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Lopez Quezada L, Mba Medie F, Luu RJ, Gaibler RB, Gabriel EP, Rubio LD, Mulhern TJ, Marr EE, Borenstein JT, Fisher CR, Gard AL. Predicting Clinical Outcomes of SARS-CoV-2 Drug Efficacy with a High-Throughput Human Airway Microphysiological System. Adv Biol (Weinh) 2024:e2300511. [PMID: 39123296 DOI: 10.1002/adbi.202300511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/23/2023] [Indexed: 08/12/2024]
Abstract
The average cost to bring a new drug from its initial discovery to a patient's bedside is estimated to surpass $2 billion and requires over a decade of research and development. There is a need for new drug screening technologies that can parse drug candidates with increased likelihood of clinical utility early in development in order to increase the cost-effectiveness of this pipeline. For example, during the COVID-19 pandemic, resources were rapidly mobilized to identify effective therapeutic treatments but many lead antiviral compounds failed to demonstrate efficacy when progressed to human trials. To address the lack of predictive preclinical drug screening tools, PREDICT96-ALI, a high-throughput (n = 96) microphysiological system (MPS) that recapitulates primary human tracheobronchial tissue,is adapted for the evaluation of differential antiviral efficacy of native SARS-CoV-2 variants of concern. Here, PREDICT96-ALI resolves both the differential viral kinetics between variants and the efficacy of antiviral compounds over a range of drug doses. PREDICT96-ALI is able to distinguish clinically efficacious antiviral therapies like remdesivir and nirmatrelvir from promising lead compounds that do not show clinical efficacy. Importantly, results from this proof-of-concept study track with known clinical outcomes, demonstrate the feasibility of this technology as a prognostic drug discovery tool.
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Affiliation(s)
| | | | - Rebeccah J Luu
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | | | | | - Logan D Rubio
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | | | | | | | | | - Ashley L Gard
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
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2
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Loveday EK, Welhaven H, Erdogan AE, Hain K, Chang CB, June RK, Taylor MP. Starve a cold or feed a fever? Identifying cellular metabolic changes following infection and exposure to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595410. [PMID: 38826440 PMCID: PMC11142155 DOI: 10.1101/2024.05.22.595410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Viral infections induce major shifts in cellular metabolism elicited by active viral replication and antiviral responses. For the virus, harnessing cellular metabolism and evading changes that limit replication are essential for productive viral replication. In contrast, the cellular response to infection disrupts metabolic pathways to prevent viral replication and promote an antiviral state in the host cell and neighboring bystander cells. This competition between the virus and cell results in measurable shifts in cellular metabolism that differ depending on the virus, cell type, and extracellular environment. The resulting metabolic shifts can be observed and analyzed using global metabolic profiling techniques to identify pathways that are critical for either viral replication or cellular defense. SARS-CoV-2 is a respiratory virus that can exhibit broad tissue tropism and diverse, yet inconsistent, symptomatology. While the factors that determine the presentation and severity of SARS-CoV-2 infection remain unclear, metabolic syndromes are associated with more severe manifestations of SARS-CoV-2 disease. Despite these observations a critical knowledge gap remains between cellular metabolic responses and SARS-CoV-2 infection. Using a well-established untargeted metabolomics analysis workflow, we compared SARS-CoV-2 infection of human lung carcinoma cells. We identified significant changes in metabolic pathways that correlate with either productive or non-productive viral infection. This information is critical for characterizing the factors that contribute to SARS-CoV-2 replication that could be targeted for therapeutic interventions to limit viral disease.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman MT 59717
- Department of Chemical and Biological Engineering, Montana State University, Bozeman MT 59717
| | - Hope Welhaven
- Chemistry and Biochemistry, Montana State University, Bozeman MT 59717
| | - Ayten Ebru Erdogan
- Department of Chemical and Biological Engineering, Montana State University, Bozeman MT 59717
| | - Kyle Hain
- Microbiology and Cell Biology, Montana State University, Bozeman MT 59717
| | - Connie B. Chang
- Center for Biofilm Engineering, Montana State University, Bozeman MT 59717
- Department of Chemical and Biological Engineering, Montana State University, Bozeman MT 59717
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905
| | - Ronald K. June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman MT 59717
| | - Matthew P. Taylor
- Microbiology and Cell Biology, Montana State University, Bozeman MT 59717
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3
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Bang LL, Tornby DR, Pham STD, Assing K, Möller S, Palarasah Y, Madsen LW, Thomsen KG, Johansen IS, Pedersen RM, Andersen TE. Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load. J Virol Methods 2024; 326:114912. [PMID: 38447645 DOI: 10.1016/j.jviromet.2024.114912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.
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Affiliation(s)
- Line L Bang
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ditte R Tornby
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Stephanie T D Pham
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Kristian Assing
- Department of Clinical Immunology, Odense University Hospital and Research Unit for Clinical Immunology, University of Southern Denmark, Odense, Denmark
| | - Sören Möller
- Open Patient Data Explorative Network (OPEN), Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense 5000, Denmark
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Lone W Madsen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark; Department of Regional Health Research, University of Southern Denmark, Denmark; Unit for Infectious Diseases, Department of medicine, Sygehus Lillebælt, Kolding, Denmark
| | - Karina G Thomsen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Rune M Pedersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas E Andersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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4
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Azevedo PHRDA, Camargo PG, Constant LEC, Costa SDS, Silva CS, Rosa AS, Souza DDC, Tucci AR, Ferreira VNS, Oliveira TKF, Borba NRR, Rodrigues CR, Albuquerque MG, Dias LRS, Garrett R, Miranda MD, Allonso D, Lima CHDS, Muri EMF. Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV‑2 Mpro). Sci Rep 2024; 14:8991. [PMID: 38637583 PMCID: PMC11026380 DOI: 10.1038/s41598-024-59442-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
COVID-19 is a multisystemic disease caused by the SARS-CoV-2 airborne virus, a member of the Coronaviridae family. It has a positive sense single-stranded RNA genome and encodes two non-structural proteins through viral cysteine-proteases processing. Blocking this step is crucial to control virus replication. In this work, we reported the synthesis of 23 statine-based peptidomimetics to determine their ability to inhibit the main protease (Mpro) activity of SARS-CoV-2. Among the 23 peptidomimetics, 15 compounds effectively inhibited Mpro activity by 50% or more, while three compounds (7d, 8e, and 9g) exhibited maximum inhibition above 70% and IC50 < 1 µM. Compounds 7d, 8e, and 9g inhibited roughly 80% of SARS-CoV-2 replication and proved no cytotoxicity. Molecular docking simulations show putative hydrogen bond and hydrophobic interactions between specific amino acids and these inhibitors. Molecular dynamics simulations further confirmed the stability and persisting interactions in Mpro's subsites, exhibiting favorable free energy binding (ΔGbind) values. These findings suggest the statine-based peptidomimetics as potential therapeutic agents against SARS-CoV-2 by targeting Mpro.
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Affiliation(s)
- Pedro Henrique R de A Azevedo
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Priscila G Camargo
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Larissa E C Constant
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Stephany da S Costa
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Celimar Sinézia Silva
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Alice S Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Daniel D C Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Amanda R Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Vivian N S Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Thamara Kelcya F Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Nathalia R R Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Carlos R Rodrigues
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Magaly G Albuquerque
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Luiza R S Dias
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Rafael Garrett
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Milene D Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Diego Allonso
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Camilo Henrique da S Lima
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil.
| | - Estela Maris F Muri
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil.
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5
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Nunberg JH, Westover JB, York J, Jung KH, Bailey KW, Boardman KM, Li M, Furnell RS, Wasson SR, Murray JS, Kaundal R, Thomas AJ, Gowen BB. Restoration of virulence in the attenuated Candid#1 vaccine virus requires reversion at both positions 168 and 427 in the envelope glycoprotein GPC. J Virol 2024; 98:e0011224. [PMID: 38506509 PMCID: PMC11019782 DOI: 10.1128/jvi.00112-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
Live-attenuated virus vaccines provide long-lived protection against viral disease but carry inherent risks of residual pathogenicity and genetic reversion. The live-attenuated Candid#1 vaccine was developed to protect Argentines against lethal infection by the Argentine hemorrhagic fever arenavirus, Junín virus. Despite its safety and efficacy in Phase III clinical study, the vaccine is not licensed in the US, in part due to concerns regarding the genetic stability of attenuation. Previous studies had identified a single F427I mutation in the transmembrane domain of the Candid#1 envelope glycoprotein GPC as the key determinant of attenuation, as well as the propensity of this mutation to revert upon passage in cell culture and neonatal mice. To ascertain the consequences of this reversion event, we introduced the I427F mutation into recombinant Candid#1 (I427F rCan) and investigated the effects in two validated small-animal models: in mice expressing the essential virus receptor (human transferrin receptor 1; huTfR1) and in the conventional guinea pig model. We report that I427F rCan displays only modest virulence in huTfR1 mice and appears attenuated in guinea pigs. Reversion at another attenuating locus in Candid#1 GPC (T168A) was also examined, and a similar pattern was observed. By contrast, virus bearing both revertant mutations (A168T+I427F rCan) approached the lethal virulence of the pathogenic Romero strain in huTfR1 mice. Virulence was less extreme in guinea pigs. Our findings suggest that genetic stabilization at both positions is required to minimize the likelihood of reversion to virulence in a second-generation Candid#1 vaccine.IMPORTANCELive-attenuated virus vaccines, such as measles/mumps/rubella and oral poliovirus, provide robust protection against disease but carry with them the risk of genetic reversion to the virulent form. Here, we analyze the genetics of reversion in the live-attenuated Candid#1 vaccine that is used to protect against Argentine hemorrhagic fever, an often-lethal disease caused by the Junín arenavirus. In two validated small-animal models, we find that restoration of virulence in recombinant Candid#1 viruses requires back-mutation at two positions specific to the Candid#1 envelope glycoprotein GPC, at positions 168 and 427. Viruses bearing only a single change showed only modest virulence. We discuss strategies to genetically harden Candid#1 GPC against these two reversion events in order to develop a safer second-generation Candid#1 vaccine virus.
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Affiliation(s)
- Jack H. Nunberg
- Montana Biotechnology Center, University of Montana, Missoula, Montana, USA
| | - Jonna B. Westover
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Joanne York
- Montana Biotechnology Center, University of Montana, Missoula, Montana, USA
| | - Kie Hoon Jung
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Kevin W. Bailey
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Kirsten M. Boardman
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Minghao Li
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Rachel S. Furnell
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Samantha R. Wasson
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Justin S. Murray
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, Utah State University, Logan, Utah, USA
- Center for Integrated BioSystems, Utah State University, Logan, Utah, USA
| | - Aaron J. Thomas
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Center for Integrated BioSystems, Utah State University, Logan, Utah, USA
| | - Brian B. Gowen
- Department of Animal Dairy and Veterinary Sciences, Utah State University, Logan, Utah, USA
- Institute for Antiviral Research, Utah State University, Logan, Utah, USA
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6
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Rokni M, Rohani Bastami T, Meshkat Z, Reza Rahimi H, Zibaee S, Meshkat M, Fotouhi F, Serki E, Khoshakhlagh M, Dabirifar Z. Rapid and sensitive detection of SARS-CoV-2 virus in human saliva samples using glycan based nanozyme: a clinical study. Mikrochim Acta 2023; 191:36. [PMID: 38108890 DOI: 10.1007/s00604-023-06120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/25/2023] [Indexed: 12/19/2023]
Abstract
A highly sensitive colorimetric method (glycan-based nano(e)zyme) was developed for sensitive and rapid detection of the SARS-CoV-2 virus based on N-acetyl neuraminic acid (sialic acid)-functionalized gold nanoparticles (SA-Au NZs). A number of techniques were used to characterize the prepared nanomaterials including XRD, FT-IR, UV-vis, DLS, and TEM. DLS analysis indicates an average hydrodynamic size of 34 nm, whereas TEM analysis indicates an average particle size of 15.78 nm. This observation confirms that water interacts with nanoparticle surfaces, resulting in a large hydrodynamic diameter. The peroxidase-like activity of SA-Au NZs was examined with SARS-CoV-2 and influenza viruses (influenza A (H1N1), influenza A (H3N2), and influenza B). UV-visible spectroscopy was used to monitor and record the results, as well as naked eye detection (photographs). SA-Au NZs exhibit a change in color from light red to purple when SARS-CoV-2 is present, and they exhibit a redshift in their spectrum. N-acetyl neuraminic acid interacts with SARS-CoV-2 spike glycoprotein, confirming its ability to bind glycans. As a result, SA-Au NZs can detect COVID-19 with sensitivity and specificity of over 95% and 98%, respectively. This method was approved by testing saliva samples from 533 suspected individuals at Ghaem Hospital of Mashhad, Mashhad, Iran. Sensitivity and specificity were calculated by comparing the results with the definitive results. The positive results were accompanied by a color change from bright red to purple within five minutes. Statistical analysis was performed based on variables such as age, gender, smoking, diabetes, hypertension, and lung involvement. In clinical trials, it was demonstrated that this method can be used to diagnose SARS-CoV-2 in a variety of places, such as medical centers, hospitals, airports, universities, and schools.
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Affiliation(s)
- Mehrdad Rokni
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran
| | - Tahereh Rohani Bastami
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran.
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Hamid Reza Rahimi
- Department of Medical Genetics and Molecular Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Zibaee
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran
| | - Mojtaba Meshkat
- Department of Community Medicine, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Serki
- Department of Clinical Biochemistry, Mashhad University of Medical Science, Mashhad, Iran Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdieh Khoshakhlagh
- Department of Clinical Biochemistry, Mashhad University of Medical Science, Mashhad, Iran Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeynab Dabirifar
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran
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7
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Jiang X, Ren W, Tian L, Ge Y, Li C, Hu X, Shi L, Jia Z. IRF9 inhibits CyHV-3 replication by regulating the PI3K-AKT signalling pathway in common carp (Cyprinus carpio) epithelial cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 148:104905. [PMID: 37549834 DOI: 10.1016/j.dci.2023.104905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
Interferon regulatory factor 9 (IRF9) is an important transcriptional regulator involved in innate and adaptive immunity. Cyprinid herpesvirus-3 (CyHV-3) is a virus causing widespread death and great economic loss in farmed common carp (Cyprinus carpio). However, the effect of IRF9 on CyHV-3 infection in common carp has not been reported. In this study, during CyHV-3 infection, IRF9 overexpression in common carp fin epithelial (CCF) cells significantly reduced the expression of viral factor thymidine kinase (TK) and open reading frame 72 (ORF72), and knockdown of IRF9 produced the opposite results (p < 0.05). In CCF cells. The IRF9 protein was expression in the nucleus and was rapidly induced in CCF cells by CyHV-3 infection. In addition, several genes associated with virus infection, including type I interferon (IFNI), IFN-stimulated gene 15 (ISG15), myxovirus resistance 1 (Mx1) and Viperin were induced in CCF cells overexpressing IRF9 upon CyHV-3 infection. IRF9 overexpression induced by CyHV-3 infection significantly increased the gene expression of Mx1 and phosphoinositide 3-kinase (PI3K) and the protein expression of protein kinase B (AKT) (p < 0.01). Interestingly, IRF9 did not significantly affect Mx1 gene expression when AKT protein levels remained unchanged during CyHV-3 infection of CCF cells. Furthermore, a significant resistance-related locus was found in the IRF9 sequence in "Longke-11" mirror carp (M11) and Yellow River carp (p < 0.05). These results indicated that IRF9 inhibited viral replication by upregulating the expression of Mx1 via the PI3K-AKT signalling pathway during CyHV-3 infection in CCF cells and provide some basis for the study of the antiviral molecular mechanisms of common carp.
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Affiliation(s)
- Xiaona Jiang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Wanying Ren
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Lijing Tian
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yanlong Ge
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Chitao Li
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xuesong Hu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Lianyu Shi
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Zhiying Jia
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China; Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.
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8
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Lewis SA, Cinco IR, Doratt BM, Blanton MB, Hoagland C, Newman N, Davies M, Grant KA, Messaoudi I. Chronic alcohol consumption dysregulates innate immune response to SARS-CoV-2 in the lung. EBioMedicine 2023; 97:104812. [PMID: 37793211 PMCID: PMC10562860 DOI: 10.1016/j.ebiom.2023.104812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Alcohol consumption is widespread with over half of the individuals over 18 years of age in the U.S. reporting alcohol use in the last 30 days. Moreover, 9 million Americans engaged in binge or chronic heavy drinking (CHD) in 2019. CHD negatively impacts pathogen clearance and tissue repair, including in the respiratory tract, thereby increasing susceptibility to infection. Although, it has been hypothesized that chronic alcohol consumption negatively impacts COVID-19 outcomes; the interplay between chronic alcohol use and SARS-CoV-2 infection outcomes has yet to be elucidated. METHODS In this study we employed luminex, scRNA sequencing, and flow cytometry to investigate the impact of chronic alcohol consumption on SARS-CoV-2 anti-viral responses in bronchoalveolar lavage cell samples from humans with alcohol use disorder and rhesus macaques that engaged in chronic drinking. FINDINGS Our data show that in both humans (n = 6) and macaques (n = 11), the induction of key antiviral cytokines and growth factors was decreased with chronic ethanol consumption. Moreover, in macaques fewer differentially expressed genes mapped to Gene Ontology terms associated with antiviral immunity following 6 month of ethanol consumption while TLR signaling pathways were upregulated. INTERPRETATION These data are indicative of aberrant inflammation and reduced antiviral responses in the lung with chronic alcohol drinking. FUNDING This study was supported by NIH 1R01AA028735-04 (Messaoudi), U01AA013510-20 (Grant), R24AA019431-14 (Grant), R24AA019661 (Burnham), P-51OD011092 (ONPRC core grant support). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Sloan A Lewis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, USA
| | - Isaac R Cinco
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA
| | - Brianna M Doratt
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA
| | - Madison B Blanton
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA; Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, USA
| | - Cherise Hoagland
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Natali Newman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Michael Davies
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Ilhem Messaoudi
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA.
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9
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Das A, Ahmed Z, Xu L, Jia W. Assessment and verification of chemical inactivation of peste des petits ruminants virus by virus isolation following virus capture using Nanotrap magnetic virus particles. Microbiol Spectr 2023; 11:e0068923. [PMID: 37655907 PMCID: PMC10580900 DOI: 10.1128/spectrum.00689-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Research including diagnosis on highly contagious viruses at the molecular level such as PCR and next-generation sequencing requires complete inactivation of the virus to ensure biosafety and biosecurity so that any accidental release of the virus does not compromise the safety of the susceptible population and the environment. In this work, peste des petits ruminants virus (PPRV) was inactivated with chemical agents, and the virus inactivation was confirmed by virus isolation (VI) using Vero cells. Since the chemical agents are cytotoxic, inactivated virus (PPRV) was diluted 1:100 to neutralize cytotoxicity, and the residual viruses (if any) were captured using Nanotrap magnetic virus particles (NMVPs). The NMVPs and the captured viruses were subjected to VI. No CPE was observed, indicating complete inactivation, and the results were further supported by real-time RT-PCR. This new protocol to verify virus inactivation can be applicable to other viruses.
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Affiliation(s)
- Amaresh Das
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Zaheer Ahmed
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Lizhe Xu
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
| | - Wei Jia
- US Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Foreign Animal Disease Diagnostic Laboratory, Reagents and Vaccine Services Section, Plum Island Animal Disease Center, Orient Point, New York, USA
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10
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Li S, Hu J, Aryee AA, Sun Y, Li Z. Three birds, one stone: Disinfecting and turning waste medical masks into valuable carbon dots for sodium hydrosulfite and Fe 3+ detection enabled by a simple hydrothermal treatment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 296:122659. [PMID: 36989697 PMCID: PMC10029333 DOI: 10.1016/j.saa.2023.122659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Disposable medical masks are widely used to prevent respiratory infections due to their ability to block virus particles from entering the human body. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of medical masks, leading to their widespread use around the world. However, a large number of disposable medical masks have been discarded, some carrying viruses, which have posed a grave threat to the environment and people's health, as well as wasting resources. In this study, a simple hydrothermal method was used for the disinfection of waste medical masks under high-temperature conditions as well as for their transformation into high-value-added carbon dots (CDs, a new type of carbon nanomaterial) with blue-emissive fluorescence, without high energy consumption or environmental pollution. Moreover, the mask-derived CDs (m-CDs) could not only be used as fluorescent probes for sensing sodium hydrosulfite (Na2S2O4), which is widely used in the food and textile industries but is seriously harmful to human health, but also be used for detecting Fe3+ which is harmful to the environment and human health due to its wide use in industries.
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Affiliation(s)
- Sen Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Jingyu Hu
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Aaron Albert Aryee
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhaohui Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
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11
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Viriyakitkosol R, Wanitchang A, Srisutthisamphan K, Saenboonreung J, Boonkrai C, Pisitkun T, Jongkaewwattana A. Impact of mAb-induced A475V substitution on viral fitness and antibody neutralization of SARS-CoV-2 omicron variants in the presence of monoclonal antibodies and human convalescent sera. Front Immunol 2023; 14:1219546. [PMID: 37593745 PMCID: PMC10427911 DOI: 10.3389/fimmu.2023.1219546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/30/2023] [Indexed: 08/19/2023] Open
Abstract
The emergence and rapid evolution of SARS-CoV-2 variants have posed a major challenge to the global efforts to control the COVID -19 pandemic. In this study, we investigated the potential of two SARS-CoV-2 variants, BA.2 and BA.5, to evade neutralization by a human monoclonal antibody targeting the virus's spike RBD (mAb 1D1). By subjecting the viruses to serial propagation in the presence of the antibody, we found that BA.2 exhibited poor growth, whereas BA.5 regained robust growth with significantly higher kinetics than the parental virus. Genetic analysis identified a single mutation, A475V, in the spike protein of BA.5 that substantially reduced the neutralizing activities of monoclonal antibodies and convalescent sera. In addition, the A475V mutation alone in BA.2 moderately reduced the neutralizing activity but completely abolished the neutralizing effect of mAb 1D1 when F486V or L452R were also present. Our results shed light on the possible evolutionary development of SARS-CoV-2 variants under selection pressure by monoclonal antibodies and have implications for the development of effective antibody therapies and vaccines against the virus.
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Affiliation(s)
- Ratchanont Viriyakitkosol
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Asawin Wanitchang
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Kanjana Srisutthisamphan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Janya Saenboonreung
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Chatikorn Boonkrai
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
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12
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Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Preparation, Purification and Performance Evaluation of Polyclonal Antibody Against SARS-CoV-2 Produced in Rat. Adv Pharm Bull 2023; 13:563-572. [PMID: 37646054 PMCID: PMC10460799 DOI: 10.34172/apb.2023.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 09/01/2023] Open
Abstract
Purpose Among all known human coronaviruses, some viruses (e.g., SARS-CoV-2) cause severe pneumonia or even death. With the regard to its spread and the importance of its rapid identification/treatment, and because pAbs are relatively cheap, able to bind to more sites on antigens and even neutralize them, this study was done for the production and purification of anti-SARS-CoV-2 polyclonal antibodies (pAb) in rats. Methods Viral antigen purification was performed by PEG/NaCl precipitation. The efficiency of the sucrose cushion method was also investigated to produce a purer antigen. Immunization was done and antibody purification was performed by ammonium sulfate precipitation (33%), dialysis, and ion-exchange chromatography. Western blotting and enzyme-linked immunosorbent assay (ELISA) were performed to verify the antibody specificity. All data were analyzed by SPSS software. Results The results showed that the amount of concentrated virus increased with the increase of PEG concentration. Moreover, the sucrose cushion method increased its purity. Besides, induction of immune response in rats for pAb production with high titers was reached via these antigens and ELISA/western blot results indicated a suitable antibody-antigen interaction. Additionally, it was shown that ion-exchange chromatography could be a suitable technique for IgG purification. Conclusion Herein, we presented a simple and cheap method for the purification of whole viral particles with relatively high quality. The results verified that these antigens could elicit a good immune response in the rat. The obtained pAbs showed a good specificity toward SARS-CoV-2 antigens. Accordingly, this study proposes a promising method for viral vaccine development.
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Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
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Caleffi GS, Rosa AS, de Souza LG, Avelar JLS, Nascimento SMR, de Almeida VM, Tucci AR, Ferreira VN, da Silva AJM, Santos-Filho OA, Miranda MD, Costa PRR. Aurones: A Promising Scaffold to Inhibit SARS-CoV-2 Replication. JOURNAL OF NATURAL PRODUCTS 2023; 86:1536-1549. [PMID: 37257024 DOI: 10.1021/acs.jnatprod.3c00249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Aurones are a small subgroup of flavonoids in which the basic C6-C3-C6 skeleton is arranged as (Z)-2-benzylidenebenzofuran-3(2H)-one. These compounds are structural isomers of flavones and flavonols, natural products reported as potent inhibitors of SARS-CoV-2 replication. Herein, we report the design, synthesis, and anti-SARS-CoV-2 activity of a series of 25 aurones bearing different oxygenated groups (OH, OCH3, OCH2OCH3, OCH2O, OCF2H, and OCH2C6H4R) at the A- and/or B-rings using cell-based screening assays. We observed that 12 of the 25 compounds exhibit EC50 < 3 μM (8e, 8h, 8j, 8k, 8l, 8m, 8p, 8q, 8r, 8w, 8x, and 8y), of which five presented EC50 < 1 μM (8h, 8m, 8p, 8q, and 8w) without evident cytotoxic effect in Calu-3 cells. The substitution of the A- and/or B-ring with OCH3, OCH2OCH3, and OCF2H groups seems beneficial for the antiviral activity, while the corresponding phenolic derivatives showed a significant decrease in the anti-SARS-CoV-2 activity. The most potent compound of the series, aurone 8q (EC50 = 0.4 μM, SI = 2441.3), is 2 to 3 times more effective than the polyphenolic flavonoids myricetin (2) and baicalein (1), respectively. Investigation of the five more active compounds as inhibitors of SARS-CoV-2 3CLpro based on molecular dynamic calculations suggested that these aurones should detach from the active site of 3CLpro, and, probably, they could bind to another SARS-CoV-2 protein target (either receptor or enzyme).
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Affiliation(s)
| | - Alice S Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-900 Rio de Janeiro, Brazil
| | | | | | | | | | - Amanda R Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-900 Rio de Janeiro, Brazil
| | - Vivian N Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-900 Rio de Janeiro, Brazil
| | | | | | - Milene D Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21040-900 Rio de Janeiro, Brazil
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14
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Couto J, Gonçalves R, Lamas S, Saraiva M. Protocol for infecting and monitoring susceptible k18-hACE2 mice with SARS-CoV-2. STAR Protoc 2023; 4:102303. [PMID: 37178116 PMCID: PMC10133884 DOI: 10.1016/j.xpro.2023.102303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/29/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Intranasal infection of k18-hACE2 mice with SARS-CoV-2 recapitulates the clinical characteristics present in severe COVID-19. Here, we present a protocol for intranasal administration of SARS-CoV-2 to k18-hACE2 mice and their subsequent daily monitoring. We describe steps for intranasal inoculation of SARS-CoV-2 and the collection of clinical scores on weight, body condition, hydration, appearance, neurological symptoms, behavior, and respiratory movements. This protocol contributes to the establishment of a model of severe SARS-CoV-2 infection that minimizes animal suffering. For complete details on the use and execution of this protocol, please refer to Gonçalves et al. (2023).1.
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Affiliation(s)
- Joana Couto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal
| | - Rute Gonçalves
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal
| | - Sofia Lamas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4200-135, Portugal.
| | - Margarida Saraiva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4200-135, Portugal.
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15
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Pilchová V, Prajeeth CK, Jendrny P, Twele F, Meller S, Pink I, Fathi A, Addo MM, Volk H, Osterhaus A, von Köckritz-Blickwede M, Schulz C. β-Propiolactone (BPL)-inactivation of SARS-Co-V-2: in vitro validation with focus on saliva from COVID-19 patients for scent dog training. J Virol Methods 2023; 317:114733. [PMID: 37068591 PMCID: PMC10105625 DOI: 10.1016/j.jviromet.2023.114733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
β-Propiolactone (BPL) is an organic compound widely used as an inactivating agent in vaccine development and production, for example for SARS-CoV, SARS-CoV-2 and Influenza viruses. Inactivation of pathogens by BPL is based on an irreversible alkylation of nucleic acids but also on acetylation and cross-linking between proteins, DNA or RNA. However, the protocols for BPL inactivation of viruses vary widely. Handling of infectious, enriched SARS-CoV-2 specimens and diagnostic samples from COVID-19 patients is recommended in biosafety level (BSL)-3 or BSL-2 laboratories, respectively. We validated BPL inactivation of SARS-CoV-2 in saliva samples with the objective to use saliva from COVID-19 patients for training of scent dogs for the detection of SARS-CoV-2 positive individuals. Therefore, saliva samples and cell culture medium buffered with NaHCO3 (pH 8.3) were comparatively spiked with SARS-CoV-2 and inactivated with 0.1% BPL for 1hour (h) or 71h (± 1h) at 2-8°C, followed by hydrolysis of BPL at 37°C for 1 or 2h, converting BPL into non-toxic beta-hydroxy-propionic acid. SARS-CoV-2 inactivation was demonstrated by a titre reduction of up to 10^4 TCID50/ml in the spiked samples for both inactivation periods using virus titration and virus isolation, respectively. The validated method was confirmed by successful inactivation of pathogens in saliva samples from COVID-19 patients. Furthermore, we reviewed the currently available literature on SARS-CoV-2 inactivation by BPL. Accordingly, BPL-inactivated, hydrolysed samples can be handled in a non-laboratory setting. Furthermore, our BPL inactivation protocols can be adapted to validation experiments with other pathogens.
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Affiliation(s)
- Veronika Pilchová
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Chittappen Kandiyil Prajeeth
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Paula Jendrny
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Friederike Twele
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Sebastian Meller
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Isabell Pink
- Department of Respiratory Medicine, Hannover Medical School, Carl-Neuberg-Straße 1, Hanover, Germany
| | - Anahita Fathi
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf, Hamburg, Germany; I(st) Department of Medicine, Division of Infectious Diseases, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Center for Infection Research, Hamburg-Lübeck, Borstel-Riems, Germany
| | - Marylyn Martina Addo
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf, Hamburg, Germany; I(st) Department of Medicine, Division of Infectious Diseases, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Center for Infection Research, Hamburg-Lübeck, Borstel-Riems, Germany
| | - Holger Volk
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Albert Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany; Department of Biochemistry, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Claudia Schulz
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany.
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Yang J, Phan VM, Heo CK, Nguyen HV, Lim WH, Cho EW, Poo H, Seo TS. Development of nucleocapsid-specific monoclonal antibodies for SARS-CoV-2 and their ELISA diagnostics on an automatic microfluidic device. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 380:133331. [PMID: 36644652 PMCID: PMC9826540 DOI: 10.1016/j.snb.2023.133331] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has threatened public health globally, and the emergence of viral variants has exacerbated an already precarious situation. To prevent further spread of the virus and determine government action required for virus control, accurate and rapid immunoassays for SARS-CoV-2 diagnosis are urgently needed. In this study, we generated monoclonal antibodies (mAbs) against the SARS-CoV-2 nucleocapsid protein (NP), compared their reactivity using an enzyme-linked immunosorbent assay (ELISA), and selected four mAbs designated 1G6, 3E10, 3F10, and 5B6 which have higher reactivity to NP and viral lysates of SARS-CoV-2 than other mAbs. Using an epitope mapping assay, we identified that 1G6 detected the C-terminal domain of SARS-CoV-2 NP (residues 248-364), while 3E10 and 3F10 bound to the N-terminal domain (residues 47-174) and 3F10 detected the N-arm region (residues 1-46) of SARS-CoV-2 NP. Based on the epitope study and sandwich ELISA, we selected the 1G6 and 3E10 Abs as an optimal Ab pair and applied them for a microfluidics-based point-of-care (POC) ELISA assay to detect the NPs of SARS-CoV-2 and its variants. The integrated and automatic microfluidic system could operate the serial injection of the sample, the washing solution, the HRP-conjugate antibody, and the TMB substrate solution simply by controlling air purge via a single syringe. The proposed Ab pair-equipped microsystem effectively detected the NPs of SARS-CoV-2 variants as well as in clinical samples. Collectively, our proposed platform provides an advanced protein-based diagnostic tool for detecting SARS-CoV-2.
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Affiliation(s)
- Jihyun Yang
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Vu Minh Phan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, South Korea
| | - Chang-Kyu Heo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Hau Van Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, South Korea
| | - Won-Hee Lim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Eun-Wie Cho
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Haryoung Poo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, South Korea
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Shahjin F, Patel M, Machhi J, Cohen JD, Nayan MU, Yeapuri P, Zhang C, Waight E, Hasan M, Abdelmoaty MM, Dash PK, Zhou Y, Andreu I, Gendelman HE, Kevadiya BD. Multipolymer microsphere delivery of SARS-CoV-2 antigens. Acta Biomater 2023; 158:493-509. [PMID: 36581007 PMCID: PMC9791794 DOI: 10.1016/j.actbio.2022.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Effective antigen delivery facilitates antiviral vaccine success defined by effective immune protective responses against viral exposures. To improve severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigen delivery, a controlled biodegradable, stable, biocompatible, and nontoxic polymeric microsphere system was developed for chemically inactivated viral proteins. SARS-CoV-2 proteins encapsulated in polymeric microspheres induced robust antiviral immunity. The viral antigen-loaded microsphere system can preclude the need for repeat administrations, highlighting its potential as an effective vaccine. STATEMENT OF SIGNIFICANCE: Successful SARS-CoV-2 vaccines were developed and quickly approved by the US Food and Drug Administration (FDA). However, each of the vaccines requires boosting as new variants arise. We posit that injectable biodegradable polymers represent a means for the sustained release of emerging viral antigens. The approach offers a means to reduce immunization frequency by predicting viral genomic variability. This strategy could lead to longer-lasting antiviral protective immunity. The current proof-of-concept multipolymer study for SARS-CoV-2 achieve these metrics.
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Affiliation(s)
- Farah Shahjin
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Jacob D Cohen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Mohammad Ullah Nayan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Pravin Yeapuri
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Chen Zhang
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Emiko Waight
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mai Mohamed Abdelmoaty
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - Prasanta K Dash
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
| | - You Zhou
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Irene Andreu
- RI Consortium of Nanoscience and Nanotechnology and Department of Chemical Engineering University of Rhode Island, RI, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA.
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
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18
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Koh ACW, Yeoh KY. Assessing the thermal stability of toolmarks casting materials through optical comparison microscopy, virtual comparison microscopy and quantitative similarity scores. Forensic Sci Res 2023; 7:782-789. [PMID: 36817232 PMCID: PMC9930827 DOI: 10.1080/20961790.2021.1991669] [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: 10/18/2022] Open
Abstract
Toolmarks, particularly those found on bulky, inaccessible or immovable items, can be recovered by casting. To allow for subsequent comparative examinations, the casting material, typically polysiloxanes or silicones, must be able to capture and preserve fine details within a toolmark accurately. To study the stability of such details after exposure to heat, toolmark casts were heated at either 60 °C for 2 h, or 90 °C for 1 h. These casts were subsequently compared to casts that had not been exposed to heat, using traditional optical comparison microscopy, as well as virtual comparison microscopy. Digitised toolmark signatures were also extracted from the casts and compared pairwise to obtain quantitative similarity scores based on cross-correlation, consecutive matching striae and Mann-Whitney U-statistic. Our results show that the fine surface details captured on all four commercial toolmark casting materials tested herein remained stable after exposure to heat. This study shows that the above heating protocols are viable viral inactivation methods for toolmark casts that are potentially contaminated with human coronaviruses, such as SARS-CoV-2. Our findings also apply to other scenarios, such as for casts that were left in a vehicle parked under the sun.
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Affiliation(s)
- Alaric C. W. Koh
- Forensic Chemistry and Physics Laboratory, Health Sciences Authority, Singapore,CONTACT Alaric C. W. Koh
| | - Kai Yuan Yeoh
- Forensic Chemistry and Physics Laboratory, Health Sciences Authority, Singapore
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19
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Amruta N, Maness NJ, Gressett TE, Tsuchiya Y, Kishi M, Bix G. Effect of acetic acid inactivation of SARS-CoV-2. PLoS One 2023; 18:e0276578. [PMID: 36753524 PMCID: PMC9907812 DOI: 10.1371/journal.pone.0276578] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/10/2022] [Indexed: 02/09/2023] Open
Abstract
Effective measures are needed to prevent the spread and infectivity of SARS-CoV-2 that causes COVID-19. Chemical inactivation may help to prevent the spread and transmission of this and other viruses. Hence, we tested the SARS-CoV-2 antiviral activity of acetic acid, the main component of vinegar, in vitro. Inactivation and binding assays suggest that acetic acid is virucidal. We found that 6% acetic acid, a concentration typically found in white distilled vinegar, effectively inactivated SARS-CoV-2 after 15-min incubation with a complete loss of replication of competent virus as measured by TCID50. Transmission electron microscopy further demonstrated that 6% acetic acid disrupts SARS-CoV-2 virion structure. In addition, 6% acetic acid significantly inhibits and disrupts the binding of SARS-CoV-2 spike protein binding to ACE2, the primary SARS-CoV-2 cell receptor, after contact with spike protein for 5, 10, 30 and 60 minutes incubation. Taken together, our findings demonstrate that acetic acid possesses inactivating activity against SARS-CoV-2 and may represent a safe alternative to commonly used chemical disinfectants to effectively control the spread of SARS-CoV-2.
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Affiliation(s)
- Narayanappa Amruta
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States of America
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Tulane University, Covington, LA, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States of America
| | - Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States of America
| | | | - Mikiya Kishi
- Central Research Institute, Mizkan Holdings Co., Ltd. Aichi, Japan
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States of America
- Department of Neurology, Tulane University School of Medicine, New Orleans, LA, United States of America
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20
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Methods to study viruses. Viruses 2023. [DOI: 10.1016/b978-0-323-90385-1.00022-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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21
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Marques M, Ferreira AR, Ribeiro D. Determining the Importance of Peroxisomal Proteins for Viral Infections in Cultured Mammalian Cells. Methods Mol Biol 2023; 2643:309-319. [PMID: 36952194 DOI: 10.1007/978-1-0716-3048-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes have recently been shown to play important roles in the context of viral infections. However, further and more detailed studies should be performed to unravel the specific mechanisms involved. The analysis of the relevance of particular peroxisomal components, such as peroxisomal proteins, for viral infections can be performed by comparing the production of new virus particles in the absence and presence of those specific components. Different methodologies are used to quantify the production of infectious virus particles, depending on the virus, cell type, and the specific characteristics of the viral infection to be analyzed. Here we provide a detailed protocol to study the importance of a putative peroxisomal protein on infection by viruses that induce the death of their host cells. We use the influenza A virus (IAV) infection in A549 cells as a model, and the quantification of the newly produced infectious virus particles is performed by a plaque assay.
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Affiliation(s)
- Mariana Marques
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Ferreira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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22
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Alp Onen E, Sonmez K, Yildirim F, Demirci EK, Gurel A. Development, analysis, and preclinical evaluation of inactivated vaccine candidate for prevention of Covid-19 disease. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2099468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Engin Alp Onen
- Kocak Pharmaceuticals, Vaccine and Biotechnology R&D, Organize Sanayi Bölgesi, Kapakli/Tekirdag, Turkey
| | - Kivilcim Sonmez
- Faculty of Veterinary Medicine, Pathology Department, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Funda Yildirim
- Faculty of Veterinary Medicine, Pathology Department, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | | | - Aydin Gurel
- Faculty of Veterinary Medicine, Pathology Department, Istanbul University-Cerrahpasa, Istanbul, Turkey
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23
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Dittmer DP, Eason AB, Juarez A. Scaling Biosafety Up During and Down After the COVID-19 Pandemic. APPLIED BIOSAFETY 2022; 27:247-254. [PMID: 36761994 PMCID: PMC9902049 DOI: 10.1089/apb.2022.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Purpose The aim of this work was to review and analyze changes to the practice of biosafety imposed by pandemics. Methods A narrative review of the COVID-19 pandemic that began in 2020 and prior pandemics from the perspective of a working virologist. Results By definition, pandemics, outbreaks, and other emergencies are transient phenomena. They manifest as waves of events that induce unforeseen needs and present unknown challenges. After a pandemic, the return to normality is as crucial as the scale-up during the exponential growth phase. The COVID-19 pandemic presents an example to study operational biosafety and biocontainment issues during community transmission of infectious agents with established pandemic potential, the propensity to induce severe disease, and the ability to disrupt aspects of human society. Conclusions Scaling down heightened biocontainment measures after a pandemic is as important as scaling up during a pandemic. The availability of preventive vaccines, and therapeutic drug regimens, should be considered in risk assessments for laboratory studies. There exists the need to preserve situational memory at the personal and institutional levels that can be served by professional societies.
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Affiliation(s)
- Dirk P. Dittmer
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anthony B. Eason
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Angelica Juarez
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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24
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Kongsomros S, Pongsakul N, Panachan J, Khowawisetsut L, Somkird J, Sangma C, Kanjanapruthipong T, Wongtrakoongate P, Chairoungdua A, Pattanapanyasat K, Newburg DS, Morrow AL, Hongeng S, Thitithanyanont A, Chutipongtanate S. Comparison of viral inactivation methods on the characteristics of extracellular vesicles from SARS-CoV-2 infected human lung epithelial cells. J Extracell Vesicles 2022; 11:e12291. [PMID: 36468940 PMCID: PMC9721205 DOI: 10.1002/jev2.12291] [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: 07/06/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
The interaction of SARS-CoV-2 infection with extracellular vesicles (EVs) is of particular interest at the moment. Studying SARS-CoV-2 contaminated-EV isolates in instruments located outside of the biosafety level-3 (BSL-3) environment requires knowing how viral inactivation methods affect the structure and function of extracellular vesicles (EVs). Therefore, three common viral inactivation methods, ultraviolet-C (UVC; 1350 mJ/cm2 ), β-propiolactone (BPL; 0.005%), heat (56°C, 45 min) were performed on defined EV particles and their proteins, RNAs, and function. Small EVs were isolated from the supernatant of SARS-CoV-2-infected human lung epithelial Calu-3 cells by stepwise centrifugation, ultrafiltration and qEV size-exclusion chromatography. The EV isolates contained SARS-CoV-2. UVC, BPL and heat completely abolished SARS-CoV-2 infectivity of the contaminated EVs. Particle detection by electron microscopy and nanoparticle tracking was less affected by UVC and BPL than heat treatment. Western blot analysis of EV markers was not affected by any of these three methods. UVC reduced SARS-CoV-2 spike detectability by quantitative RT-PCR and slightly altered EV-derived β-actin detection. Fibroblast migration-wound healing activity of the SARS-CoV-2 contaminated-EV isolate was only retained after UVC treatment. In conclusion, specific viral inactivation methods are compatible with specific measures in SARS-CoV-2 contaminated-EV isolates. UVC treatment seems preferable for studying functions of EVs released from SARS-CoV-2 infected cells.
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Affiliation(s)
- Supasek Kongsomros
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi HospitalMahidol UniversitySamut PrakanThailand,Pediatric Translational Research Unit, Department of PediatricsFaculty of Medicine Ramathibodi Hospital, Mahidol UniversityBangkokThailand,Department of Microbiology, Faculty of ScienceMahidol UniversityBangkokThailand
| | - Nutkridta Pongsakul
- Pediatric Translational Research Unit, Department of PediatricsFaculty of Medicine Ramathibodi Hospital, Mahidol UniversityBangkokThailand
| | - Jirawan Panachan
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkokThailand
| | - Ladawan Khowawisetsut
- Department of Parasitology, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Jinjuta Somkird
- Department of Parasitology, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Chak Sangma
- Department of Chemistry, Faculty of ScienceKasetsart UniversityBangkokThailand
| | | | | | - Arthit Chairoungdua
- Department of Biochemistry, Faculty of ScienceMahidol UniversityBangkokThailand
| | - Kovit Pattanapanyasat
- Center of Excellence for Microparticle and Exosome in Diseases, Research DepartmentFaculty of Medicine Siriraj Hospital, Mahidol UniversityBangkokThailand
| | - David S. Newburg
- Division of Epidemiology, Department of Environmental and Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Ardythe L. Morrow
- Division of Epidemiology, Department of Environmental and Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA,Division of Infectious Diseases, Department of PediatricsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkokThailand
| | | | - Somchai Chutipongtanate
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi HospitalMahidol UniversitySamut PrakanThailand,Pediatric Translational Research Unit, Department of PediatricsFaculty of Medicine Ramathibodi Hospital, Mahidol UniversityBangkokThailand,Division of Epidemiology, Department of Environmental and Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
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25
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Liew OW, Fanusi F, Ng JYX, Ahidjo BA, Ling SSM, Lilyanna S, Chong JPC, Lim AES, Lim WZ, Ravindran S, Chu JJH, Lim SL, Richards AM. Immunoassay-Compatible Inactivation of SARS-CoV-2 in Plasma Samples for Enhanced Handling Safety. ACS OMEGA 2022; 7:25510-25520. [PMID: 35903176 PMCID: PMC9301769 DOI: 10.1021/acsomega.2c02585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) inactivation is an important step toward enhanced biosafety in testing facilities and affords a reduction in the biocontainment level necessary for handling virus-positive biological specimens. Virus inactivation methods commonly employ heat, detergents, or combinations thereof. In this work, we address the dearth of information on the efficacy of SARS-CoV-2 inactivation procedures in plasma and their downstream impact on immunoassays. We evaluated the effects of heat (56 °C for 30 min), detergent (1-5% Triton X-100), and solvent-detergent (SD) combinations [0.3-1% tri-n-butyl phosphate (TNBP) and 1-2% Triton X-100] on 19 immunoassays across different assay formats. Treatments are deemed immunoassay-compatible when the average and range of percentage recovery (treated concentration relative to untreated concentration) lie between 90-110 and 80-120%, respectively. We show that SD treatment (0.3% TNBP/1% Triton-X100) is compatible with more than half of the downstream immunoassays tested and is effective in reducing SARS-CoV-2 infectivity in plasma to below detectable levels in plaque assays. This facile method offers enhanced safety for laboratory workers handling biological specimens in clinical and research settings.
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Affiliation(s)
- Oi Wah Liew
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Felic Fanusi
- NUS
Medicine BSL3 Core Facility, Yong Loo Lin School of Medicine, National
University of Singapore, National University
Health System, 14 Medical
Drive, Singapore 117599, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Jessica Yan Xia Ng
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Bintou Ahmadou Ahidjo
- NUS
Medicine BSL3 Core Facility, Yong Loo Lin School of Medicine, National
University of Singapore, National University
Health System, 14 Medical
Drive, Singapore 117599, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Samantha Shi Min Ling
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Shera Lilyanna
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Jenny Pek Ching Chong
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Angeline Eng Siew Lim
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Wei Zheng Lim
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
| | - Sindhu Ravindran
- NUS
Medicine BSL3 Core Facility, Yong Loo Lin School of Medicine, National
University of Singapore, National University
Health System, 14 Medical
Drive, Singapore 117599, Singapore
| | - Justin Jang Hann Chu
- NUS
Medicine BSL3 Core Facility, Yong Loo Lin School of Medicine, National
University of Singapore, National University
Health System, 14 Medical
Drive, Singapore 117599, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
- Infectious
Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Shir Lynn Lim
- Yong
Loo Lin School of Medicine, National University of Singapore, National University Health System, 1E Kent Ridge Road, Singapore 119228, Singapore
- Department
of Cardiology, National University Heart
Centre Singapore, 1E
Kent Ridge Road, Singapore 119228, Singapore
| | - Arthur Mark Richards
- Cardiovascular
Research Institute, Department of Medicine, Yong Loo Lin School of
Medicine, National University of Singapore, National University Health System, 14 Medical Drive, Singapore 117599, Singapore
- Christchurch
Heart Institute, University of Otago, Christchurch 8140, New Zealand
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26
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Kanchibhotla D, Subramanian S, Ravi Kumar RM, Venkatesh Hari KR, Pathania M. An In-vitro evaluation of a polyherbal formulation, against SARS-Cov-2. J Ayurveda Integr Med 2022; 13:100581. [PMID: 35753154 PMCID: PMC9222090 DOI: 10.1016/j.jaim.2022.100581] [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: 09/16/2021] [Revised: 02/19/2022] [Accepted: 04/16/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the last two years, COVID-19 pandemic caused by SARS-CoV-2 has created a mass destruction among humanity causing a major health crisis around the world. With the emergence of new strains of the virus, lack of targeted drugs and antimicrobial resistance, there is a dire need to discover specific antiviral with minimum side effects targeted against COVID-19. OBJECTIVE The present study evaluates the antiviral efficacy of a novel Ayurvedic polyherbal formulation, NOQ19, composed of a 13 well known herbs, in a cell-based setting. METHODOLOGY Vero E6 (CL1008), the African green monkey kidney epithelial cell, were infected with SARS-CoV-2 virus (isolate USA-WA1/2020) in a 96 well-plate. NOQ19 test material was diluted at different concentration: 0.05 mg/ml, 0.1 mg/ml, 0.2 mg/ml, 0.3 mg/ml, 0.4 mg/ml, 0.5 mg/ml, 0.6 mg/ml, 0.7 mg/ml, 0.8 mg/ml and 0.9 mg/ml. These different concentrations of NOQ19 were added to infected cells respectively and incubated for 3 days in 5% CO2 incubator. Remdesivir was used as a positive control. The cells were finally fixed with formaldehyde, stained with crystal violet and plaques were visualized. The number of plaques were counted to determine the PFU(plaque forming units)/ml. RESULTS The results of the present study demonstrated an excellent an antiviral efficacy of NOQ19 at 0.9 mg/ml concentration, eliminating 100% virus. The IC50 of the drug was found to be 0.2 mg/ml. CONCLUSION There is limited data around pre-clinical efficacy of polyherbal Ayurvedic drugs. Ayurvedic and herbal formations need to be tested in a preclinical setting to support the human data. The results of the present study demonstrated viral load reduction using NOQ19 in Vero E6 cell lines infected with SARS-CoV-2 virus. These result along with other preclinical and clinical trials could further evaluate the efficacy of NOQ19 as a potential therapeutic option in the fighting the COVID-19 challenge.
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27
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Badeti S, Jiang Q, Naghizadeh A, Tseng HC, Bushkin Y, Marras SAE, Nisa A, Tyagi S, Chen F, Romanienko P, Yehia G, Evans D, Lopez-Gonzalez M, Alland D, Russo R, Gause W, Shi L, Liu D. Development of a novel human CD147 knock-in NSG mouse model to test SARS-CoV-2 viral infection. Cell Biosci 2022; 12:88. [PMID: 35690792 PMCID: PMC9187929 DOI: 10.1186/s13578-022-00822-6] [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: 03/15/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An animal model that can mimic the SARS-CoV-2 infection in humans is critical to understanding the rapidly evolving SARS-CoV-2 virus and for development of prophylactic and therapeutic strategies to combat emerging mutants. Studies show that the spike proteins of SARS-CoV and SARS-CoV-2 bind to human angiotensin-converting enzyme 2 (hACE2, a well-recognized, functional receptor for SARS-CoV and SARS-CoV-2) to mediate viral entry. Several hACE2 transgenic (hACE2Tg) mouse models are being widely used, which are clearly invaluable. However, the hACE2Tg mouse model cannot fully explain: (1) low expression of ACE2 observed in human lung and heart, but lung or heart failure occurs frequently in severe COVID-19 patients; (2) low expression of ACE2 on immune cells, but lymphocytopenia occurs frequently in COVID-19 patients; and (3) hACE2Tg mice do not mimic the natural course of SARS-CoV-2 infection in humans. Moreover, one of most outstanding features of coronavirus infection is the diversity of receptor usage, which includes the newly proposed human CD147 (hCD147) as a possible co-receptor for SARS-CoV-2 entry. It is still debatable whether CD147 can serve as a functional receptor for SARS-CoV-2 infection or entry. RESULTS Here we successfully generated a hCD147 knock-in mouse model (hCD147KI) in the NOD-scid IL2Rgammanull (NSG) background. In this hCD147KI-NSG mouse model, the hCD147 genetic sequence was placed downstream of the endogenous mouse promoter for mouse CD147 (mCD147), which creates an in vivo model that may better recapitulate physiological expression of hCD147 proteins at the molecular level compared to the existing and well-studied K18-hACE2-B6 (JAX) model. In addition, the hCD147KI-NSG mouse model allows further study of SARS-CoV-2 in the immunodeficiency condition which may assist our understanding of this virus in the context of high-risk populations in immunosuppressed states. Our data show (1) the human CD147 protein is expressed in various organs (including bronchiolar epithelial cells) in hCD147KI-NSG mice by immunohistochemical staining and flow cytometry; (2) hCD147KI-NSG mice are marginally sensitive to SARS-CoV-2 infection compared to WT-NSG littermates characterized by increased viral copies by qRT-PCR and moderate body weight decline compared to baseline; (3) a significant increase in leukocytes in the lungs of hCD147KI-NSG mice, compared to infected WT-NSG mice. CONCLUSIONS hCD147KI-NSG mice are more sensitive to COVID-19 infection compared to WT-NSG mice. The hCD147KI-NSG mouse model can serve as an additional animal model for further interrogation whether CD147 serve as an independent functional receptor or accessory receptor for SARS-CoV-2 entry and immune responses.
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Affiliation(s)
- Saiaditya Badeti
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- School of Graduate Studies, Biomedical and Health Sciences, Rutgers University, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Qingkui Jiang
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alireza Naghizadeh
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Hsiang-Chi Tseng
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Salvatore A E Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Annuurun Nisa
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Fei Chen
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Peter Romanienko
- Genome Editing Shared Resources, Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ghassan Yehia
- Genome Editing Shared Resources, Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Deborah Evans
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Moises Lopez-Gonzalez
- Regional Bio-Containment Laboratory, Center for COVID-19 Response and Pandemic Preparedness (CCRP2), Rutgers-New Jersey Medical School, Newark, NJ, 07103, USA
| | - David Alland
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Riccardo Russo
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - William Gause
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Lanbo Shi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
| | - Dongfang Liu
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers-New Jersey Medical School, Rutgers University, 205 S. Orange Ave., CC-H1218, Newark, NJ, 07103, USA.
- School of Graduate Studies, Biomedical and Health Sciences, Rutgers University, Newark, NJ, 07103, USA.
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
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Palladino G, Chang C, Lee C, Music N, De Souza I, Nolasco J, Amoah S, Suphaphiphat P, Otten GR, Settembre EC, Wen Y. Self-amplifying mRNA SARS-CoV-2 vaccines raise cross-reactive immune response to variants and prevent infection in animal models. Mol Ther Methods Clin Dev 2022; 25:225-235. [PMID: 35345593 PMCID: PMC8942436 DOI: 10.1016/j.omtm.2022.03.013] [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: 10/11/2021] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
Abstract
The spike (S) protein of SARS-CoV-2 plays a crucial role in cell entry, and the nucleocapsid (N) protein is highly conserved among human coronavirus homologs. For potentially broad effectiveness against both original virus and emerging variants, we developed Alphavirus-based self-amplifying mRNA (sa-mRNA) SARS-CoV-2 vaccines: an sa-mRNA S encoding a full-length S protein stabilized in a prefusion conformation and an sa-mRNA S-N co-expressing S and N proteins for the original virus. We show that these sa-mRNA SARS-CoV-2 vaccines raised potent neutralizing antibody responses in mice against not only the original virus but also the Alpha, Beta, Gamma, and Delta variants. sa-mRNA S vaccines against the Alpha and Beta variants also raised robust cross-reactive neutralizing antibody responses against their homologous viruses and heterologous variants. sa-mRNA S and sa-mRNA S-N vaccines elicited Th1-dominant, antigen-specific CD4+ T cell responses to S and N proteins and robust and broad CD8+ T cell responses to S protein. Hamsters immunized with either vaccine were fully protected from lung infection and showed significant reduction of viral load in upper respiratory tract. Our findings demonstrate that sa-mRNA SARS-CoV-2 vaccines are potent in animal models with potential to be highly effective against SARS-CoV-2 infection in humans.
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Affiliation(s)
| | - Cheng Chang
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Changkeun Lee
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Nedzad Music
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Ivna De Souza
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Jonathan Nolasco
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Samuel Amoah
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | | | - Gillis R Otten
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Ethan C Settembre
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Yingxia Wen
- Seqirus, a CSL Company, 50 Hampshire Street, Cambridge, MA 02139, USA
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Identification, propagation and molecular characterization of SARS-CoV-2 delta variant isolated from Egyptian COVID-19 patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105278. [PMID: 35367360 PMCID: PMC8968185 DOI: 10.1016/j.meegid.2022.105278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/14/2022]
Abstract
The recently emerging coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Since its discovery in the city of Wahan, China, SARS-CoV-2 has spread rapidly to invade all countries. In addition to its rapid transmission rate, it is characterized by high genetic mutation rates. The aim of this study is to provide an effective method for the isolation and propagation of SARS-CoV-2 in cell lines without any induction of genetic variations. In this study, we isolated SARS-CoV-2 from oro-nasopharyngeal swabs collected from Egyptian patients who were clinically diagnosed with COVID-19. Molecular identification of SARS-CoV-2 was performed by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). The isolated virus was propagated on Vero E6 cells without applying serial viral passages to avoid any variation of the viral genome. The replication and propagation were confirmed by the results of both RT-qPCR and the cytopathic effect (CPE). Moreover, SARS-CoV-2 was completely inactivated chemically using beta-propiolactone (βPL). Whole genome sequencing (WGS) of the propagated virus was performed in order to investigate mutational patterns. The genome sequences recovered in 2020 (n = 18) were similar to the reference strain, Wuhan-Hu-1, and were clustered as clade 20A. However, the genomic sequences recovered in 2021 (n = 2) were clustered as clade 21J. These two sequences are considered the first Delta (B.1.617.2) variants detected in Egypt. This study provides a reference for researchers in Egypt to isolate and propagate SARS-CoV-2 easily and efficiently. Furthermore, the prevalence of the SARS-CoV-2 delta variant in Egypt necessitates continuous monitoring of the efficacy of the applied treatment protocol and the effectiveness of current vaccines against such variants of concern (VOC).
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Kercher L, Seiler P, Jeevan T, Franks J, Trifkovic S, Marathe B, Henry J, Gaut J, Webby RJ. It's the Wrong Virus: Rapid Adaptation of Operations Inside a Highly Pathogenic Avian Influenza Select Agent Laboratory in Response to the 2019 SARS-CoV-2 Pandemic. APPLIED BIOSAFETY 2022; 27:58-63. [PMID: 36776748 PMCID: PMC9908283 DOI: 10.1089/apb.2021.0030] [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: 11/12/2022]
Abstract
Background The Animal Biosafety Level 3 Enhanced (ABSL-3+) laboratory at St. Jude Children's Research Hospital has a long history of influenza pandemic preparedness. The emergence of SARS-CoV-2 and subsequent expansion into a pandemic has put new and unanticipated demands on laboratory operations since April 2020. Administrative changes, investigative methods requiring increased demand for inactivation and validation of sample removal, and the adoption of a new animal model into the space required all arms of our Biorisk Management System (BMS) to respond with speed and innovation. Results In this report, we describe the outcomes of three major operational changes that were implemented to adapt the ABSL-3+ select agent space into a multipathogen laboratory. First were administrative controls that were revised and developed with new Institutional Biosafety Committee protocols, laboratory space segregation, training of staff, and occupational health changes for potential exposure to SARS-CoV-2 inside the laboratory. Second were extensive inactivation and validation experiments performed for both highly pathogenic avian influenza and SARS-CoV-2 to meet the demands for sample removal to a lower biosafety level. Third was the establishment of a new caging system to house Syrian Golden hamsters for SARS-CoV-2 risk assessment modeling. Summary The demands placed on biocontainment laboratories for response to SARS-CoV-2 has highlighted the importance of a robust BMS. In a relatively short time, the ABSL-3+ was able to adapt from a single select agent space to a multipathogen laboratory and expand our pandemic response capacity.
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Affiliation(s)
- Lisa Kercher
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Address correspondence to: Lisa Kercher, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS330, Memphis, TN 38105, USA.
| | - Patrick Seiler
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Trushar Jeevan
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Franks
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bindumadhav Marathe
- Department of Environmental Health and Safety, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James Henry
- Department of Environmental Health and Safety, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James Gaut
- Department of Environmental Health and Safety, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J. Webby
- Department of Infectious Diseases and St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Martí D, Martín-Martínez E, Torras J, Betran O, Turon P, Alemán C. In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold. Colloids Surf B Biointerfaces 2022; 213:112400. [PMID: 35158221 PMCID: PMC8820101 DOI: 10.1016/j.colsurfb.2022.112400] [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: 01/10/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/26/2022]
Abstract
The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Eduard Martín-Martínez
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain.
| | - Oscar Betran
- Departament de Física, EETAC, Universitat Politècnica de Catalunya (UPC), c/ Esteve Terrades, 7, 08860 Castelldefels, Spain
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, Rubí, 08191 Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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Badeti S, Jiang Q, Naghizadeh A, Tseng HC, Bushkin Y, Marras SAE, Nisa A, Tyagi S, Chen F, Romanienko P, Yehia G, Evans D, Lopez-Gonzalez M, Alland D, Russo R, Gause W, Shi L, Liu D. Development of a Novel Human CD147 Knock-in NSG Mouse Model to Test SARS-CoV-2 Viral Infection. RESEARCH SQUARE 2022:rs.3.rs-1431484. [PMID: 35475172 PMCID: PMC9040682 DOI: 10.21203/rs.3.rs-1431484/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: An animal model that can mimic the SARS-CoV-2 infection in humans is critical to understanding the rapidly evolving SARS-CoV-2 virus and for development of prophylactic and therapeutic strategies to combat emerging mutants. Studies show that the spike proteins of SARS-CoV and SARS-CoV-2 bind to human angiotensin-converting enzyme 2 (hACE2, a well-recognized, functional receptor for SARS-CoV and SARS-CoV-2) to mediate viral entry. Several hACE2 transgenic (hACE2Tg) mouse models are being widely used, which are clearly invaluable. However, the hACE2Tg mouse model cannot fully explain: 1) low expression of ACE2 observed in human lung and heart, but lung or heart failure occurs frequently in severe COVID-19 patients; 2) low expression of ACE2 on immune cells, but lymphocytopenia occurs frequently in COVID-19 patients; and 3) hACE2Tg mice do not mimic the natural course of SARS-CoV-2 infection in humans. Moreover, one of most outstanding features of coronavirus infection is the diversity of receptor usage, which includes the newly proposed human CD147 (hCD147) as a possible co-receptor for SARS-CoV-2 entry. It is still debatable whether CD147 can serve as a functional receptor for SARS-CoV-2 infection or entry. Results: Here we successfully generated a hCD147 knock-in mouse model (hCD147KI) in the NOD- scid IL2Rgamma null (NSG) background. In this hCD147KI-NSG mouse model, the hCD147 genetic sequence was placed downstream of the endogenous mouse promoter for mouse CD147 (mCD147), which creates an in vivo model that may better recapitulate physiological expression of hCD147 proteins at the molecular level compared to the existing and well-studied K18-hACE2-B6 (JAX) model. In addition, the hCD147KI-NSG mouse model allows further study of SARS-CoV-2 in the immunodeficiency condition which may assist our understanding of this virus in the context of high-risk populations in immunosuppressed states. Our data show 1) the human CD147 protein is expressed in various organs (including bronchiolar epithelial cells) in hCD147KI-NSG mice by immunohistochemical staining and flow cytometry; 2) hCD147KI-NSG mice are marginally sensitive to SARS-CoV-2 infection compared to WT-NSG littermates characterized by increased viral copies by qRT-PCR and moderate body weight decline compared to baseline; 3) a significant increase in leukocytes in the lungs of hCD147KI-NSG mice, compared to infected WT-NSG mice. Conclusions: hCD147KI-NSG mice are more sensitive to COVID-19 infection compared to WT-NSG mice. The hCD147KI-NSG mouse model can serve as an additional animal model for further interrogation whether CD147 serve as an independent functional receptor or accessory receptor for SARS-CoV-2 entry and immune responses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fei Chen
- Rutgers New Jersey Medical School
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Inactivation of various variant types of SARS-CoV-2 by indoor-light-sensitive TiO 2-based photocatalyst. Sci Rep 2022; 12:5804. [PMID: 35422456 PMCID: PMC9010443 DOI: 10.1038/s41598-022-09402-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023] Open
Abstract
Photocatalysts are promising materials for solid-state antiviral coatings to protect against the spread of pandemic coronavirus disease (COVID-19). This paper reports that copper oxide nanoclusters grafted with titanium dioxide (CuxO/TiO2) inactivated the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, including its Delta variant, even under dark condition, and further inactivated it under illumination with a white fluorescent bulb. To investigate its inactivation mechanism, the denaturation of spike proteins of SARS-CoV-2 was examined by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS-PAGE) and enzyme-linked immunosorbent assay (ELISA). In addition to spike proteins, fragmentation of ribonucleic acids in SARS-CoV-2 was investigated by real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). As a result, both spike proteins and RNAs in the SARS-CoV-2 virus were damaged by the CuxO/TiO2 photocatalyst even under dark condition and were further damaged under white fluorescent bulb illumination. Based on the present antiviral mechanism, the CuxO/TiO2 photocatalyst will be effective in inactivating other potential mutant strains of SARS-CoV-2. The CuxO/TiO2 photocatalyst can thus be used to reduce the infectious risk of COVID-19 in an indoor environment, where light illumination is turned on during the day and off during the night.
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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Takumi-Tanimukai Y, Yamamoto S, Ogasawara N, Nakabayashi S, Mizuta K, Yamamoto K, Miyata R, Kakuki T, Jitsukawa S, Sato T, Tsutsumi H, Kojima T, Takano K, Yokota SI. A Hydroxypropyl Methylcellulose Plaque Assay for Human Respiratory Syncytial Virus. J Virol Methods 2022; 304:114528. [DOI: 10.1016/j.jviromet.2022.114528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
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Eddins DJ, Bassit LC, Chandler JD, Haddad NS, Musall KL, Yang J, Kosters A, Dobosh BS, Hernández MR, Ramonell RP, Tirouvanziam RM, Lee FEH, Zandi K, Schinazi RF, Ghosn EEB. Inactivation of SARS-CoV-2 and COVID-19 Patient Samples for Contemporary Immunology and Metabolomics Studies. Immunohorizons 2022; 6:144-155. [PMID: 35173021 PMCID: PMC9164212 DOI: 10.4049/immunohorizons.2200005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 01/13/2023] Open
Abstract
Due to the severity of COVID-19 disease, the U.S. Centers for Disease Control and Prevention and World Health Organization recommend that manipulation of active viral cultures of SARS-CoV-2 and respiratory secretions from COVID-19 patients be performed in biosafety level (BSL)3 laboratories. Therefore, it is imperative to develop viral inactivation procedures that permit samples to be transferred to lower containment levels (BSL2), while maintaining the fidelity of complex downstream assays to expedite the development of medical countermeasures. In this study, we demonstrate optimal conditions for complete viral inactivation following fixation of infected cells with commonly used reagents for flow cytometry, UVC inactivation in sera and respiratory secretions for protein and Ab detection, heat inactivation following cDNA amplification for droplet-based single-cell mRNA sequencing, and extraction with an organic solvent for metabolomic studies. Thus, we provide a suite of viral inactivation protocols for downstream contemporary assays that facilitate sample transfer to BSL2, providing a conceptual framework for rapid initiation of high-fidelity research as the COVID-19 pandemic continues.
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Affiliation(s)
- Devon J Eddins
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA
| | - Leda C Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Joshua D Chandler
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Center for Cystic Fibrosis and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; and
| | - Natalie S Haddad
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - Kathryn L Musall
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Junkai Yang
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Astrid Kosters
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Brian S Dobosh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Center for Cystic Fibrosis and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; and
| | - Mindy R Hernández
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - Richard P Ramonell
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - Rabindra M Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Center for Cystic Fibrosis and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, GA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; and
| | - F Eun-Hyung Lee
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - Keivan Zandi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA
| | - Eliver E B Ghosn
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA;
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA
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[Overview of COVID-19 vaccines licensed in the EU-from technology via clinical trial to registration]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2022; 65:1237-1243. [PMID: 36257986 PMCID: PMC9579648 DOI: 10.1007/s00103-022-03600-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Currently (as of July 2022), six different COVID-19 vaccines are licensed in the EU. These include two mRNA-based vaccines (BNT162b2, Comirnaty® and mRNA-1273, Spikevax®), two adenoviral vector-based vaccines (AZD1222, Vaxzevria® and Ad26.COV2.S, Jcovden®), the subunit vaccine Nuvaxovid® (NVX-CoV2373), and the inactivated virus vaccine VLA2001. Although these vaccines are based on different technologies, they all share the use of the spike protein of SARS-CoV‑2 as antigen.This overview describes the characteristics of their composition, their efficacy, and the impact of various factors on efficacy. Another aspect of this overview is the description of the approval process and the identification of factors that have contributed to the unprecedented speed in the development and approval of vaccines against a pandemic pathogen.
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Do T, Guran R, Adam V, Zitka O. Use of MALDI-TOF mass spectrometry for virus identification: a review. Analyst 2022; 147:3131-3154. [DOI: 10.1039/d2an00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.
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Affiliation(s)
- Tomas Do
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
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Jureka AS, Basler CF. Propagation and Quantification of SARS-CoV-2. Methods Mol Biol 2022; 2452:111-129. [PMID: 35554904 DOI: 10.1007/978-1-0716-2111-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In late 2019, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Since its emergence, SARS-CoV-2 has been responsible for a world-wide pandemic resulting in over 80 million infections and over 1.8 million deaths. The severity of the pandemic has prompted widespread research efforts to more fully understand SARS-CoV-2 and the disease it causes, COVID-19. Research into this novel virus will be facilitated by the availability of clearly described and effective protocols that enable the propagation and quantification of infectious virus. Here, we describe protocols for the propagation of SARS-CoV-2 in Vero E6 cells as well as two human cells lines, the intestinal epithelial Caco-2 cell line and the respiratory epithelial Calu-3 cell line. Additionally, we provide protocols for the quantification of SARS-CoV-2 by plaque assays and immunofocus forming assays in Vero E6 cells utilizing liquid overlays. These protocols provide a foundation for laboratories acquiring the ability to study SARS-CoV-2 to address this ongoing pandemic.
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Affiliation(s)
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Iki S, Sekiguchi K, Kurata Y, Shimizu E, Sugiura A, Yuasa H, Hanaki KI. Effects of various physical and chemical disinfection methods on the fine particle collection efficiency of N95 respirators and surgical masks. Jpn J Infect Dis 2021; 75:341-346. [PMID: 34980707 DOI: 10.7883/yoken.jjid.2021.663] [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: 11/17/2022]
Abstract
There have been many reports on the effectiveness of various disinfection methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their applicability to the disinfection of N95 respirators and surgical masks. To date, there have been no reports on the decontamination of the intermediate layers. In this study, the conditions required for the decontamination of such layers were set by simulation considering the thickness and shape of the N95 respirators or surgical masks (samples). After applying heat (steam, dry heat, or hot water) at 75°C for 60 min or chemical (benzalkonium chloride or laundry detergent) treatment, the collection efficiency of the samples was checked and evaluated. After the dry heat treatment, the time between treatment and when the heat reached the intermediate layer of the filter fiber was extended by 10 min. A dry heat disinfection method that combines hot water and a closed container was also evaluated, and satisfactory conditions were extended by 60 min. For each heat treatment, there was almost no effect on the collection efficiency, although there were cases where deformation was caused by mechanical stress. In contrast, chemical treatment resulted in a reduction in the collection efficiency of smaller particles.
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Affiliation(s)
- Shigeo Iki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Japan
| | | | | | | | | | | | - Ken-Ichi Hanaki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Japan
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Hu S, McCartney MM, Arredondo J, Sankaran-Walters S, Borras E, Harper RW, Schivo M, Davis CE, Kenyon NJ, Dandekar S. Inactivation of SARS-CoV-2 in clinical exhaled breath condensate samples for metabolomic analysis. J Breath Res 2021; 16:10.1088/1752-7163/ac3f24. [PMID: 34852327 PMCID: PMC9809239 DOI: 10.1088/1752-7163/ac3f24] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023]
Abstract
Exhaled breath condensate (EBC) is routinely collected and analyzed in breath research. Because it contains aerosol droplets, EBC samples from SARS-CoV-2 infected individuals harbor the virus and pose the threat of infectious exposure. We report for the first time a safe and consistent method to fully inactivate SARS-CoV-2 in EBC samples and make EBC samples safe for processing and analysis. EBC samples containing infectious SARS-CoV-2 were treated with several concentrations of acetonitrile. The most commonly used 10% acetonitrile treatment for EBC processing failed to completely inactivate the virus in samples and viable virus was detected by the assay of SARS-CoV-2 infection of Vero E6 cells in a biosafety level 3 laboratory. Treatment with either 50% or 90% acetonitrile was effective to completely inactivate the virus, resulting in safe, non-infectious EBC samples that can be used for metabolomic analysis. Our study provides SARS-CoV-2 inactivation protocol for the collection and processing of EBC samples in the clinical setting and for advancing to metabolic assessments in health and disease.
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Affiliation(s)
- Shuang Hu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, United States of America
| | - Mitchell M McCartney
- Mechanical and Aerospace Engineering, University of California Davis, Davis, CA 95616, United States of America,UC Davis Lung Center, Davis, CA 95616, United States of America,VA Northern California Health Care System, Mather, CA 95655, United States of America
| | - Juan Arredondo
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, United States of America
| | - Sumathi Sankaran-Walters
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, United States of America
| | - Eva Borras
- Mechanical and Aerospace Engineering, University of California Davis, Davis, CA 95616, United States of America,UC Davis Lung Center, Davis, CA 95616, United States of America
| | - Richart W Harper
- UC Davis Lung Center, Davis, CA 95616, United States of America,VA Northern California Health Care System, Mather, CA 95655, United States of America,Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, United States of America
| | - Michael Schivo
- UC Davis Lung Center, Davis, CA 95616, United States of America,VA Northern California Health Care System, Mather, CA 95655, United States of America,Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, United States of America
| | - Cristina E Davis
- Mechanical and Aerospace Engineering, University of California Davis, Davis, CA 95616, United States of America,UC Davis Lung Center, Davis, CA 95616, United States of America,VA Northern California Health Care System, Mather, CA 95655, United States of America
| | - Nicholas J Kenyon
- UC Davis Lung Center, Davis, CA 95616, United States of America,VA Northern California Health Care System, Mather, CA 95655, United States of America,Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, United States of America
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, United States of America,Author to whom any correspondence should be addressed.
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El-Sayed NS, Jureka AS, Edwards MR, Lohan S, Williams CG, Keiser PT, Davey RA, Totonchy J, Tiwari RK, Basler CF, Parang K. Synthesis and antiviral activity of fatty acyl conjugates of remdesivir against severe acute respiratory syndrome coronavirus 2 and Ebola virus. Eur J Med Chem 2021; 226:113862. [PMID: 34583312 PMCID: PMC8454092 DOI: 10.1016/j.ejmech.2021.113862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/30/2021] [Accepted: 09/18/2021] [Indexed: 01/18/2023]
Abstract
We report here the synthesis, purification, and characterization of mono- and di-fatty acyl conjugates of remdesivir (RDV) and their in vitro antiviral activity against SAR-CoV-2, an Ebola virus transcription- and replication-competent virus-like particle (trVLP) system, and infectious Ebola virus. The most potent monofatty acyl conjugate was 4b, containing a 4-oxatetradecanolyl at the 3' position. Monofatty acyl conjugates, 3'-O-tetradecanoyl (4a) (IC50(VeroE6) = 2.3 μM; IC50(Calu3) = 0.24 μM), 3'-O-4-oxatetradodecanoyl (4b) (IC50(VeroE6) = 2.0 μM; IC50(Calu3) = 0.18 μM), and 3'-O-(12-ethylthiododecanoyl) (4e) (IC50(VeroE6) = 2.4 μM; IC50(Calu3) = 0.25 μM) derivatives exhibited less activity than RDV (IC50(VeroE6) = 0.85 μM; IC50(Calu3) = 0.06 μM) in both VeroE6 and Calu3 cells. Difatty acylation led to a significant reduction in the antiviral activity of RDV (as shown in conjugates 5a and 5b) against SARS-CoV-2 when compared with monofatty acylation (3a-e and 4a-e). About 77.9% of 4c remained intact after 4 h incubation with human plasma while only 47% of parent RDV was observed at the 2 h time point. The results clearly indicate the effectiveness of fatty acylation to improve the half-life of RDV. The antiviral activities of a number of monofatty acyl conjugates of RDV, such as 3b, 3e, and 4b, were comparable with RDV against the Ebola trVLP system. Meanwhile, the corresponding physical mixtures of RDV and fatty acids 6a and 6b showed 1.6 to 2.2 times less antiviral activity than the corresponding conjugates, 4a and 4c, respectively, against SARS-CoV-2 in VeroE6 cells. A significant reduction in viral RNA synthesis was observed for selected compounds 3a and 4b consistent with the IC50 results. These studies indicate the potential of these compounds as long-acting antiviral agents or prodrugs of RDV.
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Affiliation(s)
- Naglaa Salem El-Sayed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA; Cellulose & Paper Department, National Research Centre, 33 El-Bohouth St. former (El-Tahrir St.), Dokki, Giza P.O. Box, 12622, Egypt
| | - Alexander S Jureka
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | - Megan R Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | - Sandeep Lohan
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA
| | - Caroline G Williams
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | | | - Robert A Davey
- NEIDL, 620 Albany St, Boston University, Boston, MA, 02118, USA
| | - Jennifer Totonchy
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Rakesh K Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA.
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA.
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA.
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43
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Holcar M, Kandušer M, Lenassi M. Blood Nanoparticles - Influence on Extracellular Vesicle Isolation and Characterization. Front Pharmacol 2021; 12:773844. [PMID: 34867406 PMCID: PMC8635996 DOI: 10.3389/fphar.2021.773844] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Blood is a rich source of disease biomarkers, which include extracellular vesicles (EVs). EVs are nanometer-to micrometer-sized spherical particles that are enclosed by a phospholipid bilayer and are secreted by most cell types. EVs reflect the physiological cell of origin in terms of their molecular composition and biophysical characteristics, and they accumulate in blood even when released from remote organs or tissues, while protecting their cargo from degradation. The molecular components (e.g., proteins, miRNAs) and biophysical characteristics (e.g., size, concentration) of blood EVs have been studied as biomarkers of cancers and neurodegenerative, autoimmune, and cardiovascular diseases. However, most biomarker studies do not address the problem of contaminants in EV isolates from blood plasma, and how these might affect downstream EV analysis. Indeed, nonphysiological EVs, protein aggregates, lipoproteins and viruses share many molecular and/or biophysical characteristics with EVs, and can therefore co-isolate with EVs from blood plasma. Consequently, isolation and downstream analysis of EVs from blood plasma remain a unique challenge, with important impacts on the outcomes of biomarker studies. To help improve rigor, reproducibility, and reliability of EV biomarker studies, we describe here the major contaminants of EV isolates from blood plasma, and we report on how different EV isolation methods affect their levels, and how contaminants that remain can affect the interpretation of downstream EV analysis.
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Affiliation(s)
- Marija Holcar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maša Kandušer
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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44
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Fumagalli MJ, Castro-Jorge LA, Fraga-Silva TFDC, de Azevedo PO, Capato CF, Rattis BAC, Hojo-Souza NS, Floriano VG, de Castro JT, Ramos SG, da Fonseca BAL, Bonato VLD, Gazzinelli RT, Figueiredo LTM. Protective Immunity against Gamma and Zeta Variants after Inactivated SARS-CoV-2 Virus Immunization. Viruses 2021; 13:2440. [PMID: 34960708 PMCID: PMC8707686 DOI: 10.3390/v13122440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/27/2021] [Accepted: 11/28/2021] [Indexed: 01/08/2023] Open
Abstract
The persistent circulation of SARS-CoV-2 represents an ongoing global threat due to the emergence of new viral variants that can sometimes evade the immune system of previously exposed or vaccinated individuals. We conducted a follow-up study of adult individuals that had received an inactivated SARS-CoV-2 vaccine, evaluating antibody production and neutralizing activity over a period of 6 months. In addition, we performed mice immunization with inactivated SARS-CoV-2, and evaluated the immune response and pathological outcomes against Gamma and Zeta variant infection. Vaccinated individuals produced high levels of antibodies with robust neutralizing activity, which was significantly reduced against Gamma and Zeta variants. Production of IgG anti-S antibodies and neutralizing activity robustly reduced after 6 months of vaccination. Immunized mice demonstrated cellular response against Gamma and Zeta variants, and after viral infection, reduced viral loads, IL-6 expression, and histopathological outcome in the lungs. TNF levels were unchanged in immunized or not immunized mice after infection with the Gamma variant. Furthermore, serum neutralization activity rapidly increases after infection with the Gamma and Zeta variants. Our data suggest that immunization with inactivated WT SARS-CoV-2 induces a promptly responsive cross-reactive immunity response against the Gamma and Zeta variants, reducing COVID-19 pathological outcomes.
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Affiliation(s)
- Marcilio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
- Basic and Applied Immunology Program, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (V.L.D.B.); (R.T.G.)
| | - Luiza Antunes Castro-Jorge
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
| | | | - Patrick Orestes de Azevedo
- Immunopathology Laboratory, René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Minas Gerais, Brazil; (P.O.d.A.); (N.S.H.-S.); (J.T.d.C.)
| | - Carlos Fabiano Capato
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
| | - Bruna Amanda Cruz Rattis
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (B.A.C.R.); (S.G.R.)
| | - Natália Satchiko Hojo-Souza
- Immunopathology Laboratory, René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Minas Gerais, Brazil; (P.O.d.A.); (N.S.H.-S.); (J.T.d.C.)
| | - Vitor Gonçalves Floriano
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
| | - Julia Teixeira de Castro
- Immunopathology Laboratory, René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Minas Gerais, Brazil; (P.O.d.A.); (N.S.H.-S.); (J.T.d.C.)
| | - Simone Gusmão Ramos
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (B.A.C.R.); (S.G.R.)
| | - Benedito Antônio Lopes da Fonseca
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
| | - Vânia Luiza Deperon Bonato
- Basic and Applied Immunology Program, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (V.L.D.B.); (R.T.G.)
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil;
| | - Ricardo Tostes Gazzinelli
- Basic and Applied Immunology Program, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (V.L.D.B.); (R.T.G.)
- Immunopathology Laboratory, René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Minas Gerais, Brazil; (P.O.d.A.); (N.S.H.-S.); (J.T.d.C.)
- Platform of Translational Medicine, Fundação Oswaldo Cruz, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (L.A.C.-J.); (C.F.C.); (V.G.F.); (B.A.L.d.F.); (L.T.M.F.)
- Basic and Applied Immunology Program, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (V.L.D.B.); (R.T.G.)
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Baczenas JJ, Andersen H, Rashid S, Yarmosh D, Puthuveetil N, Parker M, Bradford R, Florence C, Stemple KJ, Lewis MG, O’Connor SL. Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike. Viruses 2021; 13:v13122434. [PMID: 34960703 PMCID: PMC8704555 DOI: 10.3390/v13122434] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.
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Affiliation(s)
| | - Hanne Andersen
- BIOQUAL, Inc., Rockville, MD 20852, USA; (H.A.); (M.G.L.)
| | - Sujatha Rashid
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - David Yarmosh
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Nikhita Puthuveetil
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Michael Parker
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Rebecca Bradford
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Clint Florence
- Office of Biodefense, Research Resources and Translational Research, Division of Microbiology and Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA; (C.F.); (K.J.S.)
| | - Kimberly J. Stemple
- Office of Biodefense, Research Resources and Translational Research, Division of Microbiology and Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA; (C.F.); (K.J.S.)
| | - Mark G. Lewis
- BIOQUAL, Inc., Rockville, MD 20852, USA; (H.A.); (M.G.L.)
| | - Shelby L. O’Connor
- Wisconsin National Primate Center, UW-Madison, Madison, WI 53711, USA;
- Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53705, USA
- Correspondence: ; Tel.: +1-608-890-0843
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46
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Afaghi P, Lapolla MA, Ghandi K. Denaturation of the SARS-CoV-2 spike protein under non-thermal microwave radiation. Sci Rep 2021; 11:23373. [PMID: 34862423 PMCID: PMC8642515 DOI: 10.1038/s41598-021-02753-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/18/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19, is still a widespread threat to society. The spike protein of this virus facilitates viral entry into the host cell. Here, the denaturation of the S1 subunit of this spike protein by 2.45 GHz electromagnetic radiation was studied quantitatively. The study only pertains to the pure electromagnetic effects by eliminating the bulk heating effect of the microwave radiation in an innovative setup that is capable of controlling the temperature of the sample at any desired intensity of the electromagnetic field. This study was performed at the internal human body temperature, 37 °C, for a relatively short amount of time under a high-power electromagnetic field. The results showed that irradiating the protein with a 700 W, 2.45 GHz electromagnetic field for 2 min can denature the protein to around 95%. In comparison, this is comparable to thermal denaturation at 75 °C for 40 min. Electromagnetic denaturation of the proteins of the virus may open doors to potential therapeutic or sanitation applications.
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Affiliation(s)
- Pooya Afaghi
- Department of Chemistry, University of Gulph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
| | | | - Khashayar Ghandi
- Department of Chemistry, University of Gulph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada.
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47
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Hayashi K, Asai S, Umezawa K, Kakizoe H, Miyachi H, Morita M, Akaike T, Kuno H, Komatsu S, Watanabe T, Kawahara T. Virucidal effect of monogalactosyl diacylglyceride from a green microalga, Coccomyxa sp. KJ, against clinical isolates of SARS-CoV-2 as assessed by a plaque assay. J Clin Lab Anal 2021; 36:e24146. [PMID: 34837712 PMCID: PMC8761427 DOI: 10.1002/jcla.24146] [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: 08/20/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19) and is capable of human-to-human transmission and rapid global spread. Thus, the establishment of high-quality viral detection and quantification methods, and the development of anti-SARS-CoV-2 agents are critical. METHODS Here, we present the rapid detection of infectious SARS-CoV-2 particles using a plaque assay with 0.5% agarose-ME (Medium Electroosmosis) as an overlay medium. RESULTS The plaques were capable of detecting the virus within 36-40 h post-infection. In addition, we showed that a monogalactosyl diacylglyceride isolated from a microalga (Coccomyxa sp. KJ) could inactivate the clinical isolates of SARS-CoV-2 in a time- and concentration-dependent manner. CONCLUSIONS These results would allow rapid quantification of the infectious virus titers and help develop more potent virucidal agents against SARS-CoV-2.
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Affiliation(s)
- Kyoko Hayashi
- College of Life and Health Sciences, Chubu University, Kasugai, Japan
| | - Satomi Asai
- Department of laboratory Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Kazuo Umezawa
- Department of Emergency and Critical Care, School of Medicine, Tokai University, Isehara, Japan
| | - Hidehumi Kakizoe
- Department of laboratory Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Hayato Miyachi
- Department of laboratory Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Masanobu Morita
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takaaki Akaike
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | | | | | - Takumi Watanabe
- College of Life and Health Sciences, Chubu University, Kasugai, Japan
| | - Toshio Kawahara
- College of Life and Health Sciences, Chubu University, Kasugai, Japan
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48
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Reiterer M, Rajan M, Gómez-Banoy N, Lau JD, Gomez-Escobar LG, Ma L, Gilani A, Alvarez-Mulett S, Sholle ET, Chandar V, Bram Y, Hoffman K, Bhardwaj P, Piloco P, Rubio-Navarro A, Uhl S, Carrau L, Houhgton S, Redmond D, Shukla AP, Goyal P, Brown KA, tenOever BR, Alonso LC, Schwartz RE, Schenck EJ, Safford MM, Lo JC. Hyperglycemia in acute COVID-19 is characterized by insulin resistance and adipose tissue infectivity by SARS-CoV-2. Cell Metab 2021; 33:2174-2188.e5. [PMID: 34599884 PMCID: PMC8443335 DOI: 10.1016/j.cmet.2021.09.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023]
Abstract
Individuals infected with SARS-CoV-2 who also display hyperglycemia suffer from longer hospital stays, higher risk of developing acute respiratory distress syndrome (ARDS), and increased mortality. Nevertheless, the pathophysiological mechanism of hyperglycemia in COVID-19 remains poorly characterized. Here, we show that hyperglycemia is similarly prevalent among patients with ARDS independent of COVID-19 status. Yet among patients with ARDS and COVID-19, insulin resistance is the prevalent cause of hyperglycemia, independent of glucocorticoid treatment, which is unlike patients with ARDS but without COVID-19, where pancreatic beta cell failure predominates. A screen of glucoregulatory hormones revealed lower levels of adiponectin in patients with COVID-19. Hamsters infected with SARS-CoV-2 demonstrated a strong antiviral gene expression program in the adipose tissue and diminished expression of adiponectin. Moreover, we show that SARS-CoV-2 can infect adipocytes. Together these data suggest that SARS-CoV-2 may trigger adipose tissue dysfunction to drive insulin resistance and adverse outcomes in acute COVID-19.
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Affiliation(s)
- Moritz Reiterer
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mangala Rajan
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicolás Gómez-Banoy
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer D Lau
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luis G Gomez-Escobar
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lunkun Ma
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ankit Gilani
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergio Alvarez-Mulett
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Evan T Sholle
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Vasuretha Chandar
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Katherine Hoffman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Bhardwaj
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Phoebe Piloco
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alfonso Rubio-Navarro
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean Houhgton
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - David Redmond
- Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Alpana P Shukla
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Parag Goyal
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kristy A Brown
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura C Alonso
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Departments of Medicine and Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Monika M Safford
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - James C Lo
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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49
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Boix-Amorós A, Piras E, Bu K, Wallach D, Stapylton M, Fernández-Sesma A, Malaspina D, Clemente JC. Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner. mSystems 2021; 6:e0067421. [PMID: 34609165 PMCID: PMC8547476 DOI: 10.1128/msystems.00674-21] [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: 06/02/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022] Open
Abstract
The global emergence of novel pathogenic viruses presents an important challenge for research, as high biosafety levels are required to process samples. While inactivation of infectious agents facilitates the use of less stringent safety conditions, its effect on other biological entities of interest present in the sample is generally unknown. Here, we analyzed the effect of five inactivation methods (heat, ethanol, formaldehyde, psoralen, and TRIzol) on microbiome composition and diversity in samples collected from four different body sites (gut, nasal, oral, and skin) and compared them against untreated samples from the same tissues. We performed 16S rRNA gene sequencing and estimated abundance and diversity of bacterial taxa present in all samples. Nasal and skin samples were the most affected by inactivation, with ethanol and TRIzol inducing the largest changes in composition, and heat, formaldehyde, TRIzol, and psoralen inducing the largest changes in diversity. Oral and stool microbiomes were more robust to inactivation, with no significant changes in diversity and only moderate changes in composition. Firmicutes was the taxonomic group least affected by inactivation, while Bacteroidetes had a notable enrichment in nasal samples and moderate enrichment in fecal and oral samples. Actinobacteria were more notably depleted in fecal and skin samples, and Proteobacteria exhibited a more variable behavior depending on sample type and inactivation method. Overall, our results demonstrate that inactivation methods can alter the microbiome in a tissue-specific manner and that careful consideration should be given to the choice of method based on the sample type under study. IMPORTANCE Understanding how viral infections impact and are modulated by the microbiome is an important problem in basic research but is also of high clinical relevance under the current pandemic. To facilitate the study of interactions between microbial communities and pathogenic viruses under safe conditions, the infectious agent is generally inactivated prior to processing samples. The effect of this inactivation process in the microbiome is, however, unknown. Further, it is unclear whether biases introduced by inactivation methods are dependent on the sample type under study. Estimating the magnitude and nature of the changes induced by different methods in samples collected from various body sites thus provides important information for current and future studies that require inactivation of pathogenic agents.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Enrica Piras
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Wallach
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew Stapylton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernández-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Dolores Malaspina
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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50
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Forgacs D, Jang H, Abreu RB, Hanley HB, Gattiker JL, Jefferson AM, Ross TM. SARS-CoV-2 mRNA Vaccines Elicit Different Responses in Immunologically Naïve and Pre-Immune Humans. Front Immunol 2021; 12:728021. [PMID: 34646267 PMCID: PMC8502960 DOI: 10.3389/fimmu.2021.728021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
As the COVID-19 pandemic continues, the authorization of vaccines for emergency use has been crucial in slowing down the rate of infection and transmission of the SARS-CoV-2 virus that causes COVID-19. In order to investigate the longitudinal serological responses to SARS-CoV-2 natural infection and vaccination, a large-scale, multi-year serosurveillance program entitled SPARTA (SARS SeroPrevalence and Respiratory Tract Assessment) was initiated at 4 locations in the U.S. The serological assay presented here measuring IgG binding to the SARS-CoV-2 receptor binding domain (RBD) detected antibodies elicited by SARS-CoV-2 infection or vaccination with a 95.5% sensitivity and a 95.9% specificity. We used this assay to screen more than 3100 participants and selected 20 previously infected pre-immune and 32 immunologically naïve participants to analyze their antibody binding to RBD and viral neutralization (VN) responses following vaccination with two doses of either the Pfizer-BioNTech BNT162b2 or the Moderna mRNA-1273 vaccine. Vaccination not only elicited a more robust immune reaction than natural infection, but the level of neutralizing and anti-RBD antibody binding after vaccination is also significantly higher in pre-immune participants compared to immunologically naïve participants (p<0.0033). Furthermore, the administration of the second vaccination did not further increase the neutralizing or binding antibody levels in pre-immune participants (p=0.69). However, ~46% of the immunologically naïve participants required both vaccinations to seroconvert.
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Affiliation(s)
- David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Hyesun Jang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Rodrigo B Abreu
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Hannah B Hanley
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Jasper L Gattiker
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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