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Swaminath S, Russell AB. The use of single-cell RNA-seq to study heterogeneity at varying levels of virus-host interactions. PLoS Pathog 2024; 20:e1011898. [PMID: 38236826 PMCID: PMC10796064 DOI: 10.1371/journal.ppat.1011898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
The outcome of viral infection depends on the diversity of the infecting viral population and the heterogeneity of the cell population that is infected. Until almost a decade ago, the study of these dynamic processes during viral infection was challenging and limited to certain targeted measurements. Presently, with the use of single-cell sequencing technology, the complex interface defined by the interactions of cells with infecting virus can now be studied across the breadth of the transcriptome in thousands of individual cells simultaneously. In this review, we will describe the use of single-cell RNA sequencing (scRNA-seq) to study the heterogeneity of viral infections, ranging from individual virions to the immune response between infected individuals. In addition, we highlight certain key experimental limitations and methodological decisions that are critical to analyzing scRNA-seq data at each scale.
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Affiliation(s)
- Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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Zwygart ACA, Medaglia C, Huber R, Poli R, Marcourt L, Schnee S, Michellod E, Mazel-Sanchez B, Constant S, Huang S, Bekliz M, Clément S, Gindro K, Queiroz EF, Tapparel C. Antiviral properties of trans-δ-viniferin derivatives against enveloped viruses. Biomed Pharmacother 2023; 163:114825. [PMID: 37148860 PMCID: PMC10158552 DOI: 10.1016/j.biopha.2023.114825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
Over the last century, the number of epidemics caused by RNA viruses has increased and the current SARS-CoV-2 pandemic has taught us about the compelling need for ready-to-use broad-spectrum antivirals. In this scenario, natural products stand out as a major historical source of drugs. We analyzed the antiviral effect of 4 stilbene dimers [1 (trans-δ-viniferin); 2 (11',13'-di-O-methyl-trans-δ-viniferin), 3 (11,13-di-O-methyl-trans-δ-viniferin); and 4 (11,13,11',13'-tetra-O-methyl-trans-δ-viniferin)] obtained from plant substrates using chemoenzymatic synthesis against a panel of enveloped viruses. We report that compounds 2 and 3 display a broad-spectrum antiviral activity, being able to effectively inhibit several strains of Influenza Viruses (IV), SARS-CoV-2 Delta and, to some extent, Herpes Simplex Virus 2 (HSV-2). Interestingly, the mechanism of action differs for each virus. We observed both a direct virucidal and a cell-mediated effect against IV, with a high barrier to antiviral resistance; a restricted cell-mediated mechanism of action against SARS-CoV-2 Delta and a direct virustatic activity against HSV-2. Of note, while the effect was lost against IV in tissue culture models of human airway epithelia, the antiviral activity was confirmed in this relevant model for SARS-CoV-2 Delta. Our results suggest that stilbene dimer derivatives are good candidate models for the treatment of enveloped virus infections.
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Affiliation(s)
- Arnaud Charles-Antoine Zwygart
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Chiara Medaglia
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Robin Huber
- School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU - Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Romain Poli
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Laurence Marcourt
- School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU - Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Agroscope, Plant Protection Research Division, Mycology Group, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Emilie Michellod
- Agroscope, Plant Protection Research Division, Mycology Group, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Beryl Mazel-Sanchez
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Samuel Constant
- Epithelix Sarl, Chemin des Aulx 18, 1228 Plan-les-Ouates, Switzerland
| | - Song Huang
- Epithelix Sarl, Chemin des Aulx 18, 1228 Plan-les-Ouates, Switzerland
| | - Meriem Bekliz
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Sophie Clément
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Katia Gindro
- Agroscope, Plant Protection Research Division, Mycology Group, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Emerson Ferreira Queiroz
- School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU - Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU - Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland.
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Mathez G, Pillonel T, Bertelli C, Cagno V. Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model. Viruses 2022; 15:13. [PMID: 36680054 PMCID: PMC9864588 DOI: 10.3390/v15010013] [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: 10/14/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing an unprecedented pandemic. Although vaccines and antivirals are limiting the spread, SARS-CoV-2 is still under selective pressure in human and animal populations, as demonstrated by the emergence of variants of concern. To better understand the driving forces leading to new subtypes of SARS-CoV-2, we infected an ex vivo cell model of the human upper respiratory tract with Alpha and Omicron BA.1 variants for one month. Although viral RNA was detected during the entire course of the infection, infectious virus production decreased over time. Sequencing analysis did not show any adaptation in the spike protein, suggesting a key role for the adaptive immune response or adaptation to other anatomical sites for the evolution of SARS-CoV-2.
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Affiliation(s)
| | | | | | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
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