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Differences among HIV-1 subtypes in drug resistance against integrase inhibitors. INFECTION GENETICS AND EVOLUTION 2016; 46:286-291. [PMID: 27353185 DOI: 10.1016/j.meegid.2016.06.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/22/2022]
Abstract
Three integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG), have been approved by the FDA. Resistance against these three INSTIs have been reported and cross-resistance among them has been documented. Due to extensive and dynamic genetic diversity in different HIV-1 variants, significant differences in susceptibility to the INSTIs have been observed among HIV subtypes. This review summarizes what is known about this topic and discusses possible clinical implications.
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Lai A, Bozzi G, Franzetti M, Binda F, Simonetti FR, De Luca A, Micheli V, Meraviglia P, Bagnarelli P, Di Biagio A, Monno L, Saladini F, Zazzi M, Zehender G, Ciccozzi M, Balotta C. HIV-1 A1 Subtype Epidemic in Italy Originated from Africa and Eastern Europe and Shows a High Frequency of Transmission Chains Involving Intravenous Drug Users. PLoS One 2016; 11:e0146097. [PMID: 26752062 PMCID: PMC4709132 DOI: 10.1371/journal.pone.0146097] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/14/2015] [Indexed: 12/04/2022] Open
Abstract
Background Subtype A accounts for only 12% of HIV-1 infections worldwide but predominates in Russia and Former Soviet Union countries of Eastern Europe. After an early propagation via heterosexual contacts, this variant spread explosively among intravenous drug users. A distinct A1 variant predominates in Greece and Albania, which penetrated directly from Africa. Clade A1 accounts for 12.5% of non-B subtypes in Italy, being the most frequent after F1 subtype. Aim Aim of this study was to investigate the circulation of A1 subtype in Italy and trace its origin and diffusion through phylogenetic and phylodynamic approaches. Results The phylogenetic analysis of 113 A1 pol sequences included in the Italian ARCA database, indicated that 71 patients (62.8%) clustered within 5 clades. A higher probability to be detected in clusters was found for patients from Eastern Europe and Italy (88.9% and 60.4%, respectively) compared to those from Africa (20%) (p < .001). Higher proportions of clustering sequences were found in intravenous drug users with respect to heterosexuals (85.7% vs. 59.3%, p = .056) and in women with respect to men (81.4% vs. 53.2%, p < .006). Subtype A1 dated phylogeny indicated an East African origin around 1961. Phylogeographical reconstruction highlighted 3 significant groups. One involved East European and some Italian variants, the second encompassed some Italian and African strains, the latter included the majority of viruses carried by African and Italian subjects and all viral sequences from Albania and Greece. Conclusions Subtype A1 originated in Central Africa and spread among East European countries in 1982. It entered Italy through three introduction events: directly from East Africa, from Albania and Greece, and from the area encompassing Moldavia and Ukraine. As in previously documented A1 epidemics of East European countries, HIV-1 A1 subtype spread in Italy in part through intravenous drug users. However, Eastern European women contributed to the penetration of such variant, probably through sex work.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
- * E-mail:
| | - Giorgio Bozzi
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Marco Franzetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesca Binda
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesco R. Simonetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Valeria Micheli
- Laboratory of Microbiology, ‘L. Sacco’ Hospital, Milan, Italy
| | - Paola Meraviglia
- 2nd Division of Infectious Diseases, ‘L. Sacco’ Hospital, Milan, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Science, Section of Microbiology, Laboratory of Virology, University Politecnica delle Marche, Ancona, Italy
| | | | - Laura Monno
- Division of Infectious Disease, University of Bari, Bari, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
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Shadrina O, Krotova O, Agapkina J, Knyazhanskaya E, Korolev S, Starodubova E, Viklund A, Lukashov V, Magnani M, Medstrand P, Karpov V, Gottikh M, Isaguliants M. Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties. Biochimie 2014; 102:92-101. [PMID: 24594066 DOI: 10.1016/j.biochi.2014.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/21/2014] [Indexed: 11/28/2022]
Abstract
Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded.
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Affiliation(s)
- Olga Shadrina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Olga Krotova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Julia Agapkina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Ekaterina Knyazhanskaya
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Sergey Korolev
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Elizaveta Starodubova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Alecia Viklund
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Vladimir Lukashov
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mauro Magnani
- Department of Biomolecular Science, University of Urbino "Carla Bo", Via Saffi, 2, 61029 Urbino, Italy
| | - Patrik Medstrand
- Department of Laboratory Medicine, Lund University, Sölvegatan 19, SE-205 02 Malmö, Sweden
| | - Vadim Karpov
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia
| | - Marina Gottikh
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia.
| | - Maria Isaguliants
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden.
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Performance comparison of an in-house integrase genotyping assay versus the ViroSeq™ Integra48, and study of HIV-1 integrase polymorphisms in Hong Kong. J Clin Virol 2013; 58:299-302. [DOI: 10.1016/j.jcv.2013.06.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/17/2013] [Accepted: 06/17/2013] [Indexed: 11/17/2022]
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Dimonte S, Babakir-Mina M, Aquaro S, Perno CF. Natural polymorphisms of HIV-1 subtype-C integrase coding region in a large group of ARV-naïve infected individuals. Infection 2013; 41:1097-102. [PMID: 23620062 DOI: 10.1007/s15010-013-0464-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/15/2013] [Indexed: 11/30/2022]
Abstract
PURPOSE Integrase (IN) is an enzyme produced by human immunodeficiency virus (HIV)-1 that enables its genetic material to be integrated into the DNA of the infected cell. Still now, few data are available with detailed analysis of the natural IN polymorphisms of HIV-1 subtype-C in datasets retrieved from antiretroviral-naïve patients; this study focuses on these polymorphisms. METHODS The analysis included 335 HIV-1 subtype-C IN sequences (one per patient). Multi-alignment of IN sequences was performed, and for the definition of a polymorphism, only amino acid changes with prevalence ≥3 % among treatment-naïve patients were considered. RESULTS Seventy IN amino acid positions were fully conserved. Differently, forty-six IN amino acid polymorphic positions were observed, 12 within the N-terminal domain and 13 within the C-terminal domain. In the DDE-catalytic motif, only one mutation per site (D64G/D116G/E152K) was found, while a low variability (<1 %) was observed for IN positions interacting with LEDGF/p75. A major drug resistance mutation for raltegravir (RAL) and elvitegravir (EVG), Q148H, was retrieved from one patient and another RAL primary resistance mutation, Y143H, was also retrieved from another patient. CONCLUSIONS The results from the IN sequences analyzed underlined that some unexpected baseline substitutions affecting the susceptibility to RAL/EVG could be detected in drug-naïve individuals, and, therefore, it should be genotyped before the consideration of HIV-1 IN inhibitors (INIs). The impact of these mutations on the baseline drug susceptibility of HIV-1 subtype-C to INIs may need to be addressed prior to the introduction of these drugs in some Asiatic and African countries.
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Affiliation(s)
- S Dimonte
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy,
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Parczewski M, Bander D, Urbańska A, Boroń-Kaczmarska A. HIV-1 integrase resistance among antiretroviral treatment naive and experienced patients from Northwestern Poland. BMC Infect Dis 2012; 12:368. [PMID: 23259737 PMCID: PMC3547692 DOI: 10.1186/1471-2334-12-368] [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: 08/27/2012] [Accepted: 12/18/2012] [Indexed: 12/02/2022] Open
Abstract
Background HIV integrase inhibitor use is limited by low genetic barrier to resistance and possible cross-resistance among representatives of this class of antiretrovirals. The aim of this study was to analyse integrase sequence variability among antiretroviral treatment naive and experienced patients with no prior integrase inhibitor (InI) exposure and investigate development of the InI drug resistance mutations following the virologic failure of the raltegravir containing regimen. Methods Sequencing of HIV-1 integrase region from plasma samples of 80 integrase treatment naive patients and serial samples from 12 patients with observed virologic failure on raltegravir containing treatment whenever plasma vireamia exceeded >50 copies/ml was performed. Drug resistance mutations were called with Stanford DB database and grouped into major and minor variants. For subtyping bootstrapped phylogenetic analysis was used; Bayesian Monte Carlo Marcov Chain (MCMC) model was implemented to infer on the phylogenetic relationships between the serial sequences from patients failing on raltegravir. Results Majority of the integrase region sequences were classified as subtype B; the remaining ones being subtype D, C, G, as well as CRF01_AE , CRF02_AG and CRF13_cpx recombinants. No major integrase drug resistance mutations have been observed in InI-treatment naive patients. In 30 (38.5%) cases polymorphic variation with predominance of the E157Q mutation was observed. This mutation was more common among subtype B (26 cases, 54.2%) than non-B sequences (5 cases, 16.7%), p=0.00099, OR: 5.91 (95% CI:1.77-22.63)]. Other variants included L68V, L74IL, T97A, E138D, V151I, R263K. Among 12 (26.1%) raltegravir treated patients treatment failure was observed; major InI drug resistance mutations (G140S, Q148H and N155H, V151I, E92EQ, V151I, G163R) were noted in four of these cases (8.3% of the total InI-treated patients). Time to the development of drug resistance ranged from 2.6 to 16.3 months with mean increase of HIV viral load of 4.34 (95% CI:1.86-6.84) log HIV-RNA copies/ml at the time of emergence of the major mutations. Baseline polymorphisms, including E157Q were not associated with the virologic failure on raltegravir. Conclusions In InI treatment naive patients polymorphic integrase sequence variation was common, with no major resistance mutants. In the treatment failing patients selection of drug resistance occurred rapidly and followed the typical drug resistance pathways. Preexisting integrase polymorphisms were not associated with the treatment failure.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
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Luu QP, Dean J, Do TTD, Carr MJ, Dunford L, Coughlan S, Connell J, Nguyen HT, Hall WW, Nguyen Thi LA. HIV type 1 coreceptor tropism, CCR5 genotype, and integrase inhibitor resistance profiles in Vietnam: implications for the introduction of new antiretroviral regimens. AIDS Res Hum Retroviruses 2012; 28:1344-8. [PMID: 22264071 DOI: 10.1089/aid.2011.0396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Vietnam, where an estimated 280,000 people will be HIV-positive by 2012, recommended antiretroviral regimens do not include more recently developed therapeutics, such as Integrase inhibitors (INI) and coreceptor antagonists. This study examined HIV-1 coreceptor tropism and INI drug resistance profiles, in parallel with CCR5 genotypes, in a cohort of 60 HIV-positive individuals from different regions of Vietnam. No evidence of INI resistance was detected. Some 40% of individuals had X4-tropic HIV-1, making them unsuitable for treatment with CCR5 antagonists. We identified a novel CCR5 variant-S272P-along with other, previously reported variants: G106R, C178R, W153C, R223Q, and S336I. Interestingly, CCR5 variants known to affect HIV-1 infectivity were observed only in individuals harboring X4-tropic virus. Together, this study presents valuable baseline information on HIV-1 INI resistance, coreceptor tropism, and CCR5 variants in HIV-positive individuals in Vietnam. This should help inform policy on the future use of novel antiretrovirals in Vietnam.
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Affiliation(s)
- Quynh Phuong Luu
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Jonathan Dean
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Trinh Thi Diem Do
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Michael J Carr
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Linda Dunford
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Suzie Coughlan
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Jeff Connell
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Hien Tran Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - William W. Hall
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Lan Anh Nguyen Thi
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam
- Laboratory for Molecular Diagnostics, Department of Immunology and Molecular Biology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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