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Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic immunity from prior SARS-CoV-2 infection but not COVID-19 vaccination associates with lower endemic coronavirus incidence. Sci Transl Med 2024; 16:eado7588. [PMID: 38865483 DOI: 10.1126/scitranslmed.ado7588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Immune responses from prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and COVID-19 vaccination mitigate disease severity, but they do not fully prevent subsequent infections, especially from genetically divergent strains. We examined the incidence of and immune differences against human endemic coronaviruses (eCoVs) as a proxy for response against future genetically heterologous coronaviruses (CoVs). We assessed differences in symptomatic eCoV and non-CoV respiratory disease incidence among those with known prior SARS-CoV-2 infection or previous COVID-19 vaccination but no documented SARS-CoV-2 infection or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not previous COVID-19 vaccination alone, associates with a lower incidence of subsequent symptomatic eCoV infection. There was no difference in non-CoV incidence, implying that the observed difference was eCoV specific. In a second cohort where both cellular and humoral immunity were measured, those with prior SARS-CoV-2 spike protein exposure had lower eCoV-directed neutralizing antibodies, suggesting that neutralization is not responsible for the observed decreased eCoV disease. The three groups had similar cellular responses against the eCoV spike protein and nucleocapsid antigens. However, CD8+ T cell responses to the nonstructural eCoV proteins nsp12 and nsp13 were higher in individuals with previous SARS-CoV-2 infection as compared with the other groups. This association between prior SARS-CoV-2 infection and decreased incidence of eCoV disease may therefore be due to a boost in CD8+ T cell responses against eCoV nsp12 and nsp13, suggesting that incorporation of nonstructural viral antigens in a future pan-CoV vaccine may improve vaccine efficacy.
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Affiliation(s)
- David J Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Ella Borberg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Zoe Swank
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - David Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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2
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Sun C, Liu H, Ouyang Z, Ding J, Zhang Q, Ma H, Xu D, Zhang Q, Zhou R, Yang M, Hu W. Safety, tolerability, and pharmacokinetics of the novel RdRp inhibitor SHEN26 against SARS-CoV-2: a randomized, placebo-controlled, double-blind Phase I study in healthy subjects. Expert Opin Investig Drugs 2024:1-10. [PMID: 38662639 DOI: 10.1080/13543784.2024.2347302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND SHEN26, an oral broad-spectrum antiviral drug, possesses potent preclinical activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has a favorable safety profile. METHODS We report safety, tolerability, and pharmacokinetic data from a randomized, double-blind, placebo-controlled phase I study of SHEN26. Eighty-six healthy subjects were enrolled in the three studies: a single ascending-dose study (SAD), a multiple ascending-dose study (MAD), and a food-effect study (FE). RESULTS In the SAD trial, the maximum observed plasma concentration (Cmax) and area under the curve (AUC) of the SHEN26 rapid metabolite SHEN26-69-0 increased approximately dose-proportionally in the 50-400 mg fasting dose range. In the 800 mg dose group, standard meals increased the Cmax and AUC of SHEN26-69-0. In the MAD trial, the accumulation ratios of Cmax and AUC indicated slight accumulation upon repeated SHEN26 dosing. In the FE trial, a high-fat meal prolonged the time to maximum plasma concentration (Tmax) and increased the Cmax and AUC of SHEN26-69-0 compared with fasting administration. Most treatment-related adverse events were mild and resolved without treatment. CONCLUSION SHEN26 demonstrated satisfactory safety and tolerability in healthy subjects, which supports the continued study of SHEN26 against SARS-CoV-2. TRIAL REGISTRATION The trial is registered in ClinicalTrials.gov (CT. gov identifier: NCT05504746).
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Affiliation(s)
- Cheng Sun
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Medical University, Hefei, China
| | - Hao Liu
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Medical University, Hefei, China
| | - Ziwei Ouyang
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jie Ding
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Qin Zhang
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Hongjie Ma
- Shenzhen Kexing Pharmaceutical Co., Ltd, Shenzhen, China
| | - Dandan Xu
- Shenzhen Kexing Pharmaceutical Co., Ltd, Shenzhen, China
| | - Qian Zhang
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Renpeng Zhou
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Mingming Yang
- Shenzhen Kexing Pharmaceutical Co., Ltd, Shenzhen, China
| | - Wei Hu
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China
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3
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Koo D, Mao Z, Dimatteo R, Noguchi M, Tsubamoto N, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Burton Sojo G, Witte ON, Di Carlo D. Defining T cell receptor repertoires using nanovial-based binding and functional screening. Proc Natl Acad Sci U S A 2024; 121:e2320442121. [PMID: 38536748 PMCID: PMC10998554 DOI: 10.1073/pnas.2320442121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 04/08/2024] Open
Abstract
The ability to selectively bind to antigenic peptides and secrete effector molecules can define rare and low-affinity populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs inducing the secretion of effector molecules including IFN-γ and granzyme B that are accumulated on nanovials, allowing sorting based on both binding and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes and secretions with oligo-barcoded detection antibodies, we could accurately link TCR sequences to specific targets and rank each TCR based on the corresponding cell's secretion level. Using the technique, we identified an expanded repertoire of functional TCRs targeting viral antigens with high specificity and found rare TCRs with activity against cancer-specific splicing-enhanced epitopes.
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Affiliation(s)
- Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Natalie Tsubamoto
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
| | - Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Partillion Bioscience, Pasadena, CA91107
| | - Giselle Burton Sojo
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Owen N. Witte
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Partillion Bioscience, Pasadena, CA91107
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA90095
- California NanoSystems Institute, Los Angeles, CA90095
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4
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Hedskog C, Spinner CD, Protzer U, Hoffmann D, Ko C, Gottlieb RL, Askar M, Roestenberg M, de Vries JJC, Carbo EC, Martin R, Li J, Han D, Rodriguez L, Parvangada A, Perry JK, Ferrer R, Antón A, Andrés C, Casares V, Günthard HF, Huber M, McComsey GA, Sadri N, Aberg JA, van Bakel H, Porter DP. No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials. Viruses 2024; 16:546. [PMID: 38675889 PMCID: PMC11053423 DOI: 10.3390/v16040546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated in multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from the Phase 3 SIMPLE clinical studies evaluating RDV in hospitalized participants with severe or moderate COVID-19 disease. The severe and moderate studies enrolled participants with radiologic evidence of pneumonia and a room-air oxygen saturation of ≤94% or >94%, respectively. Virology sample collection was optional in the study protocols. Sequencing and related viral load data were obtained retrospectively from participants at a subset of study sites with local sequencing capabilities (10 of 183 sites) at timepoints with detectable viral load. Among participants with both baseline and post-baseline sequencing data treated with RDV, emergent Nsp12 substitutions were observed in 4 of 19 (21%) participants in the severe study and none of the 2 participants in the moderate study. The following 5 substitutions emerged: T76I, A526V, A554V, E665K, and C697F. The substitutions T76I, A526V, A554V, and C697F had an EC50 fold change of ≤1.5 relative to the wildtype reference using a SARS-CoV-2 subgenomic replicon system, indicating no significant change in the susceptibility to RDV. The phenotyping of E665K could not be determined due to a lack of replication. These data reveal no evidence of relevant resistance emergence and further confirm the established efficacy profile of RDV with a high resistance barrier in COVID-19 patients.
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Affiliation(s)
- Charlotte Hedskog
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Christoph D. Spinner
- TUM School of Medicine and Health, Department of Clinical Medicine—Clinical Department for Internal Medicine II, University Medical Center, Technical University of Munich, 81675 Munich, Germany;
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany; (U.P.); (D.H.)
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
- Institute of Virology, Helmholtz Munich, 85764 Munich, Germany
| | - Dieter Hoffmann
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany; (U.P.); (D.H.)
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
| | - Chunkyu Ko
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
- Institute of Virology, Helmholtz Munich, 85764 Munich, Germany
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Robert L. Gottlieb
- Center for Advanced Heart and Lung Disease, Department of Internal Medicine, Baylor University Medical Center, Dallas, TX 75246, USA; (R.L.G.); (M.A.)
- Baylor Scott & White Research Institute, Dallas, TX 75246, USA
- Department of Internal Medicine, Texas A&M Health Science Center, Dallas, TX 75246, USA
- Department of Internal Medicine, Burnett School of Medicine at TCU, Fort Worth, TX 76109, USA
| | - Medhat Askar
- Center for Advanced Heart and Lung Disease, Department of Internal Medicine, Baylor University Medical Center, Dallas, TX 75246, USA; (R.L.G.); (M.A.)
- QU Health and Department of Immunology, College of Medicine, Qatar University, Doha P.O. Box 2713, Qatar
| | - Meta Roestenberg
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Jutte J. C. de Vries
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Ellen C. Carbo
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Ross Martin
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Jiani Li
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Dong Han
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Lauren Rodriguez
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Aiyappa Parvangada
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Jason K. Perry
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Ricard Ferrer
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Andrés Antón
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Cristina Andrés
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Vanessa Casares
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8057 Zurich, Switzerland;
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Grace A. McComsey
- Department of Medicine, University Hospitals of Cleveland and Case Western Reserve University, Cleveland, OH 44106, USA; (G.A.M.); (N.S.)
| | - Navid Sadri
- Department of Medicine, University Hospitals of Cleveland and Case Western Reserve University, Cleveland, OH 44106, USA; (G.A.M.); (N.S.)
| | - Judith A. Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Danielle P. Porter
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
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5
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Saquib Q, Bakheit AH, Ahmed S, Ansari SM, Al-Salem AM, Al-Khedhairy AA. Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CL Pro and PL Pro) by Molecular Docking and Dynamic Simulation Studies. Molecules 2024; 29:998. [PMID: 38474509 DOI: 10.3390/molecules29050998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sabiha M Ansari
- Botany & Microbiology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah M Al-Salem
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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6
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Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
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Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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7
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Hedskog C, Rodriguez L, Roychoudhury P, Huang ML, Jerome KR, Hao L, Ireton RC, Li J, Perry JK, Han D, Camus G, Greninger AL, Gale M, Porter DP. Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1). J Infect Dis 2023; 228:1263-1273. [PMID: 37466213 PMCID: PMC10629708 DOI: 10.1093/infdis/jiad270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Remdesivir is approved for treatment of coronavirus disease 2019 (COVID-19) in nonhospitalized and hospitalized adult and pediatric patients. Here we present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance analyses from the phase 3 ACTT-1 randomized placebo-controlled trial conducted in adult participants hospitalized with COVID-19. METHODS Swab samples were collected at baseline and longitudinally through day 29. SARS-CoV-2 genomes were sequenced using next-generation sequencing. Phenotypic analysis was conducted directly on participant virus isolates and/or using SARS-CoV-2 subgenomic replicons expressing mutations identified in the Nsp12 target gene. RESULTS Among participants with both baseline and postbaseline sequencing data, emergent Nsp12 substitutions were observed in 12 of 31 (38.7%) and 12 of 30 (40.0%) participants in the remdesivir and placebo arms, respectively. No emergent Nsp12 substitutions in the remdesivir arm were observed in more than 1 participant. Phenotyping showed low to no change in susceptibility to remdesivir relative to wild-type Nsp12 reference for the substitutions tested: A16V (0.8-fold change in EC50), P323L + V792I (2.2-fold), C799F (2.5-fold), K59N (1.0-fold), and K59N + V792I (3.4-fold). CONCLUSIONS The similar rate of emerging Nsp12 substitutions in the remdesivir and placebo arms and the minimal change in remdesivir susceptibility among tested substitutions support a high barrier to remdesivir resistance development in COVID-19 patients. Clinical Trials Registration. NCT04280705.
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Affiliation(s)
| | | | - Pavitra Roychoudhury
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Linhui Hao
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Renee C Ireton
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Jiani Li
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Dong Han
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Alexander L Greninger
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
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8
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Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
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9
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Bakheit AH, Saquib Q, Ahmed S, Ansari SM, Al-Salem AM, Al-Khedhairy AA. Covalent Inhibitors from Saudi Medicinal Plants Target RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2. Viruses 2023; 15:2175. [PMID: 38005857 PMCID: PMC10675690 DOI: 10.3390/v15112175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
COVID-19, a disease caused by SARS-CoV-2, has caused a huge loss of human life, and the number of deaths is still continuing. Despite the lack of repurposed drugs and vaccines, the search for potential small molecules to inhibit SARS-CoV-2 is in demand. Hence, we relied on the drug-like characters of ten phytochemicals (compounds 1-10) that were previously isolated and purified by our research team from Saudi medicinal plants. We computationally evaluated the inhibition of RNA-dependent RNA polymerase (RdRp) by compounds 1-10. Non-covalent (reversible) docking of compounds 1-10 with RdRp led to the formation of a hydrogen bond with template primer nucleotides (A and U) and key amino acid residues (ASP623, LYS545, ARG555, ASN691, SER682, and ARG553) in its active pocket. Covalent (irreversible) docking revealed that compounds 7, 8, and 9 exhibited their irreversible nature of binding with CYS813, a crucial amino acid in the palm domain of RdRP. Molecular dynamic (MD) simulation analysis by RMSD, RMSF, and Rg parameters affirmed that RdRP complexes with compounds 7, 8, and 9 were stable and showed less deviation. Our data provide novel information on compounds 7, 8, and 9 that demonstrated their non-nucleoside and irreversible interaction capabilities to inhibit RdRp and shed new scaffolds as antivirals against SARS-CoV-2.
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Affiliation(s)
- Ahmed H. Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.M.A.-S.); (A.A.A.-K.)
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Sabiha M. Ansari
- Botany & Microbiology Department, College of Sciences, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Abdullah M. Al-Salem
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.M.A.-S.); (A.A.A.-K.)
| | - Abdulaziz A. Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.M.A.-S.); (A.A.A.-K.)
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10
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Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563621. [PMID: 37961343 PMCID: PMC10634759 DOI: 10.1101/2023.10.23.563621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.
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Affiliation(s)
- David J. Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Ella Borberg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Zoe Swank
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - David Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
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11
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Postovskaya A, Vujkovic A, de Block T, van Petersen L, van Frankenhuijsen M, Brosius I, Bottieau E, Van Dijck C, Theunissen C, van Ierssel SH, Vlieghe E, Bartholomeus E, Mullan K, Adriaensen W, Vanham G, Ogunjimi B, Laukens K, Vercauteren K, Meysman P. Leveraging T-cell receptor - epitope recognition models to disentangle unique and cross-reactive T-cell response to SARS-CoV-2 during COVID-19 progression/resolution. Front Immunol 2023; 14:1130876. [PMID: 37325653 PMCID: PMC10264683 DOI: 10.3389/fimmu.2023.1130876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Despite the general agreement on the significance of T cells during SARS-CoV-2 infection, the clinical impact of specific and cross-reactive T-cell responses remains uncertain. Understanding this aspect could provide insights for adjusting vaccines and maintaining robust long-term protection against continuously emerging variants. To characterize CD8+ T-cell response to SARS-CoV-2 epitopes unique to the virus (SC2-unique) or shared with other coronaviruses (CoV-common), we trained a large number of T-cell receptor (TCR) - epitope recognition models for MHC-I-presented SARS-CoV-2 epitopes from publicly available data. These models were then applied to longitudinal CD8+ TCR repertoires from critical and non-critical COVID-19 patients. In spite of comparable initial CoV-common TCR repertoire depth and CD8+ T-cell depletion, the temporal dynamics of SC2-unique TCRs differed depending on the disease severity. Specifically, while non-critical patients demonstrated a large and diverse SC2-unique TCR repertoire by the second week of the disease, critical patients did not. Furthermore, only non-critical patients exhibited redundancy in the CD8+ T-cell response to both groups of epitopes, SC2-unique and CoV-common. These findings indicate a valuable contribution of the SC2-unique CD8+ TCR repertoires. Therefore, a combination of specific and cross-reactive CD8+ T-cell responses may offer a stronger clinical advantage. Besides tracking the specific and cross-reactive SARS-CoV-2 CD8+ T cells in any TCR repertoire, our analytical framework can be expanded to more epitopes and assist in the assessment and monitoring of CD8+ T-cell response to other infections.
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Affiliation(s)
- Anna Postovskaya
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alexandra Vujkovic
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tessa de Block
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lida van Petersen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Isabel Brosius
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Caroline Theunissen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sabrina H. van Ierssel
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Erika Vlieghe
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Wim Adriaensen
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guido Vanham
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Koen Vercauteren
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
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12
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Afkhami S, Kang A, Jeyanathan V, Xing Z, Jeyanathan M. Adenoviral-vectored next-generation respiratory mucosal vaccines against COVID-19. Curr Opin Virol 2023; 61:101334. [PMID: 37276833 PMCID: PMC10172971 DOI: 10.1016/j.coviro.2023.101334] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023]
Abstract
The world is in need of next-generation COVID-19 vaccines. Although first-generation injectable COVID-19 vaccines continue to be critical tools in controlling the current global health crisis, continuous emergence of SARS-CoV-2 variants of concern has eroded the efficacy of these vaccines, leading to staggering breakthrough infections and posing threats to poor vaccine responders. This is partly because the humoral and T-cell responses generated following intramuscular injection of spike-centric monovalent vaccines are mostly confined to the periphery, failing to either access or be maintained at the portal of infection, the respiratory mucosa (RM). In contrast, respiratory mucosal-delivered vaccine can induce immunity encompassing humoral, cellular, and trained innate immunity positioned at the respiratory mucosa that may act quickly to prevent the establishment of an infection. Viral vectors, especially adenoviruses, represent the most promising platform for RM delivery that can be designed to express both structural and nonstructural antigens of SARS-CoV-2. Boosting RM immunity via the respiratory route using multivalent adenoviral-vectored vaccines would be a viable next-generation vaccine strategy.
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Affiliation(s)
- Sam Afkhami
- McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research & Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alisha Kang
- McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research & Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Vidthiya Jeyanathan
- McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research & Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Zhou Xing
- McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research & Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Mangalakumari Jeyanathan
- McMaster Immunology Research Centre, M. G. DeGroote Institute for Infectious Disease Research & Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
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13
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Westphal T, Mader M, Karsten H, Cords L, Knapp M, Schulte S, Hermanussen L, Peine S, Ditt V, Grifoni A, Addo MM, Huber S, Sette A, Lütgehetmann M, Pischke S, Kwok WW, Sidney J, Schulze zur Wiesch J. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4 + T-cell response with pre-primed responses directed against common cold coronaviruses. Front Immunol 2023; 14:1182504. [PMID: 37215095 PMCID: PMC10196118 DOI: 10.3389/fimmu.2023.1182504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction The nonstructural protein 12 (NSP12) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has a high sequence identity with common cold coronaviruses (CCC). Methods Here, we comprehensively assessed the breadth and specificity of the NSP12-specific T-cell response after in vitro T-cell expansion with 185 overlapping 15-mer peptides covering the entire SARS-CoV-2 NSP12 at single-peptide resolution in a cohort of 27 coronavirus disease 2019 (COVID-19) patients. Samples of nine uninfected seronegative individuals, as well as five pre-pandemic controls, were also examined to assess potential cross-reactivity with CCCs. Results Surprisingly, there was a comparable breadth of individual NSP12 peptide-specific CD4+ T-cell responses between COVID-19 patients (mean: 12.82 responses; range: 0-25) and seronegative controls including pre-pandemic samples (mean: 12.71 responses; range: 0-21). However, the NSP12-specific T-cell responses detected in acute COVID-19 patients were on average of a higher magnitude. The most frequently detected CD4+ T-cell peptide specificities in COVID-19 patients were aa236-250 (37%) and aa246-260 (44%), whereas the peptide specificities aa686-700 (50%) and aa741-755 (36%), were the most frequently detected in seronegative controls. In CCC-specific peptide-expanded T-cell cultures of seronegative individuals, the corresponding SARS-CoV-2 NSP12 peptide specificities also elicited responses in vitro. However, the NSP12 peptide-specific CD4+ T-cell response repertoire only partially overlapped in patients analyzed longitudinally before and after a SARS-CoV-2 infection. Discussion The results of the current study indicate the presence of pre-primed, cross-reactive CCC-specific T-cell responses targeting conserved regions of SARS-CoV-2, but they also underline the complexity of the analysis and the limited understanding of the role of the SARS-CoV-2 specific T-cell response and cross-reactivity with the CCCs.
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Affiliation(s)
- Tim Westphal
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Maria Mader
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marc Lütgehetmann
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Pischke
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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14
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Zornikova KV, Sheetikov SA, Rusinov AY, Iskhakov RN, Bogolyubova AV. Architecture of the SARS-CoV-2-specific T cell repertoire. Front Immunol 2023; 14:1070077. [PMID: 37020560 PMCID: PMC10067759 DOI: 10.3389/fimmu.2023.1070077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The T cell response plays an indispensable role in the early control and successful clearance of SARS-CoV-2 infection. However, several important questions remain about the role of cellular immunity in COVID-19, including the shape and composition of disease-specific T cell repertoires across convalescent patients and vaccinated individuals, and how pre-existing T cell responses to other pathogens—in particular, common cold coronaviruses—impact susceptibility to SARS-CoV-2 infection and the subsequent course of disease. This review focuses on how the repertoire of T cell receptors (TCR) is shaped by natural infection and vaccination over time. We also summarize current knowledge regarding cross-reactive T cell responses and their protective role, and examine the implications of TCR repertoire diversity and cross-reactivity with regard to the design of vaccines that confer broader protection against SARS-CoV-2 variants.
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Affiliation(s)
- Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Yu Rusinov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam N. Iskhakov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Apollinariya V. Bogolyubova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- *Correspondence: Apollinariya V. Bogolyubova,
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15
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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16
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Koo D, Mao Z, Dimatteo R, Tsubamoto N, Noguchi M, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Sojo GB, Witte ON, Di Carlo D. Defining T cell receptor repertoires using nanovial-based affinity and functional screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524440. [PMID: 36711524 PMCID: PMC9882161 DOI: 10.1101/2023.01.17.524440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.
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Affiliation(s)
- Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Natalie Tsubamoto
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Partillion Bioscience; Los Angeles, CA 90095, USA
| | - Giselle Burton Sojo
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Owen N. Witte
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Partillion Bioscience; Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- California NanoSystems Institute; Los Angeles, CA 90095, USA
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17
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Bubnova L, Pavlova I, Terentieva M, Glazanova T, Belyaeva E, Sidorkevich S, Bashketova N, Chkhingeria I, Kozhemyakina M, Azarov D, Kuznetsova R, Ramsay ES, Gladkikh A, Sharova A, Dedkov V, Totolian A. HLA Genotypes in Patients with Infection Caused by Different Strains of SARS-CoV-2. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14024. [PMID: 36360904 PMCID: PMC9657774 DOI: 10.3390/ijerph192114024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The aggressive infectious nature of SARS-CoV-2, its rapid spread, and the emergence of mutations necessitate investigation of factors contributing to differences in SARS-CoV-2 susceptibility and severity. The role of genetic variations in the human HLA continues to be studied in various populations in terms of both its effect on morbidity and clinical manifestation of illness. The study included 484 COVID-19 convalescents (northwest Russia residents of St. Petersburg). Cases in which the responsible strain was determined were divided in two subgroups: group 1 (n = 231) had illness caused by genovariants unrelated to variant of concern (VOC) strains; and group 2 (n = 80) had illness caused by the delta (B.1.617.2) VOC; and a control group (n = 1456). DNA typing (HLA-A, B, DRB1) was performed at the basic resolution level. HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants only but not against infection caused by delta strains. HLA-A*03 was associated with protection against infection caused by delta strains; and allele groups associated with infection by delta strains were HLA-A*30, B*49, and B*57. Thus, in northwest Russia, HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants but not against delta viral strains. HLA-A*03 was associated with a reduced risk of infection by delta SARS-CoV-2 strains. HLA-A*30, HLA-B*49, and HLA-B*57 allele groups were predisposing factors for infection by delta (B.1.617.2) strains.
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Affiliation(s)
- Ludmila Bubnova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
| | - Irina Pavlova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Maria Terentieva
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Tatiana Glazanova
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Elena Belyaeva
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Sergei Sidorkevich
- Russian Research Institute of Hematology and Transfusion Science, FMBA, 191024 St. Petersburg, Russia
| | - Nataliya Bashketova
- Saint Petersburg Office, Federal Service for Consumer Rights Protection and Human Welfare, 191025 St. Petersburg, Russia
| | - Irina Chkhingeria
- Saint Petersburg Office, Federal Service for Consumer Rights Protection and Human Welfare, 191025 St. Petersburg, Russia
| | | | - Daniil Azarov
- Saint Petersburg Center for Hygiene and Epidemiology, 191023 St. Petersburg, Russia
| | - Raisa Kuznetsova
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Edward S. Ramsay
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Anna Gladkikh
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Alena Sharova
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
| | - Vladimir Dedkov
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Areg Totolian
- Department of immunology, Faculty of medicine, Pavlov First Saint Petersburg State Medical University, Russian Ministry of Health, 197022 St. Petersburg, Russia
- Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology, 197101 St. Petersburg, Russia
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18
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Diniz MO, Mitsi E, Swadling L, Rylance J, Johnson M, Goldblatt D, Ferreira D, Maini MK. Airway-resident T cells from unexposed individuals cross-recognize SARS-CoV-2. Nat Immunol 2022; 23:1324-1329. [PMID: 36038709 PMCID: PMC9477726 DOI: 10.1038/s41590-022-01292-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/18/2022] [Indexed: 12/15/2022]
Abstract
T cells can contribute to clearance of respiratory viruses that cause acute-resolving infections such as SARS-CoV-2, helping to provide long-lived protection against disease. Recent studies have suggested an additional role for T cells in resisting overt infection: pre-existing cross-reactive responses were preferentially enriched in healthcare workers who had abortive infections1, and in household contacts protected from infection2. We hypothesize that such early viral control would require pre-existing cross-reactive memory T cells already resident at the site of infection; such airway-resident responses have been shown to be critical for mediating protection after intranasal vaccination in a murine model of SARS-CoV3. Bronchoalveolar lavage samples from the lower respiratory tract of healthy donors obtained before the COVID-19 pandemic revealed airway-resident, SARS-CoV-2-cross-reactive T cells, which correlated with the strength of human seasonal coronavirus immunity. We therefore demonstrate the potential to harness functional airway-resident SARS-CoV-2-reactive T cells in next-generation mucosal vaccines.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Elena Mitsi
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Leo Swadling
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Jamie Rylance
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Daniela Ferreira
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK.
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Mala K Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK.
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19
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Jo HY, Kim SC, Ahn DH, Lee S, Chang SH, Jung SY, Kim YJ, Kim E, Kim JE, Kim YS, Park WY, Cho NH, Park D, Lee JH, Park HY. Establishment of the large-scale longitudinal multi-omics dataset in COVID-19 patients: data profile and biospecimen. BMB Rep 2022; 55:465-471. [PMID: 35996834 PMCID: PMC9537027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/02/2022] [Accepted: 07/29/2022] [Indexed: 03/08/2024] Open
Abstract
Understanding and monitoring virus-mediated infections has gained importance since the global outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Studies of high-throughput omics-based immune profiling of COVID-19 patients can help manage the current pandemic and future virus-mediated pandemics. Although COVID-19 is being studied since past 2 years, detailed mechanisms of the initial induction of dynamic immune responses or the molecular mechanisms that characterize disease progression remains unclear. This study involved comprehensively collected biospecimens and longitudinal multi-omics data of 300 COVID-19 patients and 120 healthy controls, including whole genome sequencing (WGS), single-cell RNA sequencing combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing (scRNA(+scTCR/BCR)-seq), bulk BCR and TCR sequencing (bulk TCR/BCR-seq), and cytokine profiling. Clinical data were also collected from hospitalized COVID-19 patients, and HLA typing, laboratory characteristics, and COVID-19 viral genome sequencing were performed during the initial diagnosis. The entire set of biospecimens and multi-omics data generated in this project can be accessed by researchers from the National Biobank of Korea with prior approval. This distribution of largescale multi-omics data of COVID-19 patients can facilitate the understanding of biological crosstalk involved in COVID-19 infection and contribute to the development of potential methodologies for its diagnosis and treatment. [BMB Reports 2022; 55(9): 465-471].
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Affiliation(s)
- Hye-Yeong Jo
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Sang Cheol Kim
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Do-hwan Ahn
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | | | - Se-Hyun Chang
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - So-Young Jung
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Young-Jin Kim
- Division of Genome Science, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Eugene Kim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Jung-Eun Kim
- Division of Bio Bigdata, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Yeon-Sook Kim
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Korea
| | - Woong-Yang Park
- Geninus Inc, Seoul 05836, Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 08826, Korea
| | | | - Ju-Hee Lee
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Hyun-Young Park
- Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
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20
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Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation. Proc Natl Acad Sci U S A 2022; 119:e2203410119. [PMID: 35878026 PMCID: PMC9351518 DOI: 10.1073/pnas.2203410119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tissue-specific antigens can serve as targets for adoptive T cell transfer-based cancer immunotherapy. Recognition of tumor by T cells is mediated by interaction between peptide-major histocompatibility complexes (pMHCs) and T cell receptors (TCRs). Revealing the identity of peptides bound to MHC is critical in discovering cognate TCRs and predicting potential toxicity. We performed multimodal immunopeptidomic analyses for human prostatic acid phosphatase (PAP), a well-recognized tissue antigen. Three physical methods, including mild acid elution, coimmunoprecipitation, and secreted MHC precipitation, were used to capture a thorough signature of PAP on HLA-A*02:01. Eleven PAP peptides that are potentially A*02:01-restricted were identified, including five predicted strong binders by NetMHCpan 4.0. Peripheral blood mononuclear cells (PBMCs) from more than 20 healthy donors were screened with the PAP peptides. Seven cognate TCRs were isolated which can recognize three distinct epitopes when expressed in PBMCs. One TCR shows reactivity toward cell lines expressing both full-length PAP and HLA-A*02:01. Our results show that a combined multimodal immunopeptidomic approach is productive in revealing target peptides and defining the cloned TCR sequences reactive with prostatic acid phosphatase epitopes.
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Antonio EC, Meireles MR, Bragatte MADS, Vieira GF. Viral immunogenic footprints conferring T cell cross-protection to SARS-CoV-2 and its variants. Front Immunol 2022; 13:931372. [PMID: 35967415 PMCID: PMC9366040 DOI: 10.3389/fimmu.2022.931372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 brought scenes from sci-fi movies into real life. Infected individuals include asymptomatic cases to severe disease leading to death, suggesting the involvement of the genetic constitution of populations and pathogens contributing to differential individuals' outcomes. To investigate shared immunogenic features between SARS-CoV-2 targets and other coronaviruses, we modeled their peptides in 3D structures of HLA-A*02:01 (pMHC), comparing their molecular surfaces These structures were also compared with a panel of epitopes from unrelated viruses, looking for potential triggers conferring cross-protection in uninfected individuals. As expected, SARS-CoV 1 and 2 peptides share molecular and physicochemical features, providing an explanation for the verified experimental immunogenicity among them. Surprisingly, even discordant sequences from human coronaviruses 229E, OC43 and epitopes from unrelated viruses involved in endemic human infections exhibit similar fingerprints of immunogenicity with SARS-CoV-2 peptides. The same approach indicates a conserved CD8+ T cell recognition between Wuhan SARS-CoV-2 sequences and altered peptides from Variants of Concern. Examination of structural data over epitope sequence analysis here could explain how previous infections may produce a heterologous immunity response in a global scale against emergent diseases such as Covid-19, mitigating its full lethal potential, and paves the way for the development of wide spectrum vaccine development.
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Affiliation(s)
- Eduardo Cheuiche Antonio
- Post Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariana Rost Meireles
- Post Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Gustavo Fioravanti Vieira
- Post Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Post Graduation Program in Health and Human Development, Universidade La Salle Canoas, Canoas, Brazil
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