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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [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: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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Rodríguez-Hernández MÁ, Baena-Bustos M, Carneros D, Zurita-Palomo C, Muñoz-Pinillos P, Millán J, Padillo FJ, Smerdou C, von Kobbe C, Rose-John S, Bustos M. Targeting IL-6 trans-signalling by sgp130Fc attenuates severity in SARS-CoV-2 -infected mice and reduces endotheliopathy. EBioMedicine 2024; 103:105132. [PMID: 38677182 PMCID: PMC11061249 DOI: 10.1016/j.ebiom.2024.105132] [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: 09/06/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND SARS-CoV-2 infection is considered as a relapsing inflammatory process with a dysregulation of IL-6 signalling. Classic IL-6 signalling is thought to represent a defence mechanism against pathogens. In contrast, IL-6 trans-signalling has pro-inflammatory effects. In severe COVID-19, therapeutic strategies have focused on global inhibition of IL-6, with controversial results. We hypothesized that specific blockade of IL-6 trans-signalling could inhibit inflammatory response preserving the host defence activity inherent to IL-6 classic signalling. METHODS To test the role of the specific IL-6 trans-signalling inhibition by sgp130Fc in short- and long-term consequences of COVID-19, we used the established K18-hACE2 transgenic mouse model. Histological as well as immunohistochemical analysis, and pro-inflammatory marker profiling were performed. To investigate IL-6 trans-signalling in human cells we used primary lung microvascular endothelial cells and fibroblasts in the presence/absence of sgp130Fc. FINDINGS We report that targeting IL-6 trans-signalling by sgp130Fc attenuated SARS-CoV-2-related clinical symptoms and mortality. In surviving mice, the treatment caused a significant decrease in lung damage. In vitro, IL-6 trans-signalling induced strong and persisting JAK1/STAT3 activation in endothelial cells and lung fibroblasts with proinflammatory effects, which were attenuated by sgp130Fc. Our data also suggest that in those cells with scant amounts of IL-6R, the induction of gp130 and IL-6 by IL-6:sIL-6R complex sustains IL-6 trans-signalling. INTERPRETATION IL-6 trans-signalling fosters progression of COVID-19, and suggests that specific blockade of this signalling mode could offer a promising alternative to mitigate both short- and long-term consequences without affecting the beneficial effects of IL-6 classic signalling. These results have implications for the development of new therapies of lung injury and endotheliopathy in COVID-19. FUNDING The project was supported by ISCIII, Spain (COV-20/00792 to MB, PI23/01351 to MARH) and the European Commission-Next generation EU (European Union) (Regulation EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global, SGL2103029 to MB). PID2019-110587RB-I00 (MB) supported by MICIN/AEI/10.13039/501100011033/and PID2022-143034OB-I00 (MB) by MICIN/AEI/10.13039/501100011033/FEDER. MAR-H acknowledges support from ISCIII, Spain and the European Commission-Next generation EU (European Union), through CSIC's Global Health PTI.
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Affiliation(s)
- María Ángeles Rodríguez-Hernández
- Area of Liver, Digestive and Inflammatory Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital (HUVR), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain.
| | - Mercedes Baena-Bustos
- Pneumology Unit, Institute of Biomedicine of Seville (IBiS), Virgen Macarena University Hospital (HUVM), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain
| | - David Carneros
- Area of Liver, Digestive and Inflammatory Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital (HUVR), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain
| | - Carola Zurita-Palomo
- Area of Liver, Digestive and Inflammatory Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital (HUVR), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain
| | - Pablo Muñoz-Pinillos
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Jaime Millán
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Francisco Javier Padillo
- Area of Liver, Digestive and Inflammatory Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital (HUVR), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain
| | - Cristian Smerdou
- Division of DNA and RNA Medicine, Cima Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), and CCUN, Pamplona, Spain
| | - Cayetano von Kobbe
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, Cantoblanco, Madrid, Spain
| | | | - Matilde Bustos
- Area of Liver, Digestive and Inflammatory Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital (HUVR), Spanish National Research Council (CSIC), University of Seville (US), Seville, Spain.
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Guimaraes LC, Costa PAC, Scalzo Júnior SRA, Ferreira HAS, Braga ACS, de Oliveira LC, Figueiredo MM, Shepherd S, Hamilton A, Queiroz-Junior CM, da Silva WN, da Silva NJA, Rodrigues Alves MT, Santos AK, de Faria KKS, Marim FM, Fukumasu H, Birbrair A, Teixeira-Carvalho A, de Aguiar RS, Mitchell MJ, Teixeira MM, Vasconcelos Costa V, Frezard F, Guimaraes PPG. Nanoparticle-based DNA vaccine protects against SARS-CoV-2 variants in female preclinical models. Nat Commun 2024; 15:590. [PMID: 38238326 PMCID: PMC10796936 DOI: 10.1038/s41467-024-44830-1] [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: 03/31/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
A safe and effective vaccine with long-term protection against SARS-CoV-2 variants of concern (VOCs) is a global health priority. Here, we develop lipid nanoparticles (LNPs) to provide safe and effective delivery of plasmid DNA (pDNA) and show protection against VOCs in female small animal models. Using a library of LNPs encapsulating unique barcoded DNA (b-DNA), we screen for b-DNA delivery after intramuscular administration. The top-performing LNPs are further tested for their capacity of pDNA uptake in antigen-presenting cells in vitro. The lead LNP is used to encapsulate pDNA encoding the HexaPro version of SARS-CoV-2 spike (LNP-HPS) and immunogenicity and protection is tested in vivo. LNP-HPS elicit a robust protective effect against SARS-CoV-2 Gamma (P.1), correlating with reduced lethality, decreased viral load in the lungs and reduced lung damage. LNP-HPS induce potent humoral and T cell responses against P.1, and generate high levels of neutralizing antibodies against P.1 and Omicron (B.1.1.529). Our findings indicate that the protective efficacy and immunogenicity elicited by LNP-HPS are comparable to those achieved by the approved COVID-19 vaccine from Biontech/Pfizer in animal models. Together, these findings suggest that LNP-HPS hold great promise as a vaccine candidate against VOCs.
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Affiliation(s)
- Lays Cordeiro Guimaraes
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Pedro Augusto Carvalho Costa
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Sérgio Ricardo Aluotto Scalzo Júnior
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Heloísa Athaydes Seabra Ferreira
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Ana Carolina Soares Braga
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Leonardo Camilo de Oliveira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | | | - Sarah Shepherd
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex Hamilton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | | | - Walison Nunes da Silva
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Natália Jordana Alves da Silva
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Marco Túllio Rodrigues Alves
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Anderson Kenedy Santos
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Kevin Kelton Santos de Faria
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Fernanda Martins Marim
- Department of Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Heidge Fukumasu
- Department of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, São Paulo, Brazil
| | - Alexander Birbrair
- Department of Dermatology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Andréa Teixeira-Carvalho
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Minas Gerais, Brazil
| | - Renato Santana de Aguiar
- Department of Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Mauro Martins Teixeira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Vivian Vasconcelos Costa
- Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Frederic Frezard
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Pedro Pires Goulart Guimaraes
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil.
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Kwon DI, Park S, Jeong YL, Kim YM, Min J, Lee C, Choi JA, Choi YH, Kong HJ, Choi Y, Baek S, Lee KJ, Kang YW, Jeong C, You G, Oh Y, Im SK, Song M, Kim JK, Chang J, Choi D, Lee SW. Fc-fused IL-7 provides broad antiviral effects against respiratory virus infections through IL-17A-producing pulmonary innate-like T cells. Cell Rep Med 2024; 5:101362. [PMID: 38232693 PMCID: PMC10829794 DOI: 10.1016/j.xcrm.2023.101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/15/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Repeated pandemics caused by the influenza virus and severe acute respiratory syndrome coronavirus (SARS-CoV) have resulted in serious problems in global public health, emphasizing the need for broad-spectrum antiviral therapeutics against respiratory virus infections. Here, we show the protective effects of long-acting recombinant human interleukin-7 fused with hybrid Fc (rhIL-7-hyFc) against major respiratory viruses, including influenza virus, SARS-CoV-2, and respiratory syncytial virus. Administration of rhIL-7-hyFc in a therapeutic or prophylactic regimen induces substantial antiviral effects. During an influenza A virus (IAV) infection, rhIL-7-hyFc treatment increases pulmonary T cells composed of blood-derived interferon γ (IFNγ)+ conventional T cells and locally expanded IL-17A+ innate-like T cells. Single-cell RNA transcriptomics reveals that rhIL-7-hyFc upregulates antiviral genes in pulmonary T cells and induces clonal expansion of type 17 innate-like T cells. rhIL-7-hyFc-mediated disease prevention is dependent on IL-17A in both IAV- and SARS-CoV-2-infected mice. Collectively, we suggest that rhIL-7-hyFc can be used as a broadly active therapeutic for future respiratory virus pandemic.
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Affiliation(s)
- Dong-Il Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Subin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Yujin L Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Young-Min Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Jeongyong Min
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Changhyung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Jung-Ah Choi
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Yoon Ha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Hyun-Jung Kong
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Youngwon Choi
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seungtae Baek
- Research Institute of NeoImmuneTech Co., Ltd., Pohang 37666, Republic of Korea
| | - Kun-Joo Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Yeon-Woo Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Chaerim Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Gihoon You
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Youngsik Oh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Sun-Kyoung Im
- Research Institute of NeoImmuneTech Co., Ltd., Pohang 37666, Republic of Korea
| | - Manki Song
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea
| | - Jun Chang
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Donghoon Choi
- Research Institute of NeoImmuneTech Co., Ltd., Pohang 37666, Republic of Korea.
| | - Seung-Woo Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37666, Republic of Korea.
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Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024; 52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
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Affiliation(s)
- Yuzhou Feng
- Department of Laboratory Medicine and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiahao Yi
- School of Big Health, Guizhou Medical University, Guiyang 550025, China
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Silva BJDA, Krogstad PA, Teles RMB, Andrade PR, Rajfer J, Ferrini MG, Yang OO, Bloom BR, Modlin RL. IFN-γ-mediated control of SARS-CoV-2 infection through nitric oxide. Front Immunol 2023; 14:1284148. [PMID: 38162653 PMCID: PMC10755032 DOI: 10.3389/fimmu.2023.1284148] [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: 08/28/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The COVID-19 pandemic has highlighted the need to identify mechanisms of antiviral host defense against SARS-CoV-2. One such mediator is interferon-g (IFN-γ), which, when administered to infected patients, is reported to result in viral clearance and resolution of pulmonary symptoms. IFN-γ treatment of a human lung epithelial cell line triggered an antiviral activity against SARS-CoV-2, yet the mechanism for this antiviral response was not identified. Methods Given that IFN-γ has been shown to trigger antiviral activity via the generation of nitric oxide (NO), we investigated whether IFN-γ induction of antiviral activity against SARS-CoV-2 infection is dependent upon the generation of NO in human pulmonary epithelial cells. We treated the simian epithelial cell line Vero E6 and human pulmonary epithelial cell lines, including A549-ACE2, and Calu-3, with IFN-γ and observed the resulting induction of NO and its effects on SARS-CoV-2 replication. Pharmacological inhibition of inducible nitric oxide synthase (iNOS) was employed to assess the dependency on NO production. Additionally, the study examined the effect of interleukin-1b (IL-1β) on the IFN-g-induced NO production and its antiviral efficacy. Results Treatment of Vero E6 cells with IFN-γ resulted in a dose-responsive induction of NO and an inhibitory effect on SARS-CoV-2 replication. This antiviral activity was blocked by pharmacologic inhibition of iNOS. IFN-γ also triggered a NO-mediated antiviral activity in SARS-CoV-2 infected human lung epithelial cell lines A549-ACE2 and Calu-3. IL-1β enhanced IFN-γ induction of NO, but it had little effect on antiviral activity. Discussion Given that IFN-g has been shown to be produced by CD8+ T cells in the early response to SARS-CoV-2, our findings in human lung epithelial cell lines, of an IFN-γ-triggered, NO-dependent, links the adaptive immune response to an innate antiviral pathway in host defense against SARS-CoV-2. These results underscore the importance of IFN-γ and NO in the antiviral response and provide insights into potential therapeutic strategies for COVID-19.
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Affiliation(s)
- Bruno J. de Andrade Silva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Paul A. Krogstad
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, United States
| | - Rosane M. B. Teles
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Priscila R. Andrade
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Jacob Rajfer
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Monica G. Ferrini
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Health and Life Sciences, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| | - Otto O. Yang
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Barry R. Bloom
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Robert L. Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
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Fricke C, Pfaff F, Ulrich L, Halwe NJ, Schön J, Timm L, Hoffmann W, Rauch S, Petsch B, Hoffmann D, Beer M, Corleis B, Dorhoi A. SARS-CoV-2 variants of concern elicit divergent early immune responses in hACE2 transgenic mice. Eur J Immunol 2023; 53:e2250332. [PMID: 37609807 DOI: 10.1002/eji.202250332] [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: 12/13/2022] [Revised: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
Knowledge about early immunity to SARS-CoV-2 variants of concern mainly comes from the analysis of human blood. Such data provide limited information about host responses at the site of infection and largely miss the initial events. To gain insights into compartmentalization and the early dynamics of host responses to different SARS-CoV-2 variants, we utilized human angiotensin converting enzyme 2 (hACE2) transgenic mice and tracked immune changes during the first days after infection by RNAseq, multiplex assays, and flow cytometry. Viral challenge infection led to divergent viral loads in the lungs, distinct inflammatory patterns, and innate immune cell accumulation in response to ancestral SARS-CoV-2, Beta (B.1.351) and Delta (B.1.617.2) variant of concern (VOC). Compared to other SARS-CoV-2 variants, infection with Beta (B.1.351) VOC spread promptly to the lungs, leading to increased inflammatory responses. SARS-CoV-2-specific antibodies and T cells developed within the first 7 days postinfection and were required to reduce viral spread and replication. Our studies show that VOCs differentially trigger transcriptional profiles and inflammation. This information contributes to the basic understanding of immune responses immediately postexposure to SARS-CoV-2 and is relevant for developing pan-VOC interventions including prophylactic vaccines.
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Affiliation(s)
- Charlie Fricke
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacob Schön
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Laura Timm
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Weda Hoffmann
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | | | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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8
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Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell 2023; 186:4597-4614.e26. [PMID: 37738970 PMCID: PMC10604369 DOI: 10.1016/j.cell.2023.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.
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Affiliation(s)
- Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ann-Kathrin Reuschl
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Lucy G Thorne
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Manisha R Ummadi
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Chengjin Ye
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Romel Rosales
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M Jang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Abdullah M Syed
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noa Deutsch
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Pirak
- School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Briana L McGovern
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK
| | - Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nicholas F Liotta
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA
| | - Thomas Kehrer
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Rutkowska
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alyssa Hoffert
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Charles Ochieng' Olwal
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Weiqing Huang
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Pham
- Synthego Corporation, Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | | | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ignacia Echeverria
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kliment Verba
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Jennifer A Doudna
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Luis Martinez-Sobrido
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lisa Miorin
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris White
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Clare Jolly
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Greg J Towers
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
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Lepretre F, Gras D, Chanez P, Duez C. Natural killer cells in the lung: potential role in asthma and virus-induced exacerbation? Eur Respir Rev 2023; 32:230036. [PMID: 37437915 DOI: 10.1183/16000617.0036-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023] Open
Abstract
Asthma is a chronic inflammatory airway disorder whose pathophysiological and immunological mechanisms are not completely understood. Asthma exacerbations are mostly driven by respiratory viral infections and characterised by worsening of symptoms. Despite current therapies, asthma exacerbations can still be life-threatening. Natural killer (NK) cells are innate lymphoid cells well known for their antiviral activity and are present in the lung as circulating and resident cells. However, their functions in asthma and its exacerbations are still unclear. In this review, we will address NK cell activation and functions, which are particularly relevant for asthma and virus-induced asthma exacerbations. Then, the role of NK cells in the lungs at homeostasis in healthy individuals will be described, as well as their functions during pulmonary viral infections, with an emphasis on those associated with asthma exacerbations. Finally, we will discuss the involvement of NK cells in asthma and virus-induced exacerbations and examine the effect of asthma treatments on NK cells.
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Affiliation(s)
- Florian Lepretre
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Delphine Gras
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Pascal Chanez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
- APHM, Hôpital Nord, Clinique des Bronches, de l'allergie et du sommeil, Marseille, France
| | - Catherine Duez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
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10
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Shahbaz S, Bozorgmehr N, Lu J, Osman M, Sligl W, Tyrrell DL, Elahi S. Analysis of SARS-CoV-2 isolates, namely the Wuhan strain, Delta variant, and Omicron variant, identifies differential immune profiles. Microbiol Spectr 2023; 11:e0125623. [PMID: 37676005 PMCID: PMC10581158 DOI: 10.1128/spectrum.01256-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
There is an urgent need to better understand the impact of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on immune response and disease dynamics to facilitate better intervention strategies. Here, we show that SARS-CoV-2 variants differentially affect host immune responses. The magnitude and quantity of cytokines and chemokines were comparable in those infected with the Wuhan strain and the Delta variant. However, individuals infected with the Omicron variant had significantly lower levels of these mediators. We also found an elevation of plasma galectins (Gal-3, Gal-8, and Gal-9) in infected individuals, in particular, in those with the original strain. Soluble galectins exert a proinflammatory role in COVID-19 pathogenesis. This was illustrated by their correlation with the plasma levels of sCD14, sCD163, enhanced TNF-α/IL-6 secretion, and increased SARS-CoV-2 infectivity in vitro. Moreover, we observed enhanced CD4+ and CD8+ T cell activation in Wuhan strain-infected individuals. Surprisingly, there was a more pronounced T cell activation in those infected with the Omicron in comparison to the Delta variant. In line with T cell activation status, we observed a more pronounced expansion of T cells expressing different co-inhibitory receptors in patients infected with the Wuhan strain, followed by the Omicron and Delta variants. Individuals infected with the Wuhan strain or the Omicron variant had a similar pattern of plasma soluble immune checkpoints. Our results imply that a milder innate immune response might be beneficial and protective in those infected with the Omicron variant. Our results provide a novel insight into the differential impact of SARS-CoV-2 variants on host immunity. IMPORTANCE There is a need to better understand how different SARS-CoV-2 variants influence the immune system and disease dynamics to facilitate the development of better vaccines and therapies. We compared immune responses in 140 SARS-CoV-2-infected individuals with the Wuhan strain, the Delta variant, or the Omicron variant. All these patients were admitted to the intensive care unit and were SARS-CoV-2 vaccination naïve. We found that SARS-CoV-2 variants differentially affect the host immune response. This was done by measuring soluble biomarkers in their plasma and examining different immune cells. Overall, we found that the magnitude of cytokine storm in individuals infected with the Wuhan strain or the Delta variant was greater than in those infected with the Omicron variant. In light of enhanced cytokine release syndrome in individuals infected with the Wuhan strain or the Delta variant, we believe that a milder innate immune response might be beneficial and protective in those infected with the Omicron variant.
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Affiliation(s)
- Shima Shahbaz
- Division of Foundational Sciences, School of Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Najmeh Bozorgmehr
- Division of Foundational Sciences, School of Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Julia Lu
- Division of Foundational Sciences, School of Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohammed Osman
- Division of Rheumatology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy Sligl
- Department of Critical Care Medicine, University of Alberta, Edmonton, Alberta, Canada
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - D. Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Shokrollah Elahi
- Division of Foundational Sciences, School of Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Women and Children Health Research Institute (WCHRI), University of Alberta, Edmonton, Alberta, Canada
- Glycomics Institute of Alberta, University of Alberta, Edmonton, Alberta, Canada
- Alberta Transplant Institute, University of Alberta, Edmonton, Alberta, Canada
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11
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Corleis B, Bastian M, Hoffmann D, Beer M, Dorhoi A. Animal models for COVID-19 and tuberculosis. Front Immunol 2023; 14:1223260. [PMID: 37638020 PMCID: PMC10451089 DOI: 10.3389/fimmu.2023.1223260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Respiratory infections cause tremendous morbidity and mortality worldwide. Amongst these diseases, tuberculosis (TB), a bacterial illness caused by Mycobacterium tuberculosis which often affects the lung, and coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), stand out as major drivers of epidemics of global concern. Despite their unrelated etiology and distinct pathology, these infections affect the same vital organ and share immunopathogenesis traits and an imperative demand to model the diseases at their various progression stages and localizations. Due to the clinical spectrum and heterogeneity of both diseases experimental infections were pursued in a variety of animal models. We summarize mammalian models employed in TB and COVID-19 experimental investigations, highlighting the diversity of rodent models and species peculiarities for each infection. We discuss the utility of non-human primates for translational research and emphasize on the benefits of non-conventional experimental models such as livestock. We epitomize advances facilitated by animal models with regard to understanding disease pathophysiology and immune responses. Finally, we highlight research areas necessitating optimized models and advocate that research of pulmonary infectious diseases could benefit from cross-fertilization between studies of apparently unrelated diseases, such as TB and COVID-19.
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Affiliation(s)
- Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Max Bastian
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, Greifswald, Germany
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12
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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: 2] [Impact Index Per Article: 2.0] [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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13
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Barreto EA, Cruz AS, Veras FP, Martins R, Bernardelli RS, Paiva IM, Lima TM, Singh Y, Guimarães RC, Damasceno S, Pereira N, Alves JM, Gonçalves TT, Forato J, Muraro SP, Souza GF, Batah SS, Proenca-Modena JL, Mori MA, Cunha FQ, Louzada-Junior P, Cunha TM, Nakaya HI, Fabro A, de Oliveira RDR, Arruda E, Réa R, Réa Neto Á, Fernandes da Silva MM, Leiria LO. COVID-19-related hyperglycemia is associated with infection of hepatocytes and stimulation of gluconeogenesis. Proc Natl Acad Sci U S A 2023; 120:e2217119120. [PMID: 37186819 PMCID: PMC10214153 DOI: 10.1073/pnas.2217119120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Occurrence of hyperglycemia upon infection is associated with worse clinical outcome in COVID-19 patients. However, it is still unknown whether SARS-CoV-2 directly triggers hyperglycemia. Herein, we interrogated whether and how SARS-CoV-2 causes hyperglycemia by infecting hepatocytes and increasing glucose production. We performed a retrospective cohort study including patients that were admitted at a hospital with suspicion of COVID-19. Clinical and laboratory data were collected from the chart records and daily blood glucose values were analyzed to test the hypothesis on whether COVID-19 was independently associated with hyperglycemia. Blood glucose was collected from a subgroup of nondiabetic patients to assess pancreatic hormones. Postmortem liver biopsies were collected to assess the presence of SARS-CoV-2 and its transporters in hepatocytes. In human hepatocytes, we studied the mechanistic bases of SARS-CoV-2 entrance and its gluconeogenic effect. SARS-CoV-2 infection was independently associated with hyperglycemia, regardless of diabetic history and beta cell function. We detected replicating viruses in human hepatocytes from postmortem liver biopsies and in primary hepatocytes. We found that SARS-CoV-2 variants infected human hepatocytes in vitro with different susceptibility. SARS-CoV-2 infection in hepatocytes yields the release of new infectious viral particles, though not causing cell damage. We showed that infected hepatocytes increase glucose production and this is associated with induction of PEPCK activity. Furthermore, our results demonstrate that SARS-CoV-2 entry in hepatocytes occurs partially through ACE2- and GRP78-dependent mechanisms. SARS-CoV-2 infects and replicates in hepatocytes and exerts a PEPCK-dependent gluconeogenic effect in these cells that potentially is a key cause of hyperglycemia in infected patients.
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Affiliation(s)
- Ester A. Barreto
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Amanda S. Cruz
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Flavio P. Veras
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Ronaldo Martins
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Rafaella S. Bernardelli
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
| | - Isadora M. Paiva
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Thais M. Lima
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Youvika Singh
- Hospital Israelita Albert Einstein, São Paulo05652-900, Brazil
| | - Raphael C. Guimarães
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Samara Damasceno
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Nayara Pereira
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - João Manoel Alves
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Tiago T. Gonçalves
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Julia Forato
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Stéfanie P. Muraro
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Gabriela F. Souza
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
| | - Sabrina Setembre Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - José L. Proenca-Modena
- Department of Genetics, Microbiology and Immunology, Laboratory of Emerging Viruses, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
- Experimental Medicine Research, Cluster University of Campinas, Campinas13083-970, Brazil
| | - Marcelo A. Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas13083-970, Brazil
- Experimental Medicine Research, Cluster University of Campinas, Campinas13083-970, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas13083-864, Brazil
| | - Fernando Q. Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Paulo Louzada-Junior
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Divisions of Clinical Immunology, Emergency, Infectious Diseases, and Intensive Care Unit, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Thiago M. Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Helder I. Nakaya
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Hospital Israelita Albert Einstein, São Paulo05652-900, Brazil
| | - Alexandre Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Renê D. R. de Oliveira
- Divisions of Clinical Immunology, Emergency, Infectious Diseases, and Intensive Care Unit, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Eurico Arruda
- Department of Cell Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
| | - Rosângela Réa
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba80060-900, Brazil
| | - Álvaro Réa Neto
- Federal University of Paraná, Center for Study and Research in Intensive Care Medicine, Curitiba82530-200, Brazil
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba80060-900, Brazil
| | | | - Luiz Osório Leiria
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto14049-900, Brazil
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14
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Araújo A, Sgorlon G, Aguiar LE, Cidrão MHMC, Teixeira KS, Villalobos Salcedo JM, Passos-Silva AM, Vieira D. Influence of polymorphic variations of IFNL, HLA, and IL-6 genes in severe cases of COVID-19. Exp Biol Med (Maywood) 2023; 248:787-797. [PMID: 37452704 PMCID: PMC10350587 DOI: 10.1177/15353702231181343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
The administration of vaccination doses to the global population has led to a decrease in the incidence of COVID-19. However, the clinical picture developed by infected individuals remains extremely concerning due to the great variability in the severity of cases even in vaccinated individuals. The clinical progression of the pathology is characterized by various influential factors such as sex, age group, comorbidities, and the genetics of the individual. The immune response to viral infections can be strongly influenced by the genetics of individuals; nucleotide variations called single-nucleotide polymorphisms (SNPs) in structures involved in the innate and adaptive immune response such as interferon (IFN)-λ, human leukocyte antigen (HLA), and interleukin (IL)-6 are frequently associated with pathological progression. In this study, we conducted a review of the main SNPs of these structures that are associated with severity in COVID-19. Searches were conducted on some platforms of the National Center for Biotechnology and Information (NCBI), and 102 studies were selected for full reading according to the inclusion criteria. IFNs showed a strong association with antiviral function, specifically, IFN-λ3 (IL-28B) demonstrated genetic variants commonly related to clinical progression in various pathologies. For COVID-19, rs12979860 and rs1298275 presented frequently described unfavorable genotypes for pathological conditions of hepatitis C and hepatocellular carcinoma. The high genetic variability of HLA was reported in the studies as a crucial factor relevant to the late immune response, mainly due to its ability to recognize antigens, with the HLA-B*46:01 SNP being associated with susceptibility to COVID-19. For IL-6, rs1554606 showed a strong relationship with the clinical progression of COVID-19. In addition, rs2069837 was identified with possible host protection relationships when linked to this infection.
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Affiliation(s)
- Adrhyan Araújo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho 76812-329, Brazil
| | - Gabriella Sgorlon
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho 76801-059, Brazil
| | | | | | - Karolaine Santos Teixeira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho 76812-329, Brazil
| | - Juan Miguel Villalobos Salcedo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Universidade Federal de Rondônia (UNIR), Porto Velho 76801-059, Brazil
| | - Ana Maísa Passos-Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho 76801-059, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho 76812-329, Brazil
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho 76801-059, Brazil
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15
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da Silva Santos Y, Gamon THM, de Azevedo MSP, Telezynski BL, de Souza EE, de Oliveira DBL, Dombrowski JG, Rosa-Fernandes L, Palmisano G, de Moura Carvalho LJ, Luvizotto MCR, Wrenger C, Covas DT, Curi R, Marinho CRF, Durigon EL, Epiphanio S. Virulence Profiles of Wild-Type, P.1 and Delta SARS-CoV-2 Variants in K18-hACE2 Transgenic Mice. Viruses 2023; 15:v15040999. [PMID: 37112979 PMCID: PMC10146242 DOI: 10.3390/v15040999] [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: 02/21/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Since December 2019, the world has been experiencing the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we now face the emergence of several variants. We aimed to assess the differences between the wild-type (Wt) (Wuhan) strain and the P.1 (Gamma) and Delta variants using infected K18-hACE2 mice. The clinical manifestations, behavior, virus load, pulmonary capacity, and histopathological alterations were analyzed. The P.1-infected mice showed weight loss and more severe clinical manifestations of COVID-19 than the Wt and Delta-infected mice. The respiratory capacity was reduced in the P.1-infected mice compared to the other groups. Pulmonary histological findings demonstrated that a more aggressive disease was generated by the P.1 and Delta variants compared to the Wt strain of the virus. The quantification of the SARS-CoV-2 viral copies varied greatly among the infected mice although it was higher in P.1-infected mice on the day of death. Our data revealed that K18-hACE2 mice infected with the P.1 variant develop a more severe infectious disease than those infected with the other variants, despite the significant heterogeneity among the mice.
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Affiliation(s)
- Yasmin da Silva Santos
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Malaria Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
| | - Thais Helena Martins Gamon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Marcela Santiago Pacheco de Azevedo
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Bruna Larotonda Telezynski
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Danielle Bruna Leal de Oliveira
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
| | - Jamille Gregório Dombrowski
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
| | | | | | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05508-040, Brazil
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Rui Curi
- Interdisciplinary Program of Health Sciences, Cruzeiro do Sul University, São Paulo 08060-070, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo 05503-900, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
- Scientific Plataform Pasteur/USP, University of São Paulo, São Paulo 05508-020, Brazil
| | - Sabrina Epiphanio
- Laboratory of Cellular and Molecular Immunopathology of Malaria, Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
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16
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Payen SH, Gorzalski A, Siao DD, Pandori M, Verma SC, Rossetto CC. Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105434. [PMID: 37059256 PMCID: PMC10098042 DOI: 10.1016/j.meegid.2023.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD) and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
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Affiliation(s)
- Shannon Harger Payen
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | | | | | - Mark Pandori
- School of Medicine, University of Nevada, Reno; Nevada State Public Health Lab
| | - Subhash C Verma
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | - Cyprian C Rossetto
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno.
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17
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Capistrano KJ, Richner J, Schwartz J, Mukherjee SK, Shukla D, Naqvi AR. Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166612. [PMID: 36481486 PMCID: PMC9721271 DOI: 10.1016/j.bbadis.2022.166612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
A significant number of SARS-CoV-2-infected individuals naturally overcome viral infection, suggesting the existence of a potent endogenous antiviral mechanism. As an innate defense mechanism, microRNA (miRNA) pathways in mammals have evolved to restrict viruses, besides regulating endogenous mRNAs. In this study, we systematically examined the complete repertoire of human miRNAs for potential binding sites on SARS-CoV-2 Wuhan-Hu-1, Beta, Delta, and Omicron. Human miRNA and viral genome interaction were analyzed using RNAhybrid 2.2 with stringent parameters to identify highly bonafide miRNA targets. Using publicly available data, we filtered for miRNAs expressed in lung epithelial cells/tissue and oral keratinocytes, concentrating on the miRNAs that target SARS-CoV-2 S protein mRNAs. Our results show a significant loss of human miRNA and SARS-CoV-2 interactions in Omicron (130 miRNAs) compared to Wuhan-Hu-1 (271 miRNAs), Beta (279 miRNAs), and Delta (275 miRNAs). In particular, hsa-miR-3150b-3p and hsa-miR-4784 show binding affinity for S protein of Wuhan strain but not Beta, Delta, and Omicron. Loss of miRNA binding sites on N protein was also observed for Omicron. Through Ingenuity Pathway Analysis (IPA), we examined the experimentally validated and highly predicted functional role of these miRNAs. We found that hsa-miR-3150b-3p and hsa-miR-4784 have several experimentally validated or highly predicted target genes in the Toll-like receptor, IL-17, Th1, Th2, interferon, and coronavirus pathogenesis pathways. Focusing on the coronavirus pathogenesis pathway, we found that hsa-miR-3150b-3p and hsa-miR-4784 are highly predicted to target MAPK13. Exploring miRNAs to manipulate viral genome/gene expression can provide a promising strategy with successful outcomes by targeting specific VOCs.
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Affiliation(s)
- Kristelle J Capistrano
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Justin Richner
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Joel Schwartz
- Molecular Pathology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sunil K Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepak Shukla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA; Department of Ophthalmology and Visual Sciences, Ocular Virology Laboratory, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA.
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18
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Valyaeva AA, Zharikova AA, Sheval EV. SARS-CoV-2 cellular tropism and direct multiorgan failure in COVID-19 patients: Bioinformatic predictions, experimental observations, and open questions. Cell Biol Int 2023; 47:308-326. [PMID: 36229927 PMCID: PMC9874490 DOI: 10.1002/cbin.11928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/24/2022] [Accepted: 09/25/2022] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has led to an unprecedented public health emergency worldwide. While common cold symptoms are observed in mild cases, COVID-19 is accompanied by multiorgan failure in severe patients. Organ damage in COVID-19 patients is partially associated with the indirect effects of SARS-CoV-2 infection (e.g., systemic inflammation, hypoxic-ischemic damage, coagulopathy), but early processes in COVID-19 patients that trigger a chain of indirect effects are connected with the direct infection of cells by the virus. To understand the virus transmission routes and the reasons for the wide-spectrum of complications and severe outcomes of COVID-19, it is important to identify the cells targeted by SARS-CoV-2. This review summarizes the major steps of investigation and the most recent findings regarding SARS-CoV-2 cellular tropism and the possible connection between the early stages of infection and multiorgan failure in COVID-19. The SARS-CoV-2 pandemic is the first epidemic in which data extracted from single-cell RNA-seq (scRNA-seq) gene expression data sets have been widely used to predict cellular tropism. The analysis presented here indicates that the SARS-CoV-2 cellular tropism predictions are accurate enough for estimating the potential susceptibility of different cells to SARS-CoV-2 infection; however, it appears that not all susceptible cells may be infected in patients with COVID-19.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Anastasia A. Zharikova
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Eugene V. Sheval
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia,Department of Cell Biology and Histology, School of BiologyLomonosov Moscow State UniversityMoscowRussia
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19
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Gonçalves R, Couto J, Ferreirinha P, Costa JM, Silvério D, Silva ML, Fernandes AI, Madureira P, Alves NL, Lamas S, Saraiva M. SARS-CoV-2 variants induce distinct disease and impact in the bone marrow and thymus of mice. iScience 2023; 26:105972. [PMID: 36687317 PMCID: PMC9838028 DOI: 10.1016/j.isci.2023.105972] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to variants associated with milder disease. We employed the k18-hACE2 mouse model to study how differences in the course of infection by SARS-CoV-2 variants alpha, delta, and omicron relate to tissue pathology and the immune response triggered. We documented a variant-specific pattern of infection severity, inducing discrete lung and blood immune responses and differentially impacting primary lymphoid organs. Infections with variants alpha and delta promoted bone marrow (BM) emergency myelopoiesis, with blood and lung neutrophilia. The defects in the BM hematopoietic compartment extended to the thymus, with the infection by the alpha variant provoking a marked thymic atrophy. Importantly, the changes in the immune responses correlated with the severity of infection. Our study provides a comprehensive platform to investigate the modulation of disease by SARS-CoV-2 variants and underscores the impact of this infection on the function of primary lymphoid organs.
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Affiliation(s)
- Rute Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Joana Couto
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - José Maria Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Diogo Silvério
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana Isabel Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Pedro Madureira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,Immunethep, Biocant Park, 3060-197 Cantanhede, Portugal
| | - Nuno L. Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sofia Lamas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal,IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal,Corresponding author
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20
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Zhang GF, Meng W, Chen L, Ding L, Sun S, Wang X, Huang Y, Guo H, Gao S. Infectivity of pseudotyped SARS-CoV-2 variants of concern in different human cell types and inhibitory effects of recombinant spike protein and entry-related cellular factors. J Med Virol 2023; 95:e28437. [PMID: 36573430 PMCID: PMC9880647 DOI: 10.1002/jmv.28437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022]
Abstract
Since the report of the first COVID-19 case in 2019, SARS-CoV-2 variants of concern (VOCs) have continued to emerge, manifesting diverse infectivity, evasion of host immunity and pathology. While ACE2 is the predominant receptor of SARS-CoV-2, TMPRSS2, Kim-1, NRP-1, CD147, furin, CD209L, and CD26 have also been implicated as viral entry-related cofactors. To understand the variations in infectivity and pathogenesis of VOCs, we conducted infection analysis in human cells from different organ systems using pseudoviruses of VOCs including Alpha, Beta, Gamma, and Delta. Recombinant spike S1, RBD, ACE2, Kim-1, and NRP-1 proteins were tested for their ability to block infection to dissect their roles in SARS-CoV-2 entry into cells. Compared with wild type SARS-CoV-2 (WT), numerous VOCs had significant increases of infectivity across a wide spectrum of cell types. Recombinant ACE2 protein more effectively inhibited the infection of VOCs including Delta and Omicron (BA.1 and BA.2) than that of WT. Interestingly, recombinant S1, RBD, Kim-1, and NRP-1 proteins inhibited the infection of all pseudoviruses in a manner dependent on the levels of ACE2 expression in different cell types. These results provide insights into the diverse infectivity of SARS-CoV-2 VOCs, which might be helpful for managing the emergence of new VOCs.
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Affiliation(s)
- George Fei Zhang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Wen Meng
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Luping Chen
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Ling Ding
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Shenyu Sun
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Xian Wang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Electrical and Computer EngineeringSwanson School and EngineeringPittsburghPennsylvaniaUSA
| | - Haitao Guo
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Shou‐Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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21
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Wang SJ, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Nalabolu HS, Thota J, Thorat K, Tutaj MA, Tutaj M, Vedi M, Zacher S, Smith JR, Dwinell MR, Kwitek AE. Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal. Genes (Basel) 2022; 13:genes13122304. [PMID: 36553571 PMCID: PMC9777590 DOI: 10.3390/genes13122304] [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: 11/09/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In the COVID-19 Portal, gene-disease associations are established by manual curation of PubMed literature. The portal contains data for nine ontologies related to COVID-19, an embedded enrichment analysis tool, as well as links to a toolkit. Using these information and tools, we performed analyses on the curated COVID-19 disease genes. As expected, Disease Ontology enrichment analysis showed that the COVID-19 gene set is highly enriched with coronavirus infectious disease and related diseases. However, other less related diseases were also highly enriched, such as liver and rheumatic diseases. Using the comparison heatmap tool, we found nearly 60 percent of the COVID-19 genes were associated with nervous system disease and 40 percent were associated with gastrointestinal disease. Our analysis confirms the role of the immune system in COVID-19 pathogenesis as shown by substantial enrichment of immune system related Gene Ontology terms. The information in RGD's COVID-19 disease portal can generate new hypotheses to potentiate novel therapies and prevention of acute and long-term complications of COVID-19.
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Affiliation(s)
- Shur-Jen Wang
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C. Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L. De Pons
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M. Demos
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C. Gibson
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G. Thomas Hayman
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L. Hill
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L. Kaldunski
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J. F. Laulederkind
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S. Nalabolu
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A. Tutaj
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R. Smith
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R. Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E. Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Correspondence:
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22
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Differential transcriptomic landscapes of multiple organs from SARS-CoV-2 early infected rhesus macaques. Protein Cell 2022; 13:920-939. [PMID: 35377064 PMCID: PMC8978510 DOI: 10.1007/s13238-022-00915-5] [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: 02/23/2022] [Accepted: 03/08/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection causes complicated clinical manifestations with variable multi-organ injuries, however, the underlying mechanism, in particular immune responses in different organs, remains elusive. In this study, comprehensive transcriptomic alterations of 14 tissues from rhesus macaque infected with SARS-CoV-2 were analyzed. Compared to normal controls, SARS-CoV-2 infection resulted in dysregulation of genes involving diverse functions in various examined tissues/organs, with drastic transcriptomic changes in cerebral cortex and right ventricle. Intriguingly, cerebral cortex exhibited a hyperinflammatory state evidenced by significant upregulation of inflammation response-related genes. Meanwhile, expressions of coagulation, angiogenesis and fibrosis factors were also up-regulated in cerebral cortex. Based on our findings, neuropilin 1 (NRP1), a receptor of SARS-CoV-2, was significantly elevated in cerebral cortex post infection, accompanied by active immune response releasing inflammatory factors and signal transmission among tissues, which enhanced infection of the central nervous system (CNS) in a positive feedback way, leading to viral encephalitis. Overall, our study depicts a multi-tissue/organ transcriptomic landscapes of rhesus macaque with early infection of SARS-CoV-2, and provides important insights into the mechanistic basis for COVID-19-associated clinical complications.
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23
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Ranjbar M, Rahimi A, Baghernejadan Z, Ghorbani A, Khorramdelazad H. Role of CCL2/CCR2 axis in the pathogenesis of COVID-19 and possible Treatments: All options on the Table. Int Immunopharmacol 2022; 113:109325. [PMID: 36252475 PMCID: PMC9561120 DOI: 10.1016/j.intimp.2022.109325] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is cause of the novel coronavirus disease (COVID-19). In the last two years, SARS-CoV-2 has infected millions of people worldwide with different waves, resulting in the death of many individuals. The evidence disclosed that the host immune responses to SARS-CoV-2 play a pivotal role in COVID-19 pathogenesis and clinical manifestations. In addition to inducing antiviral immune responses, SARS-CoV-2 can also cause dysregulated inflammatory responses characterized by the noticeable release of proinflammatory mediators in COVID-19 patients. Among these proinflammatory mediators, chemokines are considered a subset of cytokines that participate in the chemotaxis process to recruit immune and non-immune cells to the site of inflammation and infection. Researchers have demonstrated that monocyte chemoattractant protein-1 (MCP-1/CCL2) and its receptor (CCR2) are involved in the recruitment of monocytes and infiltration of these cells into the lungs of patients suffering from COVID-19. Moreover, elevated levels of CCL2 have been reported in the bronchoalveolar lavage fluid (BALF) obtained from patients with severe COVID-19, initiating cytokine storm and promoting CD163+ myeloid cells infiltration in the airways and further alveolar damage. Therefore, CCL2/CCR axis plays a key role in the immunopathogenesis of COVID-19 and targeted therapy of involved molecules in this axis can be a potential therapeutic approach for these patients. This review discusses the biology of the CCL2/CCR2 axis as well as the role of this axis in COVID-19 immunopathogenesis, along with therapeutic options aimed at inhibiting CCL2/CCR2 and modulating dysregulated inflammatory responses in patients with severe SARS-CoV-2 infection.
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Affiliation(s)
- Mitra Ranjbar
- Department of Infectious Disease, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Rahimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zeinab Baghernejadan
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Atousa Ghorbani
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran,Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran,Corresponding author at: Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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24
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Mahilkar S, Agrawal S, Chaudhary S, Parikh S, Sonkar SC, Verma DK, Chitalia V, Mehta D, Koner BC, Vijay N, Shastri J, Sunil S. SARS-CoV-2 variants: Impact on biological and clinical outcome. Front Med (Lausanne) 2022; 9:995960. [PMID: 36438034 PMCID: PMC9685312 DOI: 10.3389/fmed.2022.995960] [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: 07/16/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first identified in December 2019, in Wuhan, China was found to be the etiological agent for a novel respiratory infection that led to a Coronavirus Induced Disease named COVID-19. The disease spread to pandemic magnitudes within a few weeks and since then we have been dealing with several waves across the world, due to the emergence of variants and novel mutations in this RNA virus. A direct outcome of these variants apart from the spike of cases is the diverse disease presentation and difficulty in employing effective diagnostic tools apart from confusing disease outcomes. Transmissibility rates of the variants, host response, and virus evolution are some of the features found to impact COVID-19 disease management. In this review, we will discuss the emerging variants of SARS-CoV-2, notable mutations in the viral genome, the possible impact of these mutations on detection, disease presentation, and management as well as the recent findings in the mechanisms that underlie virus-host interaction. Our aim is to invigorate a scientific debate on how pathogenic potential of the new pandemic viral strains contributes toward development in the field of virology in general and COVID-19 disease in particular.
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Affiliation(s)
- Shakuntala Mahilkar
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sakshi Chaudhary
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Swapneil Parikh
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Subash C. Sonkar
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi, India
| | - Dileep Kumar Verma
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Vidushi Chitalia
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Divya Mehta
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Bidhan Chandra Koner
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospital, New Delhi, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health and Family Welfare, New Delhi, India
| | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sujatha Sunil
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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25
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Taibe NS, Kord MA, Badawy MA, Shytaj IL, Elhefnawi MM. Progress, pitfalls, and path forward of drug repurposing for COVID-19 treatment. Ther Adv Respir Dis 2022; 16:17534666221132736. [PMID: 36282077 PMCID: PMC9597285 DOI: 10.1177/17534666221132736] [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] [Indexed: 12/15/2022] Open
Abstract
On 30 January 2020, the World Health Organization (WHO) declared the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic a public health emergency of international concern. The viral outbreak led in turn to an exponential growth of coronavirus disease 2019 (COVID-19) cases, that is, a multiorgan disease that has led to more than 6.3 million deaths worldwide, as of June 2022. There are currently few effective drugs approved for treatment of SARS-CoV-2/COVID-19 patients. Many of the compounds tested so far have been selected through a drug repurposing approach, that is, by identifying novel indications for drugs already approved for other conditions. We here present an up-to-date review of the main Food and Drug Administration (FDA)-approved drugs repurposed against SARS-CoV-2 infection, discussing their mechanism of action and their most important preclinical and clinical results. Reviewed compounds were chosen to privilege those that have been approved for use in SARS-CoV-2 patients or that have completed phase III clinical trials. Moreover, we also summarize the evidence on some novel and promising repurposed drugs in the pipeline. Finally, we discuss the current stage and possible steps toward the development of broadly effective drug combinations to suppress the onset or progression of COVID-19.
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Affiliation(s)
- Noha Samir Taibe
- Biotechnology-Biomolecular Chemistry Program, Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Maimona A. Kord
- Department of Botany, Faculty of Science, Cairo University, Giza, Egypt
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26
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Al-Mugheed K, Al Rawajfah O, Bani-Issa W, Rababa M. Acceptance, Attitudes, and Barriers of Vaccine Booster Dose among Nursing Students: A Multicounty Survey. J Nurs Manag 2022; 30:3360-3367. [PMID: 36064189 DOI: 10.1111/jonm.13791] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/07/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
AIM This study investigated the acceptance and attitudes of nursing students toward the COVID-19 vaccine booster dose in two Gulf Cooperation Countries and the potential influencing factors for taking a COVID-19 vaccine booster dose. BACKGROUND The world is still battling coronavirus because of the emerged of variants and protection against COVID-19 has waned over time. Vaccination is a powerful and effective method of reducing the outbreak of COVID-19 and decreasing the loss of lives. DESIGN This research was a survey using a cross-sectional design. METHODS The study's sample was two nursing colleges. The study tool was adopted according to recent information concerning the COVID-19 vaccine published by the World Health Organization. Data was collected through an online survey during March to April 2022. RESULTS A total of 216 nursing students completed the survey, of which 69.4 % (n = 150) were male students and more than half of the participants were from Saudi Arabia (55.1%, n = 119). Two-thirds of the students (75.5%, n = 161) reported that they agreed to receive a COVID-19 vaccine booster. The total attitude scores for the students ranged from 28 to 35, with a mean score of 15.8 (SD = 2.5), representing 73% of the highest possible score, with 79.3% were classified as 'positive attitude toward booster dose of COVID-19. Vaccine booster might cause infection, vaccine booster ineffective, worried about adverse effects, and not safe were major barriers influencing the acceptance of the COVID-19 vaccine booster. CONCLUSION Nursing students revealed high acceptance rates related to COVID-19 vaccine booster. However, more attention should be paid from nursing educators to barriers influencing the acceptance of the COVID-19 vaccine booster. Preparing nursing students with positive attitude of COVID-19 vaccine booster is very important to patient and community safety. IMPLICATIONS FOR NURSING MANAGEMENT Nursing educators and managers must make an effort to educate the nursing students regarding safety and effectiveness from COVID-19 vaccine booster and ensure that is necessary to reduce their perception of the injury of COVID-19 infection.
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Affiliation(s)
- Khalid Al-Mugheed
- Near East University. Faculty of Nursing, Surgical Nursing Department, Nicosia, Cyprus
| | - Omar Al Rawajfah
- Associate Professor of Acute Care Nursing, Dean, College of Nursing, Sultan Qaboos University, Al Khod, Muscat, Oman
| | - Wegdan Bani-Issa
- University of Sharjah. College of Health Science\ Nursing Department, United Arab Emirates
| | - Mohammad Rababa
- Department of Adult Health-Nursing, Faculty of Nursing, Jordan University of Science and Technology, Irbid, Jordan
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Lee KS, Wong TY, Russ BP, Horspool AM, Miller OA, Rader NA, Givi JP, Winters MT, Wong ZYA, Cyphert HA, Denvir J, Stoilov P, Barbier M, Roan NR, Amin MS, Martinez I, Bevere JR, Damron FH. SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice. PLoS One 2022; 17:e0273430. [PMID: 36037222 PMCID: PMC9423646 DOI: 10.1371/journal.pone.0273430] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/08/2022] [Indexed: 01/27/2023] Open
Abstract
The COVID-19 pandemic has been fueled by SARS-CoV-2 novel variants of concern (VOC) that have increased transmissibility, receptor binding affinity, and other properties that enhance disease. The goal of this study is to characterize unique pathogenesis of the Delta VOC strain in the K18-hACE2-mouse challenge model. Challenge studies suggested that the lethal dose of Delta was higher than Alpha or Beta strains. To characterize the differences in the Delta strain's pathogenesis, a time-course experiment was performed to evaluate the overall host response to Alpha or Delta variant challenge. qRT-PCR analysis of Alpha- or Delta-challenged mice revealed no significant difference between viral RNA burden in the lung, nasal wash or brain. However, histopathological analysis revealed high lung tissue inflammation and cell infiltration following Delta- but not Alpha-challenge at day 6. Additionally, pro-inflammatory cytokines were highest at day 6 in Delta-challenged mice suggesting enhanced pneumonia. Total RNA-sequencing analysis of lungs comparing challenged to no challenge mice revealed that Alpha-challenged mice have more total genes differentially activated. Conversely, Delta-challenged mice have a higher magnitude of differential gene expression. Delta-challenged mice have increased interferon-dependent gene expression and IFN-γ production compared to Alpha. Analysis of TCR clonotypes suggested that Delta challenged mice have increased T-cell infiltration compared to Alpha challenged. Our data suggest that Delta has evolved to engage interferon responses in a manner that may enhance pathogenesis. The in vivo and in silico observations of this study underscore the need to conduct experiments with VOC strains to best model COVID-19 when evaluating therapeutics and vaccines.
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Affiliation(s)
- Katherine S. Lee
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Ting Y. Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Brynnan P. Russ
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Alexander M. Horspool
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Olivia A. Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Nathaniel A. Rader
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Jerome P. Givi
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, WV, United States of America
| | - Michael T. Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
| | - Zeriel Y. A. Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Holly A. Cyphert
- Department of Biological Sciences, Marshall University, Huntington, WV, United States of America
| | - James Denvir
- Department of Biomedical Sciences, Marshall University, Huntington, WV, United States of America
| | - Peter Stoilov
- Department of Biochemistry, School of Medicine, West Virginia University Morgantown, Morgantown, WV, United States of America
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - Nadia R. Roan
- Department or Urology, University of California, San Francisco, San Francisco, CA, United States of America
- Gladstone Institute of Virology, San Francisco, CA, United States of America
| | - Md. Shahrier Amin
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, WV, United States of America
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- West Virginia University Cancer Institute, School of Medicine, Morgantown, WV, United States of America
| | - Justin R. Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, United States of America
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A SCID Mouse Model To Evaluate the Efficacy of Antivirals against SARS-CoV-2 Infection. J Virol 2022; 96:e0075822. [PMID: 35924921 PMCID: PMC9400483 DOI: 10.1128/jvi.00758-22] [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] [Indexed: 12/03/2022] Open
Abstract
Ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lacks the intrinsic ability to bind to the mouse ACE2 receptor, and therefore establishment of SARS-CoV-2 mouse models has been limited to the use of mouse-adapted viruses or genetically modified mice. Interestingly, some of the variants of concern, such as the Beta B.1.351 variant, show an improved binding to the mouse receptor and hence better replication in different wild-type (WT) mouse species. Here, we describe the establishment of a SARS-CoV-2 Beta B.1.351 variant infection model in male SCID mice as a tool to assess the antiviral efficacy of potential SARS-CoV-2 small-molecule inhibitors. Intranasal infection of male SCID mice with 105 50% tissue culture infective doses (TCID50) of the Beta B.1.351 variant resulted in high viral loads in the lungs and moderate signs of lung pathology on day 3 postinfection. Treatment of infected mice with the antiviral drugs molnupiravir (200 mg/kg, twice a day [BID]) or nirmatrelvir (300 mg/kg, BID) for 3 consecutive days significantly reduced the infectious virus titers in the lungs by 2 and 3.9 log10 TCID50/mg of tissue, respectively, and significantly improved lung pathology. Together, these data demonstrate the validity of this SCID mouse Beta B.1.351 variant infection model as a convenient preclinical model for assessment of potential activity of antivirals against SARS-CoV-2. IMPORTANCE Unlike the ancestral SARS-CoV-2 strain, the Beta (B.1.351) variant of concern has been reported to replicate to some extent in WT mice (C57BL/6 and BALB/c). We demonstrate here that infection of SCID mice with the Beta variant resulted in high viral loads in the lungs on day 3 postinfection. Treatment of infected mice with molnupiravir or nirmatrelvir for 3 consecutive days markedly reduced the infectious virus titers in the lungs and improved lung pathology. The SARS-CoV2 SCID mouse infection model, which is ideally suited for antiviral studies, offers an advantage in comparison to other SARS-CoV2 mouse models, in that there is no need for the use of mouse-adapted virus strains or genetically modified mice. Mouse models also have advantages over hamster models because (i) lower amounts of test drugs are needed, (ii) more animals can be housed in a cage, and (iii) reagents to analyze mouse samples are more readily available than those for hamsters.
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Differential Pathogenesis of SARS-CoV-2 Variants of Concern in Human ACE2-Expressing Mice. Viruses 2022; 14:v14061139. [PMID: 35746611 PMCID: PMC9231291 DOI: 10.3390/v14061139] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the current pandemic, resulting in millions of deaths worldwide. Increasingly contagious variants of concern (VoC) have fueled recurring global infection waves. A major question is the relative severity of the disease caused by previous and currently circulating variants of SARS-CoV-2. In this study, we evaluated the pathogenesis of SARS-CoV-2 variants in human ACE-2-expressing (K18-hACE2) mice. Eight-week-old K18-hACE2 mice were inoculated intranasally with a representative virus from the original B.1 lineage or from the emerging B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), or B.1.1.529 (omicron) lineages. We also infected a group of mice with the mouse-adapted SARS-CoV-2 (MA10). Our results demonstrate that B.1.1.7, B.1.351 and B.1.617.2 viruses are significantly more lethal than the B.1 strain in K18-hACE2 mice. Infection with the B.1.1.7, B.1.351, and B.1.617.2 variants resulted in significantly higher virus titers in the lungs and brain of mice compared with the B.1 virus. Interestingly, mice infected with the B.1.1.529 variant exhibited less severe clinical signs and a high survival rate. We found that B.1.1.529 replication was significantly lower in the lungs and brain of infected mice in comparison with other VoC. The transcription levels of cytokines and chemokines in the lungs of B.1- and B.1.1.529-infected mice were significantly less when compared with those challenged with other VoC. Together, our data provide insights into the pathogenesis of previous and circulating SARS-CoV-2 VoC in mice.
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The Beneficial Effect of the COVID-19 Vaccine Booster Dose among Healthcare Workers in an Infectious Diseases Center. Vaccines (Basel) 2022; 10:vaccines10040552. [PMID: 35455301 PMCID: PMC9029317 DOI: 10.3390/vaccines10040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/20/2022] Open
Abstract
Introduction: Healthcare workers in Poland received a booster dose of the BNT162b2 mRNA vaccine (Pfizer-BioNTech, Manufacturer: Pfizer, Inc., and BioNTech; Moguncja, Germany) at the beginning of October 2021. Here, we report on the preliminary results of an ongoing clinical study into the antibody response to SARS-CoV-2 of healthcare workers previously exposed to the virus, with or without evidence of past infection, in the Hospital for Infectious Diseases in Warsaw before and after the vaccine booster dose. Methods: Blood samples were collected on the day the vaccine booster dose was administered and again 14 days later. The levels of SARS-CoV-2 IgG antibodies (against the n-protein, indicative of disease) and S-RBD (indicative of a response to vaccination) were measured. Results: One hundred and ten health care workers from the Hospital for Infectious Diseases were included in the study. The percentage of subjects with a positive test for anti-n-protein IgG antibodies at both time points remained unchanged (16, 14%), while a statistically significant increase in the percentage of subjects producing high levels of S-RBD antibodies (i.e., >433 BAU/mL) was observed (from 23, 21% to 109, 99%; p = 0.00001). Conclusions: The results of the study indicate that the booster dose of the vaccine significantly increases the percentage of people with high levels of S-RBD antibodies, regardless of previous contact with the virus, which may indicate greater protection against both the disease and a severe course of COVID-19.
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