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Schlösser M, Kartashev VV, Mikkola VH, Shemshura A, Saukhat S, Kolpakov D, Suladze A, Tverdokhlebova T, Hutt K, Heger E, Knops E, Böhm M, Di Cristanziano V, Kaiser R, Sönnerborg A, Zazzi M, Bobkova M, Sierra S. HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia. Viruses 2020; 12:v12040475. [PMID: 32331438 PMCID: PMC7232409 DOI: 10.3390/v12040475] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 01/08/2023] Open
Abstract
Russia has one of the largest and fastest growing HIV epidemics. However, epidemiological data are scarce. Sub-subtype A6 is most prevalent in Russia but its identification is challenging. We analysed protease/reverse transcriptase-, integrase-sequences, and epidemiological data from 303 patients to develop a methodology for the systematisation of A6 identification and to describe the HIV epidemiology in the Russian Southern Federal District. Drug consumption (32.0%) and heterosexual contact (27.1%) were the major reported transmission risks. This study successfully established the settings for systematic identification of A6 samples. Low frequency of subtype B (3.3%) and large prevalence of sub-subtype A6 (69.6%) and subtype G (23.4%) were detected. Transmitted PI- (8.8%) and NRTI-resistance (6.4%) were detected in therapy-naive patients. In therapy-experienced patients, 17.3% of the isolates showed resistance to PIs, 50.0% to NRTI, 39.2% to NNRTIs, and 9.5% to INSTIs. Multiresistance was identified in 52 isolates, 40 corresponding to two-class resistance and seven to three-class resistance. Two resistance-associated-mutations significantly associated to sub-subtype A6 samples: A62VRT and G190SRT. This study establishes the conditions for a systematic annotation of sub-subtype A6 to normalise epidemiological studies. Accurate knowledge on South Russian epidemiology will allow for the development of efficient regional frameworks for HIV-1 infection management.
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Affiliation(s)
- Madita Schlösser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Vladimir V. Kartashev
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Visa H. Mikkola
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia;
| | - Sergey Saukhat
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
| | - Dmitriy Kolpakov
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Alexandr Suladze
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Tatiana Tverdokhlebova
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Katharina Hutt
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Michael Böhm
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy;
| | - Marina Bobkova
- Department of General Virology, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Saleta Sierra
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
- Correspondence: ; Tel.: +49-221-4788-5807
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Matsuda M, Louvel S, Sugiura W, Haas A, Pfeifer N, Yokomaku Y, Iwatani Y, Kaiser R, Klimkait T. Performance Evaluation of a Genotypic Tropism Test Using HIV-1 CRF01_AE Isolates in Japan. Jpn J Infect Dis 2018; 71:264-266. [PMID: 29709982 DOI: 10.7883/yoken.jjid.2017.482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Geno2Pheno (coreceptor), a genotypic tropism test, demonstrates excellent agreement with the phenotypic tropism test for subtype B and some other subtypes. However, potential X4-overcalling for CRF01_AE might occur with the present version. To confirm X4 overcalling for AE and to optimize the algorithm for use with AE, we compared the tropism of 22 AE samples by both genotypic and phenotypic methods. The env V3 region was analyzed by bulk sequencing, and tropism was evaluated using the Geno2Pheno algorithm. PhenXR, a phenotypic tropism test, was performed in parallel to determine chemokine receptor preferences. A high X4-overcalling for select samples and a low rate of R5-concordant samples (9.1%) were observed for AE with the current version of Geno2Pheno (coreceptor). On the other hand, the new version, namely, Geno2Pheno (Sanger), showed a high concordance rate of 81.8%, with PhenXR. Because majority of the samples were selected based on discrepancies in the genotypic tropism calls between the present version Geno2Pheno (coreceptor) (FPR<10%) and the new version Geno2Pheno (Sanger) (X4-risk<36), it remains to be determined whether the new version provides improved R5-calls for the AE sequences in general or only in this setting. Further clinical validation studies are warranted.
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Affiliation(s)
- Masakazu Matsuda
- Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center
| | | | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center
| | - Alexandra Haas
- Molecular Virology, Department Biomedicine - Petersplatz, University of Basel
| | - Nico Pfeifer
- Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center
| | - Rolf Kaiser
- Institute of Virology, University of Cologne
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine - Petersplatz, University of Basel
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Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents. PLoS One 2016; 11:e0155869. [PMID: 27196673 PMCID: PMC4873220 DOI: 10.1371/journal.pone.0155869] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/05/2016] [Indexed: 12/18/2022] Open
Abstract
The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV]) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic cell culture assays obtained from patients’ virus variants.
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Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R. Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS One 2015; 10:e0125502. [PMID: 25970632 PMCID: PMC4430318 DOI: 10.1371/journal.pone.0125502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/18/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES We analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment. METHODS 87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in triplicate, 43 samples with the ESTA assay and 45 with next-generation sequencing. The influence of the genotypic susceptibility score (GSS) and 16 MVC-resistance mutations on clinical outcome was also studied. RESULTS Concordance between single-amplification testing compared to ESTA and to NGS was in the order of 80%. Concordance with NGS was higher at lower FPR cut-offs. Detection of baseline R5 viruses in RNA and DNA samples by all methods significantly correlated with treatment success, even with FPR cut-offs of 3.75%-7.5%. Triple amplification did not improve the prediction value but reduced the number of patients eligible for MVC. No influence of the GSS or MVC-resistance mutations but adherence to treatment, on the clinical outcome was detected. CONCLUSIONS Proviral DNA is valid to select candidates for MVC treatment. FPR cut-offs of 5%-7.5% and single amplification from RNA or DNA would assure a safe administration of MVC without excluding many patients who could benefit from this drug. In addition, the new prediction system T-CUP produced reliable results.
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Affiliation(s)
- Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | - J Nikolai Dybowski
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Alejandro Pironti
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Dominik Heider
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Lisa Güney
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Alex Thielen
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Stefan Reuter
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology, University of Duisburg-Essen, Essen, Germany
| | - Gerd Fätkenheuer
- First Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Daniel Hoffmann
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Herbert Pfister
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
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HIV-1 subtypes and drug resistance profiles in a cohort of heterosexual patients in Istanbul, Turkey. Med Microbiol Immunol 2015; 204:551-5. [PMID: 25916350 DOI: 10.1007/s00430-015-0419-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/20/2015] [Indexed: 12/23/2022]
Abstract
Turkey is seeing a steady rise in rates of HIV infection in the country. The number of individuals with HIV/AIDS was greater than 7000 in 2014 according to data released by the Ministry of Health, and heterosexual contacts were reported to be the main transmission routes. Istanbul has the highest number of reported cases of HIV infection. The aim of the study was to determine the prevalence of HIV-1 drug resistance in 50 heterosexual patients from Istanbul. The most prevalent subtype was found to be subtype B (56.2 %). Resistance-associated mutations were found in 14 patients with 6/14 patients being therapy-experienced and 8/14 therapy naive at the time point of analysis. With increasing number of patients who require treatment and the rapid up-scaling of the antiretroviral therapy in Turkey, HIV-1 drug resistance testing is recommended before starting treatment in order to achieve better clinical outcomes.
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Pironti A, Sierra S, Kaiser R, Lengauer T, Pfeifer N. Effects of sequence alterations on results from genotypic tropism testing. J Clin Virol 2015; 65:68-73. [DOI: 10.1016/j.jcv.2015.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/28/2015] [Accepted: 02/06/2015] [Indexed: 11/30/2022]
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De Luca A, Di Giambenedetto S, Lo Presti A, Sierra S, Prosperi M, Cella E, Giovanetti M, Torti C, Caudai C, Vicenti I, Saladini F, Almi P, Grima P, Blanc P, Fabbiani M, Rossetti B, Gagliardini R, Kaiser R, Ciccozzi M, Zazzi M. Two Distinct Hepatitis C Virus Genotype 1a Clades Have Different Geographical Distribution and Association With Natural Resistance to NS3 Protease Inhibitors. Open Forum Infect Dis 2015; 2:ofv043. [PMID: 26213689 PMCID: PMC4511743 DOI: 10.1093/ofid/ofv043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/26/2015] [Indexed: 12/18/2022] Open
Abstract
Background. Hepatitis C virus (HCV) genotype 1 is the most prevalent worldwide. Subtype 1a, compared with 1b, shows lower response rates and higher propensity to select for drug resistance to NS3 and selected NS5A and nonnucleoside NS5B inhibitors. Two distinct clades of subtype 1a have been described. Methods. Using Bayesian methodology, we performed a time-scaled phylogeny reconstruction of clade separation and characterized the geographic distribution, phylodynamics, and association with natural resistance variants of NS3 sequences from 362 patients carrying subtype 1a HCV. Results. All sequences segregated in 2 clearly distinct clades. Clade I showed an earlier origin from the common ancestor compared with clade II. Clade I virus was more prevalent in non-European countries, represented mostly by United States, compared with European (75.7% vs 49.3%; P < .001). The prevalence of the natural NS3 variant Q80K, associated with resistance to the macrocyclic protease inhibitor simeprevir, was detected in 51.6% of clade I and 0% of clade II (P < .001); clade I showed a lower genetic barrier for Q80K, whereas no sign of selective pressure at any protease inhibitor resistance-associated codon was detected. Conclusions. Hepatitis C virus subtype 1a clades have a clearly different distribution in Europe and the United States, and the natural resistance mutation Q80K is exclusively associated with clade I.
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Affiliation(s)
- Andrea De Luca
- Unità Operativa ComplessaMalattie Infettive Universitarie, Siena University Hospital, Italy
- Institute of Clinical Infectious Diseases, Catholic University, Roma, Italy
| | | | | | - Saleta Sierra
- Partner Site of the German Center for Infection Research Deutsches Zentrum für Infektionsforschung; Institute of Virology, University of Cologne, Germany
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville
| | - Eleonora Cella
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
| | - Marta Giovanetti
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- Department of Biology, University of Rome “Tor Vergata”, Italy
| | - Carlo Torti
- University of Brescia, Italy
- Unit of Infectious Diseases, University “Magna Graecia”, Catanzaro, Italy
| | - Cinzia Caudai
- Department of Medical Biotechnologies, University of Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Italy
| | | | - Paolo Almi
- Unità Operativa Complessa Malattie Infettive ed Epatologia, Siena University Hospital, Italy
| | - Pierfrancesco Grima
- Infectious Diseases Unit, S. Caterina Novella Hospital, Galatina, Lecce, Italy
| | - Pierluigi Blanc
- Unità Operativa Malattie InfettiveOspedale Santa Maria Annunziata Azienda Sanitaria Locale 10, Firenze, Italy
| | | | - Barbara Rossetti
- Unità Operativa ComplessaMalattie Infettive Universitarie, Siena University Hospital, Italy
| | | | - Rolf Kaiser
- Partner Site of the German Center for Infection Research Deutsches Zentrum für Infektionsforschung; Institute of Virology, University of Cologne, Germany
| | - Massimo Ciccozzi
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- University Campus-Biomedico, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Italy
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Morris SR, Woods SP, Deutsch R, Little SJ, Wagner G, Morgan EE, Heaton RK, Letendre SL, Grant I, Smith DM. Dual-mixed HIV-1 coreceptor tropism and HIV-associated neurocognitive deficits. J Neurovirol 2014; 19:488-94. [PMID: 24078557 DOI: 10.1007/s13365-013-0203-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/14/2013] [Accepted: 08/20/2013] [Indexed: 11/30/2022]
Abstract
HIV coreceptor usage of CXCR4 (X4) is associated with decreased CD4+ T-cell counts and accelerated disease progression, but the role of X4 tropism in HIV-associated neurocognitive disorders (HAND) has not previously been described. This longitudinal study evaluated data on 197 visits from 72 recently HIV-infected persons who had undergone up to four sequential neurocognitive assessments over a median of 160 days (IQR, 138–192). Phenotypic tropism testing (Trofile ES, Monogram, Biosciences) was performed on stored blood samples. Multivariable mixed model repeated measures regression was used to determine the association between HAND and dual-mixed (DM) viral tropism, estimated duration of infection (EDI), HIV RNA, CD4 count, and problematic methamphetamine use. Six subjects (8.3 %) had DM at their first neurocognitive assessment and four converted to DM in subsequent sampling (for total of 10 DM) at a median EDI of 10.1 months (IQR, 7.2–12.2). There were 44 (61.1 %) subjects who demonstrated HAND on at least one study visit. HAND was associated with DM tropism (odds ratio, 4.4; 95 % CI, 0.9–20.5) and shorter EDI (odds ratio 1.1 per month earlier; 95 % CI, 1.0–1.2). This study found that recency of HIV-1 infection and the development of DM tropism may be associated with HAND in the relatively early stage of infection. Together, these data suggest that viral interaction with cellular receptors may play an important role in the early manifestation of HAND.
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Bon I, Clò A, Borderi M, Colangeli V, Calza L, Morini S, Miserocchi A, Cricca M, Gibellini D, Re MC. Prevalence of R5 strains in multi-treated HIV subjects and impact of new regimens including maraviroc in a selected group of patients with CCR5-tropic HIV-1 infection. Int J Infect Dis 2013; 17:e875-82. [PMID: 23597487 DOI: 10.1016/j.ijid.2013.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 01/21/2013] [Accepted: 02/19/2013] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Maraviroc currently represents an important antiretroviral drug for multi-experienced and viremic HIV patients. This study focused on two main points: (1) determining the prevalence of R5 and X4 HIV strains in antiretroviral-experienced patients using two main tests currently in use to determine viral tropism, and (2) the follow-up to 3 years of a limited number of patients who started a new antiretroviral protocol including maraviroc. METHODS A group of 56 HIV patients, previously multi-treated, were first analyzed by genotyping assay and Trofile™ to establish their eligibility for maraviroc treatment. In addition, 25 subjects selected to follow a new therapeutic protocol including a CCR5 antagonist were monitored by HIV RNA viral load and CD4+ cell count. RESULTS The determination of viral tropism showed a large percentage of patients with an R5 profile (72% by genotyping assay and 74% by Trofile). The follow-up of most (21 out 25) patients who started the new antiretroviral protocol showed an undetectable viral load throughout the observation period, accompanied by a major improvement in CD4 cell count (cells/mm(3)) (baseline: median CD4 cell count 365, interquartile range (IQR) 204-511; 12 months: median value 501, IQR 349-677, p=0.042; 24 months: median value 503, IQR 386-678, p=0.026; 36 months: median value 601, IQR 517-717, p=0.001). Among the four non-responder subjects, two showed a lack of drug compliance and two switched from R5 to X4. CONCLUSION Although our patient cohort was small, the results showed a high prevalence of R5 viral strains in multi-experienced patients. As well as showing the advantages of genotyping, which can be performed in plasma samples with low viral load replication, the follow-up of HIV patients selected for an alternative drug protocol, including a CCR5 antagonist, showed a persistent undetectable viral replication and a good recovery of CD4 cell count in most treated HIV patients.
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Affiliation(s)
- Isabella Bon
- Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
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Molecular epidemiology of HIV in a cohort of men having sex with men from Istanbul. Med Microbiol Immunol 2013; 202:251-5. [PMID: 23296905 DOI: 10.1007/s00430-012-0285-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/12/2012] [Indexed: 02/01/2023]
Abstract
In Turkey, the first HIV/AIDS case was reported in 1985. Since then the number of persons with HIV infection has increased, HIV is getting a public health problem. The aim of this study was to determine HIV-1 subtype diversity, drug resistance and gag cleavage site mutations among 20 HIV-infected men having sex with men from Istanbul, Turkey. The most prevalent subtype was found to be subtype B (50 %), but also the non-B subtypes A1, C and CRF02_AG, CRF03_AB and CRF06_cpx were found. Resistance-associated mutations were found in 6 patients (30 %) with 2/6 patients being therapy-experienced and 4/6 therapy-naïve at the time-point of analysis. In these patients, the nucleoside reverse transcriptase inhibitor (NRTI)-associated resistance mutations M41L, T215C, V75I, T69N, the non-NRTI associated mutations V106I, E138A, K103N and the protease inhibitor associated mutations Q58E and V82I were detected. Two virus strains also presented Gag cleavage site mutations. With increasing numbers of HIV-infected Turkish patients that require anti-retroviral treatment, HIV-1 drug-resistance testing is strongly recommended in order to choose the most active drug combination for therapy to achieve better clinical outcomes.
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Bozek K, Eckhardt M, Sierra S, Anders M, Kaiser R, Kräusslich HG, Müller B, Lengauer T. An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data. Retrovirology 2012; 9:60. [PMID: 22830600 PMCID: PMC3464718 DOI: 10.1186/1742-4690-9-60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 06/07/2012] [Indexed: 11/29/2022] Open
Abstract
Background Entry of human immunodeficiency virus type 1 (HIV-1) into the host cell involves interactions between the viral envelope glycoproteins (Env) and the cellular receptor CD4 as well as a coreceptor molecule (most importantly CCR5 or CXCR4). Viral preference for a specific coreceptor (tropism) is in particular determined by the third variable loop (V3) of the Env glycoprotein gp120. The approval and use of a coreceptor antagonist for antiretroviral therapy make detailed understanding of tropism and its accurate prediction from patient derived virus isolates essential. The aim of the present study is the development of an extended description of the HIV entry phenotype reflecting its co-dependence on several key determinants as the basis for a more accurate prediction of HIV-1 entry phenotype from genotypic data. Results Here, we established a new protocol of quantitation and computational analysis of the dependence of HIV entry efficiency on receptor and coreceptor cell surface levels as well as viral V3 loop sequence and the presence of two prototypic coreceptor antagonists in varying concentrations. Based on data collected at the single-cell level, we constructed regression models of the HIV-1 entry phenotype integrating the measured determinants. We developed a multivariate phenotype descriptor, termed phenotype vector, which facilitates a more detailed characterization of HIV entry phenotypes than currently used binary tropism classifications. For some of the tested virus variants, the multivariant phenotype vector revealed substantial divergences from existing tropism predictions. We also developed methods for computational prediction of the entry phenotypes based on the V3 sequence and performed an extrapolating calculation of the effectiveness of this computational procedure. Conclusions Our study of the HIV cell entry phenotype and the novel multivariate representation developed here contributes to a more detailed understanding of this phenotype and offers potential for future application in the effective administration of entry inhibitors in antiretroviral therapies.
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Affiliation(s)
- Katarzyna Bozek
- Department of Computational Biology and Applied Algorithmics, Max Planck for Computer Sciences, Campus E1 4 66123, Saarbrücken, Germany
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