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kristi Huik
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Maarja Sadam
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Tonis Karki
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Tonu Krispin
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Külliki Ainsalu
- Department of Infectious Diseases, Tartu University Hospital, Tartu, Estonia
| | - Piret Paap
- Hospital of Tartu Prison, Tartu, Estonia
| | | | | | - Irja Lutsar
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Rumyantseva OA, Olkhovskiy IA, Malysheva MA, Ruzaeva LA, Vasiliev AV, Kazennova EV, Bobkova MR, Lukashov VV. Epidemiological networks and drug resistance of HIV type 1 in Krasnoyarsk region, Russia. AIDS Res Hum Retroviruses 2009; 25:931-6. [PMID: 19689192 DOI: 10.1089/aid.2009.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the molecular epidemiology of HIV-1 in Krasnoyarsk region, Russia, where HIV-1 has spread rapidly since 2000, we obtained pol sequences from individuals living in this region (n = 67) as well as in the geographically closely related Altay region (n = 13). In both regions, subtype A viruses specific for the former Soviet Union (IDU-A strains) were dominant (92.5%). Virus sequences clustered according to the geographic origin of the infected individuals rather than to their risk group, demonstrating the role of geographically defined epidemiological networks in the propagation of the HIV-1 epidemic in the region. Six viruses belonged to subtype B. Three of them were phylogenetically (and therefore epidemiologically) closely related to each other, demonstrating that even though IDU-A viruses dominate the epidemic, the spread of other virus strains does occur. Most viruses (75%) had an A62V mutation in reverse transcriptase, specific for HIV-1 strains in Russia. Remarkably, 26 of 47 (55%) patients under HAART with detectable virus loads did not have any known drug-resistant mutation, indicating the need to increase compliance to therapy.
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Affiliation(s)
- Olga A. Rumyantseva
- Krasnoyarsk Regional AIDS Center, Krasnoyarsk, Russia
- D.I. Ivanovsky Institute of Virology, Moscow, Russia
| | | | | | | | | | | | | | - Vladimir V. Lukashov
- D.I. Ivanovsky Institute of Virology, Moscow, Russia
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Beyrer C, Patel Z, Stachowiak JA, Tishkova FK, Stibich MA, Eyzaguirre LM, Carr JK, Mogilnii V, Peryshkina A, Latypov A, Strathdee SA. Characterization of the emerging HIV type 1 and HCV epidemics among injecting drug users in Dushanbe, Tajikistan. AIDS Res Hum Retroviruses 2009; 25:853-60. [PMID: 19689193 DOI: 10.1089/aid.2008.0206] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study aimed to determine HIV, HCV, and syphilis prevalence and correlates, and to characterize the molecular epidemiology of HIV-1 among injecting drug users (IDUs) in Dushanbe, Tajikistan. A cross-sectional study assessing risk factors for HIV and HCV through an interview administered survey was conducted. A total of 491 active adult IDUs were recruited from May to November 2004 in Dushanbe, Tajikistan. HIV-1 antibody status was determined with rapid testing and confirmed with ELISA. HCV antibody testing was conducted using a BIOELISA HCV kit. HIV-1 subtyping was done on a subset with full-length sequencing. Correlates of HIV and HCV infection were assessed using logistic regression. Overall prevalence of HIV was 12.1%, HCV was 61.3%, and syphilis was 15.7%. In a multivariate logistic regression model controlling for gender and ethnicity, daily injection of narcotics [odds ratio (OR) OR 3.22] and Tajik nationality (OR 7.06) were significantly associated with HIV status. Tajik nationality (OR 1.91), history of arrest (OR 2.37), living/working outside Tajikistan in the past 10 years (OR 2.43), and daily injection of narcotics (OR 3.26) were significantly associated with HCV infection whereas being female (OR 0.53) and always using a sterile needle (OR 0.47) were inversely associated with HCV infection. Among 20 HIV-1-positive IDU with specimens available for typing, 10 were subtype A, 9 were CRF02_AG, and one was an A-CRF02_AG recombinant. Epidemics of HIV-1, HCV, and drug use are underway in Dushanbe. The molecular epidemiology is distinctive, with West African variants accounting for roughly 50% of prevalent infections. Targeted prevention programs offering both needle exchange programs and opiate substitution therapies are urgently called for to prevent the further spread of HIV and HCV in Tajikistan.
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Affiliation(s)
- Chris Beyrer
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland 21205
| | - Zeenat Patel
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland 21205
| | - Julie A. Stachowiak
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland 21205
| | - Farida K. Tishkova
- Tajik Scientific and Research Institute of Prevention Medicine, Federal Virology Laboratory, Dushanbe, Tajikistan
| | - Mark A. Stibich
- AIDS infoshare Russia, Dorozhny Proezd, dom 9/10, Moscow 113545, Russia
| | | | - Jean K. Carr
- Henry M. Jackson Foundation, 1401 Rockville Pike, Rockville, Maryland 20852
| | - Vladimir Mogilnii
- AIDS infoshare Russia, Dorozhny Proezd, dom 9/10, Moscow 113545, Russia
| | - Alena Peryshkina
- AIDS infoshare Russia, Dorozhny Proezd, dom 9/10, Moscow 113545, Russia
| | - Alisher Latypov
- Tajik Scientific and Research Institute of Prevention Medicine, Federal Virology Laboratory, Dushanbe, Tajikistan
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Avi R, Huik K, Sadam M, Karki T, Krispin T, Ainsalu K, Paap P, Schmidt J, Nikitina N, Lutsar I. Absence of genotypic drug resistance and presence of several naturally occurring polymorphisms of human immunodeficiency virus-1 CRF06_cpx in treatment-naive patients in Estonia. J Med Virol 2009; 81:953-8. [PMID: 19382254 DOI: 10.1002/jmv.21482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
All non-B HIV-1 subtypes and circulating recombinant forms (CRFs) are characterized by several polymorphisms in protease (PR) region. In addition, in recent years the increasing use of antiretroviral treatment (ART) has rapidly raised the spread of transmitted drug resistance. We aimed to determine the presence of naturally occurring polymorphisms and transmitted drug resistance mutations (DRMs) in ART naïve HIV-1-positive subjects in Estonia. A total of 115 drug-naive HIV-1-infected subjects (mean age 27 years; 70% male; 65% infected via intravenous drug use and 34% by heterosexual contact) were enrolled. Viral genomic RNA from plasma was directly sequenced in PR, revertase (RT), and envelope (env) regions. Phylogenetic analysis of RT and env regions revealed that 89% and 3% of sequenced viruses belonged to CRF06_cpx and subtype A1, respectively, and 6% were described as unique recombinants (signed A1-06) between CRF06_cpx and subtype A1 viruses. No primary DRMs were found in PR or RT regions indicating the absence of transmitted drug resistance. The most common polymorphisms in the PR region were K14R, M36I, H69K, and L89M seen in 96%, 100%, 99%, and 100%, respectively. The clinical relevance of these polymorphisms in terms of success of ART has to be monitored in future clinical studies.
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Affiliation(s)
- Radko Avi
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia.
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Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AMJ, van de Vijver DA, Albert J, Angarano G, Åsjö B, Balotta C, Boeri E, Camacho R, Chaix ML, Coughlan S, Costagliola D, De Luca A, de Mendoza C, Derdelinckx I, Grossman Z, Hamouda O, Hoepelman IM, Horban A, Korn K, Kücherer C, Leitner T, Loveday C, MacRae E, Maljkovic-Berry I, Meyer L, Nielsen C, Op de Coul ELM, Ormaasen V, Perrin L, Puchhammer-Stöckl E, Ruiz L, Salminen MO, Schmit JC, Schuurman R, Soriano V, Stanczak J, Stanojevic M, Struck D, Van Laethem K, Violin M, Yerly S, Zazzi M, Boucher CA, Vandamme AM. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 2009; 6:49. [PMID: 19457244 PMCID: PMC2717046 DOI: 10.1186/1742-4690-6-49] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 05/20/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The prevalence and the origin of HIV-1 subtype B, the most prevalent circulating clade among the long-term residents in Europe, have been studied extensively. However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced. RESULTS In the current study we inferred the migration history of HIV-1 subtype B by way of a phylogeography of viral sequences sampled from 16 European countries and Israel. Migration events were inferred from viral phylogenies by character reconstruction using parsimony. With regard to the spatial dispersal of the HIV subtype B sequences across viral phylogenies, in most of the countries in Europe the epidemic was introduced by multiple sources and subsequently spread within local networks. Poland provides an exception where most of the infections were the result of a single point introduction. According to the significant migratory pathways, we show that there are considerable differences across Europe. Specifically, Greece, Portugal, Serbia and Spain, provide sources shedding HIV-1; Austria, Belgium and Luxembourg, on the other hand, are migratory targets, while for Denmark, Germany, Italy, Israel, Norway, the Netherlands, Sweden, Switzerland and the UK we inferred significant bidirectional migration. For Poland no significant migratory pathways were inferred. CONCLUSION Subtype B phylogeographies provide a new insight about the geographical distribution of viral lineages, as well as the significant pathways of virus dispersal across Europe, suggesting that intervention strategies should also address tourists, travellers and migrants.
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Affiliation(s)
- Dimitrios Paraskevis
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Oliver Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Gkikas Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Angelos Hatzakis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Annemarie MJ Wensing
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - David A van de Vijver
- Department of Virology, Erasmus MC, University Medical Centre, Postbus 2040 3000 CA Rotterdam, the Netherlands
| | - Jan Albert
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - Guiseppe Angarano
- University of Foggia, Clinic of Infectious Diseases, Ospedali Riuniti – Via L. Pinto 71100 Foggia, Italy
| | - Birgitta Åsjö
- Center for Research in Virology, University of Bergen, Bergen High Technology Center, N-5020 Bergen, Norway
| | - Claudia Balotta
- University of Milano, Institute of Infectious and Tropical Diseases, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Enzo Boeri
- Diagnostica and Ricerca San Raffaele, Centro San Luigi, I.R.C.C.S. Istituto Scientifico San Raffaele, Milan, Italy
| | - Ricardo Camacho
- Universidade Nova de Lisboa, Laboratorio de Virologia, Rua da Junqueira 96 1349-008 Lisboa, Portugal
| | - Marie-Laure Chaix
- EA 3620, Universite Paris Descartes, Virologie, CHU Necker, Paris France
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College, Dublin, Ireland
| | - Dominique Costagliola
- INSERM U263 et SC4, Faculté de médecine Saint-Antoine, Université Pierre et Marie Curie, 27 rue de Chaligny, F-75571 Paris, France
| | - Andrea De Luca
- Department of Infectious Diseases, Catholic University, L.go A. Gemelli, 8 00168 Rome, Italy
| | | | | | - Zehava Grossman
- National. HIV Reference Lab, Central Virology, Public Health Laboratories, MOH Central Virology, Sheba Medical Center, 2 Ben-Tabai Street, Israel
| | - Osama Hamouda
- Robert Koch Institut (RKI), Nordufer 20, 13353 Berlin, Germany
| | - IM Hoepelman
- University Medical Center Utrecht, Department of Internal Medicine and Infectious Diseases F02.126, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Andrzej Horban
- Hospital for Infectious Diseases, Center for Diagnosis & Therapy Warsaw 37, Wolska Str. 01-201 Warszawa, Poland
| | - Klaus Korn
- University of Erlangen, Schlossplatz 4, D-91054 Erlangen, Germany
| | | | - Thomas Leitner
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - Clive Loveday
- ICVC Charity Laboratories, 3d floor, Apollo Centre Desborough Road High Wycombe, Buckinghamshire, HP11 2QW, UK
| | | | - I Maljkovic-Berry
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - Claus Nielsen
- Statens Serum Institut Copenhagen, Retrovirus Laboratory, department of virology, building 87, Division of Diagnostic Microbiology 5, Artillerivej 2300 Copenhagen, Denmark
| | - Eline LM Op de Coul
- Centre for Infectious Disease Control (Epidemiology & Surveillance), National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands
| | - Vidar Ormaasen
- Ullevaal University Hospital, Department of Infectious Diseases Kirkeveien 166, N-0407 Oslo, Norway
| | - Luc Perrin
- Laboratory of Virology, Geneva University Hospital and University of Geneva Medical School, Geneva, Switzerland
| | | | - Lidia Ruiz
- IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Ctra. de Canyet s/n, 08916 Badalona (Barcelona), Spain
| | - Mika O Salminen
- National Public Health Institute, HIV laboratory and department of infectious disease epidemiology, Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg, Retrovirology Laboratory, National service of Infectious Diseases, 4 Rue Barblé, L-1210, Luxembourg
| | - Rob Schuurman
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | | | - J Stanczak
- Hospital for Infectious Diseases, Center for Diagnosis & Therapy Warsaw 37, Wolska Str. 01-201 Warszawa, Poland
| | - Maja Stanojevic
- University of Belgrade School of Medicine, Institute of Microbiology and Immunology Virology Department, Dr Subotica 1, 11000 Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg, Retrovirology Laboratory, National service of Infectious Diseases, 4 Rue Barblé, L-1210, Luxembourg
| | - Kristel Van Laethem
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
| | - M Violin
- University of Milano, Institute of Infectious and Tropical Diseases, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospital and University of Geneva Medical School, Geneva, Switzerland
| | - Maurizio Zazzi
- Section of Microbiology, Department of Molecular Biology, University of Siena, Italy
| | - Charles A Boucher
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Department of Virology, Erasmus MC, University Medical Centre, Postbus 2040 3000 CA Rotterdam, the Netherlands
| | - Anne-Mieke Vandamme
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
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The prevalence of diverse HIV-1 strains was stable in Cameroonian blood donors from 1996 to 2004. J Acquir Immune Defic Syndr 2009; 49:432-9. [PMID: 18931623 DOI: 10.1097/qai.0b013e31818a6561] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The HIV epidemic in Cameroon is characterized by a high level of strain diversity despite a relatively low prevalence of infection. In this study, HIV strains infecting blood donors in Cameroon were characterized to determine the prevalence of subtypes and intersubtype recombinants and if strain prevalence was changing over time. METHODS From 1996 through 2004, 676 HIV-infected blood donations were collected at blood banks in Douala and Yaoundé, Cameroon. A subset of the HIV-1 group M strains (n = 574) were classified based on phylogenetic analysis of viral sequences from the gag p24, pol integrase, and env gp41 regions. RESULTS HIV-1 group M accounted for 97.3% (n = 658) of infections, whereas group O was present in 2.2% (n = 15) and HIV-2 in 0.4% (n = 3). Within the group M infections, 14 subtypes and circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified. Overall, CRFO2_AG accounted for 58.2% of infections, URFs 14.8%, and levels of subtypes, A, B, C, D, F2, and G, and CRFs, 01, 06, 09, 11, 13, 22, and 37, varied from 0.2% to 6.1%. Evaluation of HIV strains present in the donor population over this 9-year period showed no substantial changes in the proportion of infections caused by each subtype and CRF, the percentage of intersubtype recombinants, or the strain composition of the URFs. CONCLUSIONS HIV-1 strain diversity in Cameroon did not significantly change, suggesting a mature and relatively stable epidemic.
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Ding N, Guo D, Zhang C. Reidentification of the recombination map of CRF03_AB: evidence for a new additional mosaic a subtype segment. AIDS Res Hum Retroviruses 2008; 24:1337-9. [PMID: 18844466 DOI: 10.1089/aid.2008.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Na Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dongmei Guo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chiyu Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Skar H, Sylvan S, Hansson HB, Gustavsson O, Boman H, Albert J, Leitner T. Multiple HIV-1 introductions into the Swedish intravenous drug user population. INFECTION GENETICS AND EVOLUTION 2008; 8:545-52. [PMID: 18472306 DOI: 10.1016/j.meegid.2008.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 03/25/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
Abstract
In 2001, an increase of HIV-1 diagnoses among intravenous drug users (IVDU) was reported in Sweden. In nearby countries, Finland, Russia and the Baltic states, recent outbreaks had been described. Since there was a concern that these outbreaks would carry over to Sweden a study was initiated to determine the factors leading to the Swedish increase of HIV-1 diagnosed IVDUs. HIV-1 env V3 sequences were obtained from 97 patients enrolled in ongoing epidemiological studies encompassing the years 1987--2004 with a focus on 2001--2002. The sequences were used for maximum likelihood and Bayesian inference of the molecular epidemiology. Among the virus spreading in 2001--2002, we found that four different subtypes/CRFs were present in the Swedish IVDU population (A, B, CRF01_AE and CRF06_cpx). Subtype B constituted 85% of the infections, established by 12 independent introductions into the IVDU population. The worrisome increase in 2001 was mainly not a result of import of the outbreaks in nearby countries, but rather a higher detection rate of secondary cases due to efficient epidemiological tracing of the generally slow spread of established forms of subtype B in the IVDU community. However, a few of the non-subtype B cases were linked to the outbreaks in Finland, Estonia and Latvia. Because HIV-1 outbreaks can easily be exported from one country to another amongst IVDUs, this prompts continued surveillance in the Baltic Sea Region.
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Affiliation(s)
- Helena Skar
- Department of Virology, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
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Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases. J Virol 2007; 81:10625-35. [PMID: 17634235 PMCID: PMC2045441 DOI: 10.1128/jvi.00985-07] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 sequences in intravenous drug user (IDU) networks are highly homogenous even after several years, while this is not observed in most sexual epidemics. To address this disparity, we examined the human immunodeficiency virus type 1 (HIV-1) evolutionary rate on the population level for IDU and heterosexual transmissions. All available HIV-1 env V3 sequences from IDU outbreaks and heterosexual epidemics with known sampling dates were collected from the Los Alamos HIV sequence database. Evolutionary rates were calculated using phylogenetic trees with a t test root optimization of dated samples. The evolutionary rate of HIV-1 subtype A1 was found to be 8.4 times lower in fast spread among IDUs in the former Soviet Union (FSU) than in slow spread among heterosexual individuals in Africa. Mixed epidemics (IDU and heterosexual) showed intermediate evolutionary rates, indicating a combination of fast- and slow-spread patterns. Hence, if transmissions occur repeatedly during the initial stage of host infection, before selective pressures of the immune system have much impact, the rate of HIV-1 evolution on the population level will decrease. Conversely, in slow spread, where HIV-1 evolves under the pressure of the immune system before a donor infects a recipient, the virus evolution at the population level will increase. Epidemiological modeling confirmed that the evolutionary rate of HIV-1 depends on the rate of spread and predicted that the HIV-1 evolutionary rate in a fast-spreading epidemic, e.g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups.
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Affiliation(s)
- Irina Maljkovic Berry
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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Sanders-Buell E, Saad MD, Abed AM, Bose M, Todd CS, Strathdee SA, Botros BA, Safi N, Earhart KC, Scott PT, Michael N, McCutchan FE. A nascent HIV type 1 epidemic among injecting drug users in Kabul, Afghanistan is dominated by complex AD recombinant strain, CRF35_AD. AIDS Res Hum Retroviruses 2007; 23:834-9. [PMID: 17604548 DOI: 10.1089/aid.2006.0299] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Injecting drug use (IDU), common in global centers of heroin production, confers significant risk for HIV-1 infection. Once introduced into IDU networks, an explosive rise in HIV-1 infection typically occurs, fueled principally by needle sharing. New HIV-1 epidemics in IDUs have occurred in Russia, China, Thailand, Spain, Iran, and in other countries, and some have spread into other risk groups in their respective countries. In Afghanistan, the introduction of HIV-1 into IDU networks has begun, but a recent report of 3% HIV-1 prevalence suggests that the epidemic is still at an early stage. Here we establish, by complete genome sequencing and phylogenetic analysis of four viral strains from Afghan IDUs, that all are the same complex recombinant strain, combining HIV-1 subtypes A and D and herein termed CRF35_AD. Published partial HIV-1 sequences from an HIV-1 epidemic among IDUs in Iran, already at 23.2% HIV-1 prevalence, are either CRF35_AD or a related recombinant. Voluntary HIV-1 screening and harm reduction programs in Afghanistan, applied now, could limit the spread of HIV-1, both in IDUs and in other social networks.
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Affiliation(s)
- E Sanders-Buell
- US Military HIV Research Program/Division of Retrovirology, Walter Reed Army Institute of Research, Rockville Maryland 20850, USA.
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Sarrami-Forooshani R, Das SR, Sabahi F, Adeli A, Esmaeili R, Wahren B, Mohraz M, Haji-Abdolbaghi M, Rasoolinejad M, Jameel S, Mahboudi F. Molecular analysis and phylogenetic characterization of HIV in Iran. J Med Virol 2006; 78:853-63. [PMID: 16721846 DOI: 10.1002/jmv.20634] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years. While the earliest cases were found in hemophiliacs, intravenous drug users are now fueling the outbreak. In this study, both the 122 clones of HIV-1 gag p17 and the 131 clones of env V1-V5 region were obtained from 61 HIV-1 seropositives belonging to these two groups in Iran. HIV-1 subtyping and phylogenetic analysis was done by heteroduplex mobility assays (HMA) and multiple clone sequencing. The result indicated all hemophiliacs are infected with HIV-1 subtype B and all intravenous drug users are infected with HIV-1 subtype A. Since intravenous drug abuse is the major transmission route in Iran, HIV-1 subtype A is likely to be the dominant viral subtype circulating in the country. The analysis of genetic distances showed subtype B viruses in Iran to be twice as heterogeneous as the subtype A viruses. In conclusion, this first molecular study of HIV-1 genotypes in Iran suggests two parallel outbreaks in distinct high-risk populations and may offer clues to the origin and spread of infection in Iran.
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Zarandia M, Tsertsvadze T, Carr JK, Nadai Y, Sanchez JL, Nelson AK. HIV-1 genetic diversity and genotypic drug susceptibility in the Republic of Georgia. AIDS Res Hum Retroviruses 2006; 22:470-6. [PMID: 16706626 DOI: 10.1089/aid.2006.22.470] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genetic diversity and genotypic drug susceptibility of HIV-1 strains circulating in the Republic of Georgia, formerly part of the Soviet Union, were investigated for first time. Forty-eight HIV-positive drug-naive Georgian individuals contributed PBMC DNA between 1998 and 2003. On the basis of phylogenetic analyses of partial pol sequences, the predominant HIV-1 genetic forms were subtype A (70%), followed by subtype B (26%); both genetic forms were carried by injecting drug users and heterosexuals. There was also one subtype C (2%) and one CRF18_cpx (2%). The Georgian subtype A strains clustered with subtype A from Russia, designated A(FSU). Twelve of the subtype A strains (25%) contained the secondary protease inhibitor mutation V77I and 9 also had two other silent mutations. This "V77I haplotype" marks one particular genetic lineage of the epidemic in the former Soviet Union. Two strains (4%) carried antiretroviral (ARV) drug resistance mutations. Nearly full-length genome sequences of five Georgian strains were also completed. Two, 98GEMZ011 (subtype A) and 98GEMZ003 (subtype B), closely resembled the parental strains that recombined to create CRF03_AB. The use of these parental strains in the analysis revealed an additional segment of subtype A in CRF03_AB. Thus, the HIV-1 epidemic in Georgia was composed of a mixture of subtype A(FSU) and subtype B.
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Affiliation(s)
- Maia Zarandia
- Georgian Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi 38600, Georgia
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Abstract
Uma das características mais marcantes do HIV-1 é a imensa diversidade observada entre as cepas que compõem a pandemia de HIV/AIDS. Na última década, a classificação das variantes do vírus em grupos, subtipos e formas recombinantes circulantes (CRF) e a observação de padrões específicos de mutação têm provado serem ferramentas poderosas para os estudos da dinâmica molecular do vírus. O acompanhamento da distribuição mundial da diversidade do HIV-1 tem sido empregado, por exemplo, em programas de vigilância epidemiológica, bem como na reconstrução da história de epidemias regionais. Além disto, a observação de padrões específicos de distribuição espacial do vírus sugere a existência de diferenças na patogenia e transmissibilidade entre os diversos subtipos. A análise molecular das seqüências do vírus também permite a estimativa do tempo de divergência entre as variantes e das forças dinâmicas que modelam as árvores filogenéticas.
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Affiliation(s)
- Mônica Edelenyi Pinto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Irwin K, Karchevsky E, Heimer R, Badrieva L. Secondary syringe exchange as a model for HIV prevention programs in the Russian Federation. Subst Use Misuse 2006; 41:979-99. [PMID: 16809182 DOI: 10.1080/10826080600667219] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Effective prevention of syringe-borne transmission of HIV and the hepatitis viruses can be undermined if contact between injection drug users and the staff of prevention programs is impeded by police harassment, limited program resources, and the absence of an open "drug scene." All these are commonplace in the Russian Federation. In response, "Project Renewal," the harm reduction program of the AIDS Prevention and Control Center of the Tatarstan Ministry of Health in Kazan, has created a hybrid syringe exchange program that as its primary focus recruited and trained volunteers to provide secondary syringe exchange. To compensate for operational barriers, the program staff identified private venues and trained responsible individuals to work through their own and related networks of injectors to provide clean syringes, other harm reduction supplies, and educational materials, while facilitating the collection and removal of used and potentially contaminated syringes. Program staff developed a detailed set of tracking instruments to monitor, on a daily and weekly basis, the locations and types of contacts and the dissemination of trainings and materials to ensure that the secondary distribution network reaches its target audience. Data show that these secondary exchange sites have proven more productive than the primary mobile and fixed-site syringe exchanges in Kazan. Beginning in 2001, Project Renewal has trained other harm reduction programs in the Russian Federation to use this model of reaching injectors, identifying and training volunteers, and monitoring results of secondary syringe exchange.
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Affiliation(s)
- Kevin Irwin
- Department of Epidemiology and Public Health, Yale University, New Haven, CT 06510, USA.
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41
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Vázquez de Parga E, Rakhmanova A, Pérez-Alvarez L, Vinogradova A, Delgado E, Thomson MM, Casado G, Sierra M, Muñoz M, Carmona R, Vega Y, Contreras G, Medrano L, Osmanov S, Nájera R. Analysis of drug resistance-associated mutations in treatment-naïve individuals infected with different genetic forms of HIV-1 circulating in countries of the former Soviet Union. J Med Virol 2005; 77:337-44. [PMID: 16173024 DOI: 10.1002/jmv.20461] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
There are few data on drug resistance-associated mutations in the former Soviet Union since, studies have usually been focused on the env or gag genes for subtype information. This study examines the prevalence and patterns of resistance-associated mutations to reverse transcriptase and protease inhibitors (RTI, PRI) in 278 HIV-1-infected treatment-naïve subjects from countries of Eastern Europe, and defines characteristic polymorphisms of RT and PR sequences in HIV-1 subtype A viruses. Blood samples were collected between 1997 and 2004. Plasma RNA was used for PR-RT amplification by reverse transcription coupled with nested PCR and sequencing. Phylogenetic analysis was done with neighbor-joining trees and bootscanning. Analysis of drug resistance mutations, with Stanford University HIV Drug Resistance Database's algorithm, resulted in an overall prevalence of 12.9% resistance to RTI and 3.9% to PRI. The most frequent substitutions in the RT region were at positions 62 and 236. V77I substitution in PR was found in 47.8% of samples. Polymorphisms in subtype A sequences were identified. This is the first study reporting the prevalence and patterns of both PRI and RTI resistance-associated mutations in naïve HIV-1 infected patients from the former Soviet Union. These data underline the importance of genotypic resistance testing of chronically HIV-1-infected patients before initiating treatment, in order to select the most suitable drug regimen.
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42
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Lazouskaya NV, Eremin VF, Adema KW, Gasich EL, Baan E, Lukashov VV. The HIV type 1 epidemic in Belarus: predominance of Eastern European subtype A strains and circulation of subtype B viruses. AIDS Res Hum Retroviruses 2005; 21:830-3. [PMID: 16218809 DOI: 10.1089/aid.2005.21.830] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To study the molecular epidemiology of HIV-1 in Belarus, where the rapid spread of HIV-1 has been registered since 1996, we obtained HIV-1 sequences from 30 individuals living in five cities in both the main geographic areas of the epidemic (Gomel and Minsk regions) and territories where spreading of the epidemic remains limited (Grodno region). Analysis of env V3 and gag p17/p24 sequences demonstrated that infections in all 12 injecting drug users and 14 of 18 individuals infected through sexual contacts were caused by subtype A viruses that are specific for the epidemic in the former Soviet Union (IDU-A viruses), while the remaining four infections were caused by phylogenetically unrelated to each other subtype B viruses. Extrapolation of these results to the total population of HIV-1-infected individuals in Belarus allowed us to estimate that IDU-A viruses account for nearly 95% of HIV-1 infections in Belarus.
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Affiliation(s)
- Natallia V Lazouskaya
- Department of Clinical Virology, Institute for Epidemiology and Microbiology, 220114 Minsk, Belarus
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43
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Ksobiech K, Somlai AM, Kelly JA, Gore-Felton C, Benotsch E, McAuliffe T, Hackl K, Ostrovski D, Kozlov AP. Demographic characteristics, treatment history, drug risk behaviors, and condom use attitudes for U.S. and Russian injection drug users: the need for targeted sexual risk behavior interventions. AIDS Behav 2005; 9:111-20. [PMID: 15812618 DOI: 10.1007/s10461-005-1686-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 06/17/2004] [Accepted: 06/29/2004] [Indexed: 11/29/2022]
Abstract
Two separate databases, one on Russian (n = 444) injection drug users (IDUs), and the other on U.S. IDUs (n = 241), were merged, and responses were compared. Results indicated that Russian IDUs perceived themselves to be at greater risk for HIV/AIDS based upon behaviors over the past 90 days. U.S. IDUs were more likely to be tested for HIV, report a negative HIV result, and know more people with HIV. U.S. IDUs consumed greater amounts of alcohol and marijuana, and made more alcohol/drug treatment attempts than Russian IDUs. Russian IDUs injected more frequently, although were more likely to recently use clean needles. Russian and U.S. IDUs responded significantly differently to eight AIDS knowledge questions. Eight condom attitude questions were asked of each group, and each revealed significantly different responses. Gender differences for Russian IDUs were also observed. There is a clear need to create culturally targeted sexual risk reduction interventions.
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Affiliation(s)
- Kate Ksobiech
- Center for AIDS Intervention Research (CAIR), Department of Psychiatry and Behavioral Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53203-1918, USA.
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44
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Roudinskii NI, Sukhanova AL, Kazennova EV, Weber JN, Pokrovsky VV, Mikhailovich VM, Bobkov AF. Diversity of human immunodeficiency virus type 1 subtype A and CRF03_AB protease in Eastern Europe: selection of the V77I variant and its rapid spread in injecting drug user populations. J Virol 2004; 78:11276-87. [PMID: 15452247 PMCID: PMC521816 DOI: 10.1128/jvi.78.20.11276-11287.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To characterize polymorphisms of the subtype A protease in the former Soviet Union, proviral DNA samples were obtained, with informed consent, from 119 human immunodeficiency virus type 1 (HIV-1)-positive untreated injecting drug users (IDUs) from 16 regions. All individuals studied have never been treated with antiretroviral drugs. The isolates were defined as IDU-A (n = 115) and CRF03_AB (n = 4) by using gag/env HMA/sequencing. The pro region was analyzed by using sequencing and original HIV-ProteaseChip hybridization technology. The mean of pairwise nucleotide distance between 27 pro sequences (23 IDU-A and 4 CRF03_AB) was low (1.38 +/- 0.79; range, 0.00 to 3.23). All sequences contained no primary resistance mutations. However, 13 of 23 (56.5%) subtype A isolates bore the V77I substitution known as the secondary protease mutation. V77I was associated with two synonymous substitutions in triplets 31 and 78, suggesting that all V77I-bearing viruses evolved from a single source in 1997. Hybridization analysis showed that 55 of 115 (47.8%) HIV-1 isolates contained V77I, but this variant was not found in any of 31 DNA samples taken from regions, where the HIV-1 epidemic among IDUs started earlier 1997, as well as in any of four CRF03_AB isolates. The results of analysis of 12 additional samples derived from epidemiologically linked subjects showed that in all four epidemiological clusters the genotype of the donor and the recipients was the same irrespective of the route of transmission. This finding demonstrates the transmission of the V77I mutant variant, which is spreading rapidly within the circulating viral pool in Russia and Kazakhstan. The continued molecular epidemiological and virological monitoring of HIV-1 worldwide thus remains of great importance.
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Affiliation(s)
- Nikita I Roudinskii
- Laboratory of T-Lymphotropic Viruses, D. I. Ivanovsky Institute of Virology, 16 Gamaleya Street, Moscow 123098, Russia
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45
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Teixeira SLM, Bastos FI, Telles PR, Hacker MA, Brigido LF, de F Oliveira CA, Bongertz V, Morgado MG. HIV-1 infection among injection and ex-injection drug users from Rio de Janeiro, Brazil: prevalence, estimated incidence and genetic diversity. J Clin Virol 2004; 31:221-6. [PMID: 15465416 DOI: 10.1016/j.jcv.2004.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2004] [Indexed: 10/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Due to their behavioral conditions and vulnerability, injection drug users (IDUs) are prone to multiple simultaneous or sequential infections with distinct HIV-1 subtypes and variants, making them a key population for molecular epidemiology surveillance. In the present study, we evaluated HIV-1 infection seroprevalence, genetic diversity and estimated incidence among IDUs and ex-injection drug users (ex-IDUs) from Rio de Janeiro, Brazil. STUDY DESIGN Six hundred and eight IDUs and ex-IDUs, recruited between 1999 and 2001, were interviewed and agreed to donate 30 ml of blood. The serologic status for HIV infection was determined by two ELISAs and confirmed by IFA. CD4+ T-cell percentages were assessed by flow cytometry. HIV-1 positive samples were submitted to viral load quantification. DNA samples were PCR amplified and HIV-1 subtypes were determined using env and gag HMA. RESULTS AND CONCLUSIONS Forty-eight (7.89%) individuals were seropositive for HIV-1 infection. The seroincidence of HIV-1 infection was estimated as 0.76%. HIV-1 env and gag subtyping identified 29 (69%) samples as belonging to subtype B, 7 (16.7%) to subtype F, and 6 (14.3%) discordant env/gag genomes infections, indicating the circulation of recombinant viruses in this population.
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Affiliation(s)
- Sylvia Lopes Maia Teixeira
- Laboratory of AIDS and Molecular Immunology, Department of Immunology, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Leonidas Deane Building, Room #413, Rio de Janeiro 21045-900, Brazil
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46
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Bobkov AF, Kazennova EV, Selimova LM, Khanina TA, Ryabov GS, Bobkova MR, Sukhanova AL, Kravchenko AV, Ladnaya NN, Weber JN, Pokrovsky VV. Temporal trends in the HIV-1 epidemic in Russia: predominance of subtype A. J Med Virol 2004; 74:191-6. [PMID: 15332265 DOI: 10.1002/jmv.20177] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
During the period 1996-1997, three highly homogeneous variants of HIV-1 were identified, circulating among injecting drug users (IDUs) in the former Soviet Union republics. One of these belonged to HIV-1 genetic subtype A (IDU-A), another belonged to HIV-1 genetic subtype B (IDU-B) and the third was a recombinant between the first two variants (CRF03_AB). However, since 1997, the HIV-1 epidemic has affected an increasing number of geographic regions in Russia. This study was undertaken to survey the prevailing genetic variants and to estimate the current proportions of these three HIV-1 genetic subtypes in Russia. Blood samples were taken in 1999-2003 from 1090 HIV-infected individuals and analysed by gag/env HMA. The IDU-A variant was found to be the majority variant (89.7-100%) in 44 of 45 regions of the Russian Federation studied. The IDU-A variant was also found to spreading rapidly through heterosexual transmission in 1999-2003 (30/34, 88%). CRF03_AB predominates in the Kaliningrad region only (28/29, 96.6%). The IDU-B variant is currently of minor importance in the IDU epidemic but other European subtype B variants predominate among men having sex with men (18/18, 100%). Sequence analysis of the env V3 encoding regions derived from HIV-1 infected individuals in Yekaterinburg (the main centre of the HIV-1 epidemic in Russia in 2002-2003) showed that the IDU-A variant is still highly homogeneous. The mean pairwise nucleotide distance (n = 9) was 2.89 +/- 1.14 (range 1.36-6.14). However, the mean genetic distance between each sequence within the samples collected from the Yekaterinburg IDU-A variant subset and the IDU-A consensus is 2.51 +/- 1.06 (range 1.36-4.66) and considerably higher than in South Russia in 1996 (0.79 +/- 0.51, range 0.38-1.90). The current HIV-1 epidemic in Russia is almost entirely caused by a highly homogeneous A-subtype strain, which will influence vaccine development strategies and must be taken into account in the quality control of molecular tests for the diagnosis of HIV-1.
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47
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Bobkov AF, Kazennova EV, Sukhanova AL, Bobkova MR, Pokrovsky VV, Zeman VV, Kovtunenko NG, Erasilova IB. An HIV type 1 subtype A outbreak among injecting drug users in Kazakhstan. AIDS Res Hum Retroviruses 2004; 20:1134-6. [PMID: 15585106 DOI: 10.1089/aid.2004.20.1134] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Kazakhstan experienced the start of the HIV-1 outbreak among intravenous drug users (IDUs) in 1997. To characterize genetically HIV-1 strains circulating in this country, peripheral blood mononuclear cells (PBMCs) DNA samples (1999-2002) derived from HIV-infected IDUs and their sexual partners in Pavlodar (n = 19), Shymkent (n = 6), and Qaraghandy (n = 18) regions were analyzed by the gag/env heteroduplex mobility assay (HMA). The 366-bp proviral env gene fragments encoding the gp120 C2-V3 region obtained from 16 individuals were sequenced. The results of HMA revealed that all 43 HIV-1 strains studied belonged to gag/env subtype A. The nucleotide sequence analysis showed a marked genetic homogeneity with the mean genetic distance being 3.63 +/- 2.39 (range 0.00-12.13). The mean genetic distance between each sequence within the Kazakhstan set and the East-European IDU subtype A consensus was 2.94 +/- 1.92 (range 0.79-8.48). The data presented thus confirm the spreading of the same IDU subtype A virus in the former Soviet Union.
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48
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Balode D, Ferdats A, Dievberna I, Viksna L, Rozentale B, Kolupajeva T, Konicheva V, Leitner T. Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. AIDS Res Hum Retroviruses 2004; 20:245-9. [PMID: 15018713 DOI: 10.1089/088922204773004978] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the rapid HIV epidemic in Latvia, 97 newly detected individuals were sampled in 2000-2001. To establish the molecular epidemiology we sequenced the env V3 and gag p17 regions of the HIV genome and compared them with reference sequences using phylogenetic analyses. As expected, the vast majority (n = 88; 91%) were intravenous drug users (IDUs) from the Riga region. Also, the majority of the investigated individuals (n = 93; 96%) were found to carry a subtype A1 virus that may have entered the Latvian IDU population several times. In addition, one IDU was infected with CRF03_AB and three other individuals, who had been infected through sexual contacts, carried subtype B virus. Thus, subtype A1 dominates the Latvian epidemic and is strongly associated with the IDU risk group. Although some spread of subtype A1 has occurred in the heterosexual group, subtype B dominates among homosexually and heterosexually infected individuals.
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Affiliation(s)
- Dace Balode
- Department of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
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49
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Apetrei C, Descamps D, Collin G, Robertson DL, Pandrea I, Groza P, Prisecariu L, Teodorescu I, Luca V, Brun-Vézinet F. HIV type 1 diversity in northeastern Romania in 200-2001 based on phylogenic analysis of pol sequences from patient failing antiretroviral therapy. AIDS Res Hum Retroviruses 2003; 19:1155-1161. [PMID: 14714572 DOI: 10.1089/088922203771881266] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protease and the first half of reverse transcriptase from 71 Romanian patients failing highly active antiretroviral therapy (HAART) have been sequenced and phylogenetically analyzed. These analyses show that 70 patients were infected with subtype F1 and one with subtype C. The pattern of drug resistance mutations in subtype F1-infected patients failing HAART is similar to that described for subtype B strains. These results show that the diversity pattern of HIV type 1 infection in Romania has remained steady over a decade, with subtype F1 remaining the predominant viral form. The circulation of subtype F1 in Romania has the potential to be a source of this HIV-1 subtype in Europe..
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Affiliation(s)
- Cristian Apetrei
- Virology Laboratory, Pathology Laboratory and Infectious diseases Clinic, School of Medicine, Gr. T. Popa University of Iasi, Romania.
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50
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Rhodes T, Wargo H, Hu WS. High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication. J Virol 2003; 77:11193-200. [PMID: 14512567 PMCID: PMC224990 DOI: 10.1128/jvi.77.20.11193-11200.2003] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the genetic consequences of packaging two copies of full-length viral RNA into a single retroviral virion is frequent recombination during reverse transcription. Many of the currently circulating strains of human immunodeficiency virus type 1 (HIV-1) are recombinants. Recombination can also accelerate the generation of multidrug-resistant HIV-1 and therefore presents challenges to effective antiviral therapy. In this study, we determined that HIV-1 recombination rates with markers 1.0, 1.3, and 1.9 kb apart were 42.4, 50.4, and 47.4% in one round of viral replication. Because the predicted recombination rate of two unlinked markers is 50%, we conclude that markers 1 kb apart segregated in a manner similar to that for two unlinked markers in one round of retroviral replication. These recombination rates are exceedingly high even among retroviruses. Recombination rates of markers separated by 1 kb are 4 and 4.7% in one round of spleen necrosis virus and murine leukemia virus replication, respectively. Therefore, HIV-1 recombination can be 10-fold higher than that of other retroviruses. Recombination can be observed only in the proviruses derived from heterozygous virions that contain two genotypically different RNAs. The high rates of HIV-1 recombination observed in our studies also indicate that heterozygous virions are formed efficiently during HIV-1 replication and most HIV-1 virions are capable of undergoing recombination. Our results demonstrate that recombination is an effective mechanism to break the genetic linkage between neighboring sequences, thereby reassorting the HIV-1 genome and increasing the diversity in the viral population.
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Affiliation(s)
- Terence Rhodes
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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