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Ferreira RC, Reynolds SJ, Capoferri AA, Baker OR, Brown EE, Klock E, Miller J, Lai J, Saraf S, Kirby C, Lynch B, Hackman J, Gowanlock SN, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Bruno D, Martens C, Rose R, Lamers SL, Galiwango RM, Poon AFY, Quinn TC, Prodger JL, Redd AD. Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. EBioMedicine 2024; 102:105040. [PMID: 38485563 PMCID: PMC11026949 DOI: 10.1016/j.ebiom.2024.105040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The principal barrier to an HIV cure is the presence of the latent viral reservoir (LVR), which has been understudied in African populations. From 2018 to 2019, Uganda instituted a nationwide rollout of ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen of one NNRTI and the same two NRTI. METHODS Changes in the inducible replication-competent LVR (RC-LVR) of ART-suppressed Ugandans with HIV (n = 88) from 2015 to 2020 were examined using the quantitative viral outgrowth assay. Outgrowth viruses were examined for viral evolution. Changes in the RC-LVR were analyzed using three versions of a Bayesian model that estimated the decay rate over time as a single, linear rate (model A), or allowing for a change at time of DTG initiation (model B&C). FINDINGS Model A estimated the slope of RC-LVR change as a non-significant positive increase, which was due to a temporary spike in the RC-LVR that occurred 0-12 months post-DTG initiation (p < 0.005). This was confirmed with models B and C; for instance, model B estimated a significant decay pre-DTG initiation with a half-life of 6.9 years, and an ∼1.7-fold increase in the size of the RC-LVR post-DTG initiation. There was no evidence of viral failure or consistent evolution in the cohort. INTERPRETATION These data suggest that the change from NNRTI- to DTG-based ART is associated with a significant temporary increase in the circulating RC-LVR. FUNDING Supported by the NIH (grant 1-UM1AI164565); Gilead HIV Cure Grants Program (90072171); Canadian Institutes of Health Research (PJT-155990); and Ontario Genomics-Canadian Statistical Sciences Institute.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Steven J Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Rakai Health Sciences Program, Kalisizo, Uganda
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Owen R Baker
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erin E Brown
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ethan Klock
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jernelle Miller
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Daniel Bruno
- Genomics Research Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Craig Martens
- Genomics Research Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | | | | | | | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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3
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Ferreira RC, Reynolds SJ, Capoferri AA, Baker O, Brown EE, Klock E, Miller J, Lai J, Saraf S, Kirby C, Lynch B, Hackman J, Gowanlock SN, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Bruno D, Martens C, Rose R, Lamers SL, Galiwango RM, Poon AFY, Quinn TC, Prodger JL, Redd AD. Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. medRxiv 2023:2023.05.12.23289896. [PMID: 37292785 PMCID: PMC10246077 DOI: 10.1101/2023.05.12.23289896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The principal barrier to an HIV cure is the presence of a latent viral reservoir (LVR) made up primarily of latently infected resting CD4+ (rCD4) T-cells. Studies in the United States have shown that the LVR decays slowly (half-life=3.8 years), but this rate in African populations has been understudied. This study examined longitudinal changes in the inducible replication competent LVR (RC-LVR) of ART-suppressed Ugandans living with HIV (n=88) from 2015-2020 using the quantitative viral outgrowth assay, which measures infectious units per million (IUPM) rCD4 T-cells. In addition, outgrowth viruses were examined with site-directed next-generation sequencing to assess for possible ongoing viral evolution. During the study period (2018-19), Uganda instituted a nationwide rollout of first-line ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen that consisted of one NNRTI and the same two NRTI. Changes in the RC-LVR were analyzed using two versions of a novel Bayesian model that estimated the decay rate over time on ART as a single, linear rate (model A) or allowing for an inflection at time of DTG initiation (model B). Model A estimated the population-level slope of RC-LVR change as a non-significant positive increase. This positive slope was due to a temporary increase in the RC-LVR that occurred 0-12 months post-DTG initiation (p<0.0001). This was confirmed with model B, which estimated a significant decay pre-DTG initiation with a half-life of 7.7 years, but a significant positive slope post-DTG initiation leading to a transient estimated doubling-time of 8.1 years. There was no evidence of viral failure in the cohort, or consistent evolution in the outgrowth sequences associated with DTG initiation. These data suggest that either the initiation of DTG, or cessation of NNRTI use, is associated with a significant temporary increase in the circulating RC-LVR.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Steven J. Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Adam A. Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Owen Baker
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erin E. Brown
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ethan Klock
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jernelle Miller
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sarah N. Gowanlock
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Daniel Bruno
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT
| | | | | | | | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica L. Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Capoferri AA, Redd AD, Gocke CD, Clark LR, Quinn TC, Ambinder RF, Durand CM. Brief Report: Rebound HIV Viremia With Meningoencephalitis After Antiretroviral Therapy Interruption After Allogeneic Bone Marrow Transplant. J Acquir Immune Defic Syndr 2022; 89:297-302. [PMID: 34753870 PMCID: PMC10985789 DOI: 10.1097/qai.0000000000002862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Allogeneic bone marrow transplant (alloBMT) in people living with HIV can lead to the undetectable levels of HIV reservoirs in blood, even using highly sensitive assays. However, with antiretroviral therapy (ART) interruption, rebound of HIV viremia occurs. The source of this rebound viremia is of interest in HIV cure strategies. METHODS Within a trial of alloBMT in individuals with hematologic malignancies and HIV (ClinicalTrials.gov, NCT01836068), one recipient self-interrupted ART after achieving >99.5% host cell replacement in peripheral blood by day 147 and developed severe acute retroviral syndrome with meningoencephalitis at 156 days post alloBMT. We isolated replication-competent HIV using a quantitative viral outgrowth assay at 100 and 25 days before alloBMT and from the same time points before alloBMT for HIV DNA and cell-associated RNA from peripheral blood mononuclear cells and resting memory CD4+ T cells. We isolated HIV RNA in plasma and cerebrospinal fluid (CSF) at viral rebound. We sequenced the RT-region of pol and performed neighbor-joining phylogenetic reconstruction. RESULTS Phylogenetic analysis revealed an identical viral sequence at both pre-alloBMT time points accounting for 9 of 34 sequences (26%) of the sampled HIV reservoir. This sequence population grouped with viral rebound sequences from plasma and CSF with high sequence homology. DISCUSSION Despite >99.5% replacement of host cells in peripheral blood, ART interruption led to HIV viral rebound in plasma and CSF. Furthermore, the rebound virus matched replication-competent virus from resting memory CD4+ T cells before alloBMT. This case underscores that HIV-infected recipient cells can persist after alloBMT and that latent replication-competent virus can reestablish infection.
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Affiliation(s)
| | - Andrew D. Redd
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Laura R. Clark
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Thomas C. Quinn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard F. Ambinder
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Christine M. Durand
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
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5
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Capoferri AA, Shao W, Spindler J, Coffin JM, Rausch JW, Kearney MF. A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States. Viruses 2022; 14:104. [PMID: 35062308 PMCID: PMC8778900 DOI: 10.3390/v14010104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.
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Affiliation(s)
- Adam A Capoferri
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC 20007, USA
| | - Wei Shao
- Advanced Biomedical Computing Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jon Spindler
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02129, USA
| | - Jason W Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA
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Capoferri AA, Redd AD, Gocke CD, Clark LR, Ambinder RF, Durand CM. Short Communication: Persistence of HIV After Allogeneic Bone Marrow Transplant in a Dually Infected Individual. AIDS Res Hum Retroviruses 2022; 38:33-36. [PMID: 34107771 PMCID: PMC8817692 DOI: 10.1089/aid.2021.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Allogeneic bone marrow transplant (alloBMT) with continuous antiretroviral therapy alone has not been shown to completely eradicate HIV, possibly due to HIV persistence in rare residual host cells or infection of donor cells. Within a trial of alloBMT in individuals with hematological malignancies and HIV (ClinicalTrials.gov, NCT01836068), we measured HIV reservoirs longitudinally using a quantitative viral outgrowth assay. We sequenced the reverse transcriptase region of pol for replication-competent virus and performed maximum-likelihood phylogenetic reconstruction. Replacement of host cells was measured using short-tandem repeats. In one participant who had ≥99.5% donor cell replacement, HIV reservoirs declined from 2.2 infectious units per million to undetectable levels at post-alloBMT time points except for week 64. Sequence analysis revealed dual infection pre-alloBMT. Replication-competent virus isolated at week 64 post-alloBMT was identical to a pre-alloBMT variant. This report provides proof-of-concept that minor replication-competent HIV variants can persist at low levels despite ≥99.5% donor cell engraftment post-alloBMT.
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Affiliation(s)
- Adam A. Capoferri
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew D. Redd
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Laura R. Clark
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Sidney Kimmel Cancer Center, Baltimore, Maryland, USA
| | | | - Christine M. Durand
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Sidney Kimmel Cancer Center, Baltimore, Maryland, USA.,Address correspondence to: Christine M. Durand, School of Medicine, Johns Hopkins University, 725 N Wolfe Street, Baltimore, MD 21205, USA
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Capoferri AA, Shao W, Spindler J, Coffin JM, Rausch JW, Kearney MF. 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. medRxiv 2021:2021.06.01.21258185. [PMID: 34127980 PMCID: PMC8202437 DOI: 10.1101/2021.06.01.21258185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
UNLABELLED In 2020, SARS-CoV-2 spread across the United States (U.S.) in three phases distinguished by peaks in the numbers of infections and shifting geographical distribution. We investigated the viral genetic diversity in each phase using sequences publicly available prior to December 15 th , 2020, when vaccination was initiated in the U.S. In Phase 1 (winter/spring), sequences were already dominated by the D614G Spike mutation and by Phase 3 (fall), genetic diversity of the viral population had tripled and at least 54 new amino acid changes had emerged at frequencies above 5%, several of which were within known antibody epitopes. These findings highlight the need to track the evolution of SARS-CoV-2 variants in the U.S. to ensure continued efficacy of vaccines and antiviral treatments. ONE SENTENCE SUMMARY SARS-CoV-2 genetic diversity in the U.S. increased 3-fold in 2020 and 54 emergent nonsynonymous mutations were detected.
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Affiliation(s)
- Adam A. Capoferri
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
- Department of Microbiology and Immunology, Georgetown University, Washington D.C., USA
| | - Wei Shao
- Advanced Biomedical Computing Science, Frederick National Laboratory for Cancer Research (FNLCR) sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Jon Spindler
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Jason W. Rausch
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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Capoferri AA, Sorrell EM. Assessment of West Nile Virus Lineage 2 Dynamics in Greece and Future Implications. Vector Borne Zoonotic Dis 2021; 21:466-474. [PMID: 33857383 DOI: 10.1089/vbz.2020.2703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence of West Nile Virus lineage 2 (WNV-2) has contributed to multiple major human outbreaks in Greece since 2010. Studies to date investigating biological and environmental factors that contribute to West Nile Virus (WNV) transmission have resulted in complex statistical models. We sought to examine open publicly available data to ascertain if a predictive risk assessment could be employed for WNV-2 in Greece. Based on accessible data, factors such as precipitation, temperature, and range of avian host species did not yield conclusive outcomes. However, by measuring the average rate of temperature change leading up to peak caseloads, we found a predictive characteristic to the timing of outbreaks. Detailed evolutionary studies revealed possible multiple introductions of WNV-2 in Europe, and that Greece acts through a source-sink inversion model, thereby allowing continued reseeding of WNV transmission each year by overwintering the Culex pipiens mosquito vector. Greece has proven an excellent model in WNV surveillance and has demonstrated the importance of rapid reporting for proper preparedness and response to vector-borne diseases.
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Affiliation(s)
- Adam A Capoferri
- Department of Microbiology and Immunology, Georgetown University, Washington, District of Columbia, USA
| | - Erin M Sorrell
- Department of Microbiology and Immunology, Georgetown University, Washington, District of Columbia, USA.,Center for Global Health Science and Security, Georgetown University, Washington, District of Columbia, USA
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Affiliation(s)
- Jason W Rausch
- HIV Dynamics & Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Adam A Capoferri
- HIV Dynamics & Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
- Microbiology and Immunology Department, Georgetown University, Washington, DC 20007
| | - Mary Grace Katusiime
- HIV Dynamics & Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Sean C Patro
- HIV Dynamics & Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Mary F Kearney
- HIV Dynamics & Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702;
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Ramos JC, Sparano JA, Chadburn A, Reid EG, Ambinder RF, Siegel ER, Moore PC, Rubinstein PG, Durand CM, Cesarman E, Aboulafia D, Baiocchi R, Ratner L, Kaplan L, Capoferri AA, Lee JY, Mitsuyasu R, Noy A. Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial). Blood 2020; 136:1284-1297. [PMID: 32430507 PMCID: PMC7483436 DOI: 10.1182/blood.2019003959] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
EPOCH (etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin) is a preferred regimen for HIV-non-Hodgkin lymphomas (HIV-NHLs), which are frequently Epstein-Barr virus (EBV) positive or human herpesvirus type-8 (HHV-8) positive. The histone deacetylase (HDAC) inhibitor vorinostat disrupts EBV/HHV-8 latency, enhances chemotherapy-induced cell death, and may clear HIV reservoirs. We performed a randomized phase 2 study in 90 patients (45 per study arm) with aggressive HIV-NHLs, using dose-adjusted EPOCH (plus rituximab if CD20+), alone or with 300 mg vorinostat, administered on days 1 to 5 of each cycle. Up to 1 prior cycle of systemic chemotherapy was allowed. The primary end point was complete response (CR). In 86 evaluable patients with diffuse large B-cell lymphoma (DLBCL; n = 61), plasmablastic lymphoma (n = 15), primary effusion lymphoma (n = 7), unclassifiable B-cell NHL (n = 2), and Burkitt lymphoma (n = 1), CR rates were 74% vs 68% for EPOCH vs EPOCH-vorinostat (P = .72). Patients with a CD4+ count <200 cells/mm3 had a lower CR rate. EPOCH-vorinostat did not eliminate HIV reservoirs, resulted in more frequent grade 4 neutropenia and thrombocytopenia, and did not affect survival. Overall, patients with Myc+ DLBCL had a significantly lower EFS. A low diagnosis-to-treatment interval (DTI) was also associated with inferior outcomes, whereas preprotocol therapy had no negative impact. In summary, EPOCH had broad efficacy against highly aggressive HIV-NHLs, whereas vorinostat had no benefit; patients with Myc-driven DLBCL, low CD4, and low DTI had less favorable outcomes. Permitting preprotocol therapy facilitated accruals without compromising outcomes. This trial was registered at www.clinicaltrials.gov as #NCT0119384.
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MESH Headings
- Adult
- Aged
- Anti-HIV Agents/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- CD4 Lymphocyte Count
- Cyclophosphamide/administration & dosage
- Cyclophosphamide/adverse effects
- DNA, Viral/blood
- Doxorubicin/administration & dosage
- Doxorubicin/adverse effects
- Drug Administration Schedule
- Etoposide/administration & dosage
- Etoposide/adverse effects
- Female
- Genes, myc
- HIV Infections/drug therapy
- HIV-1/drug effects
- Herpesviridae Infections/complications
- Herpesviridae Infections/virology
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/isolation & purification
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/isolation & purification
- Histone Deacetylase Inhibitors/administration & dosage
- Histone Deacetylase Inhibitors/adverse effects
- Humans
- Kaplan-Meier Estimate
- Lymphoma, AIDS-Related/complications
- Lymphoma, AIDS-Related/drug therapy
- Lymphoma, AIDS-Related/genetics
- Lymphoma, AIDS-Related/virology
- Lymphoma, Non-Hodgkin/complications
- Lymphoma, Non-Hodgkin/drug therapy
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/virology
- Male
- Middle Aged
- Neutropenia/chemically induced
- Prednisone/administration & dosage
- Prednisone/adverse effects
- Progression-Free Survival
- Prospective Studies
- Rituximab/administration & dosage
- Rituximab/adverse effects
- Thrombocytopenia/chemically induced
- Treatment Outcome
- Vincristine/administration & dosage
- Vincristine/adverse effects
- Viral Load/drug effects
- Vorinostat/administration & dosage
- Vorinostat/adverse effects
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Affiliation(s)
- Juan C Ramos
- Department of Medicine, University of Miami School of Medicine, Miami, FL
| | - Joseph A Sparano
- Department of Oncology, Albert Einstein Comprehensive Cancer Center, Bronx, NY
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY
| | - Erin G Reid
- Department of Medicine, University of California, San Diego, San Diego, CA
| | | | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Page C Moore
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Paul G Rubinstein
- Section of Hematology/Oncology, John H. Stroger Jr Hospital of Cook County, Chicago, IL
| | | | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY
| | - David Aboulafia
- Division of Hematology and Oncology, Virginia Mason Medical Center, Seattle, WA
| | - Robert Baiocchi
- Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Lawrence Kaplan
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | | | - Jeannette Y Lee
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Ronald Mitsuyasu
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Ariela Noy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; and
- Department of Medicine, Weill Medical College of Cornell University, New York, NY
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11
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Durand CM, Capoferri AA, Redd AD, Zahurak M, Rosenbloom DIS, Cash A, Avery RK, Bolaños-Meade J, Bollard CM, Bullen CK, Flexner C, Fuchs EJ, Gallant J, Gladstone DE, Gocke CD, Jones RJ, Kasamon YL, Lai J, Levis M, Luznik L, Marr KA, McHugh HL, Mehta Steinke S, Pham P, Pohlmeyer C, Pratz K, Shoham S, Wagner-Johnston N, Xu D, Siliciano JD, Quinn TC, Siliciano RF, Ambinder RF. Allogeneic bone marrow transplantation with post-transplant cyclophosphamide for patients with HIV and haematological malignancies: a feasibility study. Lancet HIV 2020; 7:e602-e610. [PMID: 32649866 PMCID: PMC7484204 DOI: 10.1016/s2352-3018(20)30073-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Allogeneic blood or marrow transplantation (alloBMT) is a potentially life-saving treatment for individuals with HIV and haematological malignancies; challenges include identifying donors and maintaining antiretroviral therapy (ART). The objectives of our study were to investigate interventions to expand donor options and to prevent ART interruptions for patients with HIV in need of alloBMT. METHODS This single-arm, interventional trial took place at the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center (Baltimore, MD, USA). Individuals with HIV who were at least 18 years of age and referred for alloBMT for a standard clinical indication were eligible. The only exclusion criterion was a history of documented resistance to enfuvirtide. We used post-transplant cyclophosphamide as graft-versus-host disease (GVHD) prophylaxis to expand donor options and an optimised ART strategy of avoiding pharmacoenhancers and adding subcutaneous enfuvirtide during post-transplant cyclophosphamide and during oral medication intolerance. Our primary outcome was the proportion of participants who maintained ART through day 60 after alloBMT. We measured the HIV latent reservoir using a quantitative viral outgrowth assay. This study is registered on ClinicalTrials.gov, NCT01836068. FINDINGS Between June 1, 2013, and August 27, 2015, nine patients who were referred for transplant provided consent. Two patients had relapsed malignancy before donor searches were initiated. Seven patients had suitable donors identified (two matched sibling, two matched unrelated, two haploidentical, and one single-antigen mismatched unrelated) and proceeded to alloBMT. All patients maintained ART through day 60 and required ART changes (median 1, range 1-3) in the first 90 days. One patient stopped ART and developed HIV rebound with grade 4 meningoencephalitis at day 146. Among six patients who underwent alloBMT and had longitudinal measurements available, the HIV latent reservoir was not detected post-alloBMT in four patients with more than 95% donor chimerism, consistent with a 2·06-2·54 log10 reduction in the HIV latent reservoir. In the two patients with less than 95% donor chimerism, the HIV latent reservoir remained stable. INTERPRETATION By using post-transplant cyclophosphamide as GVHD prophylaxis, we successfully expanded alloBMT donor options for patients with HIV. Continuing ART with a regimen that includes enfuvirtide post-alloBMT was safe, but life-threatening viral rebound can occur with ART interruption. FUNDING amfAR (the Foundation for AIDS Research), Johns Hopkins University Center for AIDS Research, and National Cancer Institute.
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Affiliation(s)
- Christine M Durand
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA.
| | | | - Andrew D Redd
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Daniel I S Rosenbloom
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co, Kenilworth, NJ, USA
| | - Ayla Cash
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin K Avery
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Javier Bolaños-Meade
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Catherine M Bollard
- Sidney Kimmel Cancer Center, Baltimore, MD, USA; Program for Cell Enhancement and Technologies for Immunotherapy Children's National Health System, George Washington University Washington, DC, USA
| | - C Korin Bullen
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Flexner
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Joel Gallant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Gilead Sciences, Foster City, CA, USA
| | | | | | | | | | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark Levis
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Leo Luznik
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Kieren A Marr
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Holly L McHugh
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Paul Pham
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Keith Pratz
- Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Shmuel Shoham
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Daniel Xu
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Thomas C Quinn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert F Siliciano
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA
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12
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Ambinder RF, Capoferri AA, Durand CM. Haemopoietic cell transplantation in patients living with HIV. Lancet HIV 2020; 7:e652-e660. [PMID: 32791046 PMCID: PMC8276629 DOI: 10.1016/s2352-3018(20)30117-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/30/2020] [Accepted: 04/20/2020] [Indexed: 12/30/2022]
Abstract
Haemopoietic cell transplantation is established as a standard treatment approach for people living with HIV who have haematological malignancies with poor prognosis. Studies with autologous and allogeneic haemopoietic cell transplantation suggest that HIV status does not adversely affect outcomes, provided that there is adequate infection prophylaxis. Attention to possible drug-drug interactions is important. Allogeneic haemopoietic cell transplantation substantially reduces the long-term HIV reservoir when complete donor chimerism is established. When transplants from CCR5Δ32 homozygous donors are used, HIV cure is possible.
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Affiliation(s)
| | - Adam A Capoferri
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
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13
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Prodger JL, Capoferri AA, Yu K, Lai J, Reynolds SJ, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Kwon KJ, Schlusser K, Martens C, Scully E, Choi YH, Redd AD, Quinn TC. Reduced HIV-1 latent reservoir outgrowth and distinct immune correlates among women in Rakai, Uganda. JCI Insight 2020; 5:139287. [PMID: 32544096 DOI: 10.1172/jci.insight.139287] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 01/22/2023] Open
Abstract
HIV-1 infection remains incurable owing to the persistence of a viral reservoir that harbors integrated provirus within host cellular DNA. Increasing evidence links sex-based differences in HIV-1 immune responses and pathogenesis; however, little is known about differences in HIV-1 infection persistence. Here, we quantified persistent HIV-1 infection in 90 adults on suppressive antiretroviral therapy in Rakai, Uganda (57 female patients). Total HIV-1 DNA was quantified by PCR, and replication-competent provirus by quantitative viral outgrowth assay (QVOA). Immune phenotyping of T cell subsets and plasma biomarkers was also performed. We found that whereas both sexes had similar total HIV DNA levels, female patients had significantly fewer resting CD4+ T cells harboring replication-competent virus, as measured by viral outgrowth in the QVOA. Factors associated with viral outgrowth differed by sex; notably, frequency of programmed cell death 1 (PD1+) CD4+ T cells correlated with reservoir size in male but not female patients. The sex-based differences in HIV-1 persistence observed in this cohort warrant additional research, especially given the widespread use of the QVOA to assess reservoir size and current explorations of PD1 agonists in cure protocols. Efforts should be made to power future cure studies to assess outcomes in both male and female patients.
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Affiliation(s)
- Jessica L Prodger
- Department of Microbiology and Immunology and.,Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Yu
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven J Reynolds
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda.,Makerere University, Kampala, Uganda
| | - Kyungyoon J Kwon
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Schlusser
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | - Eileen Scully
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yun-Hee Choi
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
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14
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Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
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Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
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15
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Capoferri AA, Lynch BA, Prodger JL, Reynolds SJ, Kasule J, Serwadda D, Lamers S, Martens C, Quinn TC, Redd AD. A15 Archived ART resistance in the latent reservoir of virally suppressed Ugandans. Virus Evol 2019. [PMCID: PMC6735790 DOI: 10.1093/ve/vez002.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increased access of antiretroviral therapy (ART) has drastically improved the health of infected individuals. However, increased levels of ART resistance globally threaten ART effectiveness. Resistance monitoring is currently limited to viremic individuals or prior to ART initiation. The archival nature of the HIV latent reservoir (LR) of virally suppressed patients allows examination for the persistence of ART-resistant latent viral variants. Whole blood samples were collected longitudinally in Rakai, Uganda, from 70 virally suppressed HIV-1 infected individuals. The quantitative viral outgrowth assay was performed to measure the frequency of replication-competent latently infected resting-memory CD4 + (rCD4) T-cells. RNA was extracted from HIV p24-positive outgrowth supernatant, and the reverse transcriptase (RT) region was sequenced using a validated site-specific next-generation sequencing assay (Illumina, San Diego, CA). Consensus sequences containing >2.5 per cent of the total raw amplicons of each outgrowth well were analyzed for ART drug resistance mutations using the Stanford Database. The presence of clonal sequence is expressed as both percent clonality and Shannon Entropy. Replication-competent virus was cultured from 52/70 (74.3%) individuals, of which, RT-pol sequence data were obtained from 49/52 (94.3%) individuals. The presence of ART-resistant virus was found in the LR from one individual on second-line therapy that included a protease inhibitor. There were 20 and 44 total prominent consensus sequences from all wells at years 1 and 3 of follow-up, respectively. ART-resistant mutations for both RT-inhibitor drug classes were found in 30 per cent and 27.3 per cent of the total prominent consensus sequences of this one individual from years 1 and 3, respectively. The major ART resistance profile in this individual included: M184V, Y188L, K191E, and G190A. The percentage of total outgrowth that was clonal (percent clonality) increased from year 1 to year 3 (38.1–81.8%) and Shannon Entropy decreased (0.722–0.576). The presence of archived replication-competent ART-resistant virus in the LR was found in only one individual. There were two ART-resistant prominent consensus sequences isolated at year 3 that were not sampled 2 years earlier. The persistence of resistant, intact replication-competent proviral sequences in the LR of this individual seem to be supported by clonal expansion.
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Affiliation(s)
- A A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - B A Lynch
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J L Prodger
- Department of Microbiology and Immunology, Western University, London, Canada
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - S J Reynolds
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - J Kasule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - D Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda
- Makerere University, Kampala, Uganda
| | - S Lamers
- Bioinfo Experts Inc., Thibodaux, LA, USA
| | - C Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - T C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - A D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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16
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Cullen LM, Schmidt MR, Torres GM, Capoferri AA, Morrison TG. Comparison of Immune Responses to Different Versions of VLP Associated Stabilized RSV Pre-Fusion F Protein. Vaccines (Basel) 2019; 7:vaccines7010021. [PMID: 30769923 PMCID: PMC6466353 DOI: 10.3390/vaccines7010021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 11/16/2022] Open
Abstract
Efforts to develop a vaccine for respiratory syncytial virus (RSV) have primarily focused on the RSV fusion protein. The pre-fusion conformation of this protein induces the most potent neutralizing antibodies and is the focus of recent efforts in vaccine development. Following the first identification of mutations in the RSV F protein (DS-Cav1 mutant protein) that stabilized the pre-fusion conformation, other mutant stabilized pre-fusion F proteins have been described. To determine if there are differences in alternate versions of stabilized pre-fusion F proteins, we explored the use, as vaccine candidates, of virus-like particles (VLPs) containing five different pre-fusion F proteins, including the DS-Cav1 protein. The expression of these five pre-F proteins, their assembly into VLPs, their pre-fusion conformation stability in VLPs, their reactivity with anti-F monoclonal antibodies, and their induction of immune responses after the immunization of mice, were characterized, comparing VLPs containing the DS-Cav1 pre-F protein with VLPs containing four alternative pre-fusion F proteins. The concentrations of anti-F IgG induced by each VLP that blocked the binding of prototype monoclonal antibodies using two different soluble pre-fusion F proteins as targets were measured. Our results indicate that both the conformation and immunogenicity of alternative VLP associated stabilized pre-fusion RSV F proteins are different from those of DS-Cav1 VLPs.
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Affiliation(s)
- Lori M Cullen
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Madelyn R Schmidt
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
- Program of Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Gretel M Torres
- Program of Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Adam A Capoferri
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Trudy G Morrison
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
- Program of Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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17
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Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD. Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays. Retrovirology 2018; 15:47. [PMID: 29976219 PMCID: PMC6034329 DOI: 10.1186/s12977-018-0426-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs. RESULTS Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda. CONCLUSIONS Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Briana A Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Adam A Capoferri
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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18
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Pohlmeyer CW, Laskey SB, Beck SE, Xu DC, Capoferri AA, Garliss CC, May ME, Livingston A, Lichmira W, Moore RD, Leffell MS, Butler NJ, Thorne JE, Flynn JA, Siliciano RF, Blankson JN. Cross-reactive microbial peptides can modulate HIV-specific CD8+ T cell responses. PLoS One 2018; 13:e0192098. [PMID: 29466365 PMCID: PMC5821448 DOI: 10.1371/journal.pone.0192098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022] Open
Abstract
Heterologous immunity is an important aspect of the adaptive immune response. We hypothesized that this process could modulate the HIV-1-specific CD8+ T cell response, which has been shown to play an important role in HIV-1 immunity and control. We found that stimulation of peripheral blood mononuclear cells (PBMCs) from HIV-1-positive subjects with microbial peptides that were cross-reactive with immunodominant HIV-1 epitopes resulted in dramatic expansion of HIV-1-specific CD8+ T cells. Interestingly, the TCR repertoire of HIV-1-specific CD8+ T cells generated by ex vivo stimulation of PBMCs using HIV-1 peptide was different from that of cells stimulated with cross-reactive microbial peptides in some HIV-1-positive subjects. Despite these differences, CD8+ T cells stimulated with either HIV-1 or cross-reactive peptides effectively suppressed HIV-1 replication in autologous CD4+ T cells. These data suggest that exposure to cross-reactive microbial antigens can modulate HIV-1-specific immunity.
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Affiliation(s)
- Christopher W. Pohlmeyer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah B. Laskey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Beck
- Department of Molecular and Comparative Pathobiology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel C. Xu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Adam A. Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Caroline C. Garliss
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Megan E. May
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alison Livingston
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Walt Lichmira
- Spondylitis Association of America, Philadelphia, Pennsylvania United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - M. Sue Leffell
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nicholas J. Butler
- Department of Ophthalmology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jennifer E. Thorne
- Department of Ophthalmology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John A. Flynn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Molecular and Comparative Pathobiology. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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19
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Shan L, Deng K, Gao H, Xing S, Capoferri AA, Durand CM, Rabi SA, Laird GM, Kim M, Hosmane NN, Yang HC, Zhang H, Margolick JB, Li L, Cai W, Ke R, Flavell RA, Siliciano JD, Siliciano RF. Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4 + T Cells Permissive for Latent HIV-1 Infection. Immunity 2017; 47:766-775.e3. [PMID: 29045905 DOI: 10.1016/j.immuni.2017.09.014] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/26/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022]
Abstract
The latent reservoir for HIV-1 in resting memory CD4+ T cells is the major barrier to curing HIV-1 infection. Studies of HIV-1 latency have focused on regulation of viral gene expression in cells in which latent infection is established. However, it remains unclear how infection initially becomes latent. Here we described a unique set of properties of CD4+ T cells undergoing effector-to-memory transition including temporary upregulation of CCR5 expression and rapid downregulation of cellular gene transcription. These cells allowed completion of steps in the HIV-1 life cycle through integration but suppressed HIV-1 gene transcription, thus allowing the establishment of latency. CD4+ T cells in this stage were substantially more permissive for HIV-1 latent infection than other CD4+ T cells. Establishment of latent HIV-1 infection in CD4+ T could be inhibited by viral-specific CD8+ T cells, a result with implications for elimination of latent HIV-1 infection by T cell-based vaccines.
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Affiliation(s)
- Liang Shan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kai Deng
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Hongbo Gao
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Sifei Xing
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - S Alireza Rabi
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregory M Laird
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle Kim
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nina N Hosmane
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA.
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20
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Prodger JL, Lai J, Reynolds SJ, Keruly JC, Moore RD, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Nason M, Capoferri AA, Porcella SF, Siliciano RF, Redd AD, Siliciano JD, Quinn TC. Reduced Frequency of Cells Latently Infected With Replication-Competent Human Immunodeficiency Virus-1 in Virally Suppressed Individuals Living in Rakai, Uganda. Clin Infect Dis 2017; 65:1308-1315. [PMID: 28535179 PMCID: PMC5850010 DOI: 10.1093/cid/cix478] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/19/2017] [Indexed: 01/17/2023] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) persists in latently infected resting CD4+ T cells (rCD4 cells), posing a major barrier to curing HIV-1 infection. Previous studies have quantified this pool of latently infected cells in Americans; however, no study has quantified this reservoir in sub-Saharan Africans, who make up the largest population of HIV-1-infected individuals globally. Methods Peripheral blood was collected from 70 virally suppressed HIV-1-infected individuals from Rakai District, Uganda, who had initiated antiretroviral therapy (ART) during chronic infection. The quantitative viral outgrowth assay was used to determine frequency of latently infected rCD4 cells containing replication-competent virus. Multivariate regression was used to identify correlates of reservoir size and to compare reservoir size between this Ugandan cohort and a previously studied cohort of individuals from Baltimore, Maryland. Results The median frequency of latently infected rCD4 cells in this Ugandan cohort was 0.36 infectious units per million cells (IUPM; 95% confidence interval, 0.26-0.55 IUPM), 3-fold lower than the frequency observed in the Baltimore cohort (1.08 IUPM; .72-1.49 IUPM; P < .001). Reservoir size in Ugandans was correlated positively with set-point viral load and negatively with duration of viral suppression. Conclusions Virally suppressed Ugandans had a 3-fold lower frequency of rCD4 cells latently infected with replication-competent HIV-1, compared with previous observations in a cohort of American patients, also treated with ART during chronic infection. The biological mechanism driving the observed smaller reservoir in Ugandans is of interest and may be of significance to HIV-1 eradication efforts.
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Affiliation(s)
- Jessica L Prodger
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Steven J Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - Jeanne C Keruly
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo,Uganda
- Makerere University, Kampala, Uganda
| | - Martha Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana; and
| | - Robert F Siliciano
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Howard Hughes Medical Institute, Baltimore, Maryland
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
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21
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Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang SH, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho YC. Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell Host Microbe 2017; 21:494-506.e4. [PMID: 28407485 DOI: 10.1016/j.chom.2017.03.008] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/07/2017] [Accepted: 03/16/2017] [Indexed: 12/31/2022]
Abstract
Despite antiretroviral therapy, HIV-1 persists in memory CD4+ T cells, creating a barrier to cure. The majority of HIV-1 proviruses are defective and considered clinically irrelevant. Using cells from HIV-1-infected individuals and reconstructed patient-derived defective proviruses, we show that defective proviruses can be transcribed into RNAs that are spliced and translated. Proviruses with defective major splice donors (MSDs) can activate novel splice sites to produce HIV-1 transcripts, and cells with these proviruses can be recognized by HIV-1-specific cytotoxic T lymphocytes (CTLs). Further, cells with proviruses containing lethal mutations upstream of CTL epitopes can also be recognized by CTLs, potentially through aberrant translation. Thus, CTLs may change the landscape of HIV-1 proviruses by preferentially targeting cells with specific types of defective proviruses. Additionally, the expression of defective proviruses will need to be considered in the measurement of HIV-1 latency reversal.
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Affiliation(s)
- Ross A Pollack
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - R Brad Jones
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Mihaela Pertea
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katherine M Bruner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa R Martin
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Allison S Thomas
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Szu-Han Huang
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Sara Karandish
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Haiping Hao
- Deep Sequencing & Microarray Core, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Patrick C Yong
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Colin Kovacs
- Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Maple Leaf Medical Clinic, Toronto, ON M5G 1K2, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, ON M5G 1K2, Canada
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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22
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Hosmane NN, Kwon KJ, Bruner KM, Capoferri AA, Beg S, Rosenbloom DIS, Keele BF, Ho YC, Siliciano JD, Siliciano RF. Proliferation of latently infected CD4 + T cells carrying replication-competent HIV-1: Potential role in latent reservoir dynamics. J Exp Med 2017; 214:959-972. [PMID: 28341641 PMCID: PMC5379987 DOI: 10.1084/jem.20170193] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 12/16/2022] Open
Abstract
A latent reservoir for HIV-1 in resting CD4+ T lymphocytes precludes cure. Mechanisms underlying reservoir stability are unclear. Recent studies suggest an unexpected degree of infected cell proliferation in vivo. T cell activation drives proliferation but also reverses latency, resulting in productive infection that generally leads to cell death. In this study, we show that latently infected cells can proliferate in response to mitogens without producing virus, generating progeny cells that can release infectious virus. Thus, assays relying on one round of activation underestimate reservoir size. Sequencing of independent clonal isolates of replication-competent virus revealed that 57% had env sequences identical to other isolates from the same patient. Identity was confirmed by full-genome sequencing and was not attributable to limited viral diversity. Phylogenetic and statistical analysis suggested that identical sequences arose from in vivo proliferation of infected cells, rather than infection of multiple cells by a dominant viral species. The possibility that much of the reservoir arises by cell proliferation presents challenges to cure.
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Affiliation(s)
- Nina N Hosmane
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Katherine M Bruner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Daniel I S Rosenbloom
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Baltimore, MD 21205
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23
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Hansen EC, Ransom M, Hesselberth JR, Hosmane NN, Capoferri AA, Bruner KM, Pollack RA, Zhang H, Drummond MB, Siliciano JM, Siliciano R, Stivers JT. Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. eLife 2016; 5. [PMID: 27644592 PMCID: PMC5030084 DOI: 10.7554/elife.18447] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/23/2016] [Indexed: 12/22/2022] Open
Abstract
We report that a major subpopulation of monocyte-derived macrophages (MDMs) contains high levels of dUTP, which is incorporated into HIV-1 DNA during reverse transcription (U/A pairs), resulting in pre-integration restriction and post-integration mutagenesis. After entering the nucleus, uracilated viral DNA products are degraded by the uracil base excision repair (UBER) machinery with less than 1% of the uracilated DNA successfully integrating. Although uracilated proviral DNA showed few mutations, the viral genomic RNA was highly mutated, suggesting that errors occur during transcription. Viral DNA isolated from blood monocytes and alveolar macrophages (but not T cells) of drug-suppressed HIV-infected individuals also contained abundant uracils. The presence of viral uracils in short-lived monocytes suggests their recent infection through contact with virus producing cells in a tissue reservoir. These findings reveal new elements of a viral defense mechanism involving host UBER that may be relevant to the establishment and persistence of HIV-1 infection. DOI:http://dx.doi.org/10.7554/eLife.18447.001 Human immunodeficiency virus type 1 (HIV-1) infects and kills immune cells known as CD4+ T cells, leading to the disease AIDS. Current drug treatments enable HIV-1 infected patients to live relatively long and healthy lives. However, no cure for HIV-1 exists because the virus lives indefinitely in a resting state within the genetic material – or genome – of the infected cell, where it is not susceptible to drug treatments. Most HIV-1 research focuses on T cells, but another type of immune cell – the macrophage – may also harbor resting HIV-1 in its genome. Compared to other cells, macrophages are unusual because they produce large amounts of a molecule called deoxyuridine triphosphate (dUTP). Most cells, including T cells, keep dUTP levels very low because it closely resembles molecules that are used to make DNA and so it can be accidentally incorporated into the cell’s DNA. When this happens, the cell removes the dUTP from the DNA using enzymes in a process called uracil base excision repair (UBER). To hide inside the cell’s genome, HIV-1 needs to produce a DNA copy of its own genome, but it was not known what happens when HIV-1 tries to do this within a macrophage that contains high levels of dUTP and UBER enzymes. Here, Hansen et al. reveal that about 90% of macrophages have exceptionally high levels of dUTP and are poorly infected by HIV-1. The high levels of dUTP result in the virus incorporating dUTP into its DNA, which is then attacked and fragmented by UBER enzymes. However, about one in a hundred viral DNA molecules do manage to successfully integrate into the genome of the macrophage. This viral DNA later gives rise to new virus particles through an error-prone process that, by introducing new mutations into the virus genome, may help HIV-1 to evolve and persist. Further experiments examined cells that give rise to macrophages from infected patients who had been on anti-HIV drug therapy for several years. Hansen et al. found that there was lots of dUTP in the DNA sequences of HIV-1 viruses found in these “precursor” cells. These precursor cells only live for several days before being eliminated, so the presence of viruses containing dUTP suggests these cells were infected recently. A future challenge will be to identify new anti-HIV drugs that specifically target macrophages and to understand the role of error-prone production of new viral genomes. DOI:http://dx.doi.org/10.7554/eLife.18447.002
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Affiliation(s)
- Erik C Hansen
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Monica Ransom
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Nina N Hosmane
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Adam A Capoferri
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States.,Howard Hughes Medical Institute, The Johns Hopkins School of Medicine, Baltimore, United States
| | - Katherine M Bruner
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ross A Pollack
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Hao Zhang
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Michael Bradley Drummond
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Janet M Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Robert Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, United States.,Howard Hughes Medical Institute, The Johns Hopkins School of Medicine, Baltimore, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
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