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Horvath RM, Brumme ZL, Sadowski I. Small molecule inhibitors of transcriptional cyclin-dependent kinases impose HIV-1 latency, presenting "block and lock" treatment strategies. Antimicrob Agents Chemother 2024; 68:e0107223. [PMID: 38319085 PMCID: PMC10923280 DOI: 10.1128/aac.01072-23] [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: 08/17/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Current antiretroviral therapy for HIV-1 infection does not represent a cure for infection as viral rebound inevitably occurs following discontinuation of treatment. The "block and lock" therapeutic strategy is intended to enforce proviral latency and durably suppress viremic reemergence in the absence of other intervention. The transcription-associated cyclin-dependent protein kinases (tCDKs) are required for expression from the 5´ HIV-1 long-terminal repeat, but the therapeutic potential of inhibiting these kinases for enforcing HIV-1 latency has not been characterized. Here, we expanded previous observations to directly compare the effect of highly selective small molecule inhibitors of CDK7 (YKL-5-124), CDK9 (LDC000067), and CDK8/19 (Senexin A), and found each of these prevented HIV-1 provirus expression at concentrations that did not cause cell toxicity. Inhibition of CDK7 caused cell cycle arrest, whereas CDK9 and CDK8/19 inhibitors did not, and could be continuously administered to establish proviral latency. Upon discontinuation of drug administration, HIV immediately rebounded in cells that had been treated with the CDK9 inhibitor, while proviral latency persisted for several days in cells that had been treated with CDK8/19 inhibitors. These results identify the mediator kinases CDK8/CDK19 as potential "block and lock" targets for therapeutic suppression of HIV-1 provirus expression.
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Affiliation(s)
- Riley M. Horvath
- Department of Biochemistry and Molecular Biology Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. J Virol 2024; 98:e0165523. [PMID: 38214547 PMCID: PMC10878278 DOI: 10.1128/jvi.01655-23] [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: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Kyle Cobarrubias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Michael J. Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A. Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adaora Adimora
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Mark H. Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I. Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - the MACS/WIHS combined cohort study (MWCSS)OfotokunIghovwerha1ShethAnandi1WingoodGina1BrownTodd2MargolickJoseph2AnastosKathryn3HannaDavid3SharmaAnjali3GustafsonDeborah4WilsonTracey4D’SouzaGypsyamber5GangeStephen5TopperElizabeth5CohenMardge6FrenchAudrey6WolinskySteven7PalellaFrank7StosorValentina7AouizeratBradley8PriceJennifer8TienPhyllis8DetelsRoger9MimiagaMatthew9KassayeSeble10MerensteinDaniel10AlcaideMaria11FischlMargaret11JonesDeborah11MartinsonJeremy12RinaldoCharles12KempfMirjam-Colette13Dionne-OdomJodie13Konkle-ParkerDeborah13BrockJames B.13AdimoraAdaora14Floris-MooreMichelle14Emory University, Atlanta, Georgia, USAJohns Hopkins University, Baltimore, Maryland, USAAlbert Einstein College of Medicine, Bronx, New York, USASuny Downstate Medical Center, Brooklyn, New York, USAJohns Hopkins University, Baltimore, Maryland, USAHektoen Institute for Medical Research, Chicago, Illinois, USANorthwestern University at Chicago, Chicago, Illinois, USAUniversity of California San Francisco, San Francisco, California, USAUniversity of California Los Angeles, Los Angeles, California, USAGeorgetown University, Washington, DC, USAUniversity of Miami School of Medicine, Coral Gables, Florida, USAUniversity of Pittsburgh, Pittsburgh, Pennsylvania, USAUniversity of Alabama Birmingham, Birmingham, Alabama, USAUniversity of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- College of Dentistry, New York University, New York, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
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3
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Duncan MC, Omondi FH, Kinloch NN, Lapointe HR, Speckmaier S, Moran-Garcia N, Lawson T, DeMarco ML, Simons J, Holmes DT, Lowe CF, Bacani N, Sereda P, Barrios R, Harris M, Romney MG, Montaner JSG, Brumme CJ, Brockman MA, Brumme ZL. Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size. AIDS 2024:00002030-990000000-00434. [PMID: 38224350 DOI: 10.1097/qad.0000000000003841] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
OBJECTIVE The immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. DESIGN Longitudinal observational cohort and province-wide analysis. METHODS 62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022. RESULTS Pre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p > 0.4). There was no evidence that the magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike immune response influenced pVL nor changes in reservoir size (p > 0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. CONCLUSION We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
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Affiliation(s)
- Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Natalie N Kinloch
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nic Bacani
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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4
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Crain CR, Traunbauer AK, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Dorazio D, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Sieg S, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and host mediators of non-suppressible HIV-1 viremia. Nat Med 2023; 29:3212-3223. [PMID: 37957382 PMCID: PMC10719098 DOI: 10.1038/s41591-023-02611-1] [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: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) is defined as persistent low-level viremia on antiretroviral therapy (ART) without evidence of ART non-adherence or significant drug resistance. Unraveling the mechanisms behind NSV would broaden our understanding of HIV-1 persistence. Here we analyzed plasma virus sequences in eight ART-treated individuals with NSV (88% male) and show that they are composed of large clones without evidence of viral evolution over time in those with longitudinal samples. We defined proviruses that match plasma HIV-1 RNA sequences as 'producer proviruses', and those that did not as 'non-producer proviruses'. Non-suppressible viremia arose from expanded clones of producer proviruses that were significantly larger than the genome-intact proviral reservoir of ART-suppressed individuals. Integration sites of producer proviruses were enriched in proximity to the activating H3K36me3 epigenetic mark. CD4+ T cells from participants with NSV demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, participants with NSV showed significantly lower HIV-specific CD8+ T cell responses compared with untreated viremic controllers with similar viral loads. We identified potential critical host and viral mediators of NSV that may represent targets to disrupt HIV-1 persistence.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Valley Health System, Las Vegas, NV, USA
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Beijing Friendship Hospital Pinggu Campus, Capital Medical University, Beijing, China
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory J Bedwell
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Anna K Traunbauer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Francoise Giguel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dominic Dorazio
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Peter L Anderson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M Lederman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D Lichterfeld
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Scott Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Athe Tsibris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jose R Castillo-Mancilla
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan N Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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5
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Datwani S, Kalikawe R, Mwimanzi F, Speckmaier S, Liang R, Sang Y, Waterworth R, Yaseen F, Lapointe HR, Barad E, DeMarco ML, Holmes DT, Simons J, Montaner JS, Romney MG, Brumme ZL, Brockman MA. Dynamics of T-cell Responses Following COVID-19 mRNA Vaccination and Breakthrough Infection in Older Adults. Pathog Immun 2023; 8:117-135. [PMID: 38035132 PMCID: PMC10686373 DOI: 10.20411/pai.v8i1.613] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction While older adults generally mount weaker antibody responses to a primary COVID-19 vaccine series, T-cell responses remain less well characterized in this population. We compared SARS-CoV-2 spike-specific T-cell responses after 2- and 3-dose COVID-19 mRNA vaccination and subsequent breakthrough infection in older and younger adults. Methods We quantified CD4+ and CD8+ T-cells reactive to overlapping peptides spanning the ancestral SARS-CoV-2 spike protein in 40 older adults (median age 79) and 50 younger health care workers (median age 39), all COVID-19 naive, using an activation-induced marker assay. T-cell responses were further assessed in 24 participants, including 8 older adults, who subsequently experienced their first SARS-CoV-2 breakthrough infection. Results A third COVID-19 mRNA vaccine dose significantly boosted spike-specific CD4+ and CD8+ T-cell frequencies to above 2-dose levels in older and younger adults. T-cell frequencies did not significantly differ between older and younger adults after either dose. Multivariable analyses adjusting for sociodemographic, health, and vaccine-related variables confirmed that older age was not associated with impaired cellular responses. Instead, the strongest predictors of CD4+ and CD8+ T-cell frequencies post-third-dose were their corresponding post-second-dose frequencies. Breakthrough infection significantly increased both CD4+ and CD8+ T-cell frequencies, to comparable levels in older and younger adults. Exploratory analyses revealed an association between HLA-A*02:03 and higher post-vaccination CD8+ T-cell frequencies, which may be attributable to numerous strong-binding HLA-A*02:03-specific CD8+ T-cell epitopes in the spike protein. Conclusion Older adults mount robust T-cell responses to 2- and 3-dose COVID-19 mRNA vaccination, which are further boosted following breakthrough infection.
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Affiliation(s)
- Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Richard Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Rachel Waterworth
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mari L. DeMarco
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T. Holmes
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S.G. Montaner
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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6
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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7
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Duncan MC, Omondi FH, Kinloch NN, Lapointe HR, Speckmaier S, Moran-Garcia N, Lawson T, DeMarco ML, Simons J, Holmes DT, Lowe CF, Bacani N, Sereda P, Barrios R, Harris M, Romney MG, Montaner JSG, Brumme CJ, Brockman MA, Brumme ZL. Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size. medRxiv 2023:2023.10.08.23296718. [PMID: 37873490 PMCID: PMC10593027 DOI: 10.1101/2023.10.08.23296718] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Objective The immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign. Design Longitudinal observational cohort and province-wide analysis. Methods 62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022. Results Pre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p>0.4). The magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike antibody response did not correlate with changes in reservoir size nor detectable pVL frequency (p>0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART. Conclusion We found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.
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Affiliation(s)
- Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Natalie N Kinloch
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nic Bacani
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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8
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Costiniuk CT, Singer J, Lee T, Galipeau Y, McCluskie PS, Arnold C, Langlois MA, Needham J, Jenabian MA, Burchell AN, Samji H, Chambers C, Walmsley S, Ostrowski M, Kovacs C, Tan DH, Harris M, Hull M, Brumme ZL, Lapointe HR, Brockman MA, Margolese S, Mandarino E, Samarani S, Vulesevic B, Lebouché B, Angel JB, Routy JP, Cooper CL, Anis AH. Antibody neutralization capacity after coronavirus disease 2019 vaccination in people with HIV in Canada. AIDS 2023; 37:F25-F35. [PMID: 37534695 PMCID: PMC10481923 DOI: 10.1097/qad.0000000000003680] [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: 07/07/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Many vaccines require higher/additional doses or adjuvants to provide adequate protection for people with HIV (PWH). Here, we compare coronavirus disease 2019 (COVID-19) vaccine-induced antibody neutralization capacity in PWH vs. HIV-negative individuals following two vaccine doses. DESIGN In Canadian prospective observational cohorts, including a multicentre study of PWH receiving at least two COVID-19 vaccinations (mRNA or ChAdOx1-S), and a parallel study of HIV-negative controls (Stop the Spread Ottawa Cohort), we measured vaccine-induced neutralization capacity 3 months post dose 2 (±1 month). METHODS COVID-19 neutralization efficiency was measured by calculating the half maximal inhibitory dilution (ID50) using a high-throughput protein-based neutralization assay for Ancestral (Wuhan), Delta and Omicron (BA.1) spike variants. Univariable and multivariable quantile regression were used to compare COVID-19-specific antibody neutralization capacity by HIV status. RESULTS Neutralization assays were performed on 256 PWH and 256 controls based on specimen availability at the timepoint of interest, having received two vaccines and known date of vaccination. There was a significant interaction between HIV status and previous COVID-19 infection status in median ID50. There were no differences in median ID50 for HIV+ vs. HIV-negative persons without past COVID-19 infection. For participants with past COVID-19 infection, median ICD50 was significantly higher in controls than in PWH for ancestral SARS-CoV-2 and Omicron variants, with a trend for the Delta variant in the same direction. CONCLUSION Vaccine-induced SARS-CoV-2 neutralization capacity was similar between PWH vs. HIV-negative persons without past COVID-19 infection, demonstrating favourable humoral-mediated immunogenicity. Both HIV+ and HIV-negative persons demonstrated hybrid immunity. TRIAL REGISTRATION clinicaltrials.gov NCT04894448.
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Affiliation(s)
- Cecilia T. Costiniuk
- Division of Infectious Diseases/Chronic Viral Illness Service, McGill University Health Centre, Royal Victoria Hospital
- Infectious Diseases and Immunity in Global Health Research Program, Research Institute of McGill University Health Centre
- Department of Experimental Medicine, McGill University, Montreal, Québec
| | - Joel Singer
- School of Population and Public Health, University of British Columbia
- CIHR Canadian HIV Trials Network (CTN)
- Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia
| | - Terry Lee
- CIHR Canadian HIV Trials Network (CTN)
- Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia
| | - Yannick Galipeau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario
| | - Pauline S. McCluskie
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario
| | - Corey Arnold
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario
| | - Judy Needham
- CIHR Canadian HIV Trials Network (CTN)
- Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia
| | - Mohammad-Ali Jenabian
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, Québec
| | - Ann N. Burchell
- Department of Family and Community Medicine, St Michael's Hospital, Unity Health Toronto
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario
| | - Hasina Samji
- Faculty of Health Sciences, Simon Fraser University, Burnaby
- British Columbia Centre for Disease Control, Vancouver, British Columbia
| | - Catharine Chambers
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario
- MAP Centre for Urban Health Solutions, St Michael's Hospital
| | - Sharon Walmsley
- Division of Infectious Diseases, Department of Medicine, University of Toronto
| | - Mario Ostrowski
- Clinical Sciences Division and Department of Immunology, University of Toronto, Li Ka Shing Knowledge Institute, St. Michael's Hospital
| | | | - Darrell H.S. Tan
- MAP Centre for Urban Health Solutions, St Michael's Hospital
- Division of Infectious Diseases, Department of Medicine, University of Toronto
- Institute of Public Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver
| | | | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia
| | | | | | - Suzanne Samarani
- Division of Infectious Diseases/Chronic Viral Illness Service, McGill University Health Centre, Royal Victoria Hospital
| | - Branka Vulesevic
- CIHR Canadian HIV Trials Network (CTN)
- Division of Infectious Diseases, Department of Medicine, University of Ottawa and the Ottawa Hospital Research Institute, Ottawa, Ontario
| | - Bertrand Lebouché
- Division of Infectious Diseases/Chronic Viral Illness Service, McGill University Health Centre, Royal Victoria Hospital
- Infectious Diseases and Immunity in Global Health Research Program, Research Institute of McGill University Health Centre
- Department of Family Medicine, Faculty of Medicine and Health Sciences, McGill University
- Canadian Institutes of Health Research Strategy for Patient-Oriented Research Mentorship Chair in Innovative Clinical Trials
| | - Jonathan B. Angel
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario
- Division of Infectious Diseases, Department of Medicine, University of Ottawa and the Ottawa Hospital Research Institute, Ottawa, Ontario
| | - Jean-Pierre Routy
- Division of Infectious Diseases/Chronic Viral Illness Service, McGill University Health Centre, Royal Victoria Hospital
- Infectious Diseases and Immunity in Global Health Research Program, Research Institute of McGill University Health Centre
- Division of Hematology, Department of Medicine, McGill University Health Centre, Montreal, Québec, Canada
| | - Curtis L. Cooper
- Division of Infectious Diseases, Department of Medicine, University of Ottawa and the Ottawa Hospital Research Institute, Ottawa, Ontario
| | - Aslam H. Anis
- School of Population and Public Health, University of British Columbia
- CIHR Canadian HIV Trials Network (CTN)
- Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, British Columbia
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9
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Horvath RM, Brumme ZL, Sadowski I. CDK8 inhibitors antagonize HIV-1 reactivation and promote provirus latency in T cells. J Virol 2023; 97:e0092323. [PMID: 37671866 PMCID: PMC10537590 DOI: 10.1128/jvi.00923-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/15/2023] [Indexed: 09/07/2023] Open
Abstract
Latent HIV-1 provirus represents the barrier toward a cure for infection and is dependent upon the host RNA Polymerase (Pol) II machinery for reemergence. Here, we find that inhibitors of the RNA Pol II mediator kinases CDK8/19, Senexin A and BRD6989, inhibit induction of HIV-1 expression in response to latency-reversing agents and T cell signaling agonists. These inhibitors were found to impair recruitment of RNA Pol II to the HIV-1 LTR. Furthermore, HIV-1 expression in response to several latency reversal agents was impaired upon disruption of CDK8 by shRNA or gene knockout. However, the effects of CDK8 depletion did not entirely mimic CDK8/19 kinase inhibition suggesting that the mediator kinases are not functionally redundant. Additionally, treatment of CD4+ peripheral blood mononuclear cells isolated from people living with HIV-1 and who are receiving antiretroviral therapy with Senexin A inhibited induction of viral replication in response to T cell stimulation by PMA and ionomycin. These observations indicate that the mediator kinases, CDK8 and CDK19, play a significant role for regulation of HIV-1 transcription and that small molecule inhibitors of these enzymes may contribute to therapies designed to promote deep latency involving the durable suppression of provirus expression. IMPORTANCE A cure for HIV-1 infection will require novel therapies that can force elimination of cells that contain copies of the virus genome inserted into the cell chromosome, but which is shut off, or silenced. These are known as latently-infected cells, which represent the main reason why current treatment for HIV/AIDS cannot cure the infection because the virus in these cells is unaffected by current drugs. Our results indicate that chemical inhibitors of Cdk8 also inhibit the expression of latent HIV provirus. Cdk8 is an important enzyme that regulates the expression of genes in response to signals to which cells need to respond and which is produced by a gene that is frequently mutated in cancers. Our observations indicate that Cdk8 inhibitors may be employed in novel therapies to prevent expression from latent provirus, which might eventually enable infected individuals to cease treatment with antiretroviral drugs.
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Affiliation(s)
- Riley M. Horvath
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Dufour C, Ruiz MJ, Pagliuzza A, Richard C, Shahid A, Fromentin R, Ponte R, Cattin A, Wiche Salinas TR, Salahuddin S, Sandstrom T, Schinkel SB, Costiniuk CT, Jenabian MA, Ancuta P, Routy JP, Cohen ÉA, Brumme ZL, Power C, Angel JB, Chomont N. Near full-length HIV sequencing in multiple tissues collected postmortem reveals shared clonal expansions across distinct reservoirs during ART. Cell Rep 2023; 42:113053. [PMID: 37676762 DOI: 10.1016/j.celrep.2023.113053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 03/24/2023] [Revised: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
HIV persists in tissues during antiretroviral therapy (ART), but the relative contribution of different anatomical compartments to the viral reservoir in humans remains unknown. We performed an extensive characterization of HIV reservoirs in two men who donated their bodies to HIV cure research and who had been on suppressive ART for years. HIV DNA is detected in all tissues, with large variations across anatomical compartments and between participants. Intact HIV genomes represent 2% and 25% of all proviruses in the two participants and are mainly detected in secondary lymphoid organs, with the spleen and mediastinal lymph nodes harboring intact viral genomes in both individuals. Multiple copies of identical HIV genomes are found in all tissues, indicating that clonal expansions are common in anatomical sites. The majority (>85%) of these expanded clones are shared across multiple tissues. These findings suggest that infected cells expand, migrate, and possibly circulate between anatomical sites.
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Affiliation(s)
- Caroline Dufour
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Maria Julia Ruiz
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | | | | | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Rémi Fromentin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Rosalie Ponte
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Amélie Cattin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Tomas Raul Wiche Salinas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Syim Salahuddin
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Teslin Sandstrom
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Cecilia T Costiniuk
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Petronela Ancuta
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Jean-Pierre Routy
- Research Institute of McGill University Health Centre, Montreal, QC, Canada; Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - Éric A Cohen
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Christopher Power
- Department of Medicine (Neurology), University of Alberta, 6-11 Heritage Medical Research Center, Edmonton, AB, Canada; Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Jonathan B Angel
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada; Division of Infectious Diseases, Ottawa Hospital-General Campus, Ottawa, ON, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada.
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11
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. Res Sq 2023:rs.3.rs-3259040. [PMID: 37645749 PMCID: PMC10462229 DOI: 10.21203/rs.3.rs-3259040/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kyle Cobamibias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Nande M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, NC, USA
| | - Margaret A Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Adaora Adimora
- Departments of Medicine and Epidemiology, University of North Carolina School of Medicine, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, NY, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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12
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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13
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. bioRxiv 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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14
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Speckmaier S, Moran-Garcia N, Datwani S, Duncan MC, Agafitei O, Ennis S, Young L, Ali H, Ganase B, Omondi FH, Dong W, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes DT, DeMarco ML, Simons J, Hedgcock M, Prystajecky N, Lowe CF, Pantophlet R, Romney MG, Barrios R, Guillemi S, Brumme CJ, Montaner JSG, Hull M, Harris M, Niikura M, Brockman MA, Brumme ZL. People With Human Immunodeficiency Virus Receiving Suppressive Antiretroviral Therapy Show Typical Antibody Durability After Dual Coronavirus Disease 2019 Vaccination and Strong Third Dose Responses. J Infect Dis 2023; 227:838-849. [PMID: 35668700 PMCID: PMC9214159 DOI: 10.1093/infdis/jiac229] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Longer-term humoral responses to 2-dose coronavirus disease 2019 (COVID-19) vaccines remain incompletely characterized in people living with human immunodeficiency virus (HIV) (PLWH), as do initial responses to a third dose. METHODS We measured antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, angiotensin-converting enzyme 2 (ACE2) displacement, and viral neutralization against wild-type and Omicron strains up to 6 months after 2-dose vaccination, and 1 month after the third dose, in 99 PLWH receiving suppressive antiretroviral therapy and 152 controls. RESULTS Although humoral responses naturally decline after 2-dose vaccination, we found no evidence of lower antibody concentrations or faster rates of antibody decline in PLWH compared with controls after accounting for sociodemographic, health, and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after 2 doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though Omicron-specific responses were consistently weaker than responses against wild-type virus. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. CONCLUSION PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after 2- and 3-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.
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Affiliation(s)
- Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gisele Umviligihozo
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Nadia Moran-Garcia
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Hesham Ali
- John Ruedy Clinic, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Bruce Ganase
- AIDS Research Program, St Paul’s Hospital, Vancouver, British Columbia, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Junine Toy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
| | - Cecilia T Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Aslam H Anis
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Health Evaluation and Outcome Sciences, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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15
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Naicker D, Sonela N, Jin SW, Mulaudzi T, Ojwach D, Reddy T, Brockman MA, Brumme ZL, Ndung'u T, Mann JK. HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity. Retrovirology 2023; 20:3. [PMID: 37004071 PMCID: PMC10067162 DOI: 10.1186/s12977-023-00618-7] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. RESULTS No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. CONCLUSIONS These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics.
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Affiliation(s)
- Delon Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Nelson Sonela
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), P.O. Box 3077, Yaoundé, Cameroon
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Takalani Mulaudzi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Doty Ojwach
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Tarylee Reddy
- Medical Research Council, Biostatistics Unit, Durban, 4001, South Africa
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa.
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16
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. medRxiv 2023:2023.03.30.23287124. [PMID: 37034605 PMCID: PMC10081408 DOI: 10.1101/2023.03.30.23287124] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) can occur in persons with HIV despite adherence to combination antiretroviral therapy (ART) and in the absence of significant drug resistance. Here, we show that plasma NSV sequences are comprised primarily of large clones without evidence of viral evolution over time. We defined proviruses that contribute to plasma viremia as "producer", and those that did not as "non-producer". Compared to ART-suppressed individuals, NSV participants had a significantly larger producer reservoir. Producer proviruses were enriched in chromosome 19 and in proximity to the activating H3K36me3 epigenetic mark. CD4+ cells from NSV participants demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, NSV participants showed no elevation in HIV-specific CD8+ cell responses and producer proviruses were enriched for HLA escape mutations. We identified critical host and viral mediators of NSV that represent potential targets to disrupt HIV persistence and promote viral silencing.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rinki Deo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter L. Anderson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M. Lederman
- Center for AIDS Research, Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D. Lichterfeld
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jose R. Castillo-Mancilla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alan N. Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D. Gaiha
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Kalikawe R, Datwani S, Burns L, Young L, Leung V, Ennis S, Brumme CJ, Montaner JSG, Dong W, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Impact of Age and Severe Acute Respiratory Syndrome Coronavirus 2 Breakthrough Infection on Humoral Immune Responses After Three Doses of Coronavirus Disease 2019 mRNA Vaccine. Open Forum Infect Dis 2023; 10:ofad073. [PMID: 36910697 PMCID: PMC10003738 DOI: 10.1093/ofid/ofad073] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
Background Longer-term immune response data after 3 doses of coronavirus disease 2019 (COVID-19) mRNA vaccine remain limited, particularly among older adults and after Omicron breakthrough infection. Methods We quantified wild-type- and Omicron-specific serum immunoglobulin (Ig)G levels, angiotensin-converting enzyme 2 displacement activities, and live virus neutralization up to 6 months after third dose in 116 adults aged 24-98 years who remained COVID-19 naive or experienced their first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during this time. Results Among the 78 participants who remained COVID-19 naive throughout follow up, wild-type- and Omicron-BA.1-specific IgG concentrations were comparable between younger and older adults, although BA.1-specific responses were consistently significantly lower than wild-type-specific responses in both groups. Wild-type- and BA.1-specific IgG concentrations declined at similar rates in COVID-19-naive younger and older adults, with median half-lives ranging from 69 to 78 days. Antiviral antibody functions declined substantially over time in COVID-19-naive individuals, particularly in older adults: by 6 months, BA.1-specific neutralization was undetectable in 96% of older adults, versus 56% of younger adults. Severe acute respiratory syndrome coronavirus 2 infection, experienced by 38 participants, boosted IgG levels and neutralization above those induced by vaccination alone. Nevertheless, BA.1-specific neutralization remained significantly lower than wild-type, with BA.5-specific neutralization lower still. Higher Omicron BA.1-specific neutralization 1 month after third dose was an independent correlate of lower SARS-CoV-2 infection risk. Conclusions Results underscore the immune benefits of the third COVID-19 mRNA vaccine dose in adults of all ages and identify vaccine-induced Omicron-specific neutralization as a correlate of protective immunity. Systemic antibody responses and functions however, particularly Omicron-specific neutralization, decline rapidly in COVID-19-naive individuals, particularly in older adults, supporting the need for additional booster doses.
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Affiliation(s)
- Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | | | - Mark A Brockman
- Correspondence: Mark A. Brockman, PhD, Professor, Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada ()
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18
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Horvath RM, Brumme ZL, Sadowski I. Inhibition of the TRIM24 bromodomain reactivates latent HIV-1. Sci Rep 2023; 13:556. [PMID: 36631514 PMCID: PMC9832417 DOI: 10.1038/s41598-023-27765-3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Expression of the HIV-1 genome by RNA Polymerase II is regulated at multiple steps, as are most cellular genes, including recruitment of general transcription factors and control of transcriptional elongation from the core promoter. We recently discovered that tripartite motif protein TRIM24 is recruited to the HIV-1 Long Terminal Repeat (LTR) by interaction with TFII-I and causes transcriptional elongation by stimulating association of PTEF-b/ CDK9. Because TRIM24 is required for stimulation of transcription from the HIV-1 LTR, we were surprised to find that IACS-9571, a specific inhibitor of the TRIM24 C-terminal bromodomain, induces HIV-1 provirus expression in otherwise untreated cells. IACS-9571 reactivates HIV-1 in T cell lines bearing multiple different provirus models of HIV-1 latency. Additionally, treatment with this TRIM24 bromodomain inhibitor encourages productive HIV-1 expression in newly infected cells and inhibits formation of immediate latent transcriptionally repressed provirus. IACS-9571 synergizes with PMA, ionomycin, TNF-α and PEP005 to activate HIV-1 expression. Furthermore, co-treatment of CD4 + T cells from individuals with HIV-1 on antiretroviral therapy (ART) with PEP005 and IACS-9571 caused robust provirus expression. Notably, IACS-9571 did not cause global activation of T cells; rather, it inhibited induction of IL2 and CD69 expression in human PBMCs and Jurkat T cells treated with PEP005 or PMA. These observations indicate the TRIM24 bromodomain inhibitor IACS-9571 represents a novel HIV-1 latency reversing agent (LRA), and unlike other compounds with this activity, causes partial suppression of T cell activation while inducing expression of latent provirus.
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Affiliation(s)
- Riley M Horvath
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, UBC, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology, Molecular Epigenetics Group, LSI, University of British Columbia, UBC, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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19
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Appah A, Beelen CJ, Kirkby D, Dong W, Shahid A, Foley B, Mensah M, Ganu V, Puplampu P, Amoah LE, Nii-Trebi NI, Brumme CJ, Brumme ZL. Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage. Viruses 2022; 15:128. [PMID: 36680168 PMCID: PMC9865111 DOI: 10.3390/v15010128] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
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Affiliation(s)
- Anna Appah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Foley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Miriam Mensah
- Fevers Unit, Department of Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Vincent Ganu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Peter Puplampu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Linda E. Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
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20
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Gunst JD, Pahus MH, Rosás-Umbert M, Lu IN, Benfield T, Nielsen H, Johansen IS, Mohey R, Østergaard L, Klastrup V, Khan M, Schleimann MH, Olesen R, Støvring H, Denton PW, Kinloch NN, Copertino DC, Ward AR, Alberto WDC, Nielsen SD, Puertas MC, Ramos V, Reeves JD, Petropoulos CJ, Martinez-Picado J, Brumme ZL, Jones RB, Fox J, Tolstrup M, Nussenzweig MC, Caskey M, Fidler S, Søgaard OS. Early intervention with 3BNC117 and romidepsin at antiretroviral treatment initiation in people with HIV-1: a phase 1b/2a, randomized trial. Nat Med 2022; 28:2424-2435. [PMID: 36253609 PMCID: PMC10189540 DOI: 10.1038/s41591-022-02023-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 01/26/2023]
Abstract
Attempts to reduce the human immunodeficiency virus type 1 (HIV-1) reservoir and induce antiretroviral therapy (ART)-free virologic control have largely been unsuccessful. In this phase 1b/2a, open-label, randomized controlled trial using a four-group factorial design, we investigated whether early intervention in newly diagnosed people with HIV-1 with a monoclonal anti-HIV-1 antibody with a CD4-binding site, 3BNC117, followed by a histone deacetylase inhibitor, romidepsin, shortly after ART initiation altered the course of HIV-1 infection ( NCT03041012 ). The trial was undertaken in five hospitals in Denmark and two hospitals in the United Kingdom. The coprimary endpoints were analysis of initial virus decay kinetics and changes in the frequency of CD4+ T cells containing intact HIV-1 provirus from baseline to day 365. Secondary endpoints included changes in the frequency of infected CD4+ T cells and virus-specific CD8+ T cell immunity from baseline to day 365, pre-ART plasma HIV-1 3BNC117 sensitivity, safety and tolerability, and time to loss of virologic control during a 12-week analytical ART interruption that started at day 400. In 55 newly diagnosed people (5 females and 50 males) with HIV-1 who received random allocation treatment, we found that early 3BNC117 treatment with or without romidepsin enhanced plasma HIV-1 RNA decay rates compared to ART only. Furthermore, 3BNC117 treatment accelerated clearance of infected cells compared to ART only. All groups had significant reductions in the frequency of CD4+ T cells containing intact HIV-1 provirus. At day 365, early 3BNC117 + romidepsin was associated with enhanced HIV-1 Gag-specific CD8+ T cell immunity compared to ART only. The observed virological and immunological effects of 3BNC117 were most pronounced in individuals whose pre-ART plasma HIV-1 envelope sequences were antibody sensitive. The results were not disaggregated by sex. Adverse events were mild to moderate and similar between the groups. During a 12-week analytical ART interruption among 20 participants, 3BNC117-treated individuals harboring sensitive viruses were significantly more likely to maintain ART-free virologic control than other participants. We conclude that 3BNC117 at ART initiation enhanced elimination of plasma viruses and infected cells, enhanced HIV-1-specific CD8+ immunity and was associated with sustained ART-free virologic control among persons with 3BNC117-sensitive virus. These findings strongly support interventions administered at the time of ART initiation as a strategy to limit long-term HIV-1 persistence.
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Affiliation(s)
- Jesper D Gunst
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Marie H Pahus
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Miriam Rosás-Umbert
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital-Amager and Hvidovre, Hvidovre, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Rajesh Mohey
- Department of Internal Medicine, Regional Hospital Herning, Herning, Denmark
| | - Lars Østergaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Vibeke Klastrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maryam Khan
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Mariane H Schleimann
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Olesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Støvring
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Paul W Denton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dennis C Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Adam R Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Winiffer D Conce Alberto
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Silke D Nielsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBERINFEC, Madrid, Spain
- University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Julie Fox
- Department of Genitourinary Medicine and Infectious Disease, Guy's and St Thomas' National Health Service Trust, London, UK
- Department of Genitourinary Medicine and Infectious Disease, The National Institute for Health Research Biomedical Research Centre, King's College London, London, UK
| | - Martin Tolstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Fidler
- Department of Infectious Diseases, Imperial College Hospital, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Ole S Søgaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
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21
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Rosás-Umbert M, Gunst JD, Pahus MH, Olesen R, Schleimann M, Denton PW, Ramos V, Ward A, Kinloch NN, Copertino DC, Escribà T, Llano A, Brumme ZL, Brad Jones R, Mothe B, Brander C, Fox J, Nussenzweig MC, Fidler S, Caskey M, Tolstrup M, Søgaard OS. Administration of broadly neutralizing anti-HIV-1 antibodies at ART initiation maintains long-term CD8 + T cell immunity. Nat Commun 2022; 13:6473. [PMID: 36309514 PMCID: PMC9617872 DOI: 10.1038/s41467-022-34171-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
In simian-human immunodeficiency virus (SHIV)-infected non-human primates, broadly neutralizing antibodies (bNAbs) against the virus appear to stimulate T cell immunity. To determine whether this phenomenon also occurs in humans we measured HIV-1-specific cellular immunity longitudinally in individuals with HIV-1 starting antiviral therapy (ART) with or without adjunctive bNAb 3BNC117 treatment. Using the activation-induced marker (AIM) assay and interferon-γ release, we observe that frequencies of Pol- and Gag-specific CD8+ T cells, as well as Gag-induced interferon-γ responses, are significantly higher among individuals that received adjunctive 3BNC117 compared to ART-alone at 3 and 12 months after starting ART. The observed changes in cellular immunity were directly correlated to pre-treatment 3BNC117-sensitivity. Notably, increased HIV-1-specific immunity is associated with partial or complete ART-free virologic control during treatment interruption for up to 4 years. Our findings suggest that bNAb treatment at the time of ART initiation maintains HIV-1-specific CD8+ T cell responses that are associated with ART-free virologic control.
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Affiliation(s)
| | - Jesper D Gunst
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Marie H Pahus
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Rikke Olesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mariane Schleimann
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Paul W Denton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Adam Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Dennis C Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Tuixent Escribà
- IrsiCaixa, AIDS Research Institute, Institute for Health Science Research Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Spain
| | - Anuska Llano
- IrsiCaixa, AIDS Research Institute, Institute for Health Science Research Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Spain
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Beatriz Mothe
- IrsiCaixa, AIDS Research Institute, Institute for Health Science Research Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa, AIDS Research Institute, Institute for Health Science Research Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Julie Fox
- Department of Genitourinary Medicine and Infectious Disease, Guys and St Thomas' National Health Service Trust, London, UK
- Department of Genitourinary Medicine and Infectious Disease, The National Institute for Health Research Biomedical Research Centre, King's College London, London, UK
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Sarah Fidler
- Department of Infectious Diseases, Imperial College London, London, UK
- The National Institute for Health Research, Imperial Biomedical Research Centre, London, UK
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martin Tolstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S Søgaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
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22
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Datwani S, Omondi FH, Burns L, Young L, Leung V, Agafitei O, Ennis S, Dong W, Basra S, Lim LY, Ng K, Pantophlet R, Brumme CJ, Montaner JSG, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Older Adults Mount Less Durable Humoral Responses to Two Doses of COVID-19 mRNA Vaccine but Strong Initial Responses to a Third Dose. J Infect Dis 2022; 226:983-994. [PMID: 35543278 PMCID: PMC9129202 DOI: 10.1093/infdis/jiac199] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 02/23/2022] [Accepted: 05/10/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Third coronavirus disease 2019 (COVID-19) vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS We measured circulating antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and omicron (BA.1) strains from prevaccine up to 1 month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS Following 2 vaccine doses, humoral immunity was weaker, less functional, and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. One month after the third dose, antibody concentrations and function exceeded post-second-dose levels, and responses in older adults were comparable in magnitude to those in younger adults at this time. Humoral responses against omicron were universally weaker than against the ancestral strain after both the second and third doses. Nevertheless, after 3 doses, anti-omicron responses in older adults reached equivalence to those in younger adults. One month after 3 vaccine doses, the number of chronic health conditions, but not age, was the strongest consistent correlate of weaker humoral responses. CONCLUSIONS Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.
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Affiliation(s)
- Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel T Holmes
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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23
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Kalikawe R, Datwani S, Waterworth R, Umviligihozo G, Ennis S, Young L, Dong W, Kirkby D, Burns L, Leung V, Holmes DT, DeMarco ML, Simons J, Matic N, Montaner JS, Brumme CJ, Prystajecky N, Niikura M, Lowe CF, Romney MG, Brockman MA, Brumme ZL. Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination. Front Immunol 2022; 13:947021. [PMID: 36148225 PMCID: PMC9485663 DOI: 10.3389/fimmu.2022.947021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/18/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have immunologically assessed serial Omicron infections. We characterized SARS-CoV-2 humoral responses in an individual who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to 124 COVID-19-naive vaccinees. One month post-second and -third vaccine doses, the participant's wild-type and BA.1-specific IgG, ACE2-displacement and virus neutralization activities were average for a COVID-19-naive triple-vaccinated individual. BA.1 infection boosted the participant's responses to the cohort ≥95th percentile, but even this strong "hybrid" immunity failed to protect against BA.2. Reinfection increased BA.1 and BA.2-specific responses only modestly. Though vaccines clearly protect against severe disease, results highlight the continued importance of maintaining additional protective measures to counteract the immune-evasive Omicron variant, particularly as vaccine-induced immune responses naturally decline over time.
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Affiliation(s)
- Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel Waterworth
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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24
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Stevenson EM, Terry S, Copertino D, Leyre L, Danesh A, Weiler J, Ward AR, Khadka P, McNeil E, Bernard K, Miller IG, Ellsworth GB, Johnston CD, Finkelsztein EJ, Zumbo P, Betel D, Dündar F, Duncan MC, Lapointe HR, Speckmaier S, Moran-Garcia N, Papa MP, Nicholes S, Stover CJ, Lynch RM, Caskey M, Gaebler C, Chun TW, Bosque A, Wilkin TJ, Lee GQ, Brumme ZL, Jones RB. SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8 + T-cells. Nat Commun 2022; 13:4888. [PMID: 35985993 PMCID: PMC9389512 DOI: 10.1038/s41467-022-32376-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 06/06/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
Efforts to cure HIV have focused on reactivating latent proviruses to enable elimination by CD8+ cytotoxic T-cells. Clinical studies of latency reversing agents (LRA) in antiretroviral therapy (ART)-treated individuals have shown increases in HIV transcription, but without reductions in virologic measures, or evidence that HIV-specific CD8+ T-cells were productively engaged. Here, we show that the SARS-CoV-2 mRNA vaccine BNT162b2 activates the RIG-I/TLR - TNF - NFκb axis, resulting in transcription of HIV proviruses with minimal perturbations of T-cell activation and host transcription. T-cells specific for the early gene-product HIV-Nef uniquely increased in frequency and acquired effector function (granzyme-B) in ART-treated individuals following SARS-CoV-2 mRNA vaccination. These parameters of CD8+ T-cell induction correlated with significant decreases in cell-associated HIV mRNA, suggesting killing or suppression of cells transcribing HIV. Thus, we report the observation of an intervention-induced reduction in a measure of HIV persistence, accompanied by precise immune correlates, in ART-suppressed individuals. However, we did not observe significant depletions of intact proviruses, underscoring challenges to achieving (or measuring) HIV reservoir reductions. Overall, our results support prioritizing the measurement of granzyme-B-producing Nef-specific responses in latency reversal studies and add impetus to developing HIV-targeted mRNA therapeutic vaccines that leverage built-in LRA activity.
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Affiliation(s)
- Eva M Stevenson
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sandra Terry
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dennis Copertino
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Louise Leyre
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Ali Danesh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared Weiler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Adam R Ward
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pragya Khadka
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Evan McNeil
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kevin Bernard
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Itzayana G Miller
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Grant B Ellsworth
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carrie D Johnston
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eli J Finkelsztein
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Paul Zumbo
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Doron Betel
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Friederike Dündar
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Nadia Moran-Garcia
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Michelle Premazzi Papa
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Samuel Nicholes
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Carissa J Stover
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Rebecca M Lynch
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID, NIH, Bethesda, MD, USA
| | - Alberto Bosque
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Timothy J Wilkin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Guinevere Q Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - R Brad Jones
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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25
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Umviligihozo G, Mann JK, Jin SW, Mwimanzi FM, Hsieh HSA, Sudderuddin H, Lee GQ, Byakwaga H, Muzoora C, Hunt PW, Martin JN, Haberer JE, Karita E, Allen S, Hunter E, Brumme ZL, Brockman MA. Attenuated HIV-1 Nef But Not Vpu Function in a Cohort of Rwandan Long-Term Survivors. Front Virol 2022; 2:917902. [PMID: 35982753 PMCID: PMC9383652 DOI: 10.3389/fviro.2022.917902] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
HIV-1 accessory proteins Nef and Vpu enhance viral pathogenesis through partially overlapping immune evasion activities. Attenuated Nef or Vpu functions have been reported in individuals who display slower disease progression, but few studies have assessed the relative impact of these proteins in non-B HIV-1 subtypes or examined paired proteins from the same individuals. Here, we examined the sequence and function of matched Nef and Vpu clones isolated from 29 long-term survivors (LTS) from Rwanda living with HIV-1 subtype A and compared our results to those of 104 Nef and 62 Vpu clones isolated from individuals living with chronic untreated HIV-1 subtype A from the same geographic area. Nef and vpu coding regions were amplified from plasma HIV RNA and cloned. The function of one intact, phylogenetically-validated Nef and Vpu clone per individual was then quantified by flow cytometry following transient expression in an immortalized CD4+ T-cell line. We measured the ability of each Nef clone to downregulate CD4 and HLA class I, and of each Vpu clone to downregulate CD4 and Tetherin, from the cell surface. Results were normalized to reference clones (Nef-SF2 and Vpu-NL4.3). We observed that Nef-mediated CD4 and HLA downregulation functions were lower in LTS compared to the control cohort (Mann-Whitney p=0.03 and p<0.0001, respectively). Moreover, we found a positive correlation between Nef-mediated CD4 downregulation function and plasma viral load in LTS and controls (Spearman ρ= 0.59, p=0.03 and ρ=0.30, p=0.005, respectively). In contrast, Vpu-mediated functions were similar between groups and did not correlate with clinical markers. Further analyses identified polymorphisms at Nef codon 184 and Vpu codons 60-62 that were associated with function, which were confirmed through mutagenesis. Overall, our results support attenuated function of Nef, but not Vpu, as a contributor to slower disease progression in this cohort of long-term survivors with HIV-1 subtype A.
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Affiliation(s)
| | - Jaclyn K. Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Hua-Shiuan A. Hsieh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada
| | - Guinevere Q. Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Helen Byakwaga
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Medicine, University of California, San Francisco, CA, United States
| | - Conrad Muzoora
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Peter W. Hunt
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jeff N. Martin
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jessica E. Haberer
- Center for Global Health, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States,Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada,British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada,Correspondence: Mark A. Brockman,
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26
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Brockman MA, Mwimanzi F, Lapointe HR, Sang Y, Agafitei O, Cheung PK, Ennis S, Ng K, Basra S, Lim LY, Yaseen F, Young L, Umviligihozo G, Omondi FH, Kalikawe R, Burns L, Brumme CJ, Leung V, Montaner JSG, Holmes D, DeMarco ML, Simons J, Pantophlet R, Niikura M, Romney MG, Brumme ZL. Reduced Magnitude and Durability of Humoral Immune Responses to COVID-19 mRNA Vaccines Among Older Adults. J Infect Dis 2022; 225:1129-1140. [PMID: 34888688 PMCID: PMC8689804 DOI: 10.1093/infdis/jiab592] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 09/09/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The magnitude and durability of immune responses to coronavirus disease 2019 (COVID-19) mRNA vaccines remain incompletely characterized in the elderly. METHODS Anti-spike receptor-binding domain (RBD) antibodies, angiotensin-converting enzyme 2 (ACE2) competition, and virus neutralizing activities were assessed in plasma from 151 health care workers and older adults (range, 24-98 years of age) 1 month following the first vaccine dose, and 1 and 3 months following the second dose. RESULTS Older adults exhibited significantly weaker responses than younger health care workers for all humoral measures evaluated and at all time points tested, except for ACE2 competition activity after 1 vaccine dose. Moreover, older age remained independently associated with weaker responses even after correction for sociodemographic factors, chronic health condition burden, and vaccine-related variables. By 3 months after the second dose, all humoral responses had declined significantly in all participants, and remained significantly lower among older adults, who also displayed reduced binding antibodies and ACE2 competition activity towards the Delta variant. CONCLUSIONS Humoral responses to COVID-19 mRNA vaccines are significantly weaker in older adults, and antibody-mediated activities in plasma decline universally over time. Older adults may thus remain at elevated risk of infection despite vaccination.
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Affiliation(s)
- Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Peter K Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | | | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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27
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Lapointe HR, Mwimanzi F, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Speckmaier S, Moran-Garcia N, Datwani S, Duncan MC, Agafitei O, Ennis S, Young L, Ali H, Ganase B, Omondi FH, Dong W, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes D, DeMarco ML, Simons J, Hedgcock M, Prystajecky N, Lowe CF, Pantophlet R, Romney MG, Barrios R, Guillemi S, Brumme CJ, Montaner JSG, Hull M, Harris M, Niikura M, Brockman MA, Brumme ZL. People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses. medRxiv 2022. [PMID: 35350205 PMCID: PMC8963693 DOI: 10.1101/2022.03.22.22272793] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background: Longer-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose. Methods: We measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls. Results: Though humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though anti-Omicron responses were consistently weaker than against wild-type. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. Conclusion: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after two- and three-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.
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Affiliation(s)
- Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | | | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Maggie C Duncan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Hesham Ali
- John Ruedy Clinic, St, Paul's Hospital, Vancouver, Canada
| | - Bruce Ganase
- AIDS Research Program, St. Paul's Hospital, Vancouver, Canada
| | - F Harrison Omondi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Junine Toy
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Paul Sereda
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Cecilia T Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Hospital Research Institute, Ottawa, Canada
| | - Aslam H Anis
- School of Population and Public Health, University of British Columbia, Vancouver, Canada.,CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, Canada.,Centre for Health Evaluation and Outcome Sciences, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Mark A Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
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28
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Habermann D, Kharimzadeh H, Walker A, Li Y, Yang R, Kaiser R, Brumme ZL, Timm J, Roggendorf M, Hoffmann D. HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations. Bioinformatics 2022; 38:2428-2436. [PMID: 35238330 DOI: 10.1093/bioinformatics/btac134] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/21/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION A key process in anti-viral adaptive immunity is that the Human Leukocyte Antigen system (HLA) presents epitopes as Major Histocompatibility Complex I (MHC I) protein-peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-Lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the hosts MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature, HAMs are amenable to detection by statistical methods in paired sequence/HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this. RESULTS We present a new Bayesian regression model for the detection of HAMs that integrates a sparsity-inducing prior, epitope predictions, and phylogenetic bias assessment, and that yields easily interpretable quantitative information on HAM candidates. The model predicts experimentally confirmed HAMs as having high posterior probabilities, and it performs well in comparison to state-of-the-art models for several data sets from individuals infected with HBV, HDV, and HIV. AVAILABILITY The source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Habermann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, 45117, Germany
| | - Hadi Kharimzadeh
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, 40225, Germany
| | - Yang Li
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology,Chinese Academy of Science, Wuhan, P. R. China
| | - Rongge Yang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology,Chinese Academy of Science, Wuhan, P. R. China
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, 50935, Germany
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, 40225, Germany
| | - Michael Roggendorf
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, 45117, Germany.,Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.,Center for Computational Sciences and Simulation, University of Duisburg-Essen, Essen, Germany
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29
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Mwimanzi F, Lapointe HR, Cheung PK, Sang Y, Yaseen F, Umviligihozo G, Kalikawe R, Datwani S, Omondi FH, Burns L, Young L, Leung V, Agafitei O, Ennis S, Dong W, Basra S, Lim LY, Ng K, Pantophlet R, Brumme CJ, Montaner JS, Prystajecky N, Lowe CF, DeMarco ML, Holmes DT, Simons J, Niikura M, Romney MG, Brumme ZL, Brockman MA. Older Adults Mount Less Durable Humoral Responses to a Two-dose COVID-19 mRNA Vaccine Regimen, but Strong Initial Responses to a Third Dose. medRxiv 2022:2022.01.06.22268745. [PMID: 35018381 PMCID: PMC8750654 DOI: 10.1101/2022.01.06.22268745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Third COVID-19 vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS We measured circulating antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and Omicron (BA.1) strains from pre-vaccine up to one month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS Following two vaccine doses, humoral immunity was weaker, less functional and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. Third doses boosted antibody binding and function to higher levels than second-doses, and induced responses in older adults that were comparable in magnitude to those in younger adults. Humoral responses against Omicron were universally weaker than against the ancestral strain after both second and third doses; nevertheless, after three doses, anti-Omicron responses in older adults reached equivalence to those in younger adults. After three vaccine doses, the number of chronic health conditions, but not age per se, was the strongest consistent correlate of weaker humoral responses. CONCLUSION Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.
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Affiliation(s)
| | | | - Peter K. Cheung
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Fatima Yaseen
- Faculty of Health Sciences, Simon Fraser University, Canada
| | | | | | - Sneha Datwani
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - F. Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Laura Burns
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
| | - Victor Leung
- Department of Medicine, University of British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Canada
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Canada
- Department of Medicine, University of British Columbia, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Canada
- Department of Medicine, University of British Columbia, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Mari L. DeMarco
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Daniel T. Holmes
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Janet Simons
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | | | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Canada
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30
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Zamiri M, Cheung PK, Brockman MA, Brumme ZL, Chabot B, Cochrane A, Grierson DS. 2-Trifluoromethylthiazole-5-carboxamides: Analogues of a Stilbene-Based Anti-HIV Agent that Impact HIV mRNA Processing. ACS Med Chem Lett 2021; 12:1818-1823. [PMID: 34795872 DOI: 10.1021/acsmedchemlett.1c00428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/22/2021] [Indexed: 12/26/2022] Open
Abstract
The observation that stilbene 3 (5350150) blocks HIV replication through its impact on HIV mRNA processing prompted a program to develop non-cytotoxic analogues that maintain its mechanism of action. This initially involved replacement of the central double bond in 3 by an amide function and the quinoline motif by a 2-aminobenzothiazole subunit, as in 12jj (R' = Cl), 12pp (R = NO2), and 12vv (R = CF3). On the basis of the possible CF3 ↔ NO2 bioisostere relationship in 12vv and 12pp, compound 23 was prepared and also found to be active. In the final step, the thiazole compounds 28 (GPS488) (EC50 = 1.66 μM) and 29 (GPS491) (EC50 = 0.47 μM) were prepared and evaluated. Similar activity and cell viability values (therapeutic index (TI = CC50/EC50) values of 50-100) were observed in primary peripheral blood mononuclear cells. Furthermore, they remained active against a panel of HIV mutant strains displaying resistance to individual drugs used in antiretroviral therapy. It was determined that compound 29 suppressed expression of the HIV-1 structural protein Gag and altered HIV-1 RNA accumulation, decreasing the abundance of RNAs encoding the structural proteins while increasing levels of viral RNAs encoding the regulatory proteins, a pattern similar to that seen for compound 3.
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Affiliation(s)
- Maryam Zamiri
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter K. Cheung
- BC Centre for Excellence in HIV/AIDS, 608−1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mark A. Brockman
- BC Centre for Excellence in HIV/AIDS, 608−1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Zabrina L. Brumme
- BC Centre for Excellence in HIV/AIDS, 608−1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David S. Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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31
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McLaughlin A, Sereda P, Brumme CJ, Brumme ZL, Barrios R, Montaner JSG, Joy JB. Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering. Evol Med Public Health 2021; 9:338-348. [PMID: 34754454 PMCID: PMC8573190 DOI: 10.1093/emph/eoab028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/14/2021] [Indexed: 11/22/2022]
Abstract
Background and objectives Although HIV sequence clustering is routinely used to identify subpopulations experiencing elevated transmission, it over-simplifies transmission dynamics and is sensitive to methodology. Complementarily, viral diversification rates can be used to approximate historical transmission rates. Here, we investigated the concordance and sensitivity of HIV transmission risk factors identified by phylogenetic clustering, viral diversification rate, changes in viral diversification rate and a combined approach. Methodology Viral sequences from 9848 people living with HIV in British Columbia, Canada, sampled between 1996 and February 2019, were used to infer phylogenetic trees, from which clusters were identified and viral diversification rates of each tip were calculated. Factors associated with heightened transmission risk were compared across models of cluster membership, viral diversification rate, changes in diversification rate, and viral diversification rate among clusters. Results Viruses within larger clusters had higher diversification rates and lower changes in diversification rate than those within smaller clusters; however, rates within individual clusters, independent of size, varied widely. Risk factors for both cluster membership and elevated viral diversification rate included being male, young, a resident of health authority E, previous injection drug use, previous hepatitis C virus infection or a high recent viral load. In a sensitivity analysis, models based on cluster membership had wider confidence intervals and lower concordance of significant effects than viral diversification rate for lower sampling rates. Conclusions and implications Viral diversification rate complements phylogenetic clustering, offering a means of evaluating transmission dynamics to guide provision of treatment and prevention services. Lay Summary Understanding HIV transmission dynamics within clusters can help prioritize public health resource allocation. We compared socio-demographic and clinical risk factors associated with phylogenetic cluster membership and viral diversification rate, a historical branching rate, in order to assess their relative concordance and sampling sensitivity.
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Affiliation(s)
- Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Department of Bioinformatics, University of British Columbia, Genome Sciences Centre, British Columbia Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Faculty of Health Sciences, Simon Fraser University, Blusson Hall, Room 11300, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada.,Department of Bioinformatics, University of British Columbia, Genome Sciences Centre, British Columbia Cancer Agency, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada.,Division of Infectious Diseases, Department of Medicine, University of British Columbia, 452D, Heather Pavilion East, Vancouver General Hospital, 2733 Heather Street, Vancouver, BC V5Z 3J5, Canada
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32
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Brumme ZL, Mwimanzi F, Lapointe HR, Cheung P, Sang Y, Duncan MC, Yaseen F, Agafitei O, Ennis S, Ng K, Basra S, Lim LY, Kalikawe R, Speckmaier S, Moran-Garcia N, Young L, Ali H, Ganase B, Umviligihozo G, Omondi FH, Atkinson K, Sudderuddin H, Toy J, Sereda P, Burns L, Costiniuk CT, Cooper C, Anis AH, Leung V, Holmes D, DeMarco ML, Simons J, Hedgcock M, Romney MG, Barrios R, Guillemi S, Brumme CJ, Pantophlet R, Montaner JS, Niikura M, Harris M, Hull M, Brockman MA. Humoral immune responses to COVID-19 vaccination in people living with HIV receiving suppressive antiretroviral therapy. medRxiv 2021:2021.10.03.21264320. [PMID: 34671779 PMCID: PMC8528088 DOI: 10.1101/2021.10.03.21264320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Humoral responses to COVID-19 vaccines in people living with HIV (PLWH) remain incompletely understood. We measured circulating antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, ACE2 displacement and live viral neutralization activities one month following the first and second COVID-19 vaccine doses in 100 adult PLWH and 152 controls. All PLWH were receiving suppressive antiretroviral therapy, with median CD4+ T-cell counts of 710 (IQR 525-935) cells/mm 3 . Nadir CD4+ T-cell counts ranged as low as <10 (median 280; IQR 120-490) cells/mm 3 . After adjustment for sociodemographic, health and vaccine-related variables, HIV infection was significantly associated with 0.2 log 10 lower anti-RBD antibody concentrations (p=0.03) and ∼11% lower ACE2 displacement activity (p=0.02), but not lower viral neutralization (p=0.1) after one vaccine dose. Following two doses however, HIV was no longer significantly associated with the magnitude of any response measured. Rather, older age, a higher burden of chronic health conditions, and having received two ChAdOx1 doses (versus a heterologous or dual mRNA vaccine regimen) were independently associated with lower responses. After two vaccine doses, no significant correlation was observed between the most recent or nadir CD4+ T-cell counts and vaccine responses in PLWH. These results suggest that PLWH with well-controlled viral loads on antiretroviral therapy and CD4+ T-cell counts in a healthy range will generally not require a third COVID-19 vaccine dose as part of their initial immunization series, though other factors such as older age, co-morbidities, vaccine regimen type, and durability of vaccine responses will influence when this group may benefit from additional doses. Further studies of PLWH who are not receiving antiretroviral treatment and/or who have low CD4+ T-cell counts are needed.
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Affiliation(s)
- Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Hope R. Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Peter Cheung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Fatima Yaseen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Simran Basra
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Li Yi Lim
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Rebecca Kalikawe
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
| | - Hesham Ali
- John Ruedy Clinic, St, Paul’s Hospital, Vancouver, Canada
| | - Bruce Ganase
- AIDS Research Program, St. Paul’s Hospital, Vancouver, Canada
| | | | - F. Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Kieran Atkinson
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Junine Toy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Laura Burns
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
| | - Cecilia T. Costiniuk
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Curtis Cooper
- Department of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canadas
| | - Aslam H. Anis
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- CIHR Canadian HIV Trials Network, University of British Columbia, Vancouver, Canada
- Centre for Health Evaluation and Outcome Sciences, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Canada
| | - Mark Hull
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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Brooks K, Omondi FH, Liang RH, Sudderuddin H, Jones BR, Joy JB, Brumme CJ, Hunter E, Brumme ZL. Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART. Front Microbiol 2021; 12:719153. [PMID: 34489909 PMCID: PMC8417368 DOI: 10.3389/fmicb.2021.719153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) can persist as an integrated provirus, in a transcriptionally repressed state, within infected cells. This small yet enduring pool of cellular reservoirs that harbor replication-competent HIV is the main barrier to cure. Entry of viral sequences into cellular reservoirs begins shortly after infection, and cells containing integrated proviral DNA are extremely stable once suppressive antiretroviral therapy (ART) is initiated. During untreated HIV infection however, reservoir turnover is likely to be more dynamic. Understanding these dynamics is important because the longevity of the persisting proviral pool during untreated infection dictates reservoir composition at ART initiation. If the persisting proviral pool turns over slowly pre-ART, then HIV sequences seeded into it during early infection would have a high likelihood of persisting for long periods. However, if pre-ART turnover was rapid, the persisting proviral pool would rapidly shift toward recently circulating HIV sequences. One-way to estimate this turnover rate is from the age distributions of proviruses sampled shortly after therapy initiation: this is because, at the time of sampling, the majority of proviral turnover would have already occurred prior to ART. Recently, methods to estimate a provirus’ age from its sequence have made this possible. Using data from 12 individuals with HIV subtype C for whom proviral ages had been determined phylogenetically, we estimated that the average proviral half-life during untreated infection was 0.78 (range 0.45–2.38) years, which is >15 times faster than that of proviral DNA during suppressive ART. We further show that proviral turnover during untreated infection correlates with both viral setpoint and rate of CD4+ T-cell decline during this period. Overall, our results support dynamic proviral turnover pre-ART in most individuals, which helps explain why many individuals’ reservoirs are skewed toward younger HIV sequences. Broadly, our findings are consistent with the notion that active viral replication creates an environment less favorable to proviral persistence, while viral suppression creates conditions more favorable to persistence, where ART stabilizes the proviral pool by dramatically slowing its rate of decay. Strategies to inhibit this stabilizing effect and/or to enhance reservoir turnover during ART could represent additional strategies to reduce the HIV reservoir.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard H Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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Matic N, Lowe CF, Ritchie G, Stefanovic A, Lawson T, Jang W, Young M, Dong W, Brumme ZL, Brumme CJ, Leung V, Romney MG. Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada. Emerg Infect Dis 2021; 27:1673-1676. [PMID: 33784237 PMCID: PMC8153894 DOI: 10.3201/eid2706.210532] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To screen all severe acute respiratory syndrome coronavirus 2-positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR-based algorithm. We rapidly identified 77 samples with variants: 57 with B.1.1.7, 7 with B.1.351, and an epidemiologic cluster of 13 with B.1.1.28/P.1.
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Kinloch NN, Ritchie G, Brumme CJ, Dong W, Dong W, Lawson T, Jones RB, Montaner JSG, Leung V, Romney MG, Stefanovic A, Matic N, Lowe CF, Brumme ZL. Corrigendum to: Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results. J Infect Dis 2021; 224:184. [PMID: 34057182 PMCID: PMC8195218 DOI: 10.1093/infdis/jiab230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Weiyan Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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McCann CD, van Dorp CH, Danesh A, Ward AR, Dilling TR, Mota TM, Zale E, Stevenson EM, Patel S, Brumme CJ, Dong W, Jones DS, Andresen TL, Walker BD, Brumme ZL, Bollard CM, Perelson AS, Irvine DJ, Jones RB. A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies. J Exp Med 2021; 218:212105. [PMID: 33988715 PMCID: PMC8129803 DOI: 10.1084/jem.20201908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.
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Affiliation(s)
- Chase D McCann
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | | | - Ali Danesh
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Adam R Ward
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC.,PhD Program in Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Thomas R Dilling
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Talia M Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Elizabeth Zale
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Eva M Stevenson
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Shabnum Patel
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | | | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA.,Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Darrell J Irvine
- Howard Hughes Medical Institute, Chevy Chase, MD.,Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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Brockman MA, Mwimanzi F, Sang Y, Ng K, Agafitei O, Ennis S, Lapointe H, Young L, Umviligihozo G, Burns L, Brumme C, Leung V, Montaner JS, Holmes D, DeMarco M, Simons J, Niikura M, Pantophlet R, Romney MG, Brumme ZL. Weak humoral immune reactivity among residents of long-term care facilities following one dose of the BNT162b2 mRNA COVID-19 vaccine. medRxiv 2021:2021.03.17.21253773. [PMID: 33791737 PMCID: PMC8010769 DOI: 10.1101/2021.03.17.21253773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Several Canadian provinces are extending the interval between COVID-19 vaccine doses to increase population vaccine coverage more rapidly. However, immunogenicity of these vaccines after one dose is incompletely characterized, particularly among the elderly, who are at greatest risk of severe COVID-19. Methods We assessed SARS-CoV-2 humoral responses pre-vaccine and one month following the first dose of BNT162b2 mRNA vaccine, in 12 COVID-19 seronegative residents of long-term care facilities (median age, 82 years), 18 seronegative healthcare workers (HCW; median age, 36 years) and 4 convalescent HCW. Total antibody responses to SARS-CoV-2 nucleocapsid (N) and spike protein receptor binding domain (S/RBD) were assessed using commercial immunoassays. We quantified IgG and IgM responses to S/RBD and determined the ability of antibodies to block S/RBD binding to ACE2 receptor using ELISA. Neutralizing antibody activity was also assessed using pseudovirus and live SARS-CoV-2. Results After one vaccine dose, binding antibodies against S/RBD were ~4-fold lower in residents compared to HCW (p<0.001). Inhibition of ACE2 binding was 3-fold lower in residents compared to HCW (p=0.01) and pseudovirus neutralizing activity was 2-fold lower (p=0.003). While six (33%) seronegative HCW neutralized live SARS-CoV-2, only one (8%) resident did (p=0.19). In contrast, convalescent HCW displayed 7- to 20-fold higher levels of binding antibodies and substantial ability to neutralize live virus after one dose. Interpretation Extending the interval between COVID-19 vaccine doses may pose a risk to the elderly due to lower vaccine immunogenicity in this group. We recommend that second doses not be delayed in elderly individuals.
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Affiliation(s)
- Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
| | - Francis Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Yurou Sang
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Kurtis Ng
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Hope Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
| | - Landon Young
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver BC, Canada
| | | | - Laura Burns
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver BC, Canada
| | - Chanson Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Medicine, University of British Columbia, Vancouver BC, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver BC, Canada
| | - Julio S.G. Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver BC, Canada
| | - Daniel Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver BC, Canada
| | - Mari DeMarco
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver BC, Canada
| | - Janet Simons
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver BC, Canada
| | - Masa Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver BC, Canada
| | - Zabrina L. Brumme
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
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Akahoshi T, Gatanaga H, Kuse N, Chikata T, Koyanagi M, Ishizuka N, Brumme CJ, Murakoshi H, Brumme ZL, Oka S, Takiguchi M. T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics. PLoS Pathog 2020; 16:e1009177. [PMID: 33370400 PMCID: PMC7833229 DOI: 10.1371/journal.ppat.1009177] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
HIV-1 strains harboring immune escape mutations can persist in circulation, but the impact of selection by multiple HLA alleles on population HIV-1 dynamics remains unclear. In Japan, HIV-1 Reverse Transcriptase codon 135 (RT135) is under strong immune pressure by HLA-B*51:01-restricted and HLA-B*52:01-restricted T cells that target a key epitope in this region (TI8; spanning RT codons 128-135). Major population-level shifts have occurred at HIV-1 RT135 during the Japanese epidemic, which first affected hemophiliacs (via imported contaminated blood products) and subsequently non-hemophiliacs (via domestic transmission). Specifically, threonine accumulated at RT135 (RT135T) in hemophiliac and non-hemophiliac HLA-B*51:01+ individuals diagnosed before 1997, but since then RT135T has markedly declined while RT135L has increased among non-hemophiliac individuals. We demonstrated that RT135V selection by HLA-B*52:01-restricted TI8-specific T-cells led to the creation of a new HLA-C*12:02-restricted epitope TN9-8V. We further showed that TN9-8V-specific HLA-C*12:02-restricted T cells selected RT135L while TN9-8T-specific HLA-C*12:02-restricted T cells suppressed replication of the RT135T variant. Thus, population-level accumulation of the RT135L mutation over time in Japan can be explained by initial targeting of the TI8 epitope by HLA-B*52:01-restricted T-cells, followed by targeting of the resulting escape mutant by HLA-C*12:02-restricted T-cells. We further demonstrate that this phenomenon is particular to Japan, where the HLA-B*52:01-C*12:02 haplotype is common: RT135L did not accumulate over a 15-year longitudinal analysis of HIV sequences in British Columbia, Canada, where this haplotype is rare. Together, our observations reveal that T-cell responses to sequentially emerging viral escape mutants can shape long-term HIV-1 population dynamics in a host population-specific manner.
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Affiliation(s)
| | - Hiroyuki Gatanaga
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Shinichi Oka
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- * E-mail:
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Lima VD, Brumme ZL, Brumme C, Sereda P, Krajden M, Wong J, Guillemi SA, Henry B, Hogg RS, Barrios R, Montaner JSG. The Impact of Treatment as Prevention on the HIV Epidemic in British Columbia, Canada. Curr HIV/AIDS Rep 2020; 17:77-87. [PMID: 32124189 DOI: 10.1007/s11904-020-00482-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/24/2022]
Abstract
PURPOSE OF REVIEW This study proposes to describe the impact of a publicly funded Treatment as Prevention (TasP) strategy in British Columbia (BC), Canada, in decreasing the individual and public health impact of the HIV/AIDS Epidemic. RECENT FINDINGS In BC, TasP has been associated with a steady decline in HIV-related morbidity and mortality. At the same time, a demographic transition was observed among people living with HIV (PLWH), with the majority of those on antiretroviral treatment (ART) now ≥ 50 years of age, living with at least one comorbidity, and dying from age-associated comorbidities. We also documented a progressive increase in the proportion of viral load suppression as a result of ART expansion. While the pre-ART CD4 T cell count has increased steadily in recent years, there is still a large proportion of PLWH being diagnosed in later stages of HIV infection. New HIV diagnoses have been rapidly declining, however to a lesser extent among men who have sex with men (MSM), and BC is currently experiencing an increase in infectious syphilis cases in this population. These facts reinforce the effectiveness of TasP in decreasing HIV transmission, but at the same time, it highlights the need for further innovation to enhance the control of HIV and syphilis among MSM. This study supports the development of new approaches that address existing gaps in the TasP strategy in BC, and the future health needs of PLWH.
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Affiliation(s)
- Viviane D Lima
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Department of Medicine, Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Chanson Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Department of Medicine, Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Jason Wong
- British Columbia Centre for Disease Control, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Silvia A Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Bonnie Henry
- British Columbia Ministry of Health, Victoria, Canada
| | - Robert S Hogg
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada.,Vancouver Coastal Health, Vancouver, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Room 667, 1081 Burrard Street, Vancouver, British Columbia, V6Z 1Y6, Canada. .,Department of Medicine, Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
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Kinloch NN, Shahid A, Ritchie G, Dong W, Lawson T, Montaner JSG, Romney MG, Stefanovic A, Matic N, Brumme CJ, Lowe CF, Brumme ZL, Leung V. Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics. Open Forum Infect Dis 2020; 7:ofaa488. [PMID: 33235889 PMCID: PMC7665666 DOI: 10.1093/ofid/ofaa488] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 08/24/2020] [Accepted: 10/09/2020] [Indexed: 12/23/2022] Open
Abstract
Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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41
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Warren JA, Zhou S, Xu Y, Moeser MJ, MacMillan DR, Council O, Kirchherr J, Sung JM, Roan NR, Adimora AA, Joseph S, Kuruc JD, Gay CL, Margolis DM, Archin N, Brumme ZL, Swanstrom R, Goonetilleke N. The HIV-1 latent reservoir is largely sensitive to circulating T cells. eLife 2020; 9:57246. [PMID: 33021198 PMCID: PMC7593086 DOI: 10.7554/elife.57246] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/26/2020] [Accepted: 09/24/2020] [Indexed: 01/01/2023] Open
Abstract
HIV-1-specific CD8+ T cells are an important component of HIV-1 curative strategies. Viral variants in the HIV-1 reservoir may limit the capacity of T cells to detect and clear virus-infected cells. We investigated the patterns of T cell escape variants in the replication-competent reservoir of 25 persons living with HIV-1 (PLWH) durably suppressed on antiretroviral therapy (ART). We identified all reactive T cell epitopes in the HIV-1 proteome for each participant and sequenced HIV-1 outgrowth viruses from resting CD4+ T cells. All non-synonymous mutations in reactive T cell epitopes were tested for their effect on the size of the T cell response, with a≥50% loss defined as an escape mutation. The majority (68%) of T cell epitopes harbored no detectable escape mutations. These findings suggest that circulating T cells in PLWH on ART could contribute to control of rebound and could be targeted for boosting in curative strategies.
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Affiliation(s)
- Joanna A Warren
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States.,UNC Center For AIDS Research, University of North Carolina, Chapel Hill, United States
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States
| | - Matthew J Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States.,UNC Center For AIDS Research, University of North Carolina, Chapel Hill, United States
| | | | - Olivia Council
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Jennifer Kirchherr
- Department of Medicine, University of North Carolina, Chapel Hill, United States
| | - Julia M Sung
- Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - Nadia R Roan
- Department of Urology, University of California San Francisco, San Francisco, United States.,Gladstone Institute of Virology and Immunology, San Francisco, United States
| | - Adaora A Adimora
- Department of Medicine, University of North Carolina, Chapel Hill, United States
| | - Sarah Joseph
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - JoAnn D Kuruc
- Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - Cynthia L Gay
- Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States.,UNC Center For AIDS Research, University of North Carolina, Chapel Hill, United States.,Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - Nancie Archin
- Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Ronald Swanstrom
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States.,UNC Center For AIDS Research, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, United States.,Department of Medicine, University of North Carolina, Chapel Hill, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, United States
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42
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Jin SW, Alsahafi N, Kuang XT, Swann SA, Toyoda M, Göttlinger H, Walker BD, Ueno T, Finzi A, Brumme ZL, Brockman MA. Natural HIV-1 Nef Polymorphisms Impair SERINC5 Downregulation Activity. Cell Rep 2020; 29:1449-1457.e5. [PMID: 31693887 PMCID: PMC6925589 DOI: 10.1016/j.celrep.2019.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/01/2018] [Revised: 07/26/2019] [Accepted: 10/01/2019] [Indexed: 11/30/2022] Open
Abstract
HIV-1 Nef enhances virion infectivity by counteracting host restriction factor SERINC5; however, the impact of natural Nef polymorphisms on this function is largely unknown. We characterize SERINC5 downregulation activity of 91 primary HIV-1 subtype B nef alleles, including isolates from 45 elite controllers and 46 chronic progressors. Controller-derived Nef clones display lower ability to downregulate SERINC5 (median 80% activity) compared with progressor-derived clones (median 96% activity) (p = 0.0005). We identify 18 Nef polymorphisms associated with differential function, including two CTL escape mutations that contribute to lower SERINC5 downregulation: K94E, driven by HLA-B∗08, and H116N, driven by the protective allele HLA-B∗57. HIV-1 strains encoding Nef K94E and/or H116N display lower infectivity and replication capacity in the presence of SERINC5. Our results demonstrate that natural polymorphisms in HIV-1 Nef can impair its ability to internalize SERINC5, indicating that variation in this recently described function may contribute to differences in viral pathogenesis.
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Affiliation(s)
- Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Xiaomei T Kuang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Shayda A Swann
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Mako Toyoda
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Department of Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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43
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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44
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Kinloch NN, Ritchie G, Brumme CJ, Dong W, Dong W, Lawson T, Jones RB, Montaner JSG, Leung V, Romney MG, Stefanovic A, Matic N, Lowe CF, Brumme ZL. Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results. J Infect Dis 2020; 222:899-902. [PMID: 32594170 PMCID: PMC7337811 DOI: 10.1093/infdis/jiaa370] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [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: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 01/30/2023] Open
Abstract
False-negative severe acute respiratory syndrome coronavirus 2 test results can negatively impact the clinical and public health response to coronavirus disease 2019 (COVID-19). We used droplet digital polymerase chain reaction (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (ie, suspected false-negative test results) compared with a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Weiyan Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada.,Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
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45
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Richard K, Schonhofer C, Giron LB, Rivera-Ortiz J, Read S, Kannan T, Kinloch NN, Shahid A, Feilcke R, Wappler S, Imming P, Harris M, Brumme ZL, Brockman MA, Mounzer K, Kossenkov AV, Abdel-Mohsen M, Andrae-Marobela K, Montaner LJ, Tietjen I. The African natural product knipholone anthrone and its analogue anthralin (dithranol) enhance HIV-1 latency reversal. J Biol Chem 2020; 295:14084-14099. [PMID: 32788215 DOI: 10.1074/jbc.ra120.013031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/12/2020] [Revised: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
A sterilizing or functional cure for HIV is currently precluded by resting CD4+ T cells that harbor latent but replication-competent provirus. The "shock-and-kill" pharmacological ap-proach aims to reactivate provirus expression in the presence of antiretroviral therapy and target virus-expressing cells for elimination. However, no latency reversal agent (LRA) to date effectively clears viral reservoirs in humans, suggesting a need for new LRAs and LRA combinations. Here, we screened 216 compounds from the pan-African Natural Product Library and identified knipholone anthrone (KA) and its basic building block anthralin (dithranol) as novel LRAs that reverse viral latency at low micromolar concentrations in multiple cell lines. Neither agent's activity depends on protein kinase C; nor do they inhibit class I/II histone deacetylases. However, they are differentially modulated by oxidative stress and metal ions and induce distinct patterns of global gene expression from established LRAs. When applied in combination, both KA and anthralin synergize with LRAs representing multiple functional classes. Finally, KA induces both HIV RNA and protein in primary cells from HIV-infected donors. Taken together, we describe two novel LRAs that enhance the activities of multiple "shock-and-kill" agents, which in turn may inform ongoing LRA combination therapy efforts.
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Affiliation(s)
- Khumoekae Richard
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Cole Schonhofer
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | - Silven Read
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ruth Feilcke
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Simone Wappler
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Karam Mounzer
- Jonathan Lax Immune Disorders Treatment Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Ian Tietjen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada .,Wistar Institute, Philadelphia, Pennsylvania, USA
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46
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Umviligihozo G, Cobarrubias KD, Chandrarathna S, Jin SW, Reddy N, Byakwaga H, Muzoora C, Bwana MB, Lee GQ, Hunt PW, Martin JN, Brumme CJ, Bangsberg DR, Karita E, Allen S, Hunter E, Ndung'u T, Brumme ZL, Brockman MA. Differential Vpu-Mediated CD4 and Tetherin Downregulation Functions among Major HIV-1 Group M Subtypes. J Virol 2020; 94:e00293-20. [PMID: 32376625 PMCID: PMC7343213 DOI: 10.1128/jvi.00293-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 02/23/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Downregulation of BST-2/tetherin and CD4 by HIV-1 viral protein U (Vpu) promotes viral egress and allows infected cells to evade host immunity. Little is known however about the natural variability in these Vpu functions among the genetically diverse viral subtypes that contribute to the HIV-1 pandemic. We collected Vpu isolates from 332 treatment-naive individuals living with chronic HIV-1 infection in Uganda, Rwanda, South Africa, and Canada. Together, these Vpu isolates represent four major HIV-1 group M subtypes (A [n = 63], B [n = 84], C [n = 94], and D [n = 59]) plus intersubtype recombinants and uncommon strains (n = 32). The ability of each Vpu clone to downregulate endogenous CD4 and tetherin was quantified using flow cytometry following transfection into an immortalized T-cell line and compared to that of a reference Vpu clone derived from HIV-1 subtype B NL4.3. Overall, the median CD4 downregulation function of natural Vpu isolates was similar to that of NL4.3 (1.01 [interquartile range {IQR}, 0.86 to 1.18]), while the median tetherin downregulation function was moderately lower than that of NL4.3 (0.90 [0.79 to 0.97]). Both Vpu functions varied significantly among HIV-1 subtypes (Kruskal-Wallis P < 0.0001). Specifically, subtype C clones exhibited the lowest CD4 and tetherin downregulation activities, while subtype D and B clones were most functional for both activities. We also identified Vpu polymorphisms associated with CD4 or tetherin downregulation function and validated six of these using site-directed mutagenesis. Our results highlight the marked extent to which Vpu function varies among global HIV-1 strains, raising the possibility that natural variation in this accessory protein may contribute to viral pathogenesis and/or spread.IMPORTANCE The HIV-1 accessory protein Vpu enhances viral spread by downregulating CD4 and BST-2/tetherin on the surface of infected cells. Natural variability in these Vpu functions may contribute to HIV-1 pathogenesis, but this has not been investigated among the diverse viral subtypes that contribute to the HIV-1 pandemic. In this study, we found that Vpu function differs significantly among HIV-1 subtypes A, B, C, and D. On average, subtype C clones displayed the lowest ability to downregulate both CD4 and tetherin, while subtype B and D clones were more functional. We also identified Vpu polymorphisms that associate with functional differences among HIV-1 isolates and subtypes. Our study suggests that genetic diversity in Vpu may play an important role in the differential pathogenesis and/or spread of HIV-1.
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Affiliation(s)
- Gisele Umviligihozo
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Sandali Chandrarathna
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Nicole Reddy
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, California, USA
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - Etienne Karita
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
| | - Susan Allen
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Thumbi Ndung'u
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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47
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Brooks K, Jones BR, Dilernia DA, Wilkins DJ, Claiborne DT, McInally S, Gilmour J, Kilembe W, Joy JB, Allen SA, Brumme ZL, Hunter E. HIV-1 variants are archived throughout infection and persist in the reservoir. PLoS Pathog 2020; 16:e1008378. [PMID: 32492044 PMCID: PMC7295247 DOI: 10.1371/journal.ppat.1008378] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 08/30/2019] [Revised: 06/15/2020] [Accepted: 02/03/2020] [Indexed: 01/23/2023] Open
Abstract
The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity. Despite reducing viremia to levels below the limit of detection in standard assays, effective antiretroviral therapy (ART) does not eradicate cells latently infected with HIV-1. These cells serve as a reservoir for viral rebound if therapy is interrupted; thus, understanding the composition of the reservoir may yield further targets for HIV-1 cure strategies. We have taken a genetic approach to elucidating the reservoir in 13 Zambian subtype C seroconvertors who were followed longitudinally through ART initiation and virologic suppression. In five of the 13 individuals, provirus sequences identical to or differing by five or fewer nucleotides from the transmitted/founder virus were detected, indicating archiving and persistence of early infection variants for more than six years following infection. While the majority of proviral variants in latently infected cells were most closely related to plasma virus circulating immediately prior to treatment initiation, additional variants dating to intermediate time points in the infection were also observed. These findings demonstrate that virus is archived during all stages of ART-naïve infection, and these variants persist throughout ART. HIV-1 cure strategies to eliminate the reservoir must address the broad genetic diversity of a within-host proviral quasispecies including variants archived from acute through chronic infection.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dario A. Dilernia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel J. Wilkins
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel T. Claiborne
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha McInally
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Jill Gilmour
- Human Immunology Lab, International AIDS Vaccine Initiative, London, England, United Kingdom
| | | | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Susan A. Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Sudderuddin H, Kinloch NN, Jin SW, Miller RL, Jones BR, Brumme CJ, Joy JB, Brockman MA, Brumme ZL. Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study. Retrovirology 2020; 17:3. [PMID: 31918727 PMCID: PMC6953280 DOI: 10.1186/s12977-019-0510-1] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/26/2019] [Indexed: 11/29/2022] Open
Abstract
The HIV accessory protein Nef downregulates the viral entry receptor CD4, the Human Leukocyte Antigen (HLA)-A and -B molecules, the Serine incorporator 5 (SERINC5) protein and other molecules from the infected cell surface, thereby promoting viral infectivity, replication and immune evasion. The nef locus also represents one of the most genetically variable regions in the HIV genome, and nef sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host nef sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely naïve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of nef’s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite nef’s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.
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Affiliation(s)
- Hanwei Sudderuddin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | | | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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Kinloch NN, Ren Y, Alberto WC, Dong W, Huang SH, Wilson A, Mota TM, Kikby D, Del Rio Estrada PM, Brumme CJ, Lee GQ, Lynch RM, Brumme ZL, Jones RB. Intra- and inter-individual HIV diversity limits the application of the intact proviral detection assay (IPDA). J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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McLaughlin A, Sereda P, Oliveira N, Barrios R, Brumme CJ, Brumme ZL, Montaner JSG, Joy JB. Detection of HIV transmission hotspots in British Columbia, Canada: A novel framework for the prioritization and allocation of treatment and prevention resources. EBioMedicine 2019; 48:405-413. [PMID: 31628022 PMCID: PMC6838403 DOI: 10.1016/j.ebiom.2019.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 06/26/2019] [Accepted: 09/14/2019] [Indexed: 01/05/2023] Open
Abstract
Background Identifying populations at high risk of HIV transmission is critical for prioritizing treatment and prevention resources and achieving the UNAIDS 90-90-90 Targets. Methods HIV transmission rates can be estimated from phylogenetic trees as viral lineage-level diversification rates. To identify HIV-1 transmission foci in British Columbia, Canada, we inferred diversification rates from phylogenetic trees of 36 271 HIV-1 sequences from 9630 anonymized individuals. Diversification rates were combined with sociodemographic and clinical data, then aggregated by patients’ area of residence to predict the distribution of new HIV cases between 2008 and 2018. The predictive power of the model was compared with a phylogenetically uninformed model. Findings Aggregated diversification rate measures were predictive of new HIV cases in the subsequent year after adjusting for prevalent and incident cases in the previous year. For every one-unit increase in the mean of the top five diversification rates, the number of new HIV cases increased by on average 1·38-fold (95% CI, 1·28–1·49). In a blind prediction of 2018 cases, diversification rate improved the model's specificity by 12%, accuracy by 9%, top 20 agreement by 100%, and correlation of predicted and observed values by 162% relative to a model that incorporated epidemiological data alone. Interpretation By predicting the distribution of future HIV cases, a combined phylogenetic and epidemiological approach identifies hotspots where public health resources are needed most. Funding Canadian Institutes of Health Research, University of British Columbia, Public Health Agency of Canada, Genome Canada, Genome BC, Michael Smith Foundation for Health Research, and BC Centre for Excellence in HIV/AIDS.
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Affiliation(s)
- Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada; Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Sereda
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Natalia Oliveira
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Rolando Barrios
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Julio S G Montaner
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, University of British Columbia Department of Medicine, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada; Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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