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Piterskiy MV, Gusev AG, Khodakov OA, Zakharova YA, Semenov AV. HIV-1 subtype diversity, phylogenetic analysis and study of drug resistance in strains circulating in the Ural Federal District. JOURNAL OF MICROBIOLOGY, EPIDEMIOLOGY AND IMMUNOBIOLOGY 2022. [DOI: 10.36233/0372-9311-178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction. Ural Federal District (UFD) has been one of the most HIV-affected areas in the Russian Federation during past 20 years. The total number of people living with HIV/AIDS (PLWH) and receiving antiretroviral therapy (ART) exceeds 100,000 (61.7% of all PLWH in the UFD), which creates opportunities for the wide spread of resistant HIV strains.Research aim was to determine the distribution of HIV-1 subtypes, evaluate the genetic heterogeneity of HIV-1 strains, and analyze the prevalence of HIV-1 drug resistance mutations (DRM) and the incidence of acquired resistance to antiretroviral drugs (ARVDs) in PLWH receiving ART in the UFD.Materials and methods. 223 patients receiving ART at stage III–IV of HIV infection living in the UFD were examined. To determine the subtypes and the DRM in the HIV-1 pol gene, molecular genetic studies were performed using the AmpliSense® HIV-Resist-Seq kit by Sanger sequencing on the Applied Biosystems 3500 Genetic Analyzer. The genetic heterogeneity was evaluated by calculating the identity of the genome region of the isolated strains in comparison with the genomes of foreign HIV strains, as well as using phylogenetic analysis.Results. In the studied group of patients, 5 subtypes of HIV-1 were identified: subtype A6 prevalence was 91.03%, that of subtype B was 2.69%, 3 recombinant subtypes (CRF03_A6B, CRF02_AG, CRF63_02A6) accounted for 6.28%. Among analyzed HIV-1 strains, 43.9% had a significant genetic similarity (identity of at least 97%) with the strains isolated from patients from neighboring countries (Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Lithuania), 35.9% were similar to the strains isolated from patients from far-abroad countries (USA, China, South Korea, Australia, Sweden, Germany). A high heterogeneity of the circulating genetic variants of HIV-1 strains in the territory of the UFD region was established, which is an unfavorable factor for the diagnosis and treatment of HIV. The most common DRMs to both nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) were detected in 81 specimens (36.3%). NRTI resistance-forming M184V DRM was more common than any other DRM with statistical significance (p = 0,0008) and was detected in 88 specimens (39.5%).Conclusion. In the subtype structure of HIV-1, the dominant subtype was subtype A6, the most common in the countries that were formerly part of the USSR. The heterogeneity of the HIV-1 strains circulating in the UFD suggests that HIV-1 infection continues to be introduced into the UFD from populations outside the Russian Federation. The findings confirm the high prevalence of DRMs (62.8%) and secondary drug resistance of HIV-1 (60.1%) among PLWH in the territory of the UFD. At the same time, high-level resistance was detected in 56.5% of patients, which requires increasing the coverage of HIV resistance testing, including the introduction of monitoring for primary resistance, in order to optimize first-line ART regimens.
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Toll-like receptor 7-adapter complex modulates interferon-α production in HIV-stimulated plasmacytoid dendritic cells. PLoS One 2019; 14:e0225806. [PMID: 31830058 PMCID: PMC6907767 DOI: 10.1371/journal.pone.0225806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Plasmacytoid dendritic cells (PDCs) and their production of interferon-alpha (IFN-α) are believed to play an important role in human immunodeficiency virus, type I (HIV-1) pathogenesis. PDCs produce IFN-α and other proinflammatory cytokines through stimulation of Toll-like receptor 7 (TLR7) and TLR9 present in endosomal compartments. TLR7 recognizes single-stranded viral RNA, while TLR9 recognizes unmethylated DNA. In this study, we examined the mechanisms that may underlie variations in IFN-α production in response to HIV, and the impact of these variations on HIV pathogenesis. In four distinct cohorts, we examined PDC production of IFN-α upon stimulation with inactivated HIV-1 particles and unmethylated DNA. The signaling cascade of TLR7 bifurcates at the myeloid differentiation protein 88 (MyD88) adaptor protein to induce expression of either IFN-α or TNF-α. To determine whether variations in IFN-α production are modulated at the level of the receptor complex or downstream of it, we correlated production of IFN-α and TNF-α following stimulation of TLR7 or TLR9 receptors. Flow cytometry detection of intracellular cytokines showed strong, direct correlations between IFN-α and TNF-α expression in all four cohorts, suggesting that variations in IFN-α production are not due to variations downstream of the receptor complex. We then investigated the events upstream of TLR binding by using lipid-like vesicles to deliver TLR ligands directly to the TLR receptors, bypassing the need for CD4 binding and endocytosis. Similar tight correlations were found in IFN-α and TNF-α production in response to the TLR ligands. Taken together, these results strongly suggest that differences in IFN-α production depend on the regulatory processes at the level of the TLR7 receptor complex. Additionally, we found no association between IFN-α production before HIV infection and disease progression.
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Paraskevis D, Beloukas A, Stasinos K, Pantazis N, de Mendoza C, Bannert N, Meyer L, Zangerle R, Gill J, Prins M, d'Arminio Montforte A, Kran AMB, Porter K, Touloumi G. HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors. BMC Med 2019; 17:4. [PMID: 30616632 PMCID: PMC6323837 DOI: 10.1186/s12916-018-1241-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 12/14/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to identify MTCs and investigate factors associated with the probability of belonging to MTCs. METHODS To identify MTCs, we applied maximum likelihood inferences on partial pol sequences from 8955 HIV-positive individuals linked to demographic and clinical data. MTCs were defined using two different criteria: clusters with bootstrap support >75% (phylogenetic confidence criterion) and clusters consisting of sequences from a specific region at a proportion of >75% (geographic criterion) compared to the total number of sequences within the network. Multivariable logistic regression analysis was used to assess factors associated with MTC clustering. RESULTS Although 3700 (41%) sequences belonged to MTCs, proportions differed substantially by country and subtype, ranging from 7% among UK subtype C sequences to 63% among German subtype B sequences. The probability of belonging to an MTC was independently less likely for women than men (OR = 0.66; P < 0.001), older individuals (OR = 0.79 per 10-year increase in age; P < 0.001) and people of non-white ethnicity (OR = 0.44; P < 0.001 and OR = 0.70; P = 0.002 for black and 'other' versus white, respectively). It was also more likely among men who have sex with men (MSM) than other risk groups (OR = 0.62; P < 0.001 and OR = 0.69; P = 0.002 for people who inject drugs, and sex between men and women, respectively), subtype B (ORs 0.36-0.70 for A, C, CRF01 and CRF02 versus B; all P < 0.05), having a well-estimated date of seroconversion (OR = 1.44; P < 0.001), a later calendar year of sampling (ORs 2.01-2.61 for all post-2002 periods versus pre-2002; all P < 0.01), and being naïve to antiretroviral therapy at sampling (OR = 1.19; P = 0.010). CONCLUSIONS A high proportion (>40%) of individuals belonged to MTCs. Notably, the HIV epidemic dispersal appears to be driven by subtype B viruses spread within MSM networks. Expansion of regional epidemics seems mainly associated with recent MTCs, rather than the growth of older, established ones. This information is important for designing prevention and public health intervention strategies.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece.
| | - Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece.
- Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK.
- Department of Biomedical Sciences, School of Health Sciences, University of West Attica, Agiou Spiridonos Str (Campus 1), 12243, Athens, Greece.
| | - Kostantinos Stasinos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
| | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
| | - Carmen de Mendoza
- Department of Internal Medicine, Puerta de Hierro Research Institute and University Hospital, Alle Manuel de Falla, 1, 28222, Madrid, Majadahonda, Spain
| | | | - Laurence Meyer
- Inserm, CESP U1018, Univ Paris-Sud, Department of Epidemiology and Population Health, APHP, Hôpital Bicêtre, 78 Rue du Général Leclerc, 94270, Le Kremlin-Bicêtre, France
| | - Robert Zangerle
- Department of Dermatology and Venerology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - John Gill
- Department of Microbiology, Immunology and Infectious Diseases (MIID), University of Calgary, 269 Heritage Medical Research Building, 24 Ave NW, Calgary, Alberta, Canada
| | - Maria Prins
- Academic Medical Center, University of Amsterdam, Netherlands and Department of Infectious Diseases, Amsterdam Infection and Immunity Institute, Spui 21, 1012 WX, Amsterdam, Netherlands
| | | | - Anne-Marte Bakken Kran
- Department of Microbiology, Oslo University Hospital, OUS HF Rikshospitalet, Postboks 4950 Nydalen, 0424, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Sognsvannsveien 20, Rikshospitalet, 0372, Oslo, Norway
| | - Kholoud Porter
- University College London Institute for Global Health, Institute of Child Health, 3rd floor, 30 Guilford Street, London, WC1N 1EH, UK
| | - Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
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Klaver B, van der Velden Y, van Hemert F, van der Kuyl AC, Berkhout B. HIV-1 tolerates changes in A-count in a small segment of the pol gene. Retrovirology 2017; 14:43. [PMID: 28870251 PMCID: PMC5583962 DOI: 10.1186/s12977-017-0367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. Results To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV–SIV sequence space. Conclusions Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.
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Affiliation(s)
- Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Yme van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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Abstract
Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.
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van der Kuyl AC, Bakker M, Jurriaans S, Back NKT, Pasternak AO, Cornelissen M, Berkhout B. Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013. Retrovirology 2013; 10:93. [PMID: 23985078 PMCID: PMC3765835 DOI: 10.1186/1742-4690-10-93] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023] Open
Abstract
An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands.
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van der Knaap N, Grady BPX, Schim van der Loeff MF, Heijman T, Speksnijder A, Geskus R, Prins M. Drug users in Amsterdam: are they still at risk for HIV? PLoS One 2013; 8:e59125. [PMID: 23527107 PMCID: PMC3601054 DOI: 10.1371/journal.pone.0059125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/11/2013] [Indexed: 11/19/2022] Open
Abstract
Background and Aims To examine whether drug users (DU) in the Amsterdam Cohort Study (ACS) are still at risk for HIV, we studied trends in HIV incidence and injecting and sexual risk behaviour from 1986 to 2011. Methods The ACS is an open, prospective cohort study on HIV. Calendar time trends in HIV incidence were modelled using Poisson regression. Trends in risk behaviour were modelled via generalized estimating equations. In 2010, a screening for STI (chlamydia, gonorrhoea and syphilis) was performed. Determinants of unprotected sex were studied using logistic regression analysis. Results The HIV incidence among 1298 participants of the ACS with a total follow-up of 12,921 person-years (PY) declined from 6.0/100 PY (95% confidence interval [CI] 3.2–11.1) in 1986 to less than 1/100 PY from 1997 onwards. Both injection and sexual risk behaviour declined significantly over time. Out of 197 participants screened for STI in 2010–2011, median age 49 years (IQR 43–59), only 5 (2.5%) were diagnosed with an STI. In multivariable analysis, having a steady partner (aOR 4.1, 95% CI 1.6–10.5) was associated with unprotected sex. HIV-infected participants were less likely to report unprotected sex (aOR 0.07, 95% CI 0.02–0.37). Conclusions HIV incidence and injection risk behaviour declined from 1986 onwards. STI prevalence is low; unprotected sex is associated with steady partners and is less common among HIV-infected participants. These findings indicate a low transmission risk of HIV and STI, which suggests that DU do not play a significant role in the current spread of HIV in Amsterdam.
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Affiliation(s)
- Nienke van der Knaap
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- University of Amsterdam (UvA), Amsterdam, The Netherlands
| | - Bart P. X. Grady
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
- * E-mail:
| | - Maarten F. Schim van der Loeff
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Titia Heijman
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Arjen Speksnijder
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Laboratory of Public Health, Public Health Service, Amsterdam, The Netherlands
| | - Ronald Geskus
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Maria Prins
- Cluster of Infectious Diseases, Public Health Service, Amsterdam, The Netherlands
- Center of Infectious diseases and Immunology Amsterdam (CINIMA), Department of Internal Medicine, Academic Medical Center (AMC), Amsterdam, The Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Academic Medical Center, Amsterdam, The Netherlands
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