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Rindler AE, Kuster H, Neumann K, Leemann C, Braun DL, Metzner KJ, Günthard HF. A Novel High Throughput, Parallel Infection Assay for Determining the Replication Capacities of 346 Primary HIV-1 Isolates of the Zurich Primary HIV-1 Infection Study in Primary Cells. Viruses 2021; 13:404. [PMID: 33806576 PMCID: PMC8000554 DOI: 10.3390/v13030404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 replication capacity is an important characteristic to understand the replication competence of single variants or virus populations. It can further aid in the understanding of HIV-1 pathogenicity, disease progression, and drug resistance mutations. To effectively study RC, many assays have been established. However, there is still demand for a high throughput replication capacity assay using primary cells which is robust and reproducible. In this study, we established such an assay and validated it using 346 primary HIV-1 isolates from patients enrolled in the Zurich Primary HIV Infection study (ZPHI) and two control viruses, HIV-1 JR-CSFWT and HIV-1 JR-CSFK65R_M184V. Replication capacity was determined by measuring the viral growth on PBMCs over 10 days by longitudinally transferring cell culture supernatant to TZM-bl reporter cells. By utilizing the TZM-bl luciferase reporter assay, we determined replication capacity by measuring viral infectivity. The simplicity of the experimental setup allowed for all 346 primary HIV-1 isolates to be replicated at one time. Although the infectious input dose for each virus was normalized, a broad range of replication capacity values over 4 logs was observed. The approach was confirmed by two repeated experiments and we demonstrated that the reproducibility of the replication capacity values is statistically comparable between the two separate experiments. In summary, these results endorse our high throughput replication capacity assay as reproducible and robust and can be utilized for large scale HIV-1 replication capacity experiments in primary cells.
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Affiliation(s)
- Audrey E. Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
- Life Sciences Graduate School, University of Zürich, 8057 Zürich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
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2
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Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer AU, Müller V, Bonhoeffer S, Kouyos R, Regoes RR. Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity. Mol Biol Evol 2019; 35:27-37. [PMID: 29029206 PMCID: PMC5850767 DOI: 10.1093/molbev/msx246] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as “per-parasite pathogenicity”. Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence—measured as the rate of decline of CD4+ T cells—and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor–recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T-cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T-cell decline is 17% (5–30%), and that of the per-parasite pathogenicity is 17% (4–29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12–46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T-cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genotype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor.
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Affiliation(s)
- Frederic Bertels
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases, Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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3
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Walker-Sperling VE, Pohlmeyer CW, Veenhuis RT, May M, Luna KA, Kirkpatrick AR, Laeyendecker O, Cox AL, Carrington M, Bailey JR, Arduino RC, Blankson JN. Factors Associated With the Control of Viral Replication and Virologic Breakthrough in a Recently Infected HIV-1 Controller. EBioMedicine 2017; 16:141-149. [PMID: 28159573 PMCID: PMC5474502 DOI: 10.1016/j.ebiom.2017.01.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 01/08/2023] Open
Abstract
HIV-1 controllers are patients who control HIV-1 viral replication without antiretroviral therapy. Control is achieved very early in the course of infection, but the mechanisms through which viral replication is restricted are not fully understood. We describe a patient who presented with acute HIV-1 infection and was found to have an HIV-1 RNA level of < 100 copies/mL. She did not have any known protective HLA alleles, but significant immune activation of CD8 + T cells and natural killer (NK) cells was present, and both cell types inhibited viral replication. Virus cultured from this patient replicated as well in vitro as virus isolated from her partner, a patient with AIDS who was the source of transmission. Virologic breakthrough occurred 9 months after her initial presentation and was associated with an increase in CD4 + T cell activation levels and a significant decrease in NK cell inhibitory capacity. Remarkably, CD8 + T cell inhibitory capacity was preserved and there were no new escape mutations in targeted Gag epitopes. These findings suggest that fully replication-competent virus can be controlled in acute HIV-1 infection in some patients without protective HLA alleles and that NK cell responses may contribute to this early control of viral replication. We show that an HIV-1 controller was infected with pathogenic virus yet maintained low viral loads during primary infection. She had activated NK cells and CD8+ T cells and both cell types suppressed HIV-1 replication shortly after infection. She eventually lost control of viral replication, and this was associated with a reduction in NK cell suppressive activity.
HIV-1 controllers are patients who control the virus without HIV-1 medications. These patients may teach us how to design a vaccine against HIV-1. Little is known about how the virus is controlled in the early phase of infection in these patients. Here we show that a recently infected HIV-1 controller had a strong natural killer cell response to the virus. Interestingly, she lost control of the virus 9 months later and her natural killer cell response to the virus was diminished. Our work suggests that natural killer cells may have contributed to viral control in the early phase of infection.
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Affiliation(s)
- Victoria E Walker-Sperling
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher W Pohlmeyer
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca T Veenhuis
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Megan May
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Krystle A Luna
- Department of Medicine, University of Texas MD Anderson Cancer Center, Austin, TX, USA
| | - Allison R Kirkpatrick
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, USA
| | - Andrea L Cox
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Justin R Bailey
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roberto C Arduino
- Department of Internal Medicine, Division of Infectious Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joel N Blankson
- Department of Medicine, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Gatanag H, Oka S, Takiguchi M. Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Retrovirology 2015; 12:98. [PMID: 26585907 PMCID: PMC4653850 DOI: 10.1186/s12977-015-0223-z] [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: 04/30/2015] [Accepted: 11/08/2015] [Indexed: 01/29/2023] Open
Abstract
Background HLA class I-associated escape mutations in HIV-1 Gag can reduce viral replication, suggesting that associated fitness costs could impact HIV-1 disease progression. Previous studies in North American and African cohorts have reported reduced Gag-Protease mediated viral replication capacity (Gag-Pro RC) in individuals expressing protective HLA class I alleles including HLA-B*57:01, B*27:05, and B*81:01. These studies also reported significant positive associations between Gag-Pro RCs and plasma viral load (pVL). However, these HLA alleles are virtually absent in Japan, and the importance of Gag as an immune target is not clearly defined in this population. Results We generated chimeric NL4-3 viruses carrying patient-derived Gag-Protease from 306 treatment-naive Japanese individuals chronically infected with HIV-1 subtype B. We analyzed associations between Gag-Pro RC and clinical markers of HIV-1 infection and host HLA expression. We observed no significant correlation between Gag-Pro RC and pVL in Japan in the overall cohort. However, upon exclusion of individuals expressing Japanese protective alleles HLA-B*52:01 and B*67:01, Gag-Pro RC correlated positively with pVL and negatively with CD4 T-cell count. Our results thus contrast with studies from other global cohorts reporting significantly lower Gag-Pro RC among persons expressing protective HLA alleles, and positive relationships between Gag-Pro RC and pVL in the overall study populations. We also identified five amino acids in Gag-Protease significantly associated with Gag-Pro RC, whose effects on RC were confirmed by site-directed mutagenesis. However, of the four mutations that decreased Gag-Pro RC, none were associated with reductions in pVL in Japan though two were associated with lower pVL in North America. Conclusions These data indicate that Gag fitness does not affect clinical outcomes in subjects with protective HLA class I alleles as well as the whole Japanese population. Moreover, the impact of Gag fitness costs on HIV-1 clinical parameters in chronic infection is likely low in Japan compared to other global populations. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | | | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan. .,Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Ng OT, Laeyendecker O, Redd AD, Munshaw S, Grabowski MK, Paquet AC, Evans MC, Haddad M, Huang W, Robb ML, Reynolds SJ, Gray RH, Wawer MJ, Serwadda D, Eshleman SH, Quinn TC. HIV type 1 polymerase gene polymorphisms are associated with phenotypic differences in replication capacity and disease progression. J Infect Dis 2013; 209:66-73. [PMID: 23922373 DOI: 10.1093/infdis/jit425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Determinants of intersubtype differences in human immunodeficiency virus type 1 (HIV-1) clinical disease progression remain unknown. METHODS HIV-1 subtype was independently determined for 5 separate genomic regions in 396 HIV-1 seroconverters from Rakai, Uganda, using a multiregion hybridization assay. Replication capacities (RC) in samples from a subset of 145 of these subjects were determined. HIV-1 genomic regions and pol RC were examined for association with disease progression. Amino acid polymorphisms were examined for association with pol RC. RESULTS In multivariate analyses, the hazard for progression to the composite end point (defined as a CD4(+) T-cell count <250 cells/mm(3), antiretroviral therapy initiation, or death) among patients with subtype D pol infection was 2.4 times the hazard for those infected with subtype A pol infection (P = .001). Compared with subtype A pol (the reference group), the hazard for progression to the composite end point for subtype D pol infection with a pol RC >67% (ie, the median pol RC) was significantly greater (HR, 4.6; 95% confidence interval [CI], 1.9-11.0; P = .001), whereas the hazard for progression to the composite end point for subtype D pol infection with a pol RC ≤67% was not significantly different (HR, 2.2; 95% CI, 1.0-4.9; P = .051). Amino acid substitutions at protease positions 62 and 64 and at reverse transcriptase position 272 were associated with significant differences in pol RC. CONCLUSIONS HIV-1 pol gene intersubtype and RC differences are associated with disease progression and may be influenced by amino acid polymorphisms.
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Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver DAMC, Albert J, Åsjö B, Balotta C, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Hamouda O, Horban A, Korn K, Kostrikis LG, Kücherer C, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Liitsola K, Schmit JC, Schuurman R, Sönnerborg A, Stanekova D, Stanojevic M, Struck D, Van Laethem K, Wensing AMJ, Boucher CAB, Vandamme AM. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology 2012; 9:81. [PMID: 23031662 PMCID: PMC3487874 DOI: 10.1186/1742-4690-9-81] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. RESULTS Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. CONCLUSIONS These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level.
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Affiliation(s)
- Kristof Theys
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jurgen Vercauteren
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jan Albert
- Clinical Microbiology, Karolinska University Hospital and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Birgitta Åsjö
- Section for Microbiology and Immunology, Gade institute, University of Bergen, Bergen, Norway
| | | | - Marie Bruckova
- National Institute of Public Health, Prague, Czech Republic
| | - Ricardo J Camacho
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | | | - Zehava Grossman
- Sheba Medical Center, Tel-Hashomer, and School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Andrzei Horban
- Warsaw Medical University and Hospital for Infectious Diseases, Warsaw, Poland
| | - Klaus Korn
- Institut für Klinische und Molekulare Virologie, University of Erlangen, Erlangen, Germany
| | | | | | | | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology of Medical Statistics, University of Athens, Medical School, Athens, Greece
| | | | | | | | - Lidia Ruiz
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anders Sönnerborg
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institutet, Stockholm, Sweden
| | | | - Maja Stanojevic
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemarie MJ Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Charles AB Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Bedimo R, Kyriakides T, Brown S, Weidler J, Lie Y, Coakley E, Holodniy M. Predictive value of HIV-1 replication capacity and phenotypic susceptibility scores in antiretroviral treatment-experienced patients. HIV Med 2012; 13:345-51. [PMID: 22276745 DOI: 10.1111/j.1468-1293.2011.00981.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2011] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The aim of the study was to determine the prognostic value of HIV replication capacity (RC) for subsequent antiretroviral (ARV) treatment response in ARV-experienced patients. METHODS RC and phenotypic resistance testing were performed at baseline and week 12 on plasma samples from patients randomized to undergo a 12-week ARV drug-free period (ARDFP) or initiate immediate salvage therapy (no-ARDFP group) in the Options in Management with Antiretrovirals (OPTIMA) trial. Dichotomous and incremental phenotypic susceptibility scores (dPSSs and iPSSs, respectively) were calculated. The predictive value of RC and PSS for ARV therapy response and/or ARDFP was evaluated using multivariate regression analysis and Pearson correlations. RESULTS In 146 no-ARDFP subjects, baseline RC (50.8%) did not change at week 12 and was not correlated with CD4 cell count or viral load changes at week 12 (P=0.33 and P=0.79, respectively) or at week 24 (P=0.96 and P=0.14, respectively). dPSS predicted virological but not CD4 cell count response to ARV therapy at weeks 12, 24 and 48 (P=0.002, P<0.001 and P=0.005, respectively). RC was significantly correlated with dPSS and iPSS at baseline, but did not increase their predictive value. In the 137 ARDFP patients, RC increased significantly (from 52.4 to 85.8%), but did not predict CD4 cell count and viral load changes during ARDFP (P=0.92 and P=0.26, respectively). RC after ARDFP did not predict subsequent CD4 cell count and viral load changes 12 weeks following ARV treatment reinitiation (P=0.90 and P=0.29, respectively). CONCLUSIONS We found no additional predictive value of replication capacity for virological or immunological responses (above what PSS provides) in patients undergoing salvage ARV treatment.
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Affiliation(s)
- R Bedimo
- Veterans Affairs North Texas Health Care System, Dallas, TX 75216, USA.
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Early virologic failure and the development of antiretroviral drug resistance mutations in HIV-infected Ugandan children. J Acquir Immune Defic Syndr 2011; 56:44-50. [PMID: 21099693 DOI: 10.1097/qai.0b013e3181fbcbf7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Without virologic testing, HIV-infected African children starting antiretroviral (ARV) therapy are at risk for undetected virologic failure and the development of ARV resistance. We sought to determine the prevalence of early virologic failure (EVF), to characterize the evolution of ARV-resistance mutations and to predict the impact on second-line therapy. METHODS The prevalence of EVF (HIV RNA >400 copies/mL on sequential visits after 6 months of therapy) was identified among 120 HIV-infected Ugandan children starting ARV therapy. ARV mutations were identified by population sequencing of HIV-1 pol in sequential archived specimens. Composite discrete genotypic susceptibility scores were determined for second-line ARV regimens. RESULTS EVF occurred in 16 children (13%) and persisted throughout a median (interquartile ratio) 938 (760-1066) days of follow-up. M184V and nonnucleoside reverse transcriptase inhibitor-associated mutations emerged within 6 months of EVF; thymidine-analog-mutations arose after 12 months. Worse discrete genotypic susceptibility scores correlated with increasing duration of failure (Spearman R = -0.47; P = 0.001). Only 1 child met World Health Organization CD4 criteria for ARV failure at the time of EVF or during the follow-up period. CONCLUSIONS A significant portion of HIV-infected African children experience EVF that would be undetected using CD4/clinical monitoring and resulted in the accumulation of ARV mutations that could compromise second-line therapy options.
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