51
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Rashid F, Xie Z, Suleman M, Shah A, Khan S, Luo S. Roles and functions of SARS-CoV-2 proteins in host immune evasion. Front Immunol 2022; 13:940756. [PMID: 36003396 PMCID: PMC9394213 DOI: 10.3389/fimmu.2022.940756] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.
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Affiliation(s)
- Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- *Correspondence: Zhixun Xie,
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
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52
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Simultaneous monitoring of eight human respiratory viruses including SARS-CoV-2 using liquid chromatography-tandem mass spectrometry. Sci Rep 2022; 12:13392. [PMID: 35927299 PMCID: PMC9352774 DOI: 10.1038/s41598-022-16250-y] [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: 03/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has primarily been achieved using reverse transcriptase polymerase chain reaction (RT-PCR) for acute infection, and serology for prior infection. Assay with RT-PCR provides data on presence or absence of viral RNA, with no information on virus replication competence, infectivity, or virus characterisation. Liquid chromatography-tandem mass spectrometry (LC–MS/MS) is typically not used in clinical virology, despite its potential to provide supplemental data about the presence of viral proteins and thus the potential for replication-competent, transmissible virus. Using the SARS-CoV-2 as a model virus, we developed a fast ‘bottom-up’ proteomics workflow for discovery of target virus peptides using ‘serum-free’ culture conditions, providing high coverage of viral proteins without the need for protein or peptide fractionation techniques. This workflow was then applied to Coronaviruses OC43 and 229E, Influenza A/H1N1 and H3N2, Influenza B, and Respiratory Syncytial Viruses A and B. Finally, we created an LC–MS/MS method for targeted detection of the eight-virus panel in clinical specimens, successfully detecting peptides from the SARS-CoV-2 ORF9B and nucleoprotein in RT-PCR positive samples. The method provides specific detection of respiratory viruses from clinical samples containing moderate viral loads and is an important further step to the use of LC–MS/MS in diagnosis of viral infection.
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53
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Pedersen J, Koumakpayi IH, Babuadze G, Baz M, Ndiaye O, Faye O, Diagne CT, Dia N, Naghibosadat M, McGeer A, Muberaka S, Moukandja IP, Ndidi S, Tauil CB, Lekana-Douki JB, Loucoubar C, Faye O, Sall A, Magalhães KG, Weis N, Kozak R, Kobinger GP, Fausther-Bovendo H. Cross-reactive immunity against SARS-CoV-2 N protein in Central and West Africa precedes the COVID-19 pandemic. Sci Rep 2022; 12:12962. [PMID: 35902675 PMCID: PMC9333058 DOI: 10.1038/s41598-022-17241-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/22/2022] [Indexed: 12/22/2022] Open
Abstract
Early predictions forecasted large numbers of severe acute respiratory syndrome coronavirus (SARS-CoV-2) cases and associated deaths in Africa. To date, Africa has been relatively spared. Various hypotheses were postulated to explain the lower than anticipated impact on public health in Africa. However, the contribution of pre-existing immunity is yet to be investigated. In this study, the presence of antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins in pre-pandemic samples from Africa, Europe, South and North America was examined by ELISA. The protective efficacy of N specific antibodies isolated from Central African donors was tested by in vitro neutralization and in a mouse model of SARS-CoV-2 infection. Antibodies against SARS-CoV-2 S and N proteins were rare in all populations except in Gabon and Senegal where N specific antibodies were prevalent. However, these antibodies failed to neutralize the virus either in vitro or in vivo. Overall, this study indicates that cross-reactive immunity against SARS-CoV-2 N protein was present in Africa prior to the pandemic. However, this pre-existing humoral immunity does not impact viral fitness in rodents suggesting that other human immune defense mechanisms could be involved. In Africa, seroprevalence studies using the N protein are over-estimating SARS-CoV-2 circulation.
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Affiliation(s)
- Jannie Pedersen
- Département de Microbiologie-Infectiologie et Immunologie, Université Laval, Quebec City, Canada
| | | | - Giorgi Babuadze
- Biological Sciences Platform, University of Toronto, Sunnybrook Research Institute at Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Mariana Baz
- Département de Microbiologie-Infectiologie et Immunologie, Université Laval, Quebec City, Canada
| | | | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Ndongo Dia
- Institut Pasteur de Dakar, Dakar, Senegal
| | - Maedeh Naghibosadat
- Biological Sciences Platform, University of Toronto, Sunnybrook Research Institute at Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Microbiology, Sinai Health System/University Health Network, Toronto, Canada
| | - Samira Muberaka
- Biological Sciences Platform, University of Toronto, Sunnybrook Research Institute at Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre, Toronto, Canada
| | | | - Stella Ndidi
- Centre Hospitalier Universitaire de Libreville, Libreville, Gabon
| | - Carlos B Tauil
- Laboratory of Immunology and Inflammation, University of Brasilia, Brasilia, Brazil
| | - Jean-Bernard Lekana-Douki
- Unité d'Evolution Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | | | | | - Kelly G Magalhães
- Laboratory of Immunology and Inflammation, University of Brasilia, Brasilia, Brazil
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert Kozak
- Biological Sciences Platform, University of Toronto, Sunnybrook Research Institute at Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Gary P Kobinger
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
| | - Hugues Fausther-Bovendo
- Département de Microbiologie-Infectiologie et Immunologie, Université Laval, Quebec City, Canada. .,Global Urgent and Advanced Research and Development, 911 Rue Principale, Unit 100, Batiscan, QC, G0X 1A0, Canada.
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54
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Pandey SK, Mohanta GC, Kumar V, Gupta K. Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection. Vaccines (Basel) 2022; 10:1200. [PMID: 36016088 PMCID: PMC9414050 DOI: 10.3390/vaccines10081200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.
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Affiliation(s)
- Satish Kumar Pandey
- Department of Biotechnology, School of Life Sciences, Mizoram University (Central University), Aizawl 796004, India
| | - Girish C. Mohanta
- Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh 160030, India;
| | - Vinod Kumar
- Department of Dermatology, Venerology and Leprology, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Kuldeep Gupta
- Russel H. Morgan, Department of Radiology and Radiological Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
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Mubarak A, Almutairi S, Al-Dhabbah AD, Aldabas SY, Bhat R, Alqoufail MM, Abdel-Maksoud MA, Almanaa TN, Farrag MA, Alturaiki W. Durability of SARS-CoV-2 Specific IgG Antibody Responses Following Two Doses of Match and Mixed COVID-19 Vaccines Regimens in Saudi Population. Infect Drug Resist 2022; 15:3791-3800. [PMID: 35875613 PMCID: PMC9296867 DOI: 10.2147/idr.s369769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background SARS-CoV-2 pandemic continues to threaten the human population with millions of infections and deaths worldwide. Vaccination campaigns undertaken by several countries have resulted in a notable decrease in hospitalization and deaths. However, with the emergence of new virus variants, it is critical to determine the longevity and the protection efficiency provided by the current authorized vaccines. Aim The aims of this study are to provide data about the magnitude of immune responses in individuals fully vaccinated against COVID-19 in Riyadh province of Saudi Arabia. Also, to evaluate the continuity of specific IgG levels and compare the titers in individuals who have been received two doses of the matched and mixed vaccines, including Pfizer and AstraZeneca against SARS-CoV-2 during the period of three to six months. Moreover, we analyze the current state of immune response in terms of antibody responses in thepopulation postvaccination using homogenous or hetrogenous vaccine regimen. Methods A total of 141 healthy volunteers were recruited to our study; blood (n=63) and the saliva samples (n=78) and were collected from fully vaccinated individuals in Riyadh city. We employed a specific ELISA assay in plasma and saliva of fully vaccinated individuals. Results IgG levels varied with age groups with the highest concentration in the age group 19-29 years, but the age group (≥50) had the lowest IgG concentration. The IgG levels in both serum and saliva were higher after three months and start to wane after six months. Individuals who received mixed types of vaccines had significantly better response than Pfizer vaccine alone. Conclusion The current study investigates the status of humoral responses in different age groups, in terms of antibody measurements. These data will help to evaluate the need for further COVID-19 vaccine doses and to what extent a two-dose regimen will protect vaccinated individuals.
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Affiliation(s)
- Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Saeedah Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abulrahman D Al-Dhabbah
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shaha Y Aldabas
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Rauf Bhat
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahfoudh M Alqoufail
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Saudi Arabia
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56
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Parker MD, Stewart H, Shehata OM, Lindsey BB, Shah DR, Hsu S, Keeley AJ, Partridge DG, Leary S, Cope A, State A, Johnson K, Ali N, Raghei R, Heffer J, Smith N, Zhang P, Gallis M, Louka SF, Hornsby HR, Alamri H, Whiteley M, Foulkes BH, Christou S, Wolverson P, Pohare M, Hansford SE, Green LR, Evans C, Raza M, Wang D, Firth AE, Edgar JR, Gaudieri S, Mallal S, Collins MO, Peden AA, de Silva TI. Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections. Commun Biol 2022; 5:666. [PMID: 35790808 PMCID: PMC9255483 DOI: 10.1038/s42003-022-03565-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
Abstract
B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.
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Affiliation(s)
- Matthew D Parker
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, UK
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
| | - Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ola M Shehata
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK
| | - Benjamin B Lindsey
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Dhruv R Shah
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Sharon Hsu
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Alexander J Keeley
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | | | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Alison Cope
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Amy State
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Katie Johnson
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Nasar Ali
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Rasha Raghei
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Joe Heffer
- IT Services, The University of Sheffield, Sheffield, UK
| | - Nikki Smith
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Peijun Zhang
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Marta Gallis
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Stavroula F Louka
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Hailey R Hornsby
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Hatoon Alamri
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK
| | - Max Whiteley
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Benjamin H Foulkes
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Stella Christou
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Paige Wolverson
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Manoj Pohare
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Samantha E Hansford
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Luke R Green
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Cariad Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Mohammad Raza
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Dennis Wang
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, UK
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
- Department of Computer Science, The University of Sheffield, Sheffield, UK
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - James R Edgar
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Silvana Gaudieri
- Department of Computer Science, The University of Sheffield, Sheffield, UK
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Mark O Collins
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK
| | - Andrew A Peden
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.
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Feng W, Xiang Y, Wu L, Chen Z, Li Q, Chen J, Guo Y, Xia D, Chen N, Zhang L, Zhu S, Zhao K. Nucleocapsid protein of SARS-CoV-2 is a potential target for developing new generation of vaccine. J Clin Lab Anal 2022; 36:e24479. [PMID: 35527696 PMCID: PMC9169192 DOI: 10.1002/jcla.24479] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 04/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has spread worldwide causing more than 400 million people with virus infections since early 2020. Currently, the existing vaccines targeting the spike glycoprotein (S protein) of SARS-CoV-2 are facing great challenge from the infection of SARS-CoV-2 virus and its multiple S protein variants. Thus, we need to develop a new generation of vaccines to prevent infection of the SARS-CoV-2 variants. Compared with the S protein, the nucleocapsid protein (N protein) of SARS-CoV-2 is more conservative and less mutations, which also plays a vital role in viral infection. Therefore, the N protein may have the great potential for developing new vaccines. METHODS The N protein of SARS-CoV-2 was recombinantly expressed and purified in Escherichia coli. Western Blot and ELISA assays were used to demonstrate the immunoreactivity of the recombinant N protein with the serum of 22 COVID-19 patients. We investigated further the response of the specific serum antibodies and cytokine production in BALB/c mice immunized with recombinant N protein by Western Blot and ELISA. RESULTS The N protein had good immunoreactivity and the production of IgG antibody against N protein in COVID-19 patients was tightly correlated with disease severity. Furthermore, the N protein was used to immunize BALB/c mice to have elicited strong immune responses. Not only high levels of IgG antibody, but also cytokine-IFN-γ were produced in the N protein-immunized mice. Importantly, the N protein immunization induced a high level of IgM antibody produced in the mice. CONCLUSION SARS-CoV-2 N protein shows a great big bundle of potentiality for developing a new generation of vaccines in fighting infection of SARS-CoV-2 and its variants.
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Affiliation(s)
- Weixu Feng
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yunru Xiang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Lianpeng Wu
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Zhuo Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Qingfeng Li
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Jun Chen
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Yanru Guo
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Dandan Xia
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Na Chen
- Department of Laboratory MedicineThe Sixth People Hospital of WenzhouWenzhouChina
| | - Lifang Zhang
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Shanli Zhu
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
| | - Kong‐Nan Zhao
- School of Basic Medical ScienceWenzhou Medical UniversityWenzhouChina
- Department of Obstetrics and GynaecologyThe Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical UniversityWenzhouChina
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQueenslandAustralia
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58
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Hachim A, Gu H, Kavian O, Mori M, Kwan MYW, Chan WH, Yau YS, Chiu SS, Tsang OTY, Hui DSC, Mok CKP, Ma FNL, Lau EHY, Amarasinghe GK, Qavi AJ, Cheng SMS, Poon LLM, Peiris JSM, Valkenburg SA, Kavian N. SARS-CoV-2 accessory proteins reveal distinct serological signatures in children. Nat Commun 2022; 13:2951. [PMID: 35618731 PMCID: PMC9135746 DOI: 10.1038/s41467-022-30699-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/13/2022] [Indexed: 12/14/2022] Open
Abstract
The antibody response magnitude and kinetics may impact clinical severity, serological diagnosis and long-term protection of COVID-19, which may play a role in why children experience lower morbidity. We therefore tested samples from 122 children in Hong Kong with symptomatic (n = 78) and asymptomatic (n = 44) SARS-CoV-2 infections up to 200 days post infection, relative to 71 infected adults (symptomatic n = 61, and asymptomatic n = 10), and negative controls (n = 48). We assessed serum IgG antibodies to a 14-wide antigen panel of structural and accessory proteins by Luciferase Immuno-Precipitation System (LIPS) assay and circulating cytokines. Infected children have lower levels of Spike, Membrane, ORF3a, ORF7a, ORF7b antibodies, comparable ORF8 and elevated E-specific antibodies than adults. Combination of two unique antibody targets, ORF3d and ORF8, can accurately discriminate SARS-CoV-2 infection in children. Principal component analysis reveals distinct pediatric serological signatures, and the highest contribution to variance from adults are antibody responses to non-structural proteins ORF3d, NSP1, ORF3a and ORF8. From a diverse panel of cytokines that can modulate immune priming and relative inflammation, IL-8, MCP-1 and IL-6 correlate with the magnitude of pediatric antibody specificity and severity. Antibodies to SARS-CoV-2 internal proteins may become an important sero surveillance tool of infection with the roll-out of vaccines in the pediatric population.
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Affiliation(s)
- Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Otared Kavian
- Department of Mathematics, Université de Versailles Saint-Quentin, Versailles, France
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Mike Y W Kwan
- Department of Pediatric and Adolescent Medicine, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Wai Hung Chan
- Department of Pediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Yat Sun Yau
- Department of Pediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Susan S Chiu
- Department of Pediatric and Adolescent Medicine, The University of Hong Kong and Queen Mary Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Owen T Y Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fionn N L Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Abraham J Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Samuel M S Cheng
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L M Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Doherty Institute of Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia.
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Faculté de Médecine Université Paris Descartes, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d'Immunologie Biologique, Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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59
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Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein. Viruses 2022; 14:v14061141. [PMID: 35746613 PMCID: PMC9228376 DOI: 10.3390/v14061141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 is continuing to spread around the world and drastically affect our daily life. New strains appear, and the severity of the course of the disease itself seems to be decreasing, but even people who have been ill on an outpatient basis suffer post-COVID consequences. Partly, it is associated with the autoimmune reactions, so debates about the development of new vaccines and the need for vaccination/revaccination continue. In this study we performed an analysis of the antibody response of patients with COVID-19 to linear and conformational epitopes of viral proteins using ELISA, chip array and western blot with analysis of correlations between antibody titer, disease severity, and complications. We have shown that the presence of IgG antibodies to the nucleoprotein can deteriorate the course of the disease, induce multiple direct COVID-19 symptoms, and contribute to long-term post-covid symptoms. We analyzed the cross reactivity of antibodies to SARS-CoV-2 with own human proteins and showed that antibodies to the nucleocapsid protein can bind to human proteins. In accordance with the possibility of HLA presentation, the main possible targets of the autoantibodies were identified. People with HLA alleles A01:01; A26:01; B39:01; B15:01 are most susceptible to the development of autoimmune processes after COVID-19.
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60
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Lai YC, Cheng YW, Chao CH, Chang YY, Chen CD, Tsai WJ, Wang S, Lin YS, Chang CP, Chuang WJ, Chen LY, Wang YR, Chang SY, Huang W, Wang JR, Tseng CK, Lin CK, Chuang YC, Yeh TM. Antigenic Cross-Reactivity Between SARS-CoV-2 S1-RBD and Its Receptor ACE2. Front Immunol 2022; 13:868724. [PMID: 35603169 PMCID: PMC9114768 DOI: 10.3389/fimmu.2022.868724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus responsible for the ongoing COVID-19 pandemic. SARS-CoV-2 binds to the human cell receptor angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain in the S1 subunit of the spike protein (S1-RBD). The serum levels of autoantibodies against ACE2 are significantly higher in patients with COVID-19 than in controls and are associated with disease severity. However, the mechanisms through which these anti-ACE2 antibodies are induced during SARS-CoV-2 infection are unclear. In this study, we confirmed the increase in antibodies against ACE2 in patients with COVID-19 and found a positive correlation between the amounts of antibodies against ACE2 and S1-RBD. Moreover, antibody binding to ACE2 was significantly decreased in the sera of some COVID-19 patients after preadsorption of the sera with S1-RBD, which indicated that antibodies against S1-RBD can cross-react with ACE2. To confirm this possibility, two monoclonal antibodies (mAbs 127 and 150) which could bind to both S1-RBD and ACE2 were isolated from S1-RBD-immunized mice. Measurement of the binding affinities by Biacore showed these two mAbs bind to ACE2 much weaker than binding to S1-RBD. Epitope mapping using synthetic overlapping peptides and hydrogen deuterium exchange mass spectrometry (HDX-MS) revealed that the amino acid residues P463, F464, E465, R466, D467 and E471 of S1-RBD are critical for the recognition by mAbs 127 and 150. In addition, Western blotting analysis showed that these mAbs could recognize ACE2 only in native but not denatured form, indicating the ACE2 epitopes recognized by these mAbs were conformation-dependent. The protein-protein interaction between ACE2 and the higher affinity mAb 127 was analyzed by HDX-MS and visualized by negative-stain transmission electron microscopy imaging combined with antigen-antibody docking. Together, our results suggest that ACE2-cross-reactive anti-S1-RBD antibodies can be induced during SARS-CoV-2 infection due to potential antigenic cross-reactivity between S1-RBD and its receptor ACE2.
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Affiliation(s)
- Yen-Chung Lai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Leadgene Biomedical, Inc., Tainan, Taiwan
| | - Yu-Wei Cheng
- Leadgene Biomedical, Inc., Tainan, Taiwan
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chiao-Hsuan Chao
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Wei-Jiun Tsai
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yee-Shin Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Peng Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wenya Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Yung-Chun Chuang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Leadgene Biomedical, Inc., Tainan, Taiwan
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Trai-Ming Yeh
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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61
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Su WY, Du PX, Santos HM, Ho TS, Keskin BB, Pau CH, Yang AM, Chou YY, Shih HC, Syu GD. Antibody Profiling in COVID-19 Patients with Different Severities by Using Spike Variant Protein Microarrays. Anal Chem 2022; 94:6529-6539. [PMID: 35442638 PMCID: PMC9045038 DOI: 10.1021/acs.analchem.1c05567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/11/2022] [Indexed: 12/21/2022]
Abstract
The disease progression of COVID-19 varies from mild to severe, even death. However, the link between COVID-19 severities and humoral immune specificities is not clear. Here, we developed a multiplexed spike variant protein microarray (SVPM) and utilized it for quantifying neutralizing activity, drug screening, and profiling humoral immunity. First, we demonstrated the competition between antispike antibody and ACE2 on SVPM for measuring the neutralizing activity against multiple spike variants. Next, we collected the serums from healthy subjects and COVID-19 patients with different severities and profile the neutralizing activity as well as antibody isotypes. We identified the inhibition of ACE2 binding was stronger against multiple variants in severe compared to mild/moderate or critical patients. Moreover, the serum IgG against nonstructural protein 3 was elevated in severe but not in mild/moderate and critical cases. Finally, we evaluated two ACE2 inhibitors, Ramipril and Perindopril, and found the dose-dependent inhibition of ACE2 binding to all the spike variants except for B.1.617.3. Together, the SVPM and the assay procedures provide a tool for profiling neutralizing antibodies, antibody isotypes, and reagent specificities.
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Affiliation(s)
- Wen-Yu Su
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pin-Xian Du
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Harvey M. Santos
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- School
of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, Intramuros, Manila 1002, Philippines
| | - Tzong-Shiann Ho
- Department
of Pediatrics, National Cheng Kung University
Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center
of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
- Department
of Pediatrics, Tainan Hospital, Ministry
of Health and Welfare, Tainan 700, Taiwan
| | - Batuhan Birol Keskin
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi Ho Pau
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - An-Ming Yang
- Department
of Internal Medicine, En Chu Kong Hospital, New Taipei City 237, Taiwan
- Department
of Nursing, Yuanpei University of Medical
Technology, Hsinchu 300, Taiwan
| | - Yi-Yu Chou
- Department
of Nursing, Kaohsiung Armed Forces General
Hospital, Kaohsiung 802, Taiwan
| | - Hsi-Chang Shih
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Guan-Da Syu
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Research
Center of Excellence in Regenerative Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Medical
Device Innovation Center, National Cheng
Kung University, Tainan 701, Taiwan
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62
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Yuan Y, Feng Z, Li S, Huang Z, Wan Y, Cao C, Lin S, Wu L, Zhou J, Liao LS, Qian J, Lee CS. Molecular Programming of NIR-IIb-Emissive Semiconducting Small Molecules for In Vivo High-Contrast Bioimaging Beyond 1500 nm. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201263. [PMID: 35307885 DOI: 10.1002/adma.202201263] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Materials with long-wavelength second near-infrared (NIR-II) emission are highly desired for in vivo dynamic visualizating of microstructures in deep tissues. Herein, by employing an atom-programming strategy, a series of highly fluorescent semiconducting oligomers (SOMs) with tunable NIR-IIb emissions are developed for bioimaging applications. After self-assembly into nanoparticles (NPs), they show good brightness, high photostability, and satisfactory biocompatibility. The SOM NPs are applied as probes for high-resolution imaging of whole-body and hind-limb blood vessels, biliary tract, and bladder with their emissions over 1500 nm. This work demonstrates an atom-programming strategy for constructing semiconducting small molecules with enhanced NIR-II fluorescence for deep-tissue imaging, affording new insight for advancing molecular design of NIR-II fluorophores.
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Affiliation(s)
- Yi Yuan
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
- Center of Super-Diamond and Advanced Films (COSDAF), Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 000000, P. R. China
| | - Zhe Feng
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Shengliang Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Zhongming Huang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Yingpeng Wan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, P. R. China
| | - Chen Cao
- Center of Super-Diamond and Advanced Films (COSDAF), Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 000000, P. R. China
| | - Sien Lin
- Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, 000000, P. R. China
| | - Lan Wu
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Jing Zhou
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Liang-Sheng Liao
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Jun Qian
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Chun-Sing Lee
- Center of Super-Diamond and Advanced Films (COSDAF), Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 000000, P. R. China
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63
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Ho TS, Du PX, Su WY, Santos HM, Lin YL, Chou YY, Keskin BB, Pau CH, Syu GD. Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. Biosens Bioelectron 2022; 204:114067. [PMID: 35168024 PMCID: PMC8821029 DOI: 10.1016/j.bios.2022.114067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 is quickly evolving from wild-type to many variants and spreading around the globe. Since many people have been vaccinated with various types of vaccines, it is crucial to develop a high throughput platform for measuring the antibody responses and surrogate neutralizing activities against multiple SARS-CoV-2 variants. To meet this need, the present study developed a SARS-CoV-2 variant (CoVariant) array which consists of the extracellular domain of spike variants, e.g., wild-type, D614G, B.1.1.7, B.1.351, P.1, B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3. A surrogate virus neutralization on the CoVariant array was established to quantify the bindings of antibody and host receptor ACE2 simultaneously to spike variants. By using a chimeric anti-spike antibody, we demonstrated a broad binding spectrum of antibodies while inhibiting the bindings of ACE2 to spike variants. To monitor the humoral immunities after vaccination, we collected serums from unvaccinated, partial, or fully vaccinated individuals with either mRNA-1273 or AZD1222 (ChAdOx1). The results showed partial vaccination increased the surrogate neutralization against all the mutants while full vaccination boosted the most. Although IgG, IgA, and IgM isotypes correlated with surrogate neutralizing activities, they behave differently throughout the vaccination processes. Overall, this study developed CoVariant arrays and assays for profiling the humoral responses which are useful for immune assessment, vaccine research, and drug development.
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Affiliation(s)
- Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan, 700, Taiwan, ROC
| | - Pin-Xian Du
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Wen-Yu Su
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Harvey M Santos
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC; School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, Intramuros, Manila, 1002, Philippines
| | - Ya-Lan Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Yi-Yu Chou
- Department of Nursing, Kaohsiung Armed Forces General Hospital, Kaohsiung, 802, Taiwan, ROC
| | - Batuhan Birol Keskin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Chi Ho Pau
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Research Center of Excellence in Regenerative Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC.
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64
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A single intranasal dose of human parainfluenza virus type 3-vectored vaccine induces effective antibody and memory T cell response in the lungs and protects hamsters against SARS-CoV-2. NPJ Vaccines 2022; 7:47. [PMID: 35468973 PMCID: PMC9038905 DOI: 10.1038/s41541-022-00471-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Respiratory tract vaccination has an advantage of needle-free delivery and induction of mucosal immune response in the portal of SARS-CoV-2 entry. We utilized human parainfluenza virus type 3 vector to generate constructs expressing the full spike (S) protein of SARS-CoV-2, its S1 subunit, or the receptor-binding domain, and tested them in hamsters as single-dose intranasal vaccines. The construct bearing full-length S induced high titers of neutralizing antibodies specific to S protein domains critical to the protein functions. Robust memory T cell responses in the lungs were also induced, which represent an additional barrier to infection and should be less sensitive than the antibody responses to mutations present in SARS-CoV-2 variants. Following SARS-CoV-2 challenge, animals were protected from the disease and detectable viral replication. Vaccination prevented induction of gene pathways associated with inflammation. These results indicate advantages of respiratory vaccination against COVID-19 and inform the design of mucosal SARS-CoV-2 vaccines.
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65
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Pérez-Gómez A, Gasca-Capote C, Vitallé J, Ostos FJ, Serna-Gallego A, Trujillo-Rodríguez M, Muñoz-Muela E, Giráldez-Pérez T, Praena-Segovia J, Navarro-Amuedo MD, Paniagua-García M, García-Gutiérrez M, Aguilar-Guisado M, Rivas-Jeremías I, Jiménez-León MR, Bachiller S, Fernández-Villar A, Pérez-González A, Gutiérrez-Valencia A, Rafii-El-Idrissi Benhnia M, Weiskopf D, Sette A, López-Cortés LF, Poveda E, Ruiz-Mateos E. Deciphering the quality of SARS-CoV-2 specific T-cell response associated with disease severity, immune memory and heterologous response. Clin Transl Med 2022; 12:e802. [PMID: 35415890 PMCID: PMC9005926 DOI: 10.1002/ctm2.802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2 specific T-cell response has been associated with disease severity, immune memory and heterologous response to endemic coronaviruses. However, an integrative approach combining a comprehensive analysis of the quality of SARS-CoV-2 specific T-cell response with antibody levels in these three scenarios is needed. In the present study, we found that, in acute infection, while mild disease was associated with high T-cell polyfunctionality biased to IL-2 production and inversely correlated with anti-S IgG levels, combinations only including IFN-γ with the absence of perforin production predominated in severe disease. Seven months after infection, both non-hospitalised and previously hospitalised patients presented robust anti-S IgG levels and SARS-CoV-2 specific T-cell response. In addition, only previously hospitalised patients showed a T-cell exhaustion profile. Finally, combinations including IL-2 in response to S protein of endemic coronaviruses were the ones associated with SARS-CoV-2 S-specific T-cell response in pre-COVID-19 healthy donors' samples. These results could have implications for protective immunity against SARS-CoV-2 and recurrent COVID-19 and may help for the design of new prototypes and boosting vaccine strategies.
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Affiliation(s)
- Alberto Pérez-Gómez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Carmen Gasca-Capote
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Joana Vitallé
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Francisco J Ostos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain.,Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Ana Serna-Gallego
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - María Trujillo-Rodríguez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Esperanza Muñoz-Muela
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Teresa Giráldez-Pérez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Julia Praena-Segovia
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - María D Navarro-Amuedo
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - María Paniagua-García
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Manuel García-Gutiérrez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Manuela Aguilar-Guisado
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Inmaculada Rivas-Jeremías
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - María Reyes Jiménez-León
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Sara Bachiller
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Alberto Fernández-Villar
- Pneumology Service, Galicia Sur Health Research Instituto (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Vigo, Spain
| | - Alexandre Pérez-González
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Vigo, Spain.,Infectious Diseases Unit, Department of Internal Medicine, Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Vigo, Spain
| | - Alicia Gutiérrez-Valencia
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Mohammed Rafii-El-Idrissi Benhnia
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain.,Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, California, USA.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Luis F López-Cortés
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Eva Poveda
- Group of Virology and Pathogenesis, Galicia Sur Health Research Institute (IIS Galicia Sur), Complexo Hospitalario Universitario de Vigo, SERGAS-UVigo, Vigo, Spain
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
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- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
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66
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. JCI Insight 2022; 7:e158126. [PMID: 35133988 PMCID: PMC8986086 DOI: 10.1172/jci.insight.158126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/02/2022] [Indexed: 12/03/2022] Open
Abstract
SARS-CoV-2 provokes a robust T cell response. Peptide-based studies exclude antigen processing and presentation biology, which may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DCs to activate CD8 and CD4 T cells from convalescent people. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory tract cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the Alpha, Beta, Gamma, and Delta variant lineages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | - Chu-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Anna Wald
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, and
- Center for Innate Immunity of Immune Disease, Department of Immunology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - David M. Koelle
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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67
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Chen L, Pang P, Qi H, Yan K, Ren Y, Ma M, Cao R, Li H, Hu C, Li Y, Xia J, Lai D, Dong Y, Jiang H, Zhang H, Shan H, Tao S, Liu S. Evaluation of Spike Protein Epitopes by Assessing the Dynamics of Humoral Immune Responses in Moderate COVID-19. Front Immunol 2022; 13:770982. [PMID: 35371042 PMCID: PMC8971992 DOI: 10.3389/fimmu.2022.770982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein (S) of SARS-CoV-2 is a major target for diagnosis and vaccine development because of its essential role in viral infection and host immunity. Currently, time-dependent responses of humoral immune system against various S protein epitopes are poorly understood. In this study, enzyme-linked immunosorbent assay (ELISA), peptide microarray, and antibody binding epitope mapping (AbMap) techniques were used to systematically analyze the dynamic changes of humoral immune responses against the S protein in a small cohort of moderate COVID-19 patients who were hospitalized for approximately two months after symptom onset. Recombinant truncated S proteins, target S peptides, and random peptides were used as antigens in the analyses. The assays demonstrated the dynamic IgM- and IgG recognition and reactivity against various S protein epitopes with patient-dependent patterns. Comprehensive analysis of epitope distribution along the spike gene sequence and spatial structure of the homotrimer S protein demonstrated that most IgM- and IgG-reactive peptides were clustered into similar genomic regions and were located at accessible domains. Seven S peptides were generally recognized by IgG antibodies derived from serum samples of all COVID-19 patients. The dynamic immune recognition signals from these seven S peptides were comparable to those of the entire S protein or truncated S1 protein. This suggested that the humoral immune system recognized few conserved S protein epitopes in most COVID-19 patients during the entire duration of humoral immune response after symptom onset. Furthermore, in this cohort, individual patients demonstrated stable immune recognition to certain S protein epitopes throughout their hospitalization period. Therefore, the dynamic characteristics of humoral immune responses to S protein have provided valuable information for accurate diagnosis and immunotherapy of COVID-19 patients.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Keqiang Yan
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Yan Ren
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Ruyin Cao
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hua Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Xia
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Danyun Lai
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuliang Dong
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hainan Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hong Shan
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Siqi Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
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68
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Zhou Y, Yuan S, To KKW, Xu X, Li H, Cai JP, Luo C, Hung IFN, Chan KH, Yuen KY, Li YF, Chan JFW, Sun H. Multiplex metal-detection based assay (MMDA) for COVID-19 diagnosis and identification of disease severity biomarkers. Chem Sci 2022; 13:3216-3226. [PMID: 35414865 PMCID: PMC8926254 DOI: 10.1039/d1sc05852e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 highlights the urgent need to develop sensitive methods for diagnosis and prognosis. To achieve this, multidimensional detection of SARS-CoV-2 related parameters including virus loads, immune response, and inflammation factors is crucial. Herein, by using metal-tagged antibodies as reporting probes, we developed a multiplex metal-detection based assay (MMDA) method as a general multiplex assay strategy for biofluids. This strategy provides extremely high multiplexing capability (theoretically over 100) compared with other reported biofluid assay methods. As a proof-of-concept, MMDA was used for serologic profiling of anti-SARS-CoV-2 antibodies. The MMDA exhibits significantly higher sensitivity and specificity than ELISA for the detection of anti-SARS-CoV-2 antibodies. By integrating the high dimensional data exploration/visualization tool (tSNE) and machine learning algorithms with in-depth analysis of multiplex data, we classified COVID-19 patients into different subgroups based on their distinct antibody landscape. We unbiasedly identified anti-SARS-CoV-2-nucleocapsid IgG and IgA as the most potently induced types of antibodies for COVID-19 diagnosis, and anti-SARS-CoV-2-spike IgA as a biomarker for disease severity stratification. MMDA represents a more accurate method for the diagnosis and disease severity stratification of the ongoing COVID-19 pandemic, as well as for biomarker discovery of other diseases. A MMDA platform is developed by using metal-tagged antibodies as reporting probes combined with machine learning algorithms, as a general strategy for highly multiplexed biofluid assay.![]()
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Affiliation(s)
- Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong Special Administrative Region China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong Special Administrative Region China.,Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong Special Administrative Region China
| | - Xiaohan Xu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Ivan Fan-Ngai Hung
- Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Kwok-Hung Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong Special Administrative Region China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong Special Administrative Region China.,Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong Special Administrative Region China.,Academician Workstation of Hainan Province, Hainan Medical University Haikou Hainan China.,The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Yu-Feng Li
- CAS-HKU Joint Laboratory of Metallomics on Health and Environment, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Beijing Metallomics Facility, National Consortium for Excellence in Metallomics, Institute of High Energy Physics, Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China .,Department of Clinical Microbiology, and Infection Control, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong Province China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong Special Administrative Region China.,Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong Special Administrative Region China.,Academician Workstation of Hainan Province, Hainan Medical University Haikou Hainan China.,The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
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69
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Bartas M, Volná A, Beaudoin CA, Poulsen ET, Červeň J, Brázda V, Špunda V, Blundell TL, Pečinka P. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. Brief Bioinform 2022; 23:6539840. [PMID: 35229157 PMCID: PMC9116216 DOI: 10.1093/bib/bbac045] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Adriana Volná
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Christopher A Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 65, Czech Republic
| | - Vladimír Špunda
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic.,Global Change Research Institute, Czech Academy of Sciences, Brno, 603 00, Czech Republic
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
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70
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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71
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
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Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
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72
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Panahibakhsh M, Amiri F, Doroudi T, Sadeghi M, Kolivand P, Alipour F, Gorji A. The association between micronutrients and the SARS-CoV-2-specific antibodies in convalescent patients. Infection 2022; 50:965-972. [PMID: 35190974 PMCID: PMC8860137 DOI: 10.1007/s15010-022-01774-2] [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: 10/11/2021] [Accepted: 02/02/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Various micronutrients play key roles in the immune responses to viral infection, antibody synthesis, and susceptibility to infection. This study aimed to investigate the role of micronutrients on the immune responses following SARS-CoV-2 infection. METHODS To evaluate humoral immunity following SARS-CoV-2 infection, the levels of SARS-CoV-2-specific IgM and IgG, as well as the concentrations of different micronutrients, were determined in 36 convalescent COVID-19 patients 60 days after infection. Furthermore, the correlation between biochemical and hematological parameters, clinical features, and the changes in adiposity with SARS-CoV-2 antibodies was evaluated. RESULTS Serum IgM and IgG antibodies were detected in 38.8% and 83.3% of recovered patients after 60 days of COVID-19 infection, respectively. The values of SARS-CoV-2-specific IgG were negatively correlated with the number of the platelet. Moreover, the values of SARS-CoV-2-specific IgM were positively correlated with LDH and the vitamin B12 concentration. Furthermore, a gender-specific association of SARS-CoV-2-specific IgG and IgM with vitamins D as well as with B9 and zinc was observed. A significant negative correlation was observed between the values of IgG with vitamin D in male participants and a positive correlation was detected between IgG values and B9 in female participants. Moreover, IgM levels with serum zinc values in females were negatively correlated. CONCLUSION Our study suggests the potential role of micronutrients in gender-specific humoral immunity following SARS-CoV-2 infection. Further studies are required with a greater sample of subjects to substantiate the validity and robustness of our findings.
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Affiliation(s)
| | - Faramarz Amiri
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
| | - Taher Doroudi
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
| | - Mostafa Sadeghi
- Department of Anesthesiology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Alipour
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
| | - Ali Gorji
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Epilepsy Research Center, Westfälische Wilhelms-Universität, Münster, Germany. .,Department of Neurosurgery, Westfälische Wilhelms-Universität, Münster, Germany. .,Department of Neurology with Institute of Translational Neurology, Westfälische Wilhelms-Universität, Münster, Germany.
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73
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SARS-CoV-2-specific antibody response characteristics in COVID-19 patients of different ages. Acta Biochim Biophys Sin (Shanghai) 2022; 54:556-564. [PMID: 35607955 PMCID: PMC9828714 DOI: 10.3724/abbs.2022014] [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] [Indexed: 01/18/2023] Open
Abstract
Age has been found to be one of the main risk factors for the severity and outcome of COVID-19. However, differences in SARS-CoV-2 specific antibody responses among COVID-19 patients of different age groups remain largely unknown. In this study, we analyzed the IgG/IgM responses to 21 SARS-CoV-2 proteins and 197 peptides that fully cover the spike protein against 731 sera collected from 731 COVID-19 patients aged from 1 to We show that there is no overall difference in SARS-CoV-2 antibody responses in COVID-19 patients in the 4 age groups. By antibody response landscape maps, we find that the IgG response profiles of SARS-CoV-2 proteins are positively correlated with age. The S protein linear epitope map shows that the immunogenicity of the S-protein peptides is related to peptide sequence, disease severity and age of the COVID-19 patients. Furthermore, the enrichment analysis indicates that low S1 IgG responses are enriched in patients aged <50 and high S1 IgG responses are enriched in mild COVID-19 patients aged >60. In addition, high responses of non-structural/accessory proteins are enriched in severe COVID-19 patients aged >70. These results suggest the distinct immune response of IgG/IgM to each SARS-CoV-2 protein in patients of different age, which may facilitate a deeper understanding of the immune responses in COVID-19 patients.
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74
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Mou L, Zhang Y, Feng Y, Hong H, Xia Y, Jiang X. Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. Anal Chem 2022; 94:2510-2516. [PMID: 35080377 PMCID: PMC8805706 DOI: 10.1021/acs.analchem.1c04383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/17/2022] [Indexed: 01/04/2023]
Abstract
Neutralization assays that can measure neutralizing antibodies in serum are vital for large-scale serodiagnosis and vaccine evaluation. Here, we establish multiplexed lab-on-a-chip bioassays for testing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Compared with enzyme-linked immunosorbent assay (ELISA), our method exhibits a low consumption of sample and reagents (10 μL), a low limit of detection (LOD: 0.08 ng/mL), a quick sample-to-answer time (about 70 min), and multiplexed ability (5 targets in each of 7 samples in one assay). We can also increase the throughput as needed. The concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants after two doses of vaccines are 6.6 ± 3.6, 8.7 ± 4.6, 3.4 ± 2.8, 3.8 ± 2.8, and 2.8 ± 2.3 ng/mL, respectively. This suggests that neutralizing activities against N501Y, E484K, and L452R/E484Q-mutants were less effective than RBD and D614G-mutant. We performed a plaque reduction neutralization test (PRNT) for all volunteers. Compared with PRNT, our assay is fast, accurate, inexpensive, and multiplexed with multiple-sample processing ability, which is good for large-scale serodiagnosis and vaccine evaluation.
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Affiliation(s)
- Lei Mou
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
- Department
of Biomedical Engineering, Southern University
of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Yingying Zhang
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
- Department
of Clinical Laboratory, Bao’an Authentic
TCM Therapy Hospital, No. 99, Laian Road, Baoan District, Shenzhen, Guangdong 518101, P. R. China
| | - Yao Feng
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
| | - Honghai Hong
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
| | - Yong Xia
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
| | - Xingyu Jiang
- Department
of Clinical Laboratory, Third Affiliated
Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
- Department
of Biomedical Engineering, Southern University
of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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75
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Wei N, Wang Q, Lin Z, Xu L, Zhang Z, Wang Y, Yang Z, Li L, Zhao T, Wang L, Lou H, Han M, Ma M, Jiang Y, Lu J, Zhu S, Cui L, Li S. Systematic profiling of antigen bias in humoral response against SARS-CoV-2. Virus Res 2022; 312:198711. [PMID: 35176329 PMCID: PMC8842411 DOI: 10.1016/j.virusres.2022.198711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Nana Wei
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Qiujing Wang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Zhibing Lin
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liyun Xu
- Cell and Molecular Biology Laboratory, Zhoushan Hospital, Wenzhou medical University, Zhoushan, 316021, China
| | - Zheen Zhang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Yan Wang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Zhejuan Yang
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Lue Li
- Department of Respiratory Medicine, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316021, China
| | - Tingxiao Zhao
- Department of Infectious Disease, Zhejiang University Zhoushan Hospital, Zhoushan, 316021, China
| | - Lu Wang
- Department of Infectious Disease, Zhejiang University Zhoushan Hospital, Zhoushan, 316021, China
| | - Haifei Lou
- Department of Hospital Infection Management, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Mingfang Han
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yaosheng Jiang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinmiao Lu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Shilan Zhu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Cui
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shibo Li
- Department of Infectious Disease, Zhoushan Hospital, Wenzhou Medical University, Zhoushan 316021, China.
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76
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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77
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.23.22269497. [PMID: 35118477 PMCID: PMC8811910 DOI: 10.1101/2022.01.23.22269497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 provokes a brisk T cell response. Peptide-based studies exclude antigen processing and presentation biology and may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DC to activate CD8 and CD4 T cells from convalescent persons. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the alpha, beta, gamma, and delta variant lineages.
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78
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Huang Y, Guo L, Chen J, Wu M, Zhang C, Liu Z, Li J, Li K, Xiong Z, Wu Q, Li Z, Luo K, Yuan W, Wu X. Serum Lactate Dehydrogenase Level as a Prognostic Factor for COVID-19: A Retrospective Study Based on a Large Sample Size. Front Med (Lausanne) 2022; 8:671667. [PMID: 35059407 PMCID: PMC8763698 DOI: 10.3389/fmed.2021.671667] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 11/29/2021] [Indexed: 01/08/2023] Open
Abstract
Background: In this study, we investigated the relationship between serum lactate dehydrogenase (LDH) level and disease progression and prognosis of patients with COVID-19. Methods: We retrospectively reviewed the information of 1,751 patients with COVID-19 from Leishenshan Hospital in Wuhan, China. Univariate and multivariate Cox regression analyses as well as Logistics regression analyses, and Kaplan-Meier curves were used to determine the association between LDH levels and the prognosis of COVID-19 patients. Results: LDH was an independent risk factor for in-hospital death no matter it was taken as classified variable and continuous variable (all P = 0.001) but not for severe or critical illness status. The Kaplan-Meier curves for LDH level showed that an elevated level of LDH was associated with in-hospital death. Conclusions: In patients with COVID-19, the increased LDH level is associated with a higher risk of negative clinical prognosis and higher mortality. This will provide a reference for clinicians and researchers to understand, diagnose, and treat patients with COVID-19. Further prospective studies with larger sample sizes are needed to verify these findings.
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Affiliation(s)
- Yihui Huang
- Department of Plastic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang Guo
- Department of Plastic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiwei Chen
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Meng Wu
- Department of Ultrasound, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chao Zhang
- Department of Cardiovascular Surgery, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zeming Liu
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinpeng Li
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kun Li
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhongwei Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qian Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kuan Luo
- Department of Neurosurgery, Wuhan Puren Hospital, Wuhan, China
| | - Weiwei Yuan
- Department of Plastic and Cosmetic Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Xiaohui Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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79
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Akter A, Ahmed T, Tauheed I, Akhtar M, Rahman SIA, Khaton F, Ahmmed F, Ferdous J, Afrad MH, Kawser Z, Hossain M, Khondaker R, Hasnat MA, Sumon MA, Rashed A, Ghosh S, Calderwood SB, Charles RC, Ryan ET, Khatri P, Maecker HT, Obermoser G, Pulendran B, Clemens JD, Banu S, Shirin T, LaRocque RC, Harris JB, Bhuiyan TR, Chowdhury F, Qadri F. Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka, Bangladesh. PLoS Negl Trop Dis 2022; 16:e0010102. [PMID: 34982773 PMCID: PMC8759637 DOI: 10.1371/journal.pntd.0010102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/14/2022] [Accepted: 12/17/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND COVID-19 caused by SARS-CoV-2 ranges from asymptomatic to severe disease and can cause fatal and devastating outcome in many cases. In this study, we have compared the clinical, biochemical and immunological parameters across the different disease spectrum of COVID-19 in Bangladeshi patients. METHODOLOGY/PRINCIPAL FINDINGS This longitudinal study was conducted in two COVID-19 hospitals and also around the community in Dhaka city in Bangladesh between November 2020 to March 2021. A total of 100 patients with COVID-19 infection were enrolled and classified into asymptomatic, mild, moderate and severe cases (n = 25/group). In addition, thirty age and sex matched healthy participants were enrolled and 21 were analyzed as controls based on exclusion criteria. After enrollment (study day1), follow-up visits were conducted on day 7, 14 and 28 for the cases. Older age, male gender and co-morbid conditions were the risk factors for severe COVID-19 disease. Those with moderate and severe cases of infection had low lymphocyte counts, high neutrophil counts along with a higher neutrophil-lymphocyte ratio (NLR) at enrollment; this decreased to normal range within 42 days after the onset of symptom. At enrollment, D-dimer, CRP and ferritin levels were elevated among moderate and severe cases. The mild, moderate, and severe cases were seropositive for IgG antibody by day 14 after enrollment. Moderate and severe cases showed significantly higher IgM and IgG levels of antibodies to SARS-CoV-2 compared to mild and asymptomatic cases. CONCLUSION/SIGNIFICANCE We report on the clinical, biochemical, and hematological parameters associated with the different severity of COVID-19 infection. We also show different profile of antibody response against SARS-CoV-2 in relation to disease severity, especially in those with moderate and severe disease manifestations compared to the mild and asymptomatic infection.
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Affiliation(s)
- Afroza Akter
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Tasnuva Ahmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Imam Tauheed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Marjahan Akhtar
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Sadia Isfat Ara Rahman
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Fatema Khaton
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Faisal Ahmmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Jannatul Ferdous
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Mokibul Hassan Afrad
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Zannat Kawser
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Mohabbat Hossain
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Rabeya Khondaker
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | | | | | - Asif Rashed
- Mugda Medical College & Hospital, Dhaka, Bangladesh
| | - Shuvro Ghosh
- Mugda Medical College & Hospital, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Purvesh Khatri
- Stanford University, Stanford, California, United States of America
| | | | | | - Bali Pulendran
- Stanford University, Stanford, California, United States of America
| | - John D. Clemens
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
- UCLA Fielding School of Public Health, Los Angeles, California, United States of America (JD Clemens MD)
- Korea University School of Medicine, Seoul, South Korea (JD Clemens MD)
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Taufiqur Rahman Bhuiyan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Fahima Chowdhury
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
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80
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Jiang HW, Tao SC. Quantitative plasma proteome profiling of COVID-19 patients with mild and moderate symptoms. EBioMedicine 2021; 75:103773. [PMID: 34959132 PMCID: PMC8702381 DOI: 10.1016/j.ebiom.2021.103773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/04/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- He-Wei Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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81
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Pulido J, García-Durán M, Fernández-Antonio R, Galán C, López L, Vela C, Venteo Á, Rueda P, Rivas LA. Receptor-binding domain-based immunoassays for serosurveillance differentiate efficiently between SARS-CoV2-exposed and non-exposed farmed mink. J Vet Diagn Invest 2021; 34:190-198. [PMID: 34852683 DOI: 10.1177/10406387211057859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
During the COVID-19 pandemic, infection of farmed mink has become not only an economic issue but also a widespread public health concern. International agencies have advised the use of strict molecular and serosurveillance methods for monitoring the SARS-CoV2 status on mink farms. We developed 2 ELISAs and a duplex protein microarray immunoassay (MI), all in a double-recognition format (DR), to detect SARS-CoV2 antibodies specific to the receptor-binding domain (RBD) of the spike protein and to the full-length nucleoprotein (N) in mink sera. We collected 264 mink serum samples and 126 oropharyngeal samples from 5 Spanish mink farms. In both of the ELISAs and the MI, RBD performed better than N protein for serologic differentiation of mink from SARS-CoV2-positive and -negative farms. Therefore, RBD was the optimal antigenic target for serosurveillance of mink farms.
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Affiliation(s)
- Jorge Pulido
- Departments of R&D, Eurofins-Ingenasa, Madrid, Spain
| | | | - Ricardo Fernández-Antonio
- Department of Animal Health, Galician Mink Breeders Association (AGAVI), Santiago de Compostela, Spain
| | - Carmen Galán
- Molecular Diagnostics, Eurofins-Ingenasa, Madrid, Spain
| | | | - Carmen Vela
- Departments of R&D, Eurofins-Ingenasa, Madrid, Spain
| | - Ángel Venteo
- Departments of R&D, Eurofins-Ingenasa, Madrid, Spain
| | - Paloma Rueda
- Departments of R&D, Eurofins-Ingenasa, Madrid, Spain
| | - Luis A Rivas
- Departments of R&D, Eurofins-Ingenasa, Madrid, Spain
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82
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To KKW, Sridhar S, Chiu KHY, Hung DLL, Li X, Hung IFN, Tam AR, Chung TWH, Chan JFW, Zhang AJX, Cheng VCC, Yuen KY. Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic. Emerg Microbes Infect 2021; 10:507-535. [PMID: 33666147 PMCID: PMC8006950 DOI: 10.1080/22221751.2021.1898291] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 02/06/2023]
Abstract
Without modern medical management and vaccines, the severity of the Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) might approach the magnitude of 1894-plague (12 million deaths) and 1918-A(H1N1) influenza (50 million deaths) pandemics. The COVID-19 pandemic was heralded by the 2003 SARS epidemic which led to the discovery of human and civet SARS-CoV-1, bat SARS-related-CoVs, Middle East respiratory syndrome (MERS)-related bat CoV HKU4 and HKU5, and other novel animal coronaviruses. The suspected animal-to-human jumping of 4 betacoronaviruses including the human coronaviruses OC43(1890), SARS-CoV-1(2003), MERS-CoV(2012), and SARS-CoV-2(2019) indicates their significant pandemic potential. The presence of a large reservoir of coronaviruses in bats and other wild mammals, culture of mixing and selling them in urban markets with suboptimal hygiene, habit of eating exotic mammals in highly populated areas, and the rapid and frequent air travels from these areas are perfect ingredients for brewing rapidly exploding epidemics. The possibility of emergence of a hypothetical SARS-CoV-3 or other novel viruses from animals or laboratories, and therefore needs for global preparedness should not be ignored. We reviewed representative publications on the epidemiology, virology, clinical manifestations, pathology, laboratory diagnostics, treatment, vaccination, and infection control of COVID-19 as of 20 January 2021, which is 1 year after person-to-person transmission of SARS-CoV-2 was announced. The difficulties of mass testing, labour-intensive contact tracing, importance of compliance to universal masking, low efficacy of antiviral treatment for severe disease, possibilities of vaccine or antiviral-resistant virus variants and SARS-CoV-2 becoming another common cold coronavirus are discussed.
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Affiliation(s)
- Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kelvin Hei-Yeung Chiu
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Derek Ling-Lung Hung
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Xin Li
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Anthony Raymond Tam
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Tom Wai-Hin Chung
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Anna Jian-Xia Zhang
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
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Kwiecińska-Piróg J, Przekwas J, Kraszewska Z, Sękowska A, Brodzka S, Wiktorczyk-Kapischke N, Grudlewska-Buda K, Wałecka-Zacharska E, Zacharski M, Mańkowska-Cyl A, Gospodarek-Komkowska E, Skowron K. The Differences in the Level of Anti-SARS-CoV-2 Antibodies after mRNA Vaccine between Convalescent and Non-Previously Infected People Disappear after the Second Dose-Study in Healthcare Workers Group in Poland. Vaccines (Basel) 2021; 9:1402. [PMID: 34960148 PMCID: PMC8707727 DOI: 10.3390/vaccines9121402] [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: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 01/08/2023] Open
Abstract
(1) Background: In many infections, antibodies play a crucial role in controlling infection. In COVID-19, the dynamics of the immune system response to SARS-CoV-2 is not fully understood. (2) Methods: The study was conducted on 120 healthcare workers from Dr. Antoni Jurasz University Hospital No. 1 in Bydgoszcz, between June and December 2020. In all participants, IgA and IgG antibody serum concentrations were measured using the semi-quantitative Anti-SARS-CoV-2 ELISA test (Euroimmun). After vaccination, in January and February 2021, antibody levels were examined using the quantitative IgG Anti-SARS-CoV-2 Quantivac ELISA test (Euroimmun). (3) Results: During the whole study period, the SARS-CoV-2 infection was confirmed in 29 (24.2%) participants. In all infected participants, IgA and IgG antibodies were detectable after infection by semi-quantitative serological tests. Levels of antibodies were higher one month after the first dose in the convalescents than in the non-previously infected participants. In this second group, the level of antibodies increased significantly after the second dose of vaccines compared to the first dose. (4) Conclusions: The level of antibodies after the first dose of vaccine in the convalescents' group is higher than in the SARS-CoV-2 non-infected group, but the differences disappear after the second vaccination.
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Affiliation(s)
- Joanna Kwiecińska-Piróg
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Jana Przekwas
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Zuzanna Kraszewska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Alicja Sękowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Sylwia Brodzka
- Department of Biotechnology, Faculty of Biological Science, University of Zielona Gora, 65-417 Zielona Gora, Poland;
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wroclaw University of Environmental and Life Sciences, 50-375 Wroclaw, Poland;
| | - Maciej Zacharski
- Department of Biochemistry and Molecular Biology, Wroclaw University of Environmental and Life Sciences, 50-375 Wrocaw, Poland;
| | - Aneta Mańkowska-Cyl
- Department of Laboratory Medicine, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland;
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (J.K.-P.); (J.P.); (Z.K.); (A.S.); (N.W.-K.); (K.G.-B.); (E.G.-K.)
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Bochnia-Bueno L, De Almeida SM, Raboni SM, Adamoski D, Amadeu LLM, Carstensen S, Nogueira MB. Dynamic of humoral response to SARS-CoV-2 anti-Nucleocapsid and Spike proteins after CoronaVac vaccination. Diagn Microbiol Infect Dis 2021; 102:115597. [PMID: 34902621 PMCID: PMC8603270 DOI: 10.1016/j.diagmicrobio.2021.115597] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 11/09/2022]
Abstract
This study aimed to calculate the seroconversion rate and IgG antibody dynamic range of the CoronaVac vaccine in healthcare workers (HCWs) after immunization. Serum samples from 133 HCWs from Southern Brazil were collected 1 day before (Day 0) and +10, +20, +40, + 60, +110 days after administering the vaccine's first dose. Immunoglobulin G (IgG) was quantified using immunoassays for anti-N-protein (nucleocapsid) antibodies (Abbott, Sligo, Ireland) and for anti-S1 (spike) protein antibodies (Euroimmun, Lübeck, Germany). Seroconversion by day 40 occurred in 129 (97%) HCWs for the S1 protein, and in 69 (51.87%) HCWs for the N protein. An absence of IgG antibodies (by both methodologies), occurred in 2 (1.5%) HCWs undergoing semiannual rituximab administration, and also in another 2 (1.5%) HCWs with no apparent reason. This study showed that CoronaVac has a high seroconversion rate when evaluated in an HCW population.
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Affiliation(s)
- Lucas Bochnia-Bueno
- Virology Laboratory, Federal University of Paraná, Curitiba, Paraná, Brazil; Post-Graduate Program in Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | - Sonia Mara Raboni
- Virology Laboratory, Federal University of Paraná, Curitiba, Paraná, Brazil; Post-Graduate Program in Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | | | - Suzana Carstensen
- Virology Laboratory, Federal University of Paraná, Curitiba, Paraná, Brazil
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85
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Xu Z, Li Y, Lei Q, Huang L, Lai DY, Guo SJ, Jiang HW, Hou H, Zheng YX, Wang XN, Wu J, Ma ML, Zhang B, Chen H, Yu C, Xue JB, Zhang HN, Qi H, Yu S, Lin M, Zhang Y, Lin X, Yao Z, Sheng H, Sun Z, Wang F, Fan X, Tao SC. COVID-ONE-hi: The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:669-678. [PMID: 34748989 PMCID: PMC8570443 DOI: 10.1016/j.gpb.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/26/2021] [Accepted: 10/11/2021] [Indexed: 12/29/2022]
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, varies with regard to symptoms and mortality rates among populations. Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19. However, differences in immune responses and clinical features among COVID-19 patients remain largely unknown. Here, we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters (named COVID-ONE-hi). COVID-ONE-hi is based on the data that contain the IgG/IgM responses to 24 full-length/truncated proteins corresponding to 20 of 28 known SARS-CoV-2 proteins and 199 spike protein peptides against 2360 serum samples collected from 783 COVID-19 patients. In addition, 96 clinical parameters for the 2360 serum samples and basic information for the 783 patients are integrated into the database. Furthermore, COVID-ONE-hi provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups. A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters. After the “START” button is clicked, one can readily obtain a comprehensive analysis report for further interpretation. COVID-ONE-hi is freely available at www.COVID-ONE.cn.
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Affiliation(s)
- Zhaowei Xu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Likun Huang
- Fujian Key Laboratory of Crop Breeding by Design, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350028, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongyan Hou
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaoxiang Wu
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ming-Liang Ma
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhang
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Caizheng Yu
- Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Siqi Yu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Mingxi Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Yandi Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaosong Lin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zongjie Yao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huiming Sheng
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ziyong Sun
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Feng Wang
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xionglin Fan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.
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86
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Lei Q, Yu CZ, Li Y, Hou HY, Xu ZW, Yao ZJ, Zhang YD, Lai DY, Ndzouboukou JLB, Zhang B, Chen H, Ouyang ZQ, Xue JB, Lin XS, Zheng YX, Wang XN, Jiang HW, Zhang HN, Qi H, Guo SJ, He MA, Sun ZY, Wang F, Tao SC, Fan XL. Anti-SARS-CoV-2 IgG responses are powerful predicting signatures for the outcome of COVID-19 patients. J Adv Res 2021; 36:133-145. [PMID: 35116173 PMCID: PMC8641215 DOI: 10.1016/j.jare.2021.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/10/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Qing Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cai-zheng Yu
- Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-yan Hou
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao-wei Xu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zong-jie Yao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan-di Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan-yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jo-Lewis Banga Ndzouboukou
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Zhang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhu-qing Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun-biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao-song Lin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun-xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mei-an He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental and Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-yong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Corresponding authors at: No.13, Hangkong Rd., Wuhan 430030, China (X. Fan).
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- Corresponding authors at: No.13, Hangkong Rd., Wuhan 430030, China (X. Fan).
| | - Xiong-lin Fan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Corresponding authors at: No.13, Hangkong Rd., Wuhan 430030, China (X. Fan).
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87
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Tan HW, Xu YM, Lau ATY. Human bronchial-pulmonary proteomics in coronavirus disease 2019 (COVID-19) pandemic: applications and implications. Expert Rev Proteomics 2021; 18:925-938. [PMID: 34812694 DOI: 10.1080/14789450.2021.2010549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The outbreak of the newly discovered human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has disrupted the normal life of almost every civilization worldwide. Studies have shown that the coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 can affect multiple human organs and physiological systems, but the respiratory system remains the primary location for viral infection. AREAS COVERED We summarize how omics technologies are used in SARS-CoV-2 research and specifically review the current knowledge of COVID-19 from the aspect of human bronchial-pulmonary proteomics. Also, knowledge gaps in COVID-19 that can be fulfilled by proteomics are discussed. EXPERT OPINION Overall, human bronchial-pulmonary proteomics plays an important role in revealing the dynamics, functions, tropism, and pathogenicity of SARS-CoV-2, which is crucial for COVID-19 biomarker and therapeutic target discoveries. To more fully understand the impact of COVID-19, research from various angles using multi-omics approaches should also be conducted on the lungs as well as other organs.
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Affiliation(s)
- Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, People's Republic of China
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88
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Nasrollahi F, Haghniaz R, Hosseini V, Davoodi E, Mahmoodi M, Karamikamkar S, Darabi MA, Zhu Y, Lee J, Diltemiz SE, Montazerian H, Sangabathuni S, Tavafoghi M, Jucaud V, Sun W, Kim H, Ahadian S, Khademhosseini A. Micro and Nanoscale Technologies for Diagnosis of Viral Infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100692. [PMID: 34310048 PMCID: PMC8420309 DOI: 10.1002/smll.202100692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.
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Affiliation(s)
- Fatemeh Nasrollahi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Elham Davoodi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Mechanical and Mechatronics EngineeringUniversity of WaterlooWaterlooONN2L 3G1Canada
| | - Mahboobeh Mahmoodi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Biomedical EngineeringYazd BranchIslamic Azad UniversityYazd8915813135Iran
| | | | - Mohammad Ali Darabi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Junmin Lee
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Sibel Emir Diltemiz
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of ChemistryFaculty of ScienceEskisehir Technical UniversityEskisehir26470Turkey
| | - Hossein Montazerian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | | | - Maryam Tavafoghi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Wujin Sun
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Han‐Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
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89
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Quantification of anti-SARS-CoV-2 antibodies in human serum with LC-QTOF-MS. J Pharm Biomed Anal 2021; 205:114319. [PMID: 34416552 PMCID: PMC8354797 DOI: 10.1016/j.jpba.2021.114319] [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: 03/16/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022]
Abstract
The aim of this study was to develop the first quantitative serological test for anti-SARS-CoV-2 antibodies in human serum with liquid chromatography - quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). Other assays, mostly immunoassays, are only qualitative or semi-quantitative, and hence, actual antibody concentrations after SARS-CoV-2 infection are unknown. In our assay, anti-SARS-CoV-2 antibodies were isolated with spike protein subunit 1 (S1) coupled to magnetic beads. IgG1 signature peptide GPSVFPLAPSSK was selected for quantification using ipilimumab calibration standards and SILuMAb K1 as the stable-isotope labeled internal standard. The anti-SARS-CoV-2 IgG1 calibration range was from 1.35 to 135 nM. Inter-assay accuracies were between 98.8%− 107% with inter-assay precisions between 8.37%− 13.5% measured at 3 concentration levels on three separate occasions. Anti-SARS-CoV-2 IgG1 antibodies were quantified in PCR-positive patients with mild to severe symptoms. IgM signature peptide DGFFGVPR was detected in patients that recently recovered from COVID-19. A unique and quantitative LC-QTOF-MS method to quantify anti-SARS-CoV-2 IgG1 in serum was successfully developed and its clinical applicability has been demonstrated.
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90
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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91
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Saied EM, El-Maradny YA, Osman AA, Darwish AMG, Abo Nahas HH, Niedbała G, Piekutowska M, Abdel-Rahman MA, Balbool BA, Abdel-Azeem AM. A Comprehensive Review about the Molecular Structure of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Insights into Natural Products against COVID-19. Pharmaceutics 2021; 13:1759. [PMID: 34834174 PMCID: PMC8624722 DOI: 10.3390/pharmaceutics13111759] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
In 2019, the world suffered from the emergence of COVID-19 infection, one of the most difficult pandemics in recent history. Millions of confirmed deaths from this pandemic have been reported worldwide. This disaster was caused by SARS-CoV-2, which is the last discovered member of the family of Coronaviridae. Various studies have shown that natural compounds have effective antiviral properties against coronaviruses by inhibiting multiple viral targets, including spike proteins and viral enzymes. This review presents the classification and a detailed explanation of the SARS-CoV-2 molecular characteristics and structure-function relationships. We present all currently available crystal structures of different SARS-CoV-2 proteins and emphasized on the crystal structure of different virus proteins and the binding modes of their ligands. This review also discusses the various therapeutic approaches for COVID-19 treatment and available vaccinations. In addition, we highlight and compare the existing data about natural compounds extracted from algae, fungi, plants, and scorpion venom that were used as antiviral agents against SARS-CoV-2 infection. Moreover, we discuss the repurposing of select approved therapeutic agents that have been used in the treatment of other viruses.
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Affiliation(s)
- Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Yousra A. El-Maradny
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria 21526, Egypt;
| | - Alaa A. Osman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo 12256, Egypt;
| | - Amira M. G. Darwish
- Food Technology Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA City), Alexandria 21934, Egypt;
| | - Hebatallah H. Abo Nahas
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Partyzantów 27, 76-200 Słupsk, Poland;
| | - Mohamed A. Abdel-Rahman
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Bassem A. Balbool
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 12585, Egypt;
| | - Ahmed M. Abdel-Azeem
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
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92
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Antonini MJ, Sahasrabudhe A, Tabet A, Schwalm M, Rosenfeld D, Garwood I, Park J, Loke G, Khudiyev T, Kanik M, Corbin N, Canales A, Jasanoff AP, Fink Y, Anikeeva P. Customizing MRI-Compatible Multifunctional Neural Interfaces through Fiber Drawing. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2104857. [PMID: 34924913 PMCID: PMC8673858 DOI: 10.1002/adfm.202104857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Indexed: 05/11/2023]
Abstract
Fiber drawing enables scalable fabrication of multifunctional flexible fibers that integrate electrical, optical and microfluidic modalities to record and modulate neural activity. Constraints on thermomechanical properties of materials, however, have prevented integrated drawing of metal electrodes with low-loss polymer waveguides for concurrent electrical recording and optical neuromodulation. Here we introduce two fabrication approaches: (1) an iterative thermal drawing with a soft, low melting temperature (Tm) metal indium, and (2) a metal convergence drawing with traditionally non-drawable high Tm metal tungsten. Both approaches deliver multifunctional flexible neural interfaces with low-impedance metallic electrodes and low-loss waveguides, capable of recording optically-evoked and spontaneous neural activity in mice over several weeks. We couple these fibers with a light-weight mechanical microdrive (1g) that enables depth-specific interrogation of neural circuits in mice following chronic implantation. Finally, we demonstrate the compatibility of these fibers with magnetic resonance imaging (MRI) and apply them to visualize the delivery of chemical payloads through the integrated channels in real time. Together, these advances expand the domains of application of the fiber-based neural probes in neuroscience and neuroengineering.
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Affiliation(s)
- Marc-Joseph Antonini
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard/MIT Health Science & Technology Graduate Program, Cambridge, MA, 02139, USA
| | - Atharva Sahasrabudhe
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Anthony Tabet
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Miriam Schwalm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dekel Rosenfeld
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Indie Garwood
- Harvard/MIT Health Science & Technology Graduate Program, Cambridge, MA, 02139, USA
| | - Jimin Park
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gabriel Loke
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tural Khudiyev
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mehmet Kanik
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Kinetik Therapeutics LLC, Newton, MA, 02459, USA
| | - Nathan Corbin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Alan P. Jasanoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Nuclear Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yoel Fink
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Advanced Functional Fabrics of America, Cambridge, MA, 02139 USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - Polina Anikeeva
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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93
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SARS-CoV-2 immune repertoire in MIS-C and pediatric COVID-19. Nat Immunol 2021; 22:1452-1464. [PMID: 34611361 DOI: 10.1038/s41590-021-01051-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/14/2021] [Indexed: 01/22/2023]
Abstract
There is limited understanding of the viral antibody fingerprint following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children. Herein, SARS-CoV-2 proteome-wide immunoprofiling of children with mild/moderate or severe coronavirus disease 2019 (COVID-19) versus multisystem inflammatory syndrome in children versus hospitalized control patients revealed differential cytokine responses, IgM/IgG/IgA epitope diversity, antibody binding and avidity. Apart from spike and nucleocapsid, IgG/IgA recognized epitopes in nonstructural protein (NSP) 2, NSP3, NSP12-NSP14 and open reading frame (ORF) 3a-ORF9. Peptides representing epitopes in NSP12, ORF3a and ORF8 demonstrated SARS-CoV-2 serodiagnosis. Antibody-binding kinetics with 24 SARS-CoV-2 proteins revealed antibody parameters that distinguish children with mild/moderate versus severe COVID-19 or multisystem inflammatory syndrome in children. Antibody avidity to prefusion spike correlated with decreased illness severity and served as a clinical disease indicator. The fusion peptide and heptad repeat 2 region induced SARS-CoV-2-neutralizing antibodies in rabbits. Thus, we identified SARS-CoV-2 antibody signatures in children associated with disease severity and delineate promising serodiagnostic and virus neutralization targets. These findings might guide the design of serodiagnostic assays, prognostic algorithms, therapeutics and vaccines in this important but understudied population.
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94
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Hachim A, Kavian N, Valkenburg SA. Antibody landscapes of SARS-CoV-2 can reveal novel vaccine and diagnostic targets. Curr Opin Virol 2021; 50:139-146. [PMID: 34464844 PMCID: PMC8376662 DOI: 10.1016/j.coviro.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 virions are composed of structural proteins, but during virus infection, an additional 30 proteins could be expressed according to putative open reading frames (ORFs) of the viral genome. Some of these additional proteins modulate cellular processes through direct interactions, their truncations can affect disease pathogenesis and they can also serve as antigenic targets for more specific serology. In addition to structural proteins, the ORF1a/b polyprotein and accessory proteins can stimulate antibody responses during infection. Antibodies that target non-structural proteins can impact viral infection, through Fc mediated effector functions, through interactions during virus entry, fusion, replication and egress within infected cells. Characterization of the serological responses to additional proteins, provides a snapshot of the 'antibody landscape', which includes the antibody magnitude, antigenic specificity and informs the biological relevance of SARS-CoV-2 proteins.
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Affiliation(s)
- Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China,Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d’Immunologie Biologique, Paris, France,Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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95
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Sinha K, Som Chaudhury S, Sharma P, Ruidas B. COVID-19 rhapsody: Rage towards advanced diagnostics and therapeutic strategy. J Pharm Anal 2021; 11:529-540. [PMID: 34178413 PMCID: PMC8214321 DOI: 10.1016/j.jpha.2021.06.004] [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: 12/21/2020] [Revised: 05/29/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The deadly global outbreak of coronavirus disease-2019 (COVID-19) has forged an unrivaled threat to human civilization. Contemplating its profuse impact, initial risk management and therapies are needed, as well as rapid detection strategies alongside treatments with existing drugs or traditional treatments to provide better clinical support for critical patients. Conventional detection techniques have been considered but do not sufficiently meet the current challenges of effective COVID-19 diagnosis. Therefore, several modern techniques including point-of-care diagnosis with a biosensor, clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins that function as nuclease (Cas) technology, next-generation sequencing, serological, digital, and imaging approaches have delivered improved and noteworthy success compared to that using traditional strategies. Conventional drug treatment, plasma therapy, and vaccine development are also ongoing. However, alternative medicines including Ayurveda, herbal drugs, homeopathy, and Unani have also been enlisted as prominent treatment strategies for developing herd immunity and physical defenses against COVID-19. All considered, this review can help develop rapid and simplified diagnostic strategies, as well as advanced evidence-based modern therapeutic approaches that will aid in combating the global pandemic.
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Affiliation(s)
- Koel Sinha
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science Technology, Shibpur, Howrah, 711103, India
| | - Sutapa Som Chaudhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science Technology, Shibpur, Howrah, 711103, India
| | - Pramita Sharma
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science Technology, Shibpur, Howrah, 711103, India
- Department of Zoology, Hooghly Mohsin College Affiliated to University of Burdwan, Hooghly, 712101, India
| | - Bhuban Ruidas
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science Technology, Shibpur, Howrah, 711103, India
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96
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Zhou Y, Chen Y, Liu W, Fang H, Li X, Hou L, Liu Y, Lai W, Huang X, Xiong Y. Development of a rapid and sensitive quantum dot nanobead-based double-antigen sandwich lateral flow immunoassay and its clinical performance for the detection of SARS-CoV-2 total antibodies. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 343:130139. [PMID: 34035562 DOI: 10.1016/j.snb.2021.130169] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 05/28/2023]
Abstract
Owing to the over-increasing demands in resisting and managing the coronavirus disease 2019 (COVID-19) pandemic, development of rapid, highly sensitive, accurate, and versatile tools for monitoring total antibody concentrations at the population level has been evolved as an urgent challenge on measuring the fatality rate, tracking the changes in incidence and prevalence, comprehending medical sequelae after recovery, as well as characterizing seroprevalence and vaccine coverage. To this end, herein we prepared highly luminescent quantum dot nanobeads (QBs) by embedding numerous quantum dots into polymer matrix, and then applied it as a signal-amplification label in lateral flow immunoassay (LFIA). After covalently linkage with the expressed recombinant SARS-CoV-2 spike protein (RSSP), the synthesized QBs were used to determine the total antibody levels in sera by virtue of a double-antigen sandwich immunoassay. Under the developed condition, the QB-LFIA can allow the rapid detection of SARS-CoV-2 total antibodies within 15 min with about one order of magnitude improvement in analytical sensitivity compared to conventional gold nanoparticle-based LFIA. In addition, the developed QB-LFIA performed well in clinical study in dynamic monitoring of serum antibody levels in the whole course of SARS-CoV-2 infection. In conclusion, we successfully developed a promising fluorescent immunological sensing tool for characterizing the host immune response to SARS-CoV-2 infection and confirming the acquired immunity to COVID-19 by evaluating the SRAS-CoV-2 total antibody level in the crowd.
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Affiliation(s)
- Yaofeng Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Yuan Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi YeLi Medical Device Co., Ltd, Nanchang 330096, PR China
| | - Wenjuan Liu
- Jiangxi Weibang Biological Technology Co. Ltd, Nanchang 330096, PR China
| | - Hao Fang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Xiangmin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, PR China
| | - Li Hou
- Jiangxi YeLi Medical Device Co., Ltd, Nanchang 330096, PR China
| | - Yuanjie Liu
- College of Information and Electrical Engineering, China Agricultural University, Haidian, Beijing 100083, PR China
| | - Weihua Lai
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, PR China
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97
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Zhou Y, Chen Y, Liu W, Fang H, Li X, Hou L, Liu Y, Lai W, Huang X, Xiong Y. Development of a rapid and sensitive quantum dot nanobead-based double-antigen sandwich lateral flow immunoassay and its clinical performance for the detection of SARS-CoV-2 total antibodies. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 343:130139. [PMID: 34035562 PMCID: PMC8137357 DOI: 10.1016/j.snb.2021.130139] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 05/18/2023]
Abstract
Owing to the over-increasing demands in resisting and managing the coronavirus disease 2019 (COVID-19) pandemic, development of rapid, highly sensitive, accurate, and versatile tools for monitoring total antibody concentrations at the population level has been evolved as an urgent challenge on measuring the fatality rate, tracking the changes in incidence and prevalence, comprehending medical sequelae after recovery, as well as characterizing seroprevalence and vaccine coverage. To this end, herein we prepared highly luminescent quantum dot nanobeads (QBs) by embedding numerous quantum dots into polymer matrix, and then applied it as a signal-amplification label in lateral flow immunoassay (LFIA). After covalently linkage with the expressed recombinant SARS-CoV-2 spike protein (RSSP), the synthesized QBs were used to determine the total antibody levels in sera by virtue of a double-antigen sandwich immunoassay. Under the developed condition, the QB-LFIA can allow the rapid detection of SARS-CoV-2 total antibodies within 15 min with about one order of magnitude improvement in analytical sensitivity compared to conventional gold nanoparticle-based LFIA. In addition, the developed QB-LFIA performed well in clinical study in dynamic monitoring of serum antibody levels in the whole course of SARS-CoV-2 infection. In conclusion, we successfully developed a promising fluorescent immunological sensing tool for characterizing the host immune response to SARS-CoV-2 infection and confirming the acquired immunity to COVID-19 by evaluating the SRAS-CoV-2 total antibody level in the crowd.
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Affiliation(s)
- Yaofeng Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Yuan Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi YeLi Medical Device Co., Ltd, Nanchang 330096, PR China
| | - Wenjuan Liu
- Jiangxi Weibang Biological Technology Co. Ltd, Nanchang 330096, PR China
| | - Hao Fang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Xiangmin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, PR China
| | - Li Hou
- Jiangxi YeLi Medical Device Co., Ltd, Nanchang 330096, PR China
| | - Yuanjie Liu
- College of Information and Electrical Engineering, China Agricultural University, Haidian, Beijing 100083, PR China
| | - Weihua Lai
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, PR China
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98
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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99
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Lv H, Tsang OT, So RTY, Wang Y, Yuan M, Liu H, Yip GK, Teo QW, Lin Y, Liang W, Wang J, Ng WW, Wilson IA, Peiris JSM, Wu NC, Mok CKP. Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2 in humans and mice. Eur J Immunol 2021; 51:2296-2305. [PMID: 34089541 PMCID: PMC8237060 DOI: 10.1002/eji.202149234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/14/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022]
Abstract
The increasing numbers of infected cases of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses serious threats to public health and the global economy. Most SARS-CoV-2 neutralizing antibodies target the receptor binding domain (RBD) and some the N-terminal domain (NTD) of the spike protein, which is the major antigen of SARS-CoV-2. While the antibody response to RBD has been extensively characterized, the antigenicity and immunogenicity of the NTD protein are less well studied. Using 227 plasma samples from COVID-19 patients, we showed that SARS-CoV-2 NTD-specific antibodies could be induced during infection. As compared to the results of SARS-CoV-2 RBD, the serological response of SARS-CoV-2 NTD is less cross-reactive with SARS-CoV, a pandemic strain that was identified in 2003. Furthermore, neutralizing antibodies are rarely elicited in a mice model when NTD is used as an immunogen. We subsequently demonstrate that NTD has an altered antigenicity when expressed alone. Overall, our results suggest that while NTD offers a supplementary strategy for serology testing, it may not be suitable as an immunogen for vaccine development.
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Affiliation(s)
- Huibin Lv
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Owen Tak‐Yin Tsang
- Infectious Diseases Centre, Princess Margaret HospitalHospital Authority of Hong Kong
| | - Ray T. Y. So
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Yiquan Wang
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Meng Yuan
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Hejun Liu
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Garrick K. Yip
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Qi Wen Teo
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Yihan Lin
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Weiwen Liang
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Jinlin Wang
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Wilson W. Ng
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Ian A. Wilson
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - J. S. Malik Peiris
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
| | - Nicholas C. Wu
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Biophysics and Quantitative BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Chris K. P. Mok
- HKU‐Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- Li Ka Shing Institute of Health SciencesFaculty of MedicineThe Chinese University of Hong KongShatinHong Kong SARChina
- The Jockey Club School of Public Health and Primary CareThe Chinese University of Hong KongHong KongSARChina
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100
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Zheng YX, Wang L, Kong WS, Chen H, Wang XN, Meng Q, Zhang HN, Guo SJ, Jiang HW, Tao SC. Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1134-1141. [PMID: 34159380 DOI: 10.1093/abbs/gmab088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health threat since December 2019, and there is still no highly effective drug to control the pandemic. To facilitate drug target identification for drug development, studies on molecular mechanisms, such as SARS-CoV-2 protein interactions, are urgently needed. In this study, we focused on Nsp2, a non-structural protein with largely unknown function and mechanism. The interactome of Nsp2 was revealed through the combination of affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), and 84 proteins of high-confidence were identified. Gene ontology analysis demonstrated that Nsp2-interacting proteins are involved in several biological processes such as endosome transport and translation. Network analysis generated two clusters, including ribosome assembly and vesicular transport. Bio-layer interferometry (BLI) assay confirmed the bindings between Nsp2- and 4-interacting proteins, i.e. STAU2 (Staufen2), HNRNPLL, ATP6V1B2, and RAP1GDS1 (SmgGDS), which were randomly selected from the list of 84 proteins. Our findings provide insights into the Nsp2-host interplay and indicate that Nsp2 may play important roles in SARS-CoV-2 infection and serve as a potential drug target for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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