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Zhu Y, Yu M, Aisikaer M, Zhang C, He Y, Chen Z, Yang Y, Han R, Li Z, Zhang F, Ding J, Lu X. Contriving a novel of CHB therapeutic vaccine based on IgV_CTLA-4 and L protein via immunoinformatics approach. J Biomol Struct Dyn 2024; 42:6323-6341. [PMID: 37424209 DOI: 10.1080/07391102.2023.2234043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Chronic infection induced by immune tolerance to hepatitis B virus (HBV) is one of the most common causes of hepatic cirrhosis and hepatoma. Fortunately, the application of therapeutic vaccine can not only reverse HBV-tolerance, but also serve a potentially effective therapeutic strategy for treating chronic hepatitis B (CHB). However, the clinical effect of the currently developed CHB therapeutic vaccine is not optimistic due to the weak immunogenicity. Given that the human leukocyte antigen CTLA-4 owns strong binding ability to the surface B7 molecules (CD80 and CD86) of antigen presenting cell (APCs), the immunoglobulin variable region of CTLA-4 (IgV_CTLA-4) was fused with the L protein of HBV to contrive a novel therapeutic vaccine (V_C4HBL) for CHB in this study. We found that the addition of IgV_CTLA-4 did not interfere with the formation of L protein T cell and B cell epitopes after analysis by means of immunoinformatics approaches. Meanwhile, we also found that the IgV_CTLA-4 had strong binding force to B7 molecules through molecular docking and molecular dynamics (MD) simulation. Notably, our vaccine V_C4HBL showed good immunogenicity and antigenicity by in vitro and in vivo experiments. Therefore, the V_C4HBL is promising to again effectively activate the cellular and humoral immunity of CHB patients, and provides a potentially effective therapeutic strategy for the treatment of CHB in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Infectious Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Maierhaba Aisikaer
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Chuntao Zhang
- Department of Microbiology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yinyin Yang
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Rui Han
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Xiaobo Lu
- Infectious Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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2
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Ponne S, Kumar R, Vanmathi SM, Brilhante RSN, Kumar CR. Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens. Vaccine 2024; 42:2503-2518. [PMID: 38523003 DOI: 10.1016/j.vaccine.2024.02.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain viruses is challenging due to various factors, notably the inability to culture certain viruses in cell cultures and the wide-ranging diversity of MHC profiles in humans. Fortunately, reverse vaccinology (RV) efficiently overcomes these limitations and has simplified the identification of epitopes from antigenic proteins across the entire proteome, streamlining the vaccine development process. Furthermore, it enables the creation of multiepitope vaccines that can effectively account for the variations in MHC profiles within the human population. The RV approach offers numerous advantages in developing precise and effective vaccines against viral pathogens, including extensive proteome coverage, accurate epitope identification, cross-protection capabilities, and MHC compatibility. With the introduction of RV, there is a growing emphasis among researchers on creating multiepitope-based vaccines aiming to stimulate the host's immune responses against multiple serotypes, as opposed to single-component monovalent alternatives. Regardless of how promising the RV-based vaccine candidates may appear, they must undergo experimental validation to probe their protection efficacy for real-world applications. The time, effort, and resources allocated to the laborious epitope identification process can now be redirected toward validating vaccine candidates identified through the RV approach. However, to overcome failures in the RV-based approach, efforts must be made to incorporate immunological principles and consider targeting the epitope regions involved in disease pathogenesis, immune responses, and neutralizing antibody maturation. Integrating multi-omics and incorporating artificial intelligence and machine learning-based tools and techniques in RV would increase the chances of developing an effective vaccine. This review thoroughly explains the RV approach, ideal RV-based vaccine construct components, RV-based vaccines designed to combat viral pathogens, its challenges, and future perspectives.
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Affiliation(s)
- Saravanaraman Ponne
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (Deemed to be University), Kirumampakkam, Puducherry 607402, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 106 91, Sweden
| | - S M Vanmathi
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India
| | - Raimunda Sâmia Nogueira Brilhante
- Medical Mycology Specialized Center, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Chinnadurai Raj Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India.
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Shoute LCT, Charlton CL, Kanji JN, Babiuk S, Babiuk L, Chen J. Faradaic Impedimetric Immunosensor for Label-Free Point-of-Care Detection of COVID-19 Antibodies Using Gold-Interdigitated Electrode Array. BIOSENSORS 2023; 14:6. [PMID: 38248383 PMCID: PMC10812953 DOI: 10.3390/bios14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024]
Abstract
Label-free electrochemical biosensors have many desirable characteristics in terms of miniaturization, scalability, digitization, and other attributes associated with point-of-care (POC) applications. In the era of COVID-19 and pandemic preparedness, further development of such biosensors will be immensely beneficial for rapid testing and disease management. Label-free electrochemical biosensors often employ [Fe(CN)6]-3/4 redox probes to detect low-concentration target analytes as they dramatically enhance sensitivity. However, such Faradaic-based sensors are reported to experience baseline signal drift, which compromises the performance of these devices. Here, we describe the use of a mecaptohexanoic (MHA) self-assembled monolayer (SAM) modified Au-interdigitated electrode arrays (IDA) to investigate the origin of the baseline signal drift, developed a protocol to resolve the issue, and presented insights into the underlying mechanism on the working of label-free electrochemical biosensors. Using this protocol, we demonstrate the application of MHA SAM-modified Au-IDA for POC analysis of human serum samples. We describe the use of a label-free electrochemical biosensor based on covalently conjugated SARS-CoV-2 spike protein for POC detection of COVID-19 antibodies. The test requires a short incubation time (10 min), and has a sensitivity of 35.4/decade (35.4%/10 ng mL-1) and LOD of 21 ng/mL. Negligible cross reactivity to seasonal human coronavirus or other endogenous antibodies was observed. Our studies also show that Faradaic biosensors are ~17 times more sensitive than non-Faradaic biosensors. We believe the work presented here contributes to the fundamental understanding of the underlying mechanisms of baseline signal drift and will be applicable to future development of electrochemical biosensors for POC applications.
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Affiliation(s)
- Lian C. T. Shoute
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada;
| | - Carmen L. Charlton
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada; (C.L.C.); (J.N.K.)
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB T2N 1M7, Canada
- Li Ka Shing Institute for Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Jamil N. Kanji
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada; (C.L.C.); (J.N.K.)
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB T2N 1M7, Canada
- Division of Infectious Diseases, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada;
- Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Lorne Babiuk
- Vaccine and Infectious Disease Organization, University of Alberta, Edmonton, AB T6G 2G3, Canada;
| | - Jie Chen
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada;
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
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Cioffi VB, de Castro-Amarante MF, Lulla A, Andreata-Santos R, Cruz MC, Moreno ACR, de Oliveira Silva M, de Miranda Peres B, de Freitas Junior LHG, Moraes CB, Durigon EL, Gordon NC, Hyvönen M, de Souza Ferreira LC, Balan A. SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies. Sci Rep 2023; 13:16821. [PMID: 37798298 PMCID: PMC10556064 DOI: 10.1038/s41598-023-43720-8] [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: 07/28/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
Amongst the potential contribution of protein or peptide-display systems to study epitopes with relevant immunological features, the RAD display system stands out as a highly stable scaffold protein that allows the presentation of constrained target peptides. Here, we employed the RAD display system to present peptides derived from the SARS-CoV-2 Spike (S) protein as a tool to detect specific serum antibodies and to generate polyclonal antibodies capable of inhibiting SARS-CoV-2 infectivity in vitro. 44 linear S-derived peptides were genetically fused with the RAD scaffold (RAD-SCoV-epitopes) and screened for antigenicity with sera collected from COVID-19-infected patients. In a second step, selected RAD-SCoV-epitopes were used to immunize mice and generate antibodies. Phenotypic screening showed that some of these antibodies were able to recognize replicating viral particles in VERO CCL-81 and most notably seven of the RAD-SCoV-epitopes were able to induce antibodies that inhibited viral infection. Our findings highlight the RAD display system as an useful platform for the immunological characterization of peptides and a potentially valuable strategy for the design of antigens for peptide-based vaccines, for epitope-specific antibody mapping, and for the development of antibodies for diagnostic and therapeutic purposes.
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Affiliation(s)
- Victor Bolsanelli Cioffi
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Maria Fernanda de Castro-Amarante
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Robert Andreata-Santos
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Mario Costa Cruz
- Core Facilities to Support Research (CEFAP), Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, São Paulo, 173005508-000, Brazil
| | - Ana Carolina Ramos Moreno
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Vaccine Development Laboratory, Butantan Institute, Av. Vital Brasil, 1500, São Paulo, SP, 05503-900, Brazil
| | - Mariângela de Oliveira Silva
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Bianca de Miranda Peres
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Lucio Holanda Gondim de Freitas Junior
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Carolina Borsoi Moraes
- Phenotypic Screening Platform, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Nicola Coker Gordon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Luís Carlos de Souza Ferreira
- Laboratory of Vaccine Development, Department of Microbiology, University of São Paulo, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil
- Institut Pasteur de São Paulo, Av. Prof. Lucio Martins Rodrigues, 370, São Paulo, 05508-020, Brazil
| | - Andrea Balan
- Laboratory of Applied Structural Biology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, 05508-000, Brazil.
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5
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Hou W, Wu H, Wang S, Wang W, Wang B, Wang H. Designing a multi-epitope vaccine to control porcine epidemic diarrhea virus infection using immunoinformatics approaches. Front Microbiol 2023; 14:1264612. [PMID: 37779715 PMCID: PMC10538973 DOI: 10.3389/fmicb.2023.1264612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), a continuously evolving pathogen, causes severe diarrhea in piglets with high mortality rates. However, current vaccines cannot provide complete protection against PEDV, so vaccine development is still necessary and urgent. Here, with the help of immunoinformatics approaches, we attempted to design a multi-epitope vaccine named rPMEV to prevent and control PEDV infection. The epitopes of rPMEV were constructed by 9 cytotoxic T lymphocyte epitopes (CTLs), 11 helper T lymphocyte epitopes (HTLs), 6 linear B cell epitopes (LBEs), and 4 conformational B cell epitopes (CBEs) based on the S proteins from the four representative PEDV G2 strains. To enhance immunogenicity, porcine β-defensin-2 (PBD-2) was adjoined to the N-terminal of the vaccine as an adjuvant. All of the epitopes and PBD-2 were joined by corresponding linkers and recombined into the multivalent vaccine, which is stable, antigenic, and non-allergenic. Furthermore, we adopted molecular docking and molecular dynamics simulation methods to analyze the interaction of rPMEV with the Toll-like receptor 4 (TLR4): a stable interaction between them created by 13 hydrogen bonds. In addition, the results of the immune simulation showed that rPMEV could stimulate both cellular and humoral immune responses. Finally, to raise the expression efficiency, the sequence of the vaccine protein was cloned into the pET28a (+) vector after the codon optimization. These studies indicate that the designed multi-epitope vaccine has a potential protective effect, providing a theoretical basis for further confirmation of its protective effect against PEDV infection in vitro and in vivo studies.
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Affiliation(s)
- Wei Hou
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Heqiong Wu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Sibei Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Wenting Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Bin Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
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Designing multi-epitope mRNA construct as a universal influenza vaccine candidate for future epidemic/pandemic preparedness. Int J Biol Macromol 2023; 226:885-899. [PMID: 36521707 DOI: 10.1016/j.ijbiomac.2022.12.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Despite the availability of prevention and treatment strategies and advancing immunization approaches, the influenza virus remains a global threat that continues to plague humanity with unpredictable pandemics. Due to the unusual genetic variability and segmented genome, the reassortment between different strains of influenza is facilitated and the viruses continuously evolve and adapt to the host cell's immunity. This underlies the seasonal vaccine mismatches that decrease the vaccine efficacy and increase the risk of outbreaks. Thus, the development of a universal vaccine covering all the influenza A and B strains would reduce the pervasiveness of the influenza virus. In the current study, a potentially universal influenza multi-epitope vaccine was designed based on the experimentally tested conserved T cell and B cell epitopes of hemagglutinin (HA), neuraminidase (NA), nucleoprotein (NP), and matrix-2 proton channel (M2) of the virus. The immune simulation and molecular docking of the vaccine construct with TLR2, TLR3, and TLR4 elicited the favorable immunogenicity of the vaccine and the formation of stable complexes, respectively. Ultimately, based on the immunoinformatics analysis, the universal mRNA multi-epitope vaccine designed in this study might have a protection potential against the various subtypes of influenza A and B.
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Pereira GC. An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part II: In Vitro Transcribed mRNA Vector Design for Inoculation Against Infectious Agent Variants. Methods Mol Biol 2023; 2575:323-340. [PMID: 36301484 DOI: 10.1007/978-1-0716-2716-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A fully automated strategy to handle antigenic variability in immunisation protocols is here presented. The method comprises of (1) nanopore sequencing of infectious agent variants, with focus on the SARS-CoV-2 and its variants, followed by (2) in-vitro transcribed mRNA vector design for immunotherapy. This chapter introduces the mRNA vector design protocol and Chapter 16 presents the nano-pore sequencing step.
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Pal A, Pyne N, Paul S. In-Silico Designing of a Multi-Epitope Vaccine against SARS-CoV2 and Studying the Interaction of the Vaccine with Alpha, Beta, Delta and Omicron Variants of Concern. Curr Drug Discov Technol 2023; 20:67-88. [PMID: 36093818 DOI: 10.2174/1570163819666220909114900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND The sudden appearance of the SARS-CoV2 virus has almost changed the future of vaccine development. There have been many different approaches to vaccination; among them, computational vaccinology in the form of multi-epitope vaccines with excellent immunological properties and minimal contamination or other adverse reactions has emerged as a promising strategy with a lot of room for further study in this area. OBJECTIVE Designing a multi-epitope vaccine from the spike protein of SARS-CoV2 based on immunoinformatics and in-silico techniques. Evaluating the binding affinity of the constructed vaccine against the major variants of concern (alpha, beta, delta, and omicron) using docking studies. METHODS The potential antigenic, immunogenic, and non-allergic T-cell epitopes were thoroughly explored using IEDB, NetCTL1.2, and NetMHCII pan 3.2 servers. The best suitable linker was identified using the ExPASy Protparam tool and VERIFY 3D. The 3D model of the vaccine was developed by RaptorX and the model was validated using ERRAT, Z-score, and Ramachandran Plot. Docking studies of the vaccine with TLR-2, 3, 4, and 7 and alpha, beta, delta, and omicron variants were performed using HADDOCK 2.4. RESULTS The vaccine construct showed good antigenic and immunogenic scores and was non-allergic as well. The model was capable of binding to all four selected Toll-like receptors. Docking scores with variants were also promising. CONCLUSION All the variants showed good binding ability with the vaccine construct. Interaction with the alpha variant was found to be the most intense, followed by delta, beta, and omicron.
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Affiliation(s)
- Aranya Pal
- Department of Botany, Laboratory of Cell and Molecular Biology, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India
| | - Nibedita Pyne
- Department of Botany, Laboratory of Cell and Molecular Biology, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India
| | - Santanu Paul
- Department of Botany, Laboratory of Cell and Molecular Biology, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India
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Li L, Gao M, Li J, Xie X, Zhao H, Wang Y, Xu X, Zu S, Chen C, Wan D, Duan J, Wang J, Aliyari SR, Gold S, Zhang J, Qin CF, Shi PY, Yang H, Cheng G. Identification of an immunogenic epitope and protective antibody against the furin cleavage site of SARS-CoV-2. EBioMedicine 2022; 87:104401. [PMID: 36508877 PMCID: PMC9732504 DOI: 10.1016/j.ebiom.2022.104401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the global coronavirus disease 2019 (COVID-19) pandemic, contains a unique, four amino acid (aa) "PRRA" insertion in the spike (S) protein that creates a transmembrane protease serine 2 (TMPRSS2)/furin cleavage site and enhances viral infectivity. More research into immunogenic epitopes and protective antibodies against this SARS-CoV-2 furin cleavage site is needed. METHODS Combining computational and experimental methods, we identified and characterized an immunogenic epitope overlapping the furin cleavage site that detects antibodies in COVID-19 patients and elicits strong antibody responses in immunized mice. We also identified a high-affinity monoclonal antibody from COVID-19 patient peripheral blood mononuclear cells; the antibody directly binds the furin cleavage site and protects against SARS-CoV-2 infection in a mouse model. FINDINGS The presence of "PRRA" amino acids in the S protein of SARS-CoV-2 not only creates a furin cleavage site but also generates an immunogenic epitope that elicits an antibody response in COVID-19 patients. An antibody against this epitope protected against SARS-CoV-2 infection in mice. INTERPRETATION The immunogenic epitope and protective antibody we have identified may augment our strategy in handling COVID-19 epidemic. FUNDING The National Natural Science Foundation of China (82102371, 91542201, 81925025, 82073181, and 81802870), the Chinese Academy of Medical Sciences Initiative for Innovative Medicine (2021-I2M-1-047 and 2022-I2M-2-004), the Non-profit Central Research Institute Fund of the Chinese Academy of Medical Sciences (2020-PT310-006, 2019XK310002, and 2018TX31001), the National Key Research and Development Project of China (2020YFC0841700), US National Institute of Health (NIH) funds grant AI158154, University of California Los Angeles (UCLA) AI and Charity Treks, and UCLA DGSOM BSCRC COVID-19 Award Program. H.Y. is supported by Natural Science Foundation of Jiangsu Province (BK20211554 andBE2022728).
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Affiliation(s)
- Lili Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Meiling Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Jie Li
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xuping Xie
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Hui Zhao
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | | | - Xin Xu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Shulong Zu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China
| | | | - Dingyi Wan
- AtaGenix Laboratories (Wuhan) Co., Ltd., Wuhan, China
| | - Jing Duan
- AtaGenix Laboratories (Wuhan) Co., Ltd., Wuhan, China
| | - Jingfeng Wang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Saba R. Aliyari
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Sarah Gold
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Jicai Zhang
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China,Corresponding author.
| | - Pei-Yong Shi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA,Corresponding author.
| | - Heng Yang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China,Suzhou Institute of Systems Medicine, Suzhou, China,Corresponding author.
| | - Genhong Cheng
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA,Corresponding author.
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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11
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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12
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Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production. Sci Rep 2022; 12:15057. [PMID: 36064951 PMCID: PMC9442563 DOI: 10.1038/s41598-022-18517-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/12/2022] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 contains four structural proteins, two of which, the spike and nucleocapsid, are commonly used for the standardization of novel methods for antibody detection; however, some limitations in their use have been observed due to the homology of this virus with other phylogenetically-related viruses. We performed in silico analysis to search for novel immunogenic and antigenic peptides. A total of twenty-five peptides were preliminarily selected, located in the 3D structure of both proteins. Finally, eight peptides were selected: one located in the N protein and seven in the S1 domain of the spike protein. Additionally, the localization of selected peptides in 2D structures and possible changes in the sequences of these peptides in SARS-CoV-2 variants of concern were analyzed. All peptides were synthetized in MAP8 format, and recombinant S (trimer and RBD) and N proteins were used as antigens to search for antibodies in serum samples derived from COVID-19 patients, and for antibody response in New Zealand rabbits. Results showed high recognition of the serum derived from COVID-19 patients to all selected peptides; however, only the RBD3 peptide induced antibody production. In conclusion, this work provides evidence for a new strategy in peptide selection and its use for antibody detection or antibody production in animals.
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13
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Sharma A, Virmani T, Pathak V, Sharma A, Pathak K, Kumar G, Pathak D. Artificial Intelligence-Based Data-Driven Strategy to Accelerate Research, Development, and Clinical Trials of COVID Vaccine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7205241. [PMID: 35845955 PMCID: PMC9279074 DOI: 10.1155/2022/7205241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5-15 years to 1-2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
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Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Vipluv Pathak
- GL Bajaj Institute of Technology and Management, Greater Noida, Uttar Pradesh, India
| | | | - Kamla Pathak
- Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh 206001, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Devender Pathak
- Rajiv Academy for Pharmacy, NH. #2, Mathura Delhi Road P.O, Chhatikara, Mathura, Uttar Pradesh 281001, India
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14
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Success of Current COVID-19 Vaccine Strategies vs. the Epitope Topology of SARS-CoV-2 Spike Protein-Receptor Binding Domain (RBD): A Computational Study of RBD Topology to Guide Future Vaccine Design. Vaccines (Basel) 2022; 10:vaccines10060841. [PMID: 35746449 PMCID: PMC9228374 DOI: 10.3390/vaccines10060841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 05/21/2022] [Indexed: 12/05/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19) is a pandemic with a high morbidity rate occurring over recent years. COVID-19 is caused by the severe acute respiratory syndrome causing coronavirus type-2 (SARS-CoV-2). COVID-19 not only challenged mankind but also gave scope to the evolution of various vaccine design technologies. Although these vaccines protected and saved many lives, with the emerging viral strains, some of the strains may pose a threat to the currently existing vaccine design that is primarily based on the wild type spike protein of SARS-CoV-2. To evaluate the risk involved from such mutant viral strains, we performed a systematic in silico amino acid substitution of critical residues in the receptor binding domain (RBD) of the spike protein. Our molecular modeling analysis revealed significant topological changes in the RBD of spike protein suggesting that they could potentially contribute to the loss of antigen specificity for the currently existing therapeutic antibodies/vaccines, thus posing a challenge to the current vaccine strategies that are based on wild type viral spike protein epitopes. The structural deviations discussed in this article should be considered carefully in the future vaccine design.
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15
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Diaz-Hernandez A, Gonzalez-Vazquez MC, Arce-Fonseca M, Rodríguez-Morales O, Cedillo-Ramirez ML, Carabarin-Lima A. Consensus Enolase of Trypanosoma Cruzi: Evaluation of Their Immunogenic Properties Using a Bioinformatics Approach. Life (Basel) 2022; 12:life12050746. [PMID: 35629412 PMCID: PMC9148029 DOI: 10.3390/life12050746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 12/23/2022] Open
Abstract
There is currently no vaccine against American trypanosomiasis, caused by the parasite Trypanosoma cruzi. This is due to the genomic variation observed in the six DTUs of T. cruzi. This work aims to propose a consensus sequence of the enolase protein from different strains of T. cruzi and mainly evaluate its immunogenic properties at the bioinformatic level. From specialized databases, 15 sequences of the enolase gene were aligned to obtain a consensus sequence, where this sequence was modeled and then evaluated and validated through different bioinformatic programs to learn their immunogenic potential. Finally, chimeric peptides were designed with the most representative epitopes. The results showed high immunogenic potential with six epitopes for MHC-I, and seven epitopes for MHC-II, all of which were highly representative of the enolase present in strains from the American continent as well as five epitopes for B cells. Regarding the computational modeling, molecular docking with Toll-like receptors showed a high affinity and low constant of dissociation, which could lead to an innate-type immune response that helps to eliminate the parasite. In conclusion, the consensus sequence proposed for enolase is capable of providing an ideal immune response; however, the experimental evaluation of this enolase consensus and their chimeric peptides should be a high priority to develop a vaccine against Chagas disease.
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Affiliation(s)
- Alejandro Diaz-Hernandez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 14 Sury Avenida San Claudio, Ciudad Universitaria, Puebla 72570, Mexico; (A.D.-H.); (M.L.C.-R.)
| | - Maria Cristina Gonzalez-Vazquez
- Herbario y Jardín Botánico Universitario, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla 72570, Mexico;
| | - Minerva Arce-Fonseca
- Departamento de Biología Molecular, Instituto Nacional de Cardiología “Ignacio Chávez”, Juan Badiano No. 1, Col. Sección XVI, Tlalpan, México City 14080, Mexico; (M.A.-F.); (O.R.-M.)
| | - Olivia Rodríguez-Morales
- Departamento de Biología Molecular, Instituto Nacional de Cardiología “Ignacio Chávez”, Juan Badiano No. 1, Col. Sección XVI, Tlalpan, México City 14080, Mexico; (M.A.-F.); (O.R.-M.)
| | - Maria Lilia Cedillo-Ramirez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 14 Sury Avenida San Claudio, Ciudad Universitaria, Puebla 72570, Mexico; (A.D.-H.); (M.L.C.-R.)
| | - Alejandro Carabarin-Lima
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 14 Sury Avenida San Claudio, Ciudad Universitaria, Puebla 72570, Mexico; (A.D.-H.); (M.L.C.-R.)
- Correspondence: ; Tel.: +52-222-2295-500 (ext. 3965)
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16
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Yu M, Zhu Y, Li Y, Chen Z, Li Z, Wang J, Li Z, Zhang F, Ding J. Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches. Front Immunol 2022; 13:884433. [PMID: 35603198 PMCID: PMC9120605 DOI: 10.3389/fimmu.2022.884433] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023] Open
Abstract
The development of an effective multivalent vaccine against SARS-CoV-2 variants is an important means to improve the global public health situation caused by COVID-19. In this study, we identified the antigen epitopes of the main global epidemic SARS-CoV-2 and mutated virus strains using immunoinformatics approach, and screened out 8 cytotoxic T lymphocyte epitopes (CTLEs), 17 helper T lymphocyte epitopes (HTLEs), 9 linear B-cell epitopes (LBEs) and 4 conformational B-cell epitopes (CBEs). The global population coverage of CTLEs and HTLEs was 93.16% and 99.9% respectively. These epitopes were spliced together by corresponding linkers and recombined into multivalent vaccine. In silico tests, the vaccine protein was a non-allergen and the docking with TLR-3 molecule showed a strong interaction. The results of immune simulation showed that the vaccine may be helpful to initiate both cellular and humoral immunity against all VOC. The optimistic immunogenicity of the vaccine was confirmed in vivo and in vitro finally. Therefore, our vaccine may have potential protection against SARS-CoV-2 and its variants.
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jing Wang
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Zheng Li
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
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Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron. Biochem Res Int 2022; 2022:2164749. [PMID: 35450296 PMCID: PMC9017565 DOI: 10.1155/2022/2164749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
The prolonged global spread and community transmission of severe acute respiratory syndrome virus 2 (SARS-CoV-2) has led to the emergence of variants and brought questions regarding disease severity and vaccine effectiveness. We conducted simple bioinformatics on the spike gene of a representative of each variant. The data show that a number of polymorphic amino acids are located mostly on the amino-terminal side of the S1/S2 cleavage site. The Omicron variant diverges from the others, with the highest number of amino acid substitutions, including the receptor-binding site (RBS), epitopes, S1/S2 cleavage site, fusion peptide, and heptad repeat 1. The current sharp global increase in the frequency of the Omicron genome constitutes evidence of its high community transmissibility. In conclusion, the proposed guideline could give an immediate insight of the probable biological nature of any variant of SARS-Cov-2. As the Omicron diverged the farthest from the original pandemic strain, Wuhan-Hu-1, we expect different epidemiological and clinical patterns of Omicron cases. On vaccine efficacy, slight changes in some epitopes while others are conserved should not lead to a significant reduction in the effectiveness of an approved vaccine.
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Immunoinformatics approach for designing a universal multiepitope vaccine against Chandipura Virus. Microb Pathog 2021; 162:105358. [PMID: 34902539 DOI: 10.1016/j.micpath.2021.105358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022]
Abstract
Chandipura vesiculovirus (CHPV) is a fast-emerging virus that causes acute encephalitis with a high death rate. Because of its extensive prevalence in African and Asian countries, this infection has become a global hazard, and there is an urgent need to create an effective and non-allergenic vaccine or appropriate treatment to combat it. A vaccine candidate is offered utilizing a computational technique in this study. To build a potential vaccine candidate, viral protein sequences were acquired from the National Center for Biotechnology Information database and evaluated with several bioinformatics techniques to identify B-cell and T-cell epitopes. V1 was shown to be superior in terms of various physicochemical qualities, as well as highly immunogenic and non-allergic. Molecular docking revealed that the CHPV vaccine construct had a greater binding affinity with human Toll-like receptors (TLR-3 and TLR-8) and that it was stable in molecular dynamics simulations. MEC-CHPV was in silico cloned in the pET28a (+) expression vector using codon optimization. The current research identifies potential antigenic epitopes that could be used as vaccine candidates to eradicate the CHPV. This in-silico development of a CHPV vaccine with multiple epitopes could open the path for future rapid laboratory tests.
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Laha S, Chatterjee R. Temporal variations of country-specific mutational profile of SARS-CoV-2: effect on vaccine efficacy. Future Virol 2021; 0. [PMID: 34824595 PMCID: PMC8603786 DOI: 10.2217/fvl-2021-0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022]
Abstract
Aim: In order to curb the transmission of SARS-CoV-2, nation-wide travel restrictions at different levels were implemented in different countries. Country-specific mutational profile may exist and have an impact on vaccine efficacy. Materials & methods: We identified nonsynonymous mutations in approximately 215,000 SARS-CoV-2 sequences during the 1st year of the pandemic in 35 countries. Mutational profiles on a bimonthly basis were traced over time. We also examined the mutations that overlapped with the spike protein vaccine epitopes. Results: Several new mutations emerged over time and were dominating in specific countries. Many nonsynonymous mutations were within multiple spike protein epitopes that might impact the vaccine efficacy. Conclusion: Our study advocates requirement of active monitoring of country-specific mutations and vaccine efficacies in respective countries.
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Affiliation(s)
- Sayantan Laha
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
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20
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Uttamrao PP, Sathyaseelan C, Patro LPP, Rathinavelan T. Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach. Front Immunol 2021; 12:692937. [PMID: 34497604 PMCID: PMC8419283 DOI: 10.3389/fimmu.2021.692937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kills thousands of people worldwide every day, thus necessitating rapid development of countermeasures. Immunoinformatics analyses carried out here in search of immunodominant regions in recently identified SARS-CoV-2 unannotated open reading frames (uORFs) have identified eight linear B-cell, one conformational B-cell, 10 CD4+ T-cell, and 12 CD8+ T-cell promising epitopes. Among them, ORF9b B-cell and T-cell epitopes are the most promising followed by M.ext and ORF3c epitopes. ORF9b40-48 (CD8+ T-cell epitope) is found to be highly immunogenic and antigenic with the highest allele coverage. Furthermore, it has overlap with four potent CD4+ T-cell epitopes. Structure-based B-cell epitope prediction has identified ORF9b61-68 to be immunodominant, which partially overlaps with one of the linear B-cell epitopes (ORF9b65-69). ORF3c CD4+ T-cell epitopes (ORF3c2-16, ORF3c3-17, and ORF3c4-18) and linear B-cell epitope (ORF3c14-22) have also been identified as the candidate epitopes. Similarly, M.ext and 7a.iORF1 (overlap with M and ORF7a) proteins have promising immunogenic regions. By considering the level of antigen expression, four ORF9b and five M.ext epitopes are finally shortlisted as potent epitopes. Mutation analysis has further revealed that the shortlisted potent uORF epitopes are resistant to recurrent mutations. Additionally, four N-protein (expressed by canonical ORF) epitopes are found to be potent. Thus, SARS-CoV-2 uORF B-cell and T-cell epitopes identified here along with canonical ORF epitopes may aid in the design of a promising epitope-based polyvalent vaccine (when connected through appropriate linkers) against SARS-CoV-2. Such a vaccine can act as a bulwark against SARS-CoV-2, especially in the scenario of emergence of variants with recurring mutations in the spike protein.
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21
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De Pace V, Caligiuri P, Ricucci V, Nigro N, Galano B, Visconti V, Da Rin G, Bruzzone B. Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens. BMC Infect Dis 2021; 21:926. [PMID: 34493222 PMCID: PMC8423595 DOI: 10.1186/s12879-021-06591-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens. Methods Consecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values. Results The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.Demographic characteristics and data sample type of the study cases (N = 75) Male, N (%) | 56 (74.6%) | Age (yr), Median (IQR) | 65 (31–81) | BAS, N (%) | 43 (57.3%) | Negative | 30.2% | Positive—High viral load [Ct ≤ 30] | 27.9% | Positive—Low viral load [Ct 31–35] | 41.9% | BAL, N (%) | 32 (42.7%) | Negative | 37.5% | Positive—High viral load [Ct ≤ 30] | 40.6% | Positive—Low viral load [Ct 31–35] | 21.9% |
Data were expressed as proportions for categorical variables. Specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). BAS bronchoaspirates, BAL bronchoalveolar lavage, Ct cycle threshold Distribution of E gene cycle threshold values of the rapid PCR and RT-PCR ![]() Conclusions Vivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.
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Affiliation(s)
- Vanessa De Pace
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Patrizia Caligiuri
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy.
| | - Nicola Nigro
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Barbara Galano
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Valeria Visconti
- Laboratory Medicine, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Giorgio Da Rin
- Laboratory Medicine, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
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22
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Hussain M, Shabbir S, Amanullah A, Raza F, Imdad MJ, Zahid S. Immunoinformatic analysis of structural and epitope variations in the spike and Orf8 proteins of SARS-CoV-2/B.1.1.7. J Med Virol 2021; 93:4461-4468. [PMID: 33704818 PMCID: PMC8206967 DOI: 10.1002/jmv.26931] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/17/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022]
Abstract
A newly emerged strain of SARS‐CoV‐2 of B.1.1.7 lineage has caused a significant surge in the SARS‐CoV‐2 infections in the UK. In this study, changes in the epitopes of spike and orf8 proteins in SARS‐CoV‐2 of B.1.1.7 lineage were investigated. Genomic alignment of the SARS‐CoV‐2/B.1.1.7 with SARS‐CoV‐2/Wuhan showed the presence of several mutations in orf1a/b, spike, orf8, and N proteins of SARS‐CoV‐2/B.1.1.7. Molecular models of spike and orf8 proteins were constructed by homology modeling. Superimposition between the spike proteins of SARS‐CoV‐2/Wuhan and SARS‐CoV‐2/B.1.1.7 showed noticeable variations in the spatial orientation in Val70‐Asn74 and Thr250‐Ser255 regions. This may have also resulted in the extension of the epitopic region at Ser244‐Gly249 in the SARS‐CoV‐2/B.1.1.7 spike protein. Superimposition of the SARS‐CoV‐2/B.1.1.7 spike protein over Fab‐spike protein complexes of SARS‐CoV‐2/Wuhan also showed subtle variations in the antibody binding affinity targeting the N‐terminal domain of the spike protein. Epitopic variations were also observed between the corresponding orf8 regions of SARS‐CoV‐2/Wuhan and SARS‐CoV‐2/B.1.1.7. Moreover, the presence of a stop codon at position 27 in orf8 connotes the emergence of two frames (orf8a and orf8b) in SARS‐CoV‐2, which further hampers its extracellular secretion, and in turn, immunogenicity. The findings of the present study could further be used to develop targeted immunotherapeutics.
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Affiliation(s)
- Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Sanya Shabbir
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.,Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Anusha Amanullah
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Fozia Raza
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Muhammad J Imdad
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.,Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Sahar Zahid
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
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23
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Baisa G, Rancour D, Mansfield K, Burns M, Martin L, Cunha D, Fischer J, Muecksch F, Hatziioannou T, Bieniasz PD, Schomburg F, Luke K. A Recombinant Protein SARS-CoV-2 Candidate Vaccine Elicits High-titer Neutralizing Antibodies in Macaques. RESEARCH SQUARE 2021:rs.3.rs-137857. [PMID: 33442678 PMCID: PMC7805460 DOI: 10.21203/rs.3.rs-137857/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Background Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. Methods We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain or an extended C-terminal domain containing the receptor-binding domain and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. Results A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the N-terminal domain alone lacked this activity. Crucially, sera from animals immunized with the extended receptor binding domain but not the N-terminal domain had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. Conclusions These data support the utility of spike subunit-based antigens as a vaccine for use in humans.
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Affiliation(s)
| | | | | | | | - Lori Martin
- Novartis Institutes for BioMedical Research Inc
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24
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Baisa G, Rancour D, Mansfield K, Burns M, Martin L, Cunha D, Fischer J, Muecksch F, Hatziioannou T, Bieniasz PD, Schomburg F, Luke K. "A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.20.422693. [PMID: 33398285 PMCID: PMC7781324 DOI: 10.1101/2020.12.20.422693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.
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Affiliation(s)
- Gary Baisa
- Intuitive Biosciences, 918 Deming Way, Madison WI 53717
| | | | - Keith Mansfield
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139
| | - Monika Burns
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139
| | - Lori Martin
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139
| | - Daise Cunha
- Covance Greenfield Laboratories, 671 South Meridian Road Greenfield, IN 46140
| | - Jessica Fischer
- Covance Greenfield Laboratories, 671 South Meridian Road Greenfield, IN 46140
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York NY 10065
| | | | - Kimberly Luke
- Intuitive Biosciences, 918 Deming Way, Madison WI 53717
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25
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Shaw B, Daskareh M, Gholamrezanezhad A. The lingering manifestations of COVID-19 during and after convalescence: update on long-term pulmonary consequences of coronavirus disease 2019 (COVID-19). Radiol Med 2020; 126:40-46. [PMID: 33006087 PMCID: PMC7529085 DOI: 10.1007/s11547-020-01295-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
The long-term sequelae of coronavirus disease 2019 (COVID-19) are still unknown. Lessons from past viral epidemics reveal that, after recovery, patients with viral pulmonary infections can suffer from irreversible pulmonary dysfunction and demonstrate residual imaging or functional abnormalities. Residual ground glass opacities, consolidations, reticular and linear opacities, residual crazy paving pattern, melted sugar sign, and parenchymal fibrotic bands are several features found in the late or remission stages of COVID-19. These radiologic findings have been observed weeks after symptom onset, even after hospital discharge, and they may or may not correlate with clinical manifestations. High-resolution CT may be indicated to establish new baselines and track changes in residual impairments. In our previous review, we observed significant pulmonary sequelae in some COVID-19 survivors at follow-up. In this update, we review the current literature on the clinical and radiologic manifestations of post-recovery COVID-19 toward the end of hospital admission and after discharge.
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Affiliation(s)
- Brian Shaw
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Ali Gholamrezanezhad
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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