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Wieczorek L, Chang D, Sanders-Buell E, Zemil M, Martinez E, Schoen J, Chenine AL, Molnar S, Barrows B, Poltavee K, Charurat ME, Abimiku A, Blattner W, Iroezindu M, Kokogho A, Michael NL, Crowell TA, Ake JA, Tovanabutra S, Polonis VR. Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG. Virol J 2024; 21:148. [PMID: 38951814 PMCID: PMC11218331 DOI: 10.1186/s12985-024-02394-y] [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: 02/23/2024] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.
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Affiliation(s)
- Lindsay Wieczorek
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - David Chang
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Office of AIDS Research, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Martinez
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Jesse Schoen
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Integrated Biotherapeutics, Rockville, MD, 20850, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Brittani Barrows
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Lentigen Technology, Gaithersburg, MD, 20878, USA
| | - Kultida Poltavee
- SEARCH, Insititute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alash'le Abimiku
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Blattner
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Afoke Kokogho
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Trevor A Crowell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA.
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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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Sivay MV, Totmenin AV, Zyryanova DP, Osipova IP, Nalimova TM, Gashnikova MP, Ivlev VV, Meshkov IO, Chokmorova UZ, Narmatova E, Motorov U, Akmatova Z, Asybalieva N, Bekbolotov AA, Kadyrbekov UK, Maksutov RA, Gashnikova NM. Characterization of HIV-1 Epidemic in Kyrgyzstan. Front Microbiol 2021; 12:753675. [PMID: 34721358 PMCID: PMC8554114 DOI: 10.3389/fmicb.2021.753675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Kyrgyzstan has one of the highest rates of HIV-1 spread in Central Asia. In this study, we used molecular–epidemiological approaches to examine the HIV-1 epidemic in Kyrgyzstan. Samples were obtained from HIV-positive individuals who visited HIV/AIDS clinics. Partial pol gene sequences were used to identify HIV-1 subtypes and drug resistance mutations (DRMs) and to perform phylogenetic analysis. Genetic diversity and history reconstruction of the major HIV-1 subtypes were explored using BEAST. This study includes an analysis of 555 HIV-positive individuals. The study population was equally represented by men and women aged 1–72 years. Heterosexual transmission was the most frequent, followed by nosocomial infection. Men were more likely to acquire HIV-1 during injection drug use and while getting clinical services, while women were more likely to be infected through sexual contacts (p < 0.01). Heterosexual transmission was the more prevalent among individuals 25–49 years old; individuals over 49 years old were more likely to be persons who inject drugs (PWID). The major HIV-1 variants were CRF02_AG, CRF63_02A, and sub-subtype A6. Major DRMs were detected in 26.9% of the study individuals; 62.2% of those had DRMs to at least two antiretroviral (ARV) drug classes. Phylogenetic analysis revealed a well-defined structure of CRF02_AG, indicating locally evolving sub-epidemics. The lack of well-defined phylogenetic structure was observed for sub-subtype A6. The estimated origin date of CRF02_AG was January 1997; CRF63_02A, April 2004; and A6, June 1995. A rapid evolutionary dynamic of CRF02_AG and A6 among Kyrgyz population since the mid-1990s was observed. We observed the high levels of HIV-1 genetic diversity and drug resistance in the study population. Complex patterns of HIV-1 phylogenetics in Kyrgyzstan were found. This study highlights the importance of molecular–epidemiological analysis for HIV-1 surveillance and treatment implementation to reduce new HIV-1 infections.
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Affiliation(s)
- Mariya V Sivay
- 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
| | - Daria P Zyryanova
- 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
| | - Tatyana M Nalimova
- 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
| | - Vladimir V Ivlev
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | | | - Umut Z Chokmorova
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Elmira Narmatova
- Osh Regional Center of AIDS Treatment and Prevention, Osh, Kyrgyzstan
| | - Ulukbek Motorov
- Osh Regional Center of AIDS Treatment and Prevention, Osh, Kyrgyzstan
| | - Zhyldyz Akmatova
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Nazgul Asybalieva
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Aybek A Bekbolotov
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Ulan K Kadyrbekov
- Republican Center of AIDS, Ministry of Health of Kyrgyzstan, Bishkek, Kyrgyzstan
| | - 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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4
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Maksimenko LV, Totmenin AV, Gashnikova MP, Astakhova EM, Skudarnov SE, Ostapova TS, Yaschenko SV, Meshkov IO, Bocharov EF, Maksyutov RА, Gashnikova NM. Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9057541. [PMID: 32964045 PMCID: PMC7501552 DOI: 10.1155/2020/9057541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/28/2019] [Indexed: 12/31/2022]
Abstract
More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75-85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.
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Affiliation(s)
- Lada V. Maksimenko
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Aleksey V. Totmenin
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Mariya P. Gashnikova
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | | | - Sergey E. Skudarnov
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Tatyana S. Ostapova
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Svetlana V. Yaschenko
- Krasnoyarsk Regional Center for Prevention and Control of AIDS, Krasnoyarsk 660049, Russia
| | - Ivan O. Meshkov
- Novosibirsk Tuberculosis Research Institute, Novosibirsk 630040, Russia
| | - Evgeniy F. Bocharov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
| | - Rinat А. Maksyutov
- State Research Center of Virology and Biotechnology Vector, Koltsovo 630559, Russia
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Kazennova EV, Antonova AA, Ozhmegova EN, Demyanenko ER, Minakova MV, Belousova OV, Gromov KB, Bobkova MR. GENETIC ANALYSIS OF HIV-1 IN THE ALTAI KRAY: THE FURTHER SPREAD OF THE CRF63_02A1 VARIANT IN WESTERN SIBERIA. ACTA ACUST UNITED AC 2020. [DOI: 10.22328/2077-9828-2020-12-1-47-57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
IThe aim of this study was to characterize HIV-1 genetic strains currently circulating in Altay Kray (Western Siberia) and to analyze the HIV resistance on this territory.Materials and methods. Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences of pol gene fragments coding protease and part of reverse transcriptase were obtained by in house system and Sanger sequencing. Genotyping, phylogenetic and recombinant analyses were carried out by HIVdbProgram: Sequence Analysis, COMET HIV-1, REGA HIV-1 Subtyping Tool (V 3.0), MEGA 5.05, RIP and jpHMM.Results and discussion. The results of genotype analysis revealed that the circulating recombinant form CRF63_02A1 dominated in Altay Kray (61%), subtype А was identified in 33%, the remaining subtypes, such as B, G, URF, accounted for 6%. According to phylogenetic analysis results, CRF63_02A1 sequences formed the common branch with nucleotide sequences of strains found in other regions of Siberia and Far East. All of HIV-1 variants belonging to subtype A clustered together with nucleotide sequences of A6 dominating in Russia. RIP analysis allowed to identify three unique recombinant forms (URFs), formed by CRF63_02A1 and A6. Drug resistance mutations were identified in 8 of 21 ART patients (8/21, 38%). The prevalence of drug resistance mutations in naïve patients equaled to 5,1%. Conclusion. Currently, the process of changing the dominant strain to CRF63_02A1 is ongoing in the Altai Kray, where 13 years ago the main variant was HIV sub-subtype A6 (IDU-A).
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Affiliation(s)
- E. V. Kazennova
- National Research Center оf Epidemiology and Microbiology named after honorary academician N. F. Gamalei
| | - A. A. Antonova
- National Research Center оf Epidemiology and Microbiology named after honorary academician N. F. Gamalei
| | - E. N. Ozhmegova
- National Research Center оf Epidemiology and Microbiology named after honorary academician N. F. Gamalei
| | - E. R. Demyanenko
- Altai regional center for prevention and control of AIDS and infectious diseases
| | - M. V. Minakova
- Altai regional center for prevention and control of AIDS and infectious diseases
| | - O. V. Belousova
- Altai regional center for prevention and control of AIDS and infectious diseases
| | - K. B. Gromov
- National Research Center оf Epidemiology and Microbiology named after honorary academician N. F. Gamalei
| | - M. R. Bobkova
- National Research Center оf Epidemiology and Microbiology named after honorary academician N. F. Gamalei
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Zyryanova DP, Totmenin AV, Bogacheva NV, Gashnikova NM. Construction and Characterization of Infectious Molecular Clones of HIV-1 CRF63_02A6. AIDS Res Hum Retroviruses 2020; 36:227-233. [PMID: 31482716 DOI: 10.1089/aid.2019.0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Currently, HIV-1 CRF63_02A6 is the prevalent genetic variant of the HIV-infected subjects in the major part of the Siberian Federal District (Russia). The HIV-1 CRF63_02A6 R5-tropic pT11.17 and X4-tropic pMtBs.18 infectious molecular clones (IMCs) were constructed using the virus isolates recovered in 2015 and 2017 of male HIV-infected Russian residents (from Tomsk and Novosibirsk, respectively). Near full-length proviral HIV-1 sequences (9,644 and 9,748 bp) were subcloned in pBluescript II KS(-). The CRF63_02A6 IMC virions were obtained by transfecting HEK293T cells with the constructed plasmids and demonstrated a stable growth in peripheral blood mononuclear cell culture (p24 concentration increased >1,000-fold and the virus protein accumulation in culture liquid exceeded 100,000 pg/mL). The tropism of CRF63_02A6 IMCs was determined genotypically (using Geno2pheno) and phenotypically by cultivating the IMC virions in MT-2, U87-CD4-CCR5, and U87-CD4-CXCR4 cell cultures. The obtained HIV-1 CRF63_02A6 IMCs may be useful in basic and applied research.
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Affiliation(s)
- Daria P Zyryanova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Alexei V Totmenin
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Natalia V Bogacheva
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - Natalya M Gashnikova
- Department of Retroviruses, State Research Center of Virology and Biotechnology "Vector", Koltsovo, Russia
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Neshumaev D, Lebedev A, Malysheva M, Boyko A, Skudarnov S, Ozhmegova E, Antonova A, Kazennova E, Bobkova M. Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography. Curr HIV Res 2020; 17:114-125. [PMID: 31210113 DOI: 10.2174/1570162x17666190618155816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/27/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions. OBJECTIVE The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region. METHODS The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods. RESULTS The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s. CONCLUSION This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.
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Affiliation(s)
- Dmitry Neshumaev
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Aleksey Lebedev
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Marina Malysheva
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Anatoly Boyko
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Sergey Skudarnov
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Anastasia Antonova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Elena Kazennova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Marina Bobkova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
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8
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Agapkina YY, Pustovarova MA, Korolev SP, Zyryanova DP, Ivlev VV, Totmenin AV, Gashnikova NM, Gottikh MB. Consensus Integrase of a New HIV-1 Genetic Variant CRF63_02A1. Acta Naturae 2019; 11:14-22. [PMID: 31024744 PMCID: PMC6475865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
The high genetic variability of the human immunodeficiency virus (HIV-1) leads to a constant emergence of new genetic variants, including the recombinant virus CRF63_02A1, which is widespread in the Siberian Federal District of Russia. We studied HIV-1 CRF63_02A1 integrase (IN_CRF) catalyzing the incorporation of viral DNA into the genome of an infected cell. The consensus sequence was designed, recombinant integrase was obtained, and its DNA-binding and catalytic activities were characterized. The stability of the IN_CRF complex with the DNA substrate did not differ from the complex stability for subtype A and B integrases; however, the rate of complex formation was significantly higher. The rates and efficiencies of 3'-processing and strand transfer reactions catalyzed by IN_CRF were found to be higher, too. Apparently, all these distinctive features of IN_CRF may result from specific amino acid substitutions in its N-terminal domain, which plays an important role in enzyme multimerization and binding to the DNA substrate. It was also found that the drug resistance mutations Q148K/G140S and G118R/E138K significantly reduce the catalytic activity of IN_CRF and its sensitivity to the strand transfer inhibitor raltegravir. Reduction in sensitivity to raltegravir was found to be much stronger in the case of double-mutation Q148K/G140S.
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Affiliation(s)
- Y. Y. Agapkina
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - M. A. Pustovarova
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - S. P. Korolev
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
| | - D. P. Zyryanova
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - V. V. Ivlev
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - A. V. Totmenin
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - N. M. Gashnikova
- State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Russia
| | - M. B. Gottikh
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical Chemical Biology, Leninskie gory 1/40, 119991, Moscow, Russia
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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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Kostaki EG, Karamitros T, Bobkova M, Oikonomopoulou M, Magiorkinis G, Garcia F, Hatzakis A, Paraskevis D. Spatiotemporal Characteristics of the HIV-1 CRF02_AG/CRF63_02A1 Epidemic in Russia and Central Asia. AIDS Res Hum Retroviruses 2018; 34:415-420. [PMID: 29455562 DOI: 10.1089/aid.2017.0233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eastern European countries, including Russia, Ukraine, and other former Soviet Union (FSU) countries, have experienced a human immunodeficiency virus (HIV) epidemic spreading mostly among people who inject drugs (PWID). We aimed to investigate the origin and the dispersal patterns of HIV-1 CRF02_AG in Russia and other FSU countries. We studied 136 CRF02_AG sequences originating from Russia, and FSU countries along with a globally sampled dataset of 3,580 CRF02_AG sequences. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation was conducted in RAxML. Bayesian phylogeographic analysis was performed in BEAST v1.8 using the discrete trait model. We found that all CRF02_AG sequences from Russia and other FSU countries formed a single monophyletic cluster within CRF02_AG radiation. The Russian/FSU clade was classified as CRF63_02A1. Sequences from the FSU countries clustered further within distinct subclades (two from Russia, three from Uzbekistan, and one Kazakhstan) according to the geographic origin of sampling. Molecular clock analysis revealed that the time to the most recent common ancestor (tMRCA) of the CRF63_02A1 epidemic was in 1996 [95% higher posterior density (95% HPD): 1992-1999], while for the two Russian subclades, tMRCA was estimated in 2003 (95% HPD: 2001-2004) and in 2007 (95% HPD: 2005-2008). Phylogeographic analysis suggested that the potential origin of the epidemic was in Uzbekistan. Early dispersal of CRF63_02A1 occurred in Kazakhstan and Uzbekistan and thereafter the epidemic spread to Russia. Notably, spillover transmissions to Russia kept occurring from both countries. Previous studies have shown that Russia and Ukraine have provided the source for the PWID-driven, HIV-1 subtype-A epidemic, spreading across the FSU countries (AFSU). In great contrast, CRF63_02A1 established an epidemic in central Asia (Uzbekistan and Kazakhstan), from where it subsequently disseminated to Russia. Our study suggests that cross-border transmissions among PWID occur bidirectionally between Russian and other FSU populations. These results are of public health importance and suggest that prevention actions have to be reinforced in this area to assist the management of high-risk practices.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | | | - Marina Bobkova
- 3 Ivanovsky Institute of Virology , FSBI "N.F. Gamaleya FRCEM" of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Martha Oikonomopoulou
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Gkikas Magiorkinis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
- 2 Department of Zoology, University of Oxford , Oxford, United Kingdom
| | - Federico Garcia
- 4 Servicio de Microbiología, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada, Cohorte de Adultos de la Red de Investigación en SIDA-CoRIS, Instituto de Investigación Ibs , Granada, Granada (Andalucía), Spain
| | - Angelos Hatzakis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Dimitrios Paraskevis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
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11
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Lapovok IA, Lopatukhin AE, Kireev DE, Kazennova EV, Lebedev AV, Bobkova MR, Kolomeets AN, Turbina GI, Shipulin GA, Ladnaya NN, Pokrovsky VV. [Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015]. TERAPEVT ARKH 2018; 89:44-49. [PMID: 29260745 DOI: 10.17116/terarkh2017891144-49] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. SUBJECTS AND METHODS The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. RESULTS The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. CONCLUSION The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.
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Affiliation(s)
- I A Lapovok
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - A E Lopatukhin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - D E Kireev
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - E V Kazennova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A V Lebedev
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A N Kolomeets
- Omsk Research Institute of Natural Focal Infections, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G I Turbina
- Lipetsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Lipetsk, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - N N Ladnaya
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V V Pokrovsky
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
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12
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HIV-1 Epidemiology, Genetic Diversity, and Primary Drug Resistance in the Tyumen Oblast, Russia. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2496280. [PMID: 27957489 PMCID: PMC5124469 DOI: 10.1155/2016/2496280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023]
Abstract
Introduction. Specific molecular epidemic features of HIV infection in Tyumen Oblast (TO), Russia, were studied. Methods. The genome sequences encoding HIV-1 protease-reverse transcriptase, integrase, and major envelope protein were examined for 72 HIV-1 specimens isolated from the TO resident infected in 2000-2015. Results. The recorded prevalence of HIV-1 subtype A (A1) is 93.1%; HIV-1 subtype B continues to circulate in MSM risk group (1.4%). Solitary instances of HIV-1 recombinant forms, CRF63_02A1 (1.4%) and CRF03_AB (1.4%), were detected as well as two cases of HIV-1 URF63_A1 (2.8%). Phylogenetic analysis showed no HIV-1 clustering according to the duration of infection and risk groups but revealed different epidemic networks confirming that HIV infection spread within local epidemic foci. A high incidence of CXCR4-tropic HIV-1 variants and a higher rate of secondary mutations influencing the virus fitness (K20R, L10V, and I) are observed among the virus specimens isolated from newly infected individuals. Conclusions. The current HIV-1 epidemic in TO develops within the local epidemic networks. Similar to the previous period, HIV-1 subtype A is predominant in TO with sporadic cases of importation of HIV-1 recombinant forms circulating in adjacent areas.
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Predominance of CRF63_02A1 and multiple patterns of unique recombinant forms of CRF63_A1 among individuals with newly diagnosed HIV-1 infection in Kemerovo Oblast, Russia. Arch Virol 2016; 162:379-390. [PMID: 27761744 DOI: 10.1007/s00705-016-3120-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/18/2022]
Abstract
Kemerovo Oblast (KO) has had the highest rate of HIV spread in Russia since 2011. The aim of this work was to study the genetic variation of HIV-1 in Kemerovo Oblast. Blood was sampled from a total of 91 HIV-positive antiretroviral-therapy-naïve individuals in 2013 (38) and 2015 (53). HIV-1 subtypes, pol gene drug resistance mutations, and viral tropism were analyzed. In 2013-2015, the prevalence of HIV-1 subtype A decreased in KO from 60.5 to 7.5 %. The samples collected in 2015 from the patients with newly diagnosed HIV demonstrate the current dominance of HIV-1 CRF63_02A1 (71.7 %) and HIV-1 URF63_A1 (20.8 %), their parental viruses being CRF63_02A1 and subtype A. The initially predominant genetic variant, HIV-1 subtype A, was replaced in KO. An unusually high incidence of HIV-1 unique recombinant forms is probably the result of HIV-1 CRF63_02A1 introduction in the group of injection drug users with the initial HIV-1 subtype A infection and the practice of risky behavior that promotes reinfection. HIV-1 CRF63_02A1, which recently emerged in Siberia, and its recombinant forms have an ever-increasing impact on the current HIV epidemic in Russia, making urgent the need for in-depth study of this HIV-1 genetic variant.
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Jackson PE, Tebit DM, Rekosh D, Hammarskjold ML. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates. AIDS Res Hum Retroviruses 2016; 32:923-34. [PMID: 27147495 DOI: 10.1089/aid.2016.0047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 replication cycle requires the nucleocytoplasmic export of intron-containing viral RNAs, a process that is ordinarily restricted. HIV overcomes this by means of the viral Rev protein, which binds to an RNA secondary structure called the Rev response element (RRE) present in all unspliced or incompletely spliced viral RNA transcripts. The resulting mRNP complex is exported through interaction with cellular factors. The Rev-RRE binding interaction is increasingly understood to display remarkable structural plasticity, but little is known about how Rev-RRE sequence differences affect functional activity. To study this issue, we utilized a lentiviral vector assay in which vector titer is dependent on the activity of selected Rev-RRE pairs. We found that Rev-RRE functional activity varies significantly (up to 24-fold) between naturally occurring viral isolates. The activity differences of the Rev-RRE cognate pairs track closely with Rev, but not with RRE activity. This variation in Rev activity is not correlated with differences in Rev steady state protein levels. These data suggest that Rev sequence differences drive substantial variation in Rev-RRE functional activity between patients. Such variation may play a role in viral adaptation to different immune milieus within and between patients and may be significant in the establishment of latency. The identification of differences in Rev-RRE functional activity in naturally occurring isolates may also permit more efficient production of lentiviral vectors.
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Affiliation(s)
- Patrick E. Jackson
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Denis M. Tebit
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - David Rekosh
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Mir D, Jung M, Delatorre E, Vidal N, Peeters M, Bello G. Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global dissemination. INFECTION GENETICS AND EVOLUTION 2016; 46:190-199. [PMID: 27180893 DOI: 10.1016/j.meegid.2016.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/09/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022]
Abstract
The HIV-1 CRF02_AG clade is the most prevalent HIV variant in West and West-Central Africa and its detection outside Africa is increasingly common. Little is known, however, about the number and phylodynamics of major CRF02_AG lineages circulating worldwide. To this end, a total of 3170 HIV-1 CRF02_AG-like pol sequences isolated around the world, over a period of 25years (1989 to 2013), were analyzed using Maximum Likelihood and Bayesian coalescent-based methods. Our results suggest that most of the current CRF02_AG diversity comes from the dissemination of a few founder strains out of Central Africa into West Africa and Cameroon between the late 1960s and the middle 1980s. The CRF02_AG strain introduced into West Africa established a large regional epidemic with low phylogeographic structure. This strain was also successfully disseminated out of the West African region and originated at least three large secondary outbreaks in Cameroon at around the late 1970s, in the former Soviet Union (FSU) countries at around the late 1990s, and in Bulgaria/Germany at around the early 2000s. The CRF02_AG African lineages introduced into Cameroon remained mostly restricted to this country and its neighbors. Demographic reconstructions indicate that major CRF02_AG clades circulating in Africa exhibited a decline in growth rate since the middle 1980s/1990s, whereas CRF02_AG clades in Europe and the FSU countries continue to grow exponentially until the middle to late 2000s. Substantial differences in the median estimated growth rate of the same CRF02_AG clade circulating in different regions (0.63-2.00year-1), and of different CRF02_AG clades circulating in the same country (0.41-0.75year-1) were observed. Thus, the cause of the epidemic outcome of the different HIV-1 CRF02_AG lineages is probably multifactorial.
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Affiliation(s)
- Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Matthieu Jung
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicole Vidal
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
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Gashnikova NM, Bogachev VV, Baryshev PB, Totmenin AV, Gashnikova MP, Kazachinskaya AG, Ismailova TN, Stepanova SA, Chernov AS, Mikheev VN. A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia. AIDS Res Hum Retroviruses 2015; 31:456-60. [PMID: 25738513 DOI: 10.1089/aid.2014.0375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of HIV infection in different Russian regions is nonuniform. In the Tomsk region (TR), 2020 HIV new infection cases were recorded in 2013, the morbidity having increased 5.9-fold as compared to 2012. In total, 64 blood plasma samples from primary HIV cases have been examined. HIV-specific fragments of the pol gene have been obtained for 61 samples (of protease for 58 and of integrase for 23) and of the env gene V3 region for 40 samples. Phylogenetic analysis of the determined HIV-1 sequences has detected CRF63_02A1 in 55 (90.2%) cases, whereas HIV subtype A1, characteristic of Russia, has been observed in only three (4.9%) patients. Three (4.9%) cases contain CRF63_02A1/A recombinant variants. This article demonstrates that a drastic activation of the epidemic in the Tomsk region is accompanied by a rapid spreading of the recently described HIV-1 CRF63_02A1, which we detected in the Novosibirsk region outbreak of 2008.
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Affiliation(s)
- Natalya M Gashnikova
- 1 Department of Retroviruses, State Research Center of Virology and Biotechnology Vector , Koltsovo, Russia
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A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS 2014; 28:F1-8. [PMID: 25259833 DOI: 10.1097/qad.0000000000000485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The subtype A variant in the Former Soviet Union (A(FSU)) causes most of Russia's HIV-1 infections. However, the spectrum of drug-resistance mutations (DRMs) in antiretroviral experienced patients with this variant has not been studied. METHODS Between 2010 and 2013, genotypic resistance testing was performed on plasma samples from 366 antiretroviral-experienced patients in Siberia. RESULTS Three-hundred patients (82%) had subtype A(FSU) and 55 (15%) had CRF02_AG viruses. The pattern of DRMs was consistent with patient antiretroviral history with one exception. G190S was the most common nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, occurring in 55 (33%) subtype A(FSU) viruses from 167 NNRTI-experienced patients compared with none of 37 CRF02_AG viruses from NNRTI-experienced patients (P < 0.001). The next most common subtype A(FSU) NNRTI-resistance mutation, K103N, occurred in 25 (15%) viruses. Wild-type glycine (G) at position 190 is encoded by GGC in more than 99% of published A(FSU) strains. By contrast, G190 is encoded by GGA or GGG in 97% of other subtypes and in subtype A strains outside of the FSU. Therefore, G190S results from a single G→A transition: G (GGC) → S (AGC) almost exclusively in subtype A(FSU) viruses. CONCLUSION The predisposition of subtype A(FSU) to G190S is concerning because G→A is the most common HIV-1 mutation and because G190S causes higher levels of nevirapine and efavirenz resistance than K103N. This study exemplifies the need for characterizing the genetic mechanisms of resistance in diverse populations and warrants studies to verify that NRTI/NNRTI regimens are as efficacious in treating subtype A(FSU) as viruses belonging to other subtypes.
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Shcherbakova NS, Shalamova LA, Delgado E, Fernández-García A, Vega Y, Karpenko LI, Ilyichev AA, Sokolov YV, Shcherbakov DN, Pérez-Álvarez L, Thomson MM. Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:912-9. [PMID: 25050828 DOI: 10.1089/aid.2014.0075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.
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Affiliation(s)
- Nadezhda S. Shcherbakova
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Lyudmila A. Shalamova
- Department of Zoonotic Infections and Influenza, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Larissa I. Karpenko
- Laboratory of Recombinant Vaccine, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Alexander A. Ilyichev
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Yuri V. Sokolov
- Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk, Russia
| | | | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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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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Baryshev PB, Bogachev VV, Gashnikova NM. HIV-1 genetic diversity in Russia: CRF63_02A1, a new HIV type 1 genetic variant spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:592-7. [PMID: 24279614 DOI: 10.1089/aid.2013.0196] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the factors determining a high degree of heterogeneity in the HIV population is recombination-based variation, which leads to the emergence of the virus variants with a mosaic genome. An example is CRF63_02A1, an HIV-1 variant currently spreading in the Siberian region of Russia. To prove that this HIV-1 variant is a new circulating recombinant form that had emerged as a result of repeated recombination between CRF02_AG and subtype A, we have isolated seven full-length HIV genomes and theoretically analyzed them, that is, reconstructed the phylogenetic relationships, determined recombination breakpoints and regions, and compared them with the regions known for CRF02_AG.
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Affiliation(s)
- Pavel B. Baryshev
- State Research Center of Virology and Biotechnology Vector, Novosibirsk, Russia
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