1
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Marichannegowda MH, Zemil M, Wieczorek L, Sanders-Buell E, Bose M, O'Sullivan AM, King D, Francisco L, Diaz-Mendez F, Setua S, Chomont N, Phanuphak N, Ananworanich J, Hsu D, Vasan S, Michael NL, Eller LA, Tovanabutra S, Tagaya Y, Robb ML, Polonis VR, Song H. Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting: the RV217 acute infection cohort study. EBioMedicine 2023; 98:104867. [PMID: 37939456 PMCID: PMC10665704 DOI: 10.1016/j.ebiom.2023.104867] [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: 06/02/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The CCR5 (R5) to CXCR4 (X4) coreceptor switch in natural HIV-1 infection is associated with faster progression to AIDS, but the mechanisms remain unclear. The difficulty in elucidating the evolutionary origin of the earliest X4 viruses limits our understanding of this phenomenon. METHODS We tracked the evolution of the transmitted/founder (T/F) HIV-1 in RV217 participants identified in acute infection. The origin of the X4 viruses was elucidated by single genome amplification, deep sequencing and coreceptor assay. Mutations responsible for coreceptor switch were confirmed by mutagenesis. Viral susceptibility to neutralization was determined by neutralization assay. Virus CD4 subset preference was demonstrated by sequencing HIV-1 RNA in sorted CD4 subsets. FINDINGS We demonstrated that the earliest X4 viruses evolved de novo from the T/F strains. Strong X4 usage can be conferred by a single mutation. The mutations responsible for coreceptor switch can confer escape to neutralization and drive the X4 variants to replicate mainly in the central memory (CM) and naïve CD4 subsets. Likely due to the smaller viral burst size of the CM and naïve subsets, the X4 variants existed at low frequency in plasma. The origin of the X4 viruses preceded accelerated CD4 decline. All except one X4 virus identified in the current study lost the conserved V3 N301 glycan site. INTERPRETATIONS The findings demonstrate co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting which have implications for HIV-1 therapeutics and functional cure. The observations provide evidence that coreceptor switch can function as an evolutionary mechanism of immune evasion. FUNDING Institute of Human Virology, National Institutes of Health, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Thai Red Cross AIDS Research Centre, Gilead Sciences, Merck, and ViiV Healthcare.
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Affiliation(s)
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Anne Marie O'Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - David King
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leilani Francisco
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Felisa Diaz-Mendez
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Saini Setua
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Canada
| | | | | | - Denise Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Yutaka Tagaya
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Hongshuo Song
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA.
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2
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Marichannegowda MH, Song H. Immune escape mutations selected by neutralizing antibodies in natural HIV-1 infection can alter coreceptor usage repertoire of the transmitted/founder virus. Virology 2022; 568:72-76. [DOI: 10.1016/j.virol.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022]
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3
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Judicate GP, Barabona G, Kamori D, Mahiti M, Tan TS, Ozono S, Mgunya AS, Kuwata T, Matsushita S, Sunguya B, Lyamuya E, Tokunaga K, Ueno T. Phenotypic and Genotypic Co-receptor Tropism Testing in HIV-1 Epidemic Region of Tanzania Where Multiple Non-B Subtypes Co-circulate. Front Microbiol 2021; 12:703041. [PMID: 34305873 PMCID: PMC8292895 DOI: 10.3389/fmicb.2021.703041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
HIV human immunodeficiency virus type I (HIV-1) entry inhibitor potency is dependent on viral co-receptor tropisms and thereby tropism determination is clinically important. However, phenotypic tropisms of HIV-1 non-B subtypes have been poorly investigated and the genotypic prediction algorithms remain insufficiently validated. To clarify this issue, we recruited 52 treatment-naïve, HIV-1-infected patients in Tanzania, where multiple HIV-1 non-B subtypes co-circulate. Sequence analysis of 93 infectious envelope clones isolated from their plasma viral RNA revealed the co-circulation of subtypes A1, C, D, and inter-subtype recombinant forms (isRFs). Phenotypic tropism assays revealed that lentivirus reporters pseudotyped with 75 (80.6%) and 5 (5.4%) envelope clones could establish infection toward U87.CD4 cells expressing CCR5 (R5) and CXCR4 (X4), respectively; whereas the remaining 13 (14%) clones could infect both cells. Genotypic analyses by widely used algorithms including V3 net charge, Geno2pheno, WebPSSM, and PhenoSeq showed that almost all phenotypic X4-tropic clones and only 15 of 75 phenotypic R5-tropic clones were concordantly predicted. However, the remaining 60 phenotypic R5-tropic clones were discordantly predicted by at least one algorithm. In particular, 2 phenotypic R5-tropic clones were discordantly predicted by all algorithms tested. Taken together, the results demonstrate the limitation of currently available genotypic algorithms for predicting co-receptor inference among co-circulating multiple non-B subtypes and emerging isRFs. Also, the phenotypic tropism dataset presented here could be valuable for retraining of the widely used genotypic prediction algorithms to enhance their performance.
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Affiliation(s)
- George P Judicate
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Doreen Kamori
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Macdonald Mahiti
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Toong Seng Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Takeo Kuwata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Shuzo Matsushita
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Bruno Sunguya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius Lyamuya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Kenzo Tokunaga
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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4
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Sutar J, Deshpande S, Mullick R, Hingankar N, Patel V, Bhattacharya J. Geospatial HIV-1 subtype C gp120 sequence diversity and its predicted impact on broadly neutralizing antibody sensitivity. PLoS One 2021; 16:e0251969. [PMID: 34029329 PMCID: PMC8143386 DOI: 10.1371/journal.pone.0251969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/06/2021] [Indexed: 11/28/2022] Open
Abstract
Evolving diversity in globally circulating HIV-1 subtypes presents a formidable challenge in defining and developing neutralizing antibodies for prevention and treatment. HIV-1 subtype C is responsible for majority of global HIV-1 infections. In the present study, we examined the diversity in genetic signatures and attributes that differentiate region-specific HIV-1 subtype C gp120 sequences associated with virus neutralization outcomes to key bnAbs having distinct epitope specificities. A total of 1814 full length HIV-1 subtype C gp120 sequence from 37 countries were retrieved from Los Alamos National Laboratory HIV database (www.hiv.lanl.gov). The amino acid sequences were assessed for their phylogenetic association, variable loop lengths and prevalence of potential N-linked glycosylation sites (pNLGS). Responses of these sequences to bnAbs were predicted with a machine learning algorithm ‘bNAb-ReP’ and compared with those reported in the CATNAP database. Subtype C sequences from Asian countries including India differed phylogenetically when compared with that from African countries. Variable loop lengths and charges within Indian and African clusters were also found to be distinct from each other, specifically for V1, V2 and V4 loops. Pairwise analyses at each of the 25 pNLG sites indicated distinct country specific profiles. Highly significant differences (p<0.001***) were observed in prevalence of four pNLGS (N130, N295, N392 and N448) between South Africa and India, having most disease burden associated with subtype C. Our findings highlight that distinctly evolving clusters within global intra-subtype C gp120 sequences are likely to influence the disparate region-specific sensitivity of circulating HIV-1 subtype C to bnAbs.
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Affiliation(s)
- Jyoti Sutar
- HIV Vaccine Translational Research Laboratory, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
- International AIDS Vaccine Initiative, New Delhi, India
| | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Ranajoy Mullick
- HIV Vaccine Translational Research Laboratory, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
- International AIDS Vaccine Initiative, New Delhi, India
| | - Nitin Hingankar
- HIV Vaccine Translational Research Laboratory, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Vainav Patel
- ICMR-National Institute for Research in Reproductive Health, Mumbai, India
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
- International AIDS Vaccine Initiative, New Delhi, India
- * E-mail: ,
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5
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Dimeglio C, Raymond S, Jeanne N, Reynes C, Carcenac R, Lefebvre C, Cazabat M, Nicot F, Delobel P, Izopet J. THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage. Bioinformatics 2020; 36:416-421. [PMID: 31350559 DOI: 10.1093/bioinformatics/btz585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/28/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION The circulating recombinant form of HIV-1 CRF02-AG is the most frequent non-B subtype in Europe. Anti-HIV therapy and pathophysiological studies on the impact of HIV-1 tropism require genotypic determination of HIV-1 tropism for non-B subtypes. But genotypic approaches based on analysis of the V3 envelope region perform poorly when used to determine the tropism of CRF02-AG. We, therefore, designed an algorithm based on information from the gp120 and gp41 ectodomain that better predicts the tropism of HIV-1 subtype CRF02-AG. RESULTS We used a bio-statistical method to identify the genotypic determinants of CRF02-AG coreceptor use. Toulouse HIV Extended Tropism Algorithm (THETA), based on a Least Absolute Shrinkage and Selection Operator method, uses HIV envelope sequence from phenotypically characterized clones. Prediction of R5X4/X4 viruses was 86% sensitive and that of R5 viruses was 89% specific with our model. The overall accuracy of THETA was 88%, making it sufficiently reliable for predicting the tropism of subtype CRF02-AG sequences. AVAILABILITY AND IMPLEMENTATION Binaries are freely available for download at https://github.com/viro-tls/THETA. It was implemented in Matlab and supported on MS Windows platform. The sequence data used in this work are available from GenBank under the accession numbers MK618182-MK618417.
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Affiliation(s)
- Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Stéphanie Raymond
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Christelle Reynes
- Institut de Génomique Fonctionnelle, 34090 Montpellier, France.,UM-Université de Montpellier, 34090 Montpellier, France.,Faculté de Pharmacie, 34090 Montpellier, France
| | | | | | | | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Pierre Delobel
- CHU de Toulouse, Service de Maladies Infectieuses et Tropicales, 31059 Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
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6
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Digban TO, Iweriebor BC, Nwodo UU, Okoh AI, Obi LC. Chemokine Coreceptor Usage Among HIV-1 Drug-Naive Patients Residing in the Rural Eastern Cape, South Africa. AIDS Res Hum Retroviruses 2020; 36:688-696. [PMID: 32466656 DOI: 10.1089/aid.2020.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sub-Saharan region in Africa still holds the highest burden of HIV/AIDS globally. HIV-1 requires coreceptor to gain entry into permissive cells to initiate infection. Molecular analysis of the chemokine coreceptor usage is important clinically and in the effective management of AIDS virus. This study aims to determine the coreceptor usage among HIV-1 drug-naive patients residing in the rural Eastern cape, South Africa. We collected blood samples from 55 HIV-infected patients into an anticoagulant vacutainer. RNA was extracted from separated plasma, and reverse transcription-polymerase chain reaction (RT-PCR) was performed followed by nested polymerase chain reaction to amplify the partial envelope fragment spanning the C2-C3 region. Sanger sequencing was done on the amplicons using the BigDye Terminator V3.1 sequencing kit (Applied Biosystems, Foster City, CA) while sequences were manually edited using BioEdit and Geneious 10.2.6 tools. The WebPSSM and Geno2pheno online tools were also utilized to predict coreceptor tropism while the phylogenetic analysis of the isolates was determined using MEGA 7. Of the 55 blood samples collected for the study, 50 (91%) were successfully amplified and sequenced. The mean age of the patients was 32 (18-56) years while the ratio of men to women was 35% and 65% correspondingly. Phylogenetic analysis revealed that all 50 sequences clustered with HIV-1 subtype C reference strains. Viral tropism of the V3 loop revealed 47 sequences to be R5 strains, while three sequences (T1E, T10E, and T11E,) were classified as X4 strains based on the WebPSSM and the Geno2pheno algorithm. HIV-1 R5 tropic strains were the most dominant virus obtained from this study, while HIV-1 subtype C still drives the epidemic in South Africa suggesting greater in vivo and host pathogen fitness. Documented data on mapping out cellular tropism based on viral tropism are important as maraviroc and the other CCR5 antagonist could be introduced as part of the treatment regimen in South Africa.
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Affiliation(s)
- Tennison Onoriode Digban
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied Environmental and Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Benson Chucks Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Uchechukwu U. Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied Environmental and Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Larry Chikwelu Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
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7
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Existence of Replication-Competent Minor Variants with Different Coreceptor Usage in Plasma from HIV-1-Infected Individuals. J Virol 2020; 94:JVI.00193-20. [PMID: 32295903 DOI: 10.1128/jvi.00193-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/04/2020] [Indexed: 12/20/2022] Open
Abstract
Cell entry by HIV-1 is mediated by its principal receptor, CD4, and a coreceptor, either CCR5 or CXCR4, with viral envelope glycoprotein gp120. Generally, CCR5-using HIV-1 variants, called R5, predominate over most of the course of infection, while CXCR4-using HIV-1 variants (variants that utilize both CCR5 and CXCR4 [R5X4, or dual] or CXCR4 alone [X4]) emerge at late-stage infection in half of HIV-1-infected individuals and are associated with disease progression. Although X4 variants also appear during acute-phase infection in some cases, these variants apparently fall to undetectable levels thereafter. In this study, replication-competent X4 variants were isolated from plasma of drug treatment-naive individuals infected with HIV-1 strain CRF01_AE, which dominantly carries viral RNA (vRNA) of R5 variants. Next-generation sequencing (NGS) confirmed that sequences of X4 variants were indeed present in plasma vRNA from these individuals as a minor population. On the other hand, in one individual with a mixed infection in which X4 variants were dominant, only R5 replication-competent variants were isolated from plasma. These results indicate the existence of replication-competent variants with different coreceptor usage as minor populations.IMPORTANCE The coreceptor switch of HIV-1 from R5 to CXCR4-using variants (R5X4 or X4) has been observed in about half of HIV-1-infected individuals at late-stage infection with loss of CD4 cell count and disease progression. However, the mechanisms that underlie the emergence of CXCR4-using variants at this stage are unclear. In the present study, CXCR4-using X4 variants were isolated from plasma samples of HIV-1-infected individuals that dominantly carried vRNA of R5 variants. The sequences of the X4 variants were detected as a minor population using next-generation sequencing. Taken together, CXCR4-using variants at late-stage infection are likely to emerge when replication-competent CXCR4-using variants are maintained as a minor population during the course of infection. The present study may support the hypothesis that R5-to-X4 switching is mediated by the expansion of preexisting X4 variants in some cases.
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8
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Fabrizio C, Bavaro DF, Scudeller L, Lepore L, Balena F, Lagioia A, Angarano G, Monno L, Saracino A. Variability OF HIV-1 V2 env domain for integrin binding: Clinical correlates. Virology 2019; 535:266-271. [PMID: 31357165 DOI: 10.1016/j.virol.2019.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 11/27/2022]
Abstract
The HIV V2179-181 (HXB2 numbering) tripeptide mediates binding to α4β7 integrin, which is responsible for GALT homing. Our study aimed to assess V2 variability in naive HIV-1 infected patients and its association with clinical and viro-immunological features. Gp120 sequences were obtained from 322 subjects; length, potential N-linked glycosylation sites (PNGs), net-charge (NC) and 179-181tripeptide α4β7-binding-motif of V2 were evaluated. At multivariate analysis, lower V2 length and higher NC correlated with low CD4 cells; no association was found with PNGs. A greater variability pertained positions 162-163, 164-167, 169, 175-179, 187, 194 and 195 in B sequences, and 163 and 177 in X4 tropic viruses. LDV was the most common tripeptide. Asp180 was highly conserved; Leu179 was more frequently observed in non-B and in recent infections compared to others, while Val181 was found in recent infections and in MSM. Further studies to deeply explore the clinical significance of these associations are warranted.
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Affiliation(s)
- Claudia Fabrizio
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy; Malattie Infettive e Tropicali Ospedale Oncologico San Giuseppe Moscati, Taranto, Italy
| | - Davide F Bavaro
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Luigia Scudeller
- Scientific Direction, Clinical Epidemiology Unit, IRCCS San Matteo Foundation, Viale Camillo Golgi, 19, 27100, Pavia, Italy
| | - Luciana Lepore
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Flavia Balena
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Antonella Lagioia
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Gioacchino Angarano
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy.
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9
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Ortega V, Stone JA, Contreras EM, Iorio RM, Aguilar HC. Addicted to sugar: roles of glycans in the order Mononegavirales. Glycobiology 2019; 29:2-21. [PMID: 29878112 PMCID: PMC6291800 DOI: 10.1093/glycob/cwy053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/29/2018] [Accepted: 06/05/2018] [Indexed: 12/25/2022] Open
Abstract
Glycosylation is a biologically important protein modification process by which a carbohydrate chain is enzymatically added to a protein at a specific amino acid residue. This process plays roles in many cellular functions, including intracellular trafficking, cell-cell signaling, protein folding and receptor binding. While glycosylation is a common host cell process, it is utilized by many pathogens as well. Protein glycosylation is widely employed by viruses for both host invasion and evasion of host immune responses. Thus better understanding of viral glycosylation functions has potential applications for improved antiviral therapeutic and vaccine development. Here, we summarize our current knowledge on the broad biological functions of glycans for the Mononegavirales, an order of enveloped negative-sense single-stranded RNA viruses of high medical importance that includes Ebola, rabies, measles and Nipah viruses. We discuss glycobiological findings by genera in alphabetical order within each of eight Mononegavirales families, namely, the bornaviruses, filoviruses, mymonaviruses, nyamiviruses, paramyxoviruses, pneumoviruses, rhabdoviruses and sunviruses.
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Affiliation(s)
- Victoria Ortega
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jacquelyn A Stone
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Erik M Contreras
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ronald M Iorio
- Department of Microbiology and Physiological Systems and Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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10
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Narasimhulu VGS, Bellamy-McIntyre AK, Laumaea AE, Lay CS, Harrison DN, King HAD, Drummer HE, Poumbourios P. Distinct functions for the membrane-proximal ectodomain region (MPER) of HIV-1 gp41 in cell-free and cell-cell viral transmission and cell-cell fusion. J Biol Chem 2018; 293:6099-6120. [PMID: 29496992 DOI: 10.1074/jbc.ra117.000537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/21/2018] [Indexed: 11/06/2022] Open
Abstract
HIV-1 is spread by cell-free virions and by cell-cell viral transfer. We asked whether the structure and function of a broad neutralizing antibody (bNAb) epitope, the membrane-proximal ectodomain region (MPER) of the viral gp41 transmembrane glycoprotein, differ in cell-free and cell-cell-transmitted viruses and whether this difference could be related to Ab neutralization sensitivity. Whereas cell-free viruses bearing W666A and I675A substitutions in the MPER lacked infectivity, cell-associated mutant viruses were able to initiate robust spreading infection. Infectivity was restored to cell-free viruses by additional substitutions in the cytoplasmic tail (CT) of gp41 known to disrupt interactions with the viral matrix protein. We observed contrasting effects on cell-free virus infectivity when W666A was introduced to two transmitted/founder isolates, but both mutants could still mediate cell-cell spread. Domain swapping indicated that the disparate W666A phenotypes of the cell-free transmitted/founder viruses are controlled by sequences in variable regions 1, 2, and 4 of gp120. The sequential passaging of an MPER mutant (W672A) in peripheral blood mononuclear cells enabled selection of viral revertants with loss-of-glycan suppressor mutations in variable region 1, suggesting a functional interaction between variable region 1 and the MPER. An MPER-directed bNAb neutralized cell-free virus but not cell-cell viral spread. Our results suggest that the MPER of cell-cell-transmitted virions has a malleable structure that tolerates mutagenic disruption but is not accessible to bNAbs. In cell-free virions, interactions mediated by the CT impose an alternative MPER structure that is less tolerant of mutagenic alteration and is efficiently targeted by bNAbs.
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Affiliation(s)
- Vani G S Narasimhulu
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004.,the Department of Microbiology and Immunology at the Peter Doherty Institute, University of Melbourne, Parkville, Victoria 3010, and
| | - Anna K Bellamy-McIntyre
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004.,the Departments of Microbiology and
| | - Annamarie E Laumaea
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004.,the Department of Microbiology and Immunology at the Peter Doherty Institute, University of Melbourne, Parkville, Victoria 3010, and
| | - Chan-Sien Lay
- Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - David N Harrison
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004
| | - Hannah A D King
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004.,the Department of Microbiology and Immunology at the Peter Doherty Institute, University of Melbourne, Parkville, Victoria 3010, and
| | - Heidi E Drummer
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004.,the Department of Microbiology and Immunology at the Peter Doherty Institute, University of Melbourne, Parkville, Victoria 3010, and.,the Departments of Microbiology and
| | - Pantelis Poumbourios
- From the Virus Entry and Vaccines Laboratory, Burnet Institute, Melbourne, Victoria 3004, .,the Departments of Microbiology and.,Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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RNA Sequencing Reveals Xyr1 as a Transcription Factor Regulating Gene Expression beyond Carbohydrate Metabolism. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4841756. [PMID: 28116297 PMCID: PMC5223008 DOI: 10.1155/2016/4841756] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/06/2016] [Indexed: 12/04/2022]
Abstract
Xyr1 has been demonstrated to be the main transcription activator of (hemi)cellulases in the well-known cellulase producer Trichoderma reesei. This study comprehensively investigates the genes regulated by Xyr1 through RNA sequencing to produce the transcription profiles of T. reesei Rut-C30 and its xyr1 deletion mutant (Δxyr1), cultured on lignocellulose or glucose. xyr1 deletion resulted in 467 differentially expressed genes on inducing medium. Almost all functional genes involved in (hemi)cellulose degradation and many transporters belonging to the sugar porter family in the major facilitator superfamily (MFS) were downregulated in Δxyr1. By contrast, all differentially expressed protease, lipase, chitinase, some ATP-binding cassette transporters, and heat shock protein-encoding genes were upregulated in Δxyr1. When cultured on glucose, a total of 281 genes were expressed differentially in Δxyr1, most of which were involved in energy, solute transport, lipid, amino acid, and monosaccharide as well as secondary metabolism. Electrophoretic mobility shift assays confirmed that the intracellular β-glucosidase bgl2, the putative nonenzymatic cellulose-attacking gene cip1, the MFS lactose transporter lp, the nmrA-like gene, endo T, the acid protease pepA, and the small heat shock protein hsp23 were probable Xyr1-targets. These results might help elucidate the regulation system for synthesis and secretion of (hemi)cellulases in T. reesei Rut-C30.
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Tian J, López CA, Derdeyn CA, Jones MS, Pinter A, Korber B, Gnanakaran S. Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein. PLoS Comput Biol 2016; 12:e1005094. [PMID: 27716795 PMCID: PMC5055340 DOI: 10.1371/journal.pcbi.1005094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/01/2016] [Indexed: 12/14/2022] Open
Abstract
Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes. Heavy glycosylation of the envelope surface subunit, gp120, is a key adaptation of HIV-1, however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. The network of glycans on gp120 is of particular interest with regards to vaccine design, because the glycans both serve as targets for many classes of broadly neutralizing antibodies, and contribute to patterns of immune evasion and escape during HIV-1 infection. In this manuscript, we report on how glycosylation influences an immunogenic but disordered region of gp120. Glycosylation stabilizes the pre-existing conformation, and reduces its propensity to form other secondary structures. It also stabilizes preformed conformation against thermal unfolding. These complementary effects originate from a combination of multiple factors, including the observation that having a glycosylation site adjacent to the disulfide bond further promotes the formation of beta-strand structure in this peptide.
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Affiliation(s)
- Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Biomolecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Cesar A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Morris S. Jones
- University of California Berkeley, School of Public Health, Berkeley, California, United States of America
| | - Abraham Pinter
- New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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13
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Dimonte S. Different HIV-1 env frames: gp120 and ASP (antisense protein) biosynthesis, and theirs co-variation tropic amino acid signatures in X4- and R5-viruses. J Med Virol 2016; 89:112-122. [PMID: 27328810 DOI: 10.1002/jmv.24611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 11/07/2022]
Abstract
Antisense protein (ASP) is the new actor of viral life of Human Immunodeficiency Virus type 1 (HIV-1) although proposed above 20 years ago. The asp ORF is into complementary strand of the gp120/gp41 junction of env gene. The ASP biological role remains little known. Knowing the Env markers of viral tropism, a dataset of sequences (660 strains) was used to analyze the hypothetical ASP involvement in CCR5 (R5) and/or CXCR4 (X4) co-receptor interaction. Preliminarily, prevalence of ASP and gp120V3 mutations was performed; following association among mutations were elaborate. The classical V3 tropic-signatures were confirmed, and 36 R5- and 22 X4-tropic ASP mutations were found. Moreover, by analyzing the ASP sequences, 36 out of 179 amino acid positions significantly associated with different co-receptor usage were found. Several statistically significant associations between gp120V3 and ASP mutations were observed. The dendrogram showed the existence of a cluster associated with R5-usage and a large cluster associated with X4-usage. These results show that gp120V3 and specific amino acid changes in ASP are associated together with CXCR4 and/or CCR5-usage. These findings implement previous observations on unclear ASP functions. J. Med. Virol. 89:112-122, 2017. © 2016 Wiley Periodicals, Inc.
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14
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Hikichi Y, Yokoyama M, Takemura T, Fujino M, Kumakura S, Maeda Y, Yamamoto N, Sato H, Matano T, Murakami T. Increased HIV-1 sensitivity to neutralizing antibodies by mutations in the Env V3-coding region for resistance to CXCR4 antagonists. J Gen Virol 2016; 97:2427-2440. [PMID: 27368421 DOI: 10.1099/jgv.0.000536] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV-1 passage in cell culture in the presence of chemokine receptor antagonists can result in selection of viruses with env mutations that confer resistance to these inhibitors. In the present study, we examined the effect of HIV-1env mutations that confer resistance to CXCR4 antagonists on envelope (Env) sensitivity to neutralizing antibodies (NAbs). Serial passage of CXCR4-tropic HIV-1 NL4-3 in PM1/CCR5 cells under CXCR4 antagonists KRH-3955, AMD3100 and AMD070 yielded two KRH-3955-resistant, one AMD3100-resistant and one AMD070-resistant viruses. These viruses had multiple env mutations including the Env gp120 V3 region. The majority of viruses having these CXCR4 antagonist-resistant Envs showed higher sensitivity to NAbs 447-52D, b12 and 2F5 targeting the V3 region, the gp120 CD4-binding site and the gp41 membrane proximal region, respectively, compared to NL4-3 WT virus. Recombinant NL4-3 viruses with the V3-coding region replaced with those derived from the CXCR4 antagonist-resistant viruses showed increased sensitivity to NAbs b12, 2F5 and 447-52D. Molecular dynamics simulations of Env gp120 outer domains predicted that the V3 mutations increased levels of fluctuations at the tip and stem of the V3 loop. These results indicate that mutations in the V3-coding region that result in loss of viral sensitivity to CXCR4 antagonists increase viral sensitivity to NAbs, providing insights into our understanding of the interplay of viral Env accessibility to chemokine receptors and sensitivity to NAbs.
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Affiliation(s)
- Yuta Hikichi
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640 Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639 Tokyo, Japan
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi Murayama-shi, 208-0011 Tokyo, Japan
| | - Taichiro Takemura
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, 852-8523 Nagasaki, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640 Tokyo, Japan
| | - Sei Kumakura
- Kureha Corporation, 3-26-2, Hyakunin-cho, Shinjuku-ku, 169-8503 Tokyo, Japan
| | - Yosuke Maeda
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, 860-8556 Kumamoto, Japan
| | - Naoki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640 Tokyo, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi Murayama-shi, 208-0011 Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640 Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639 Tokyo, Japan
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640 Tokyo, Japan
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15
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Garg H, Lee RT, Maurer-Stroh S, Joshi A. HIV-1 adaptation to low levels of CCR5 results in V3 and V2 loop changes that increase envelope pathogenicity, CCR5 affinity and decrease susceptibility to Maraviroc. Virology 2016; 493:86-99. [DOI: 10.1016/j.virol.2016.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 11/26/2022]
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16
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Pandey SS, Cherian S, Thakar M, Paranjape RS. Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1. AIDS Res Hum Retroviruses 2016; 32:489-502. [PMID: 26756665 DOI: 10.1089/aid.2015.0207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
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Affiliation(s)
| | - Sarah Cherian
- Bioinformatics Group, National Institute of Virology (ICMR), Pune, India
| | - Madhuri Thakar
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Ramesh S. Paranjape
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
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Yokoyama M, Nomaguchi M, Doi N, Kanda T, Adachi A, Sato H. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells. Front Microbiol 2016; 7:110. [PMID: 26903989 PMCID: PMC4746247 DOI: 10.3389/fmicb.2016.00110] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/21/2016] [Indexed: 12/17/2022] Open
Abstract
Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness.
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Affiliation(s)
- Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Naoya Doi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Tadahito Kanda
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan; Department of Research Promotion, Division of Infectious Disease Research, Japan Agency for Medical Research and DevelopmentTokyo, Japan
| | - Akio Adachi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
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18
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Bagdonaite I, Nordén R, Joshi HJ, Dabelsteen S, Nyström K, Vakhrushev SY, Olofsson S, Wandall HH. A strategy for O-glycoproteomics of enveloped viruses--the O-glycoproteome of herpes simplex virus type 1. PLoS Pathog 2015; 11:e1004784. [PMID: 25830354 PMCID: PMC4382219 DOI: 10.1371/journal.ppat.1004784] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/04/2015] [Indexed: 12/12/2022] Open
Abstract
Glycosylation of viral envelope proteins is important for infectivity and interaction with host immunity, however, our current knowledge of the functions of glycosylation is largely limited to N-glycosylation because it is difficult to predict and identify site-specific O-glycosylation. Here, we present a novel proteome-wide discovery strategy for O-glycosylation sites on viral envelope proteins using herpes simplex virus type 1 (HSV-1) as a model. We identified 74 O-linked glycosylation sites on 8 out of the 12 HSV-1 envelope proteins. Two of the identified glycosites found in glycoprotein B were previously implicated in virus attachment to immune cells. We show that HSV-1 infection distorts the secretory pathway and that infected cells accumulate glycoproteins with truncated O-glycans, nonetheless retaining the ability to elongate most of the surface glycans. With the use of precise gene editing, we further demonstrate that elongated O-glycans are essential for HSV-1 in human HaCaT keratinocytes, where HSV-1 produced markedly lower viral titers in HaCaT with abrogated O-glycans compared to the isogenic counterpart with normal O-glycans. The roles of O-linked glycosylation for viral entry, formation, secretion, and immune recognition are poorly understood, and the O-glycoproteomics strategy presented here now opens for unbiased discovery on all enveloped viruses. Information on site-specific O-glycosylation of viral envelope glycoproteins is generally very limited despite important functions. We present a powerful mass-spectrometry based strategy to globally identify O-glycosylation sites on viral envelope proteins of a given virus in the context of a productive infection. We successfully utilized the strategy to map O-linked glycosylation sites on the complex HSV-1 virus demonstrating that O-glycosylation is widely distributed on most envelope proteins. Moreover, we used genetically engineered keratinocytes lacking O-glycan elongation capacity to demonstrate that O-linked glycans are indeed important for HSV-1 biology as HSV-1 particles produced in these cells had significantly lower titers compared to wild-type keratinocytes. These tools enable wider discovery and detailed analysis of the role of site-specific O-glycosylation in virology.
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Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rickard Nordén
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- Institute of Odontology, University of Copenhagen, Copenhagen, Denmark
| | - Kristina Nyström
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sigvard Olofsson
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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19
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IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol 2014; 10:e1003842. [PMID: 25254639 PMCID: PMC4177671 DOI: 10.1371/journal.pcbi.1003842] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/01/2014] [Indexed: 11/19/2022] Open
Abstract
Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals--a cure and a vaccine--remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.
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20
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Sede MM, Moretti FA, Laufer NL, Jones LR, Quarleri JF. HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants. PLoS One 2014; 9:e102857. [PMID: 25032817 PMCID: PMC4102574 DOI: 10.1371/journal.pone.0102857] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/25/2014] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships. METHODS Here, we characterized C2-V3-C3 sequences of HIV obtained from 19 patients followed up for 54 to 114 months using UDPS, with further genotyping and phylogenetic analysis for coreceptor usage. HIV quasispecies diversity and variability as well as HIV plasma viral load were measured longitudinally and their relationship with the HIV coreceptor usage was analyzed. The longitudinal UDPS data were submitted to phylogenetic analysis and sampling times and coreceptor usage were mapped onto the trees obtained. RESULTS Although a temporal viral genetic structuring was evident, the persistence of several viral lineages evolving independently along the infection was statistically supported, indicating a complex scenario for the evolution of viral quasispecies. HIV X4-using variants were present in most of our patients, exhibiting a dissimilar inter- and intra-patient predominance as the component of quasispecies even on antiretroviral therapy. The viral populations from some of the patients studied displayed evidences of the evolution of X4 variants through fitness valleys, whereas for other patients the data favored a gradual mode of emergence. CONCLUSIONS CXCR4 usage can emerge independently, in multiple lineages, along the course of HIV infection. The mode of emergence, i.e. gradual or through fitness valleys seems to depend on both virus and patient factors. Furthermore, our analyses suggest that, besides becoming dominant after population-level switches, minor proportions of X4 viruses might exist along the infection, perhaps even at early stages of it. The fate of these minor variants might depend on both viral and host factors.
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Affiliation(s)
- Mariano M. Sede
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco A. Moretti
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia L. Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Leandro R. Jones
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales, sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Chubut, Argentina
| | - Jorge F. Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Andrianov AM, Kornoushenko YV, Kashyn IA, Kisel MA, Tuzikov AV. In silico design of novel broad anti-HIV-1 agents based on glycosphingolipid β-galactosylceramide, a high-affinity receptor for the envelope gp120 V3 loop. J Biomol Struct Dyn 2014; 33:1051-66. [PMID: 24942968 DOI: 10.1080/07391102.2014.926832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Novel anti-Human immunodeficiency virus (HIV)-1 agents targeting the V3 loop of envelope protein gp120 were designed by computer modeling based on glycosphingolipid β-galactosylceramide (β-GalCer), which is an alternative receptor allowing HIV-1 entry into CD4-negative cells of neural and colonic origin. Models of these β-GalCer analogs bound to the V3 loops from five various HIV-1 variants were generated by molecular docking and their stability was estimated by molecular dynamics (MDs) and binding free energy simulations. Specific binding to the V3 loop was accomplished primarily by non-conventional XH…π interactions between CH/OH sugar groups of the glycolipids and the conserved V3 residues with π-conjugated side chains. The designed compounds were found to block the tip and/or the base of the V3 loop, which form invariant structural motifs that contain residues critical for cell tropism. With the MDs calculations, the docked models of the complexes of the β-GalCer analogs with V3 are energetically stable in all of the cases of interest and exhibit low values of free energy of their formation. Based on the data obtained, these compounds are considered as promising basic structures for the rational design of novel, potent, and broad-spectrum anti-HIV-1 therapeutics.
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Affiliation(s)
- Alexander M Andrianov
- a Institute of Bioorganic Chemistry , National Academy of Sciences of Belarus , Kuprevich Street 5/2, Minsk 220141 , Republic of Belarus
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Yen PJ, Mefford ME, Hoxie JA, Williams KC, Desrosiers RC, Gabuzda D. Identification and characterization of a macrophage-tropic SIV envelope glycoprotein variant in blood from early infection in SIVmac251-infected macaques. Virology 2014; 458-459:53-68. [PMID: 24928039 DOI: 10.1016/j.virol.2014.03.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 02/23/2014] [Accepted: 03/22/2014] [Indexed: 12/01/2022]
Abstract
Macrophages play an important role in HIV/SIV pathogenesis by serving as a reservoir for viral persistence in brain and other tissues. Infected macrophages have been detected in brain early after infection, but macrophage-tropic viruses are rarely isolated until late-stage infection. Little is known about early variants that establish persistent infection in brain. Here, we characterize a unique macrophage-tropic SIV envelope glycoprotein (Env) variant from two weeks post-infection in blood of an SIVmac251-infected macaque that is closely related to sequences in brain from animals with neurological disease. SIVmac251 clones expressing this Env are highly fusogenic, and replicate efficiently in T cells and macrophages. N173 and N481 were identified as novel determinants of macrophage tropism and neutralization sensitivity. These results imply that macrophage-tropic SIV capable of establishing viral reservoirs in brain can be present in blood during early infection. Furthermore, these SIVmac251 clones will be useful for studies on pathogenesis, eradication, and vaccines.
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Affiliation(s)
- Po-Jen Yen
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Medical Sciences Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Megan E Mefford
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Medical Sciences Program in Virology, Harvard Medical School, Boston, MA, USA
| | - James A Hoxie
- Department of Medicine, Hematology-Oncology Division, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ronald C Desrosiers
- New England Primate Research Center, Department of Microbiology and Immunobiology, Harvard Medical School, Southborough, MA, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA.
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23
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Cenci A, D'Avenio G, Tavoschi L, Chiappi M, Becattini S, Narino MDP, Picconi O, Bernasconi D, Fanales-Belasio E, Vardas E, Sukati H, Lo Presti A, Ciccozzi M, Monini P, Ensoli B, Grigioni M, Buttò S. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms. PLoS One 2014; 9:e95183. [PMID: 24788065 PMCID: PMC4005737 DOI: 10.1371/journal.pone.0095183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/24/2014] [Indexed: 11/17/2022] Open
Abstract
The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of “shifting” putative N-glycosylation sites (PNGSs) in the α2 helix (in C3) and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.
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Affiliation(s)
| | - Giuseppe D'Avenio
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Lara Tavoschi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Michele Chiappi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Orietta Picconi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Eftyhia Vardas
- Stellenbosch University, Division of Medical Virology, Stellenbosch, South Africa; Lancet Laboratories, Johannesburg, South Africa
| | - Hosea Sukati
- National Center Public Health Laboratory, Manzini, Swaziland
| | - Alessandra Lo Presti
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy
| | - Massimo Ciccozzi
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy; University of Biomedical Campus, Rome, Italy
| | - Paolo Monini
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Barbara Ensoli
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Mauro Grigioni
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Stefano Buttò
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
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24
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Symons J, Vandekerckhove L, Hütter G, Wensing AMJ, van Ham PM, Deeks SG, Nijhuis M. Dependence on the CCR5 coreceptor for viral replication explains the lack of rebound of CXCR4-predicted HIV variants in the Berlin patient. Clin Infect Dis 2014; 59:596-600. [PMID: 24759824 DOI: 10.1093/cid/ciu284] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The "Berlin patient" is the first patient cured of HIV-1 infection after allogeneic transplantation with nonfunctional CCR5 coreceptor stem cells. We demonstrate that CXCR4-predicted minority viruses present prior to transplantation were unable to rebound after transplantation due to their dependence on CCR5 for replication and high genetic barrier toward CXCR4 usage.
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Affiliation(s)
- Jori Symons
- Department of Medical Microbiology and Virology, University Medical Center, Utrecht, The Netherlands
| | - Linos Vandekerckhove
- Department of Internal Medicine, Infectious Diseases and Psychosomatic Medicine, Ghent University Hospital, Belgium
| | - Gero Hütter
- Institute of Transfusion Medicine and Immunology, Heidelberg, Germany
| | - Annemarie M J Wensing
- Department of Medical Microbiology and Virology, University Medical Center, Utrecht, The Netherlands
| | - Petra M van Ham
- Department of Medical Microbiology and Virology, University Medical Center, Utrecht, The Netherlands
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco
| | - Monique Nijhuis
- Department of Medical Microbiology and Virology, University Medical Center, Utrecht, The Netherlands
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25
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HIV-1 tropism testing and clinical management of CCR5 antagonists: Quebec review and recommendations. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:202-8. [PMID: 24489562 DOI: 10.1155/2013/982759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 tropism assays play a crucial role in determining the response to CCR5 receptor antagonists. Initially, phenotypic tests were used, but limited access to these tests prompted the development of alternative strategies. Recently, genotyping tropism has been validated using a Canadian technology in clinical trials investigating the use of maraviroc in both experienced and treatment-naive patients. The present guidelines review the evidence supporting the use of genotypic assays and provide recommendations regarding tropism testing in daily clinical management.
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Loss of a conserved N-linked glycosylation site in the simian immunodeficiency virus envelope glycoprotein V2 region enhances macrophage tropism by increasing CD4-independent cell-to-cell transmission. J Virol 2014; 88:5014-28. [PMID: 24554659 DOI: 10.1128/jvi.02785-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) strains differ in their capacity to replicate in macrophages, but mechanisms underlying these differences are not fully understood. Here, we identify a highly conserved N-linked glycosylation site (N173 in SIV, corresponding to N160 in HIV) in the V2 region of the SIV envelope glycoprotein (Env) as a novel determinant of macrophage tropism and characterize mechanisms underlying this phenotype. Loss of the N173 glycosylation site in the non-macrophage-tropic SIVmac239 by introducing an N173Q mutation enhanced viral replication and multinucleated giant cell formation upon infection of rhesus macrophages, while the addition of N173 to SIVmac251 had the opposite effect. The removal of N173 in SIVmac239 enhanced CD4-independent cell-to-cell transmission to CCR5-expressing cells. SIVmac239 with N173Q mediated CD4-independent cell-cell fusion but could not infect CD4-negative cells in single-round infections. Thus, CD4-independent phenotypes were detected only in the context of cell-to-cell contact. Similar results were obtained in SIVmac251 with and without N173. N173 decreased the neutralization sensitivity of SIVmac251 but had no effect on the neutralization sensitivity of SIVmac239. The N173Q mutation had no effect on SIVmac239 binding to CD4 in Biacore assays, coimmunoprecipitation assays, and enzyme-linked immunosorbent assays (ELISAs). These findings suggest that the loss of the N173 N-linked glycosylation site increases SIVmac239 replication in macrophages by enhancing CD4-independent cell-to-cell virus transmission through CCR5-mediated fusion. This mechanism may facilitate the escape of macrophage-tropic viruses from neutralizing antibodies while promoting spreading infection by these viruses in vivo. IMPORTANCE In this study, we identify a genetic determinant in the viral envelope (N173) that increases replication and spreading infection of SIV strains in macrophages by enhancing cell-to-cell virus transmission. This effect is explained by a novel mechanism involving increased cell-to-cell fusion in the absence of CD4, the primary receptor that normally mediates virus entry. The same genetic determinant also affects the sensitivity of these viruses to inhibition by neutralizing antibodies. Most macrophage-tropic HIV/SIV strains are known to be neutralization sensitive. Together, these findings suggest that this efficient mode of virus transmission may facilitate the escape of macrophage-tropic viruses from neutralizing antibodies while promoting spreading infection by these viruses to cells expressing little or no CD4 in vivo.
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27
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Maeda Y, Terasawa H, Nakano Y, Monde K, Yusa K, Oka S, Takiguchi M, Harada S. V3-independent competitive resistance of a dual-X4 HIV-1 to the CXCR4 inhibitor AMD3100. PLoS One 2014; 9:e89515. [PMID: 24586840 PMCID: PMC3929750 DOI: 10.1371/journal.pone.0089515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/23/2014] [Indexed: 12/16/2022] Open
Abstract
A CXCR4 inhibitor-resistant HIV-1 was isolated from a dual-X4 HIV-1 in vitro. The resistant variant displayed competitive resistance to the CXCR4 inhibitor AMD3100, indicating that the resistant variant had a higher affinity for CXCR4 than that of the wild-type HIV-1. Amino acid sequence analyses revealed that the resistant variant harbored amino acid substitutions in the V2, C2, and C4 regions, but no remarkable changes in the V3 loop. Site-directed mutagenesis confirmed that the changes in the C2 and C4 regions were principally involved in the reduced sensitivity to AMD3100. Furthermore, the change in the C4 region was associated with increased sensitivity to soluble CD4, and profoundly enhanced the entry efficiency of the virus. Therefore, it is likely that the resistant variant acquired the higher affinity for CD4/CXCR4 by the changes in non-V3 regions. Taken together, a CXCR4 inhibitor-resistant HIV-1 can evolve using a non-V3 pathway.
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Affiliation(s)
- Yosuke Maeda
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- * E-mail:
| | - Hiromi Terasawa
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yusuke Nakano
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuaki Monde
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Keisuke Yusa
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Shinji Harada
- Department of Medical Virology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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28
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Enhanced fusion and virion incorporation for HIV-1 subtype C envelope glycoproteins with compact V1/V2 domains. J Virol 2013; 88:2083-94. [PMID: 24335304 DOI: 10.1128/jvi.02308-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In infected people, the HIV-1 envelope glycoprotein (Env) constantly evolves to escape the immune response while retaining the essential elements needed to mediate viral entry into target cells. The extensive genetic variation of Env is particularly striking in the V1/V2 hypervariable domains. In this study, we investigated the trade-off, in terms of fusion efficiency, for encoding V1/V2 domains of different lengths. We found that natural variations in V1/V2 length exert a profound impact on HIV-1 entry. Variants encoding compact V1/V2 domains mediated fusion with higher efficiencies than related Envs encoding longer V1/V2 domains. By exchanging the V1/V2 domains between Envs of the same infected person or between two persons linked by a transmission event, we further demonstrated that V1/V2 domains critically influence both Env incorporation into viral particles and fusion to primary CD4 T cells and monocyte-derived dendritic cells. Shortening the V1/V2 domains consistently increased Env incorporation and fusion, whereas lengthening the V1/V2 domains decreased Env incorporation and fusion. Given that in a new host transmitted founder viruses are distinguished by compact Envs with fewer glycosylation sites, our study points to fusion and possibly Env incorporation into virions as limiting steps for transmission of HIV-1 to a new host and suggests that the length and/or the N-glycosylation profile of the V1/V2 domain influences these early steps in the HIV life cycle.
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29
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Ho YS, Saksena NK. Glycosylation in HIV-1 envelope glycoprotein and its biological implications. Future Virol 2013. [DOI: 10.2217/fvl.13.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Glycosylation of HIV-1 envelope proteins (Env gp120/gp41) plays a vital role in viral evasion from the host immune response, which occurs through the masking of key neutralization epitopes and the presentation of the Env glycosylation as ‘self’ to the host immune system. Env glycosylation is generally conserved, yet its continual evolution plays an important role in modulating viral infectivity and Env immunogenicity. Thus, it is believed that Env glycosylation, which is a vital part of the HIV-1 architecture, also controls intra- and inter-clade genetic variations. Discerning intra- and inter-clade glycosylation variations could therefore yield important information for understanding the molecular and biological differences between HIV clades and may assist in effectively designing Env-based immunogens and in clearly understanding HIV vaccines. This review provides an in-depth perspective of various aspects of Env glycosylation in the context of HIV-1 pathogenesis.
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Affiliation(s)
- Yung Shwen Ho
- Computational Bioscience Research Center, Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Instiute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW 2145, Australia
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30
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Pou C, Codoñer FM, Thielen A, Bellido R, Pérez-Álvarez S, Cabrera C, Dalmau J, Curriu M, Lie Y, Noguera-Julian M, Puig J, Martínez-Picado J, Blanco J, Coakley E, Däumer M, Clotet B, Paredes R. HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization. PLoS One 2013; 8:e67085. [PMID: 23936293 PMCID: PMC3731261 DOI: 10.1371/journal.pone.0067085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/15/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Technically, HIV-1 tropism can be evaluated in plasma or peripheral blood mononuclear cells (PBMCs). However, only tropism testing of plasma HIV-1 has been validated as a tool to predict virological response to CCR5 antagonists in clinical trials. The preferable tropism testing strategy in subjects with undetectable HIV-1 viremia, in whom plasma tropism testing is not feasible, remains uncertain. METHODS & RESULTS We designed a proof-of-concept study including 30 chronically HIV-1-infected individuals who achieved HIV-1 RNA <50 copies/mL during at least 2 years after first-line ART initiation. First, we determined the diagnostic accuracy of 454 and population sequencing of gp120 V3-loops in plasma and PBMCs, as well as of MT-2 assays before ART initiation. The Enhanced Sensitivity Trofile Assay (ESTA) was used as the technical reference standard. 454 sequencing of plasma viruses provided the highest agreement with ESTA. The accuracy of 454 sequencing decreased in PBMCs due to reduced specificity. Population sequencing in plasma and PBMCs was slightly less accurate than plasma 454 sequencing, being less sensitive but more specific. MT-2 assays had low sensitivity but 100% specificity. Then, we used optimized 454 sequence data to investigate viral evolution in PBMCs during viremia suppression and only found evolution of R5 viruses in one subject. No de novo CXCR4-using HIV-1 production was observed over time. Finally, Slatkin-Maddison tests suggested that plasma and cell-associated V3 forms were sometimes compartmentalized. CONCLUSIONS The absence of tropism shifts during viremia suppression suggests that, when available, testing of stored plasma samples is generally safe and informative, provided that HIV-1 suppression is maintained. Tropism testing in PBMCs may not necessarily produce equivalent biological results to plasma, because the structure of viral populations and the diagnostic performance of tropism assays may sometimes vary between compartments. Thereby, proviral DNA tropism testing should be specifically validated in clinical trials before it can be applied to routine clinical decision-making.
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Affiliation(s)
- Christian Pou
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- * E-mail: (CP); (RP)
| | - Francisco M. Codoñer
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | | | - Rocío Bellido
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Susana Pérez-Álvarez
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Cecilia Cabrera
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Judith Dalmau
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Marta Curriu
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Yolanda Lie
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Jordi Puig
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Javier Martínez-Picado
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Julià Blanco
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Eoin Coakley
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserlautern, Germany
| | - Bonaventura Clotet
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Roger Paredes
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- * E-mail: (CP); (RP)
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31
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Andrianov AM, Kornoushenko YV, Anishchenko IV, Eremin VF, Tuzikov AV. Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe. J Biomol Struct Dyn 2013; 31:665-83. [DOI: 10.1080/07391102.2012.706455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Mild M, Gray RR, Kvist A, Lemey P, Goodenow MM, Fenyö EM, Albert J, Salemi M, Esbjörnsson J, Medstrand P. High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch. INFECTION GENETICS AND EVOLUTION 2013; 19:369-77. [PMID: 23672855 DOI: 10.1016/j.meegid.2013.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 04/29/2013] [Accepted: 05/04/2013] [Indexed: 12/20/2022]
Abstract
In approximately 70% of individuals infected with HIV-1 subtype B, the virus switches coreceptor use from exclusively CCR5 use (R5 virus) to either inclusion of or exclusively CXCR4 use (X4 virus) during infection. This switch is associated with an accelerated loss of CD4(+) T-cells and a faster progression to AIDS. Despite intensive research, the mechanisms responsible for coreceptor switch remains elusive. In the present study, we investigated associations between viral evolutionary rate and selection pressure versus viral coreceptor use and rate of disease progression in eight patients with longitudinally sampled HIV-1 env V1-V3 sequences. By employing a Bayesian hierarchical phylogenetic model, we found that the HIV-1 evolutionary rate was more strongly associated with coreceptor switch than with rate of disease progression in terms of CD4(+)T-cell decline. Phylogenetic analyses showed that X4 variants evolved from R5 populations. In addition, coreceptor switch was associated with higher evolutionary rates on both the synonymous and non-synonymous substitution level, but not with dN/dS ratio rates. Our findings suggest that X4 viruses evolved from pre-existing R5 viral populations and that the evolution of coreceptor switch is governed by high replication rates rather than by selective pressure. Furthermore, the association of viral evolutionary rate was more strongly associated with coreceptor switch than disease progression. This adds to the understanding of the complex virus-host interplay that influences the evolutionary dynamics of HIV-1 coreceptor use.
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Affiliation(s)
- Mattias Mild
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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33
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Ren W, Mumbauer A, Zhuang K, Harbison C, Knight H, Westmoreland S, Gettie A, Blanchard J, Cheng-Mayer C. Mucosal transmissibility, disease induction and coreceptor switching of R5 SHIVSF162P3N molecular clones in rhesus macaques. Retrovirology 2013; 10:9. [PMID: 23369442 PMCID: PMC3571932 DOI: 10.1186/1742-4690-10-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/25/2013] [Indexed: 11/18/2022] Open
Abstract
Background Mucosally transmissible and pathogenic CCR5 (R5)-tropic simian-human immunodeficiency virus (SHIV) molecular clones are useful reagents to identity neutralization escape in HIV-1 vaccine experiments and to study the envelope evolutionary process and mechanistic basis for coreceptor switch during the course of natural infection. Results We observed progression to AIDS in rhesus macaques infected intrarectally with molecular clones of the pathogenic R5 SHIVSF162P3N isolate. Expansion to CXCR4 usage was documented in one diseased macaque that mounted a neutralizing antibody response and in another that failed to do so, with the latter displaying a rapid progressor phenotype. V3 loop envelop glycoprotein gp120 sequence changes that are predictive of a CXCR4 (X4)-using phenotype in HIV-1 subtype B primary isolates, specifically basic amino acid substations at positions 11 (S11R), 24 (G24R) and 25 (D25K) of the loop were detected in the two infected macaques. Functional assays showed that envelopes with V3 S11R or D25K mutation were dual-tropic, infecting CD4+ target cells that expressed either the CCR5 or CXCR4 coreceptor. And, consistent with findings of coreceptor switching in macaques infected with the pathogenic isolate, CXCR4-using variant was first detected in the lymph node of the chronically infected rhesus monkey several weeks prior to its presence in peripheral blood. Moreover, X4 emergence in this macaque coincided with persistent peripheral CD4+ T cell loss and a decline in neutralizing antibody titer that are suggestive of immune deterioration, with macrophages as the major virus-producing cells at the end-stage of disease. Conclusions The data showed that molecular clones derived from the R5 SHIVSF162P3N isolate are mucosally transmissible and induced disease in a manner similar to that observed in HIV-1 infected individuals, providing a relevant and useful animal infection model for in-depth analyses of host selection pressures and the env evolutionary changes that influence disease outcome, coreceptor switching and vaccine escape.
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Affiliation(s)
- Wuze Ren
- Aaron Diamond AIDS Research Center, 455 First Ave,, 7th Floor, New York, NY 10016, USA
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Xiang SH, Pacheco B, Bowder D, Yuan W, Sodroski J. Characterization of a dual-tropic human immunodeficiency virus (HIV-1) strain derived from the prototypical X4 isolate HXBc2. Virology 2013; 438:5-13. [PMID: 23369572 DOI: 10.1016/j.virol.2013.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/21/2012] [Accepted: 01/02/2013] [Indexed: 11/25/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) coreceptor usage and tropism can be modulated by the V3 loop sequence of the gp120 exterior envelope glycoprotein. For coreceptors, R5 viruses use CCR5, X4 viruses use CXCR4, and dual-tropic (R5X4) viruses use either CCR5 or CXCR4. To understand the requirements for dual tropism, we derived and analyzed a dual-tropic variant of an X4 virus. Changes in the V3 base, which allow gp120 to interact with the tyrosine-sulfated CCR5 N-terminus, and deletion of residues 310/311 in the V3 tip were necessary for efficient CCR5 binding and utilization. Thus, both sets of V3 changes allowed CCR5 utilization with retention of the ability to use CXCR4. We also found that the stable association of gp120 with the trimeric envelope glycoprotein complex in R5X4 viruses, as in X4 viruses, is less sensitive to V3 loop changes than gp120-trimer association in R5 viruses.
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Affiliation(s)
- Shi-hua Xiang
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02215, USA.
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Abstract
HIV-1 subtype CRF01-AE predominates in south Asia and has spread throughout the world. The virus tropism must be determined before using CCR5 antagonists. Genotypic methods could be used, but the prediction algorithms may be inaccurate for non-B subtypes like CRF01-AE and the correlation with the phenotypic approach has not been assessed. We analyzed 61 CRF01-AE V3 clonal sequences of known phenotype from the GenBank database. The sensitivity of the Geno2pheno10 genotypic algorithm was 91%, but its specificity was poor (54%). In contrast, the combined 11/25 and net charge rule was highly specific (98%) but rather insensitive (64%). We thus identified subtype CRF01-AE determinants in the V3 region that are associated with CXCR4 use and developed a new simple rule for optimizing the genotypic prediction of CRF01-AE tropism. The concordance between the predicted CRF01-AE genotype and the phenotype was 95% for the clonal data set. We then validated this algorithm by analyzing the data from 44 patients infected with subtype CRF01-AE, whose tropism was determined using a recombinant phenotypic entry assay and V3-loop bulk sequencing. The CRF01-AE genotypic tool was 70% sensitive and 96% specific for predicting CXCR4 use, and the concordance between genotype and phenotype was 84%, approaching the concordance obtained for predicting the tropism of HIV-1 subtype B. Genotypic predictions that use a subtype CRF01-AE-specific algorithm appear to be preferable for characterizing coreceptor usage both in pathophysiological studies and for ensuring the appropriate use of CCR5 antagonists.
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Yokoyama M, Naganawa S, Yoshimura K, Matsushita S, Sato H. Structural dynamics of HIV-1 envelope Gp120 outer domain with V3 loop. PLoS One 2012; 7:e37530. [PMID: 22624045 PMCID: PMC3356331 DOI: 10.1371/journal.pone.0037530] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/20/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The net charge of the hypervariable V3 loop on the HIV-1 envelope gp120 outer domain plays a key role in modulating viral phenotype. However, the molecular mechanisms underlying the modulation remain poorly understood. METHODOLOGY/PRINCIPAL FINDINGS By combining computational and experimental approaches, we examined how V3 net charge could influence the phenotype of the gp120 interaction surface. Molecular dynamics simulations of the identical gp120 outer domain, carrying a V3 loop with net charge of +3 or +7, showed that the V3 change alone could induce global changes in fluctuation and conformation of the loops involved in binding to CD4, coreceptor and antibodies. A neutralization study using the V3 recombinant HIV-1 infectious clones showed that the virus carrying the gp120 with +3 V3, but not with +7 V3, was resistant to neutralization by anti-CD4 binding site monoclonal antibodies. An information entropy study shows that otherwise variable surface of the gp120 outer domain, such as V3 and a region around the CD4 binding loop, are less heterogeneous in the gp120 subpopulation with +3 V3. CONCLUSIONS/SIGNIFICANCE These results suggest that the HIV-1 gp120 V3 loop acts as an electrostatic modulator that influences the global structure and diversity of the interaction surface of the gp120 outer domain. Our findings will provide a novel structural basis to understand how HIV-1 adjusts relative replication fitness by V3 mutations.
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Affiliation(s)
- Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi Murayama-shi, Tokyo, Japan
- * E-mail: (MY); (HS)
| | - Satoshi Naganawa
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Kazuhisa Yoshimura
- Division of Clinical Retrovirology and Infectious Diseases, Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Kumamoto, Japan
| | - Shuzo Matsushita
- Division of Clinical Retrovirology and Infectious Diseases, Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Kumamoto, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi Murayama-shi, Tokyo, Japan
- * E-mail: (MY); (HS)
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Andrianov AM, Anishchenko IV. Computational Model of the HIV-1 Subtype A V3 Loop: Study on the Conformational Mobility for Structure-Based Anti-AIDS Drug Design. J Biomol Struct Dyn 2012; 27:179-93. [DOI: 10.1080/07391102.2009.10507308] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Alexander M. Andrianov
- a Institute of Bioorganic Chemistry National Academy of Sciences of Belarus , Kuprevich Street 5/2, 220141 , Minsk , Republic of Belarus
| | - Ivan V. Anishchenko
- b United Institute of Informatics Problems National Academy of Sciences of Belarus , Surganov Street 6, 220012 , Minsk , Republic of Belarus
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Huang X, Jin W, Hu K, Luo S, Du T, Griffin GE, Shattock RJ, Hu Q. Highly conserved HIV-1 gp120 glycans proximal to CD4-binding region affect viral infectivity and neutralizing antibody induction. Virology 2012; 423:97-106. [DOI: 10.1016/j.virol.2011.11.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/15/2011] [Accepted: 11/28/2011] [Indexed: 10/14/2022]
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39
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Bialuk I, Whitney S, Andresen V, Florese RH, Nacsa J, Cecchinato V, Valeri VW, Heraud JM, Gordon S, Parks RW, Montefiori DC, Venzon D, Demberg T, Guroff MR, Landucci G, Forthal DN, Franchini G. Vaccine induced antibodies to the first variable loop of human immunodeficiency virus type 1 gp120, mediate antibody-dependent virus inhibition in macaques. Vaccine 2011; 30:78-94. [PMID: 22037204 DOI: 10.1016/j.vaccine.2011.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 10/11/2011] [Accepted: 10/17/2011] [Indexed: 12/21/2022]
Abstract
The role of antibodies directed against the hyper variable envelope region V1 of human immunodeficiency virus type 1 (HIV-1), has not been thoroughly studied. We show that a vaccine able to elicit strain-specific non-neutralizing antibodies to this region of gp120 is associated with control of highly pathogenic chimeric SHIV(89.6P) replication in rhesus macaques. The vaccinated animal that had the highest titers of antibodies to the amino terminus portion of V1, prior to challenge, had secondary antibody responses that mediated cell killing by antibody-dependent cellular cytotoxicity (ADCC), as early as 2 weeks after infection and inhibited viral replication by antibody-dependent cell-mediated virus inhibition (ADCVI), by 4 weeks after infection. There was a significant inverse correlation between virus level and binding antibody titers to the envelope protein, (R=-0.83, p=0.015), and ADCVI (R=-0.84 p=0.044). Genotyping of plasma virus demonstrated in vivo selection of three SHIV(89.6P) variants with changes in potential N-linked glycosylation sites in V1. We found a significant inverse correlation between virus levels and titers of antibodies that mediated ADCVI against all the identified V1 virus variants. A significant inverse correlation was also found between neutralizing antibody titers to SHIV(89.6) and virus levels (R=-0.72 p=0.0050). However, passive inoculation of purified immunoglobulin from animal M316, the macaque that best controlled virus, to a naïve macaque, resulted in a low serum neutralizing antibodies and low ADCVI activity that failed to protect from SHIV(89.6P) challenge. Collectively, while our data suggest that anti-envelope antibodies with neutralizing and non-neutralizing Fc(R-dependent activities may be important in the control of SHIV replication, they also demonstrate that low levels of these antibodies alone are not sufficient to protect from infection.
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Affiliation(s)
- Izabela Bialuk
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
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Naturally Occurring Polymorphisms of the Mouse Gammaretrovirus Receptors CAT-1 and XPR1 Alter Virus Tropism and Pathogenicity. Adv Virol 2011; 2011:975801. [PMID: 22312361 PMCID: PMC3265322 DOI: 10.1155/2011/975801] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/12/2011] [Indexed: 01/29/2023] Open
Abstract
Gammaretroviruses of several different host range subgroups have been isolated from laboratory mice. The ecotropic viruses infect mouse cells and rely on the host CAT-1 receptor. The xenotropic/polytropic viruses, and the related human-derived XMRV, can infect cells of other mammalian species and use the XPR1 receptor for entry. The coevolution of these viruses and their receptors in infected mouse populations provides a good example of how genetic conflicts can drive diversifying selection. Genetic and epigenetic variations in the virus envelope glycoproteins can result in altered host range and pathogenicity, and changes in the virus binding sites of the receptors are responsible for host restrictions that reduce virus entry or block it altogether. These battleground regions are marked by mutational changes that have produced 2 functionally distinct variants of the CAT-1 receptor and 5 variants of the XPR1 receptor in mice, as well as a diverse set of infectious viruses, and several endogenous retroviruses coopted by the host to interfere with entry.
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41
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Andrianov AM, Anishchenko IV, Tuzikov AV. Discovery of Novel Promising Targets for Anti-AIDS Drug Developments by Computer Modeling: Application to the HIV-1 gp120 V3 Loop. J Chem Inf Model 2011; 51:2760-7. [DOI: 10.1021/ci200255t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander M. Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Kuprevich Str. 5/2, 220141, Minsk, Belarus
| | - Ivan V. Anishchenko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Surganov Str. 6, 220012, Minsk, Belarus
| | - Alexander V. Tuzikov
- Laboratory of Mathematical Cybernetics, United Institute of Informatics Problems, National Academy of Sciences of Belarus, Surganov Str. 6, 220012, Minsk, Belarus
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42
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Andrianov AM, Anishchenko IV. [Computer modeling of the promising inhibitors of the HIV-1 subtype A replication as a framework for the rational anti-aids drug design]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2011; 57:161-73. [PMID: 21870601 DOI: 10.18097/pbmc20115702161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The model of the structural complex of cyclophilin B belonging to the immunophilins family with the HIV-1 subtype A V3 loop presenting the principal neutralizing determinant of the virus gp120 envelope protein as well as determinants of cell tropism and syncutium formation was generated by molecular docking methods. Basing on the conformational and energy characteristics of the built complex, computer-aided design of the polypeptide able to block effectively the functionally crucial V3 segments was implemented. From the joint analysis of the results derived with the data of literature, the generated molecule was suggested to offer a promising pharmacological substance for making a reality of the protein engineering projects aimed at developing the anti-AIDS drugs able to stop the HIV's spread.
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Characterization of structural features and diversity of variable-region determinants of related quaternary epitopes recognized by human and rhesus macaque monoclonal antibodies possessing unusually potent neutralizing activities. J Virol 2011; 85:10730-40. [PMID: 21835798 DOI: 10.1128/jvi.00365-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A series of potently neutralizing monoclonal antibodies (MAbs) that target quaternary epitopes on the native Env trimer have recently been described. A common feature shared by these antibodies is the critical involvement of sites in both the V2 and V3 variable domains in antibody recognition. In this study the gp120 variable-region determinants were mapped for eight rhesus macaque monoclonal antibodies (RhMAbs) possessing potently neutralizing activity specific for a quaternary target in SF162 Env and compared to those originally identified for human MAb 2909. These studies showed that determinants for the epitopes defined by the RhMAbs differed in both the V2 (positions 160, 167, and 169) and V3 (positions 313 and 315) regions from 2909, and in a number of cases, from each other. Attempts to reconstitute expression of these epitopes on the cell surface by cotransfecting Envs containing either the V2 or the V3 determinant of the epitope were not successful, suggesting that these epitopes were expressed on individual protomers in a trimer-dependent manner. Several of the V2 positions found to be critical for expression of these quaternary epitopes also significantly affected exposure and neutralization sensitivity of targets in the V3 and CD4-binding domains. These results demonstrated a considerable diversity in the fine structure of this class of epitopes and further suggested a potentially important relationship between the expression of such quaternary epitopes and V1/V2-mediated masking of immunodominant epitopes.
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Pramanik L, Fried U, Clevestig P, Ehrnst A. Charged amino acid patterns of coreceptor use in the major subtypes of human immunodeficiency virus type 1. J Gen Virol 2011; 92:1917-1922. [PMID: 21525208 DOI: 10.1099/vir.0.029447-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 has several genetic subtypes and two coreceptor use phenotypes: R5 that uses CCR5, while X4 uses CXCR4. A high amino acid charge of the envelope glycoprotein 120 V3 region, common at positions 11 and 25, is important for CXCR4 use. We characterized charged V3 amino acids, retrieving all biologically phenotyped sequences from the HIV Sequence Database. Selecting individually unique ones randomly yielded 48 subtype A, 231 B, 180 C, 37 D and 32 CRF01_AE sequences; 482 were R5 and 46 were X4. Charged amino acids were conserved in both R5 and X4 with general and subtype-specific patterns. X4 viruses gained a higher charge from positive amino acids at positions other than in R5, and through the loss of negative amino acids. Other positions than 11/25 had a greater impact on charge (P<0.001). This describes how R5 evolves into X4 in a subtype-specific context, useful for computer-based predictions and vaccine design.
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Affiliation(s)
- Lotta Pramanik
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Ulrik Fried
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Peter Clevestig
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Anneka Ehrnst
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
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45
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Andrianov AM. Human immunodeficiency virus-1 gp120 V3 loop for anti-acquired immune deficiency syndrome drug discovery: computer-aided approaches to the problem solving. Expert Opin Drug Discov 2011; 6:419-35. [DOI: 10.1517/17460441.2011.560603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Kuprevich Street 5/2, 220141 Minsk, Republic of Belarus +375 17 2678263 ; +375 17 2241214 ;
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46
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Gharu L, Ringe R, Satyakumar A, Patil A, Bhattacharya J. Short communication: evidence of HIV type 1 clade C env clones containing low V3 loop charge obtained from an AIDS patient in India that uses CXCR6 and CCR8 for entry in addition to CCR5. AIDS Res Hum Retroviruses 2011; 27:211-9. [PMID: 20854195 DOI: 10.1089/aid.2009.0180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract HIV-1 clade C is the major subtype circulating in India and preferentially uses CCR5 during the entire disease course. We have recently shown that env clones from an Indian patient; NARI-VB105 uses multiple coreceptors for entry and was presented with an unusual V3 loop sequence giving rise to high net V3 loop positive charges. Here we show that env clones belonging to subtype C obtained from an AIDS patient, NARI-VB52, use CXCR6 and CCR8 in addition to CCR5 for entry. However, unlike the NARI-105 patient, the env clones contained a low V3 loop net charge of +3 with a conserved GPGQ motif typical of CCR5 using subtype C strains, indicating that residues outside the V3 loop contributed to extended coreceptor use in this particular patient.
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Affiliation(s)
- Lavina Gharu
- Department of Molecular Virology, National AIDS Research Institute, G-73 MIDC, Bhosari, Pune, India
| | - Rajesh Ringe
- Department of Molecular Virology, National AIDS Research Institute, G-73 MIDC, Bhosari, Pune, India
| | - Anupindi Satyakumar
- Department of Molecular Virology, National AIDS Research Institute, G-73 MIDC, Bhosari, Pune, India
| | - Ajit Patil
- Department of Molecular Virology, National AIDS Research Institute, G-73 MIDC, Bhosari, Pune, India
| | - Jayanta Bhattacharya
- Department of Molecular Virology, National AIDS Research Institute, G-73 MIDC, Bhosari, Pune, India
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47
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Zhang H, Tully DC, Zhang T, Moriyama H, Thompson J, Wood C. Molecular determinants of HIV-1 subtype C coreceptor transition from R5 to R5X4. Virology 2010; 407:68-79. [PMID: 20797755 DOI: 10.1016/j.virol.2010.07.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/01/2010] [Accepted: 07/28/2010] [Indexed: 11/18/2022]
Abstract
The molecular mechanism(s) underlying transition from CCR5 to CXCR4 usage of subtype C viruses remain largely unknown. We previously identified a subtype C HIV-1 infected child whose virus demonstrated CXCR4 usage along with CCR5 upon longitudinal follow-up. Here we delineated the molecular determinants of Env involved in expanded coreceptor usage. Residue changes in three positions of Env V3 domain are critical for the dual tropic phenotype. These include: substitution of arginine at position 11, MG or LG insertion between positions 13 and 14, and substitution of threonine at the position immediately downstream of the GPGQ crown. Introducing these mutations into V3 region of a heterologous R5 virus also conferred dual tropism. Molecular modeling of V3 revealed a possible structural basis for the dual tropic phenotype. Determining what defines a subtype C X4 virus will lead to a better understanding of subtype C HIV-1 pathogenesis, and will provide important information relevant to anti-retroviral therapy.
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Affiliation(s)
- Hong Zhang
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA
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48
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Heeregrave EJ, Ampofo WK, Tetteh JKA, Ofori M, Ofori SB, Shah AS, Pollakis G, Paxton WA. Generation of HIV-1 primary isolates representative of plasma variants using the U87.CD4 cell line. J Virol Methods 2010; 169:341-50. [PMID: 20705104 DOI: 10.1016/j.jviromet.2010.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/28/2010] [Accepted: 08/03/2010] [Indexed: 11/26/2022]
Abstract
In order to obtain HIV-1 primary isolates in settings with limited access to donor PBMCs, a culture method was developed where patient PBMCs infected with HIV-1 were cultured together with U87.CD4 cells. Using this non-laborious method, it is possible to harvest virus solely on the basis of syncytia formation and circumventing monitoring of viral replication by CA-p24 ELISA. Primary isolates from 23 out of 33 patients (70%) were isolated successfully. From PCR amplification and sequencing of the V1V5 region of the viral gp120 envelope gene, primary isolates were compared with variants obtained from plasma and PBMCs of 13 patients. The primary isolates of seven patients (54%) resembled closely the plasma viral quasispecies, whereas different variants were isolated from the other patients (46%). Three patients harboured a dual infection, while this remained unnoticed from sequencing the plasma or PBMC compartment. The primary isolates were highly infectious for TZM-bl cells and could infect CD4-enriched lymphocytes. This study demonstrates that it is possible to grow viral isolates using a non-laborious and simple method. These isolates may be used in the field for studies on antiretroviral therapy or for vaccine trials.
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Affiliation(s)
- Edwin J Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
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Variable loop glycan dependency of the broad and potent HIV-1-neutralizing antibodies PG9 and PG16. J Virol 2010; 84:10510-21. [PMID: 20686044 DOI: 10.1128/jvi.00552-10] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The HIV-1-specific antibodies PG9 and PG16 show marked cross-isolate neutralization breadth and potency. Antibody neutralization has been shown to be dependent on the presence of N-linked glycosylation at position 160 in gp120. We show here that (i) the loss of several key glycosylation sites in the V1, V2, and V3 loops; (ii) the generation of pseudoviruses in the presence of various glycosidase inhibitors; and (iii) the growth of pseudoviruses in a mutant cell line (GnT1(-/-)) that alters envelope glycosylation patterns all have significant effects on the sensitivity of virus to neutralization by PG9 and PG16. However, the interaction of antibody is not inhibited by sugar monosaccharides corresponding to those found in glycans on the HIV surface. We show that some of the glycosylation effects described are isolate dependent and others are universal and can be used as diagnostic for the presence of PG9 and PG16-like antibodies in the sera of HIV-1-infected patients. The results suggest that PG9 and PG16 recognize a conformational epitope that is dependent on glycosylation at specific variable loop N-linked sites. This information may be valuable for the design of immunogens to elicit PG9 and PG16-like antibodies, as well as constructs for cocrystallization studies.
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50
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Distinct molecular pathways to X4 tropism for a V3-truncated human immunodeficiency virus type 1 lead to differential coreceptor interactions and sensitivity to a CXCR4 antagonist. J Virol 2010; 84:8777-89. [PMID: 20573813 DOI: 10.1128/jvi.00333-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
During the course of infection, transmitted HIV-1 isolates that initially use CCR5 can acquire the ability to use CXCR4, which is associated with an accelerated progression to AIDS. Although this coreceptor switch is often associated with mutations in the stem of the viral envelope (Env) V3 loop, domains outside V3 can also play a role, and the underlying mechanisms and structural basis for how X4 tropism is acquired remain unknown. In this study we used a V3 truncated R5-tropic Env as a starting point to derive two X4-tropic Envs, termed DeltaV3-X4A.c5 and DeltaV3-X4B.c7, which took distinct molecular pathways for this change. The DeltaV3-X4A.c5 Env clone acquired a 7-amino-acid insertion in V3 that included three positively charged residues, reestablishing an interaction with the CXCR4 extracellular loops (ECLs) and rendering it highly susceptible to the CXCR4 antagonist AMD3100. In contrast, the DeltaV3-X4B.c7 Env maintained the V3 truncation but acquired mutations outside V3 that were critical for X4 tropism. In contrast to DeltaV3-X4A.c5, DeltaV3-X4B.c7 showed increased dependence on the CXCR4 N terminus (NT) and was completely resistant to AMD3100. These results indicate that HIV-1 X4 coreceptor switching can involve (i) V3 loop mutations that establish interactions with the CXCR4 ECLs, and/or (ii) mutations outside V3 that enhance interactions with the CXCR4 NT. The cooperative contributions of CXCR4 NT and ECL interactions with gp120 in acquiring X4 tropism likely impart flexibility on pathways for viral evolution and suggest novel approaches to isolate these interactions for drug discovery.
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