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Domingo E, Martínez-González B, García-Crespo C, Somovilla P, de Ávila AI, Soria ME, Durán-Pastor A, Perales C. Reply to Qu et al., "Quasispecies are constantly selected through virus-encoded intracellular reproductive population bottlenecking". J Virol 2024; 98:e0004624. [PMID: 38445886 PMCID: PMC11019780 DOI: 10.1128/jvi.00046-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Brenda Martínez-González
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
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2
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Zhang Y, Zhang H, Xu T, Zeng L, Liu F, Huang X, Liu Q. Interactions among microorganisms open up a new world for anti-infectious therapy. FEBS J 2024; 291:1615-1631. [PMID: 36527169 DOI: 10.1111/febs.16705] [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: 09/04/2022] [Revised: 11/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The human microbiome, containing bacteria, fungi, and viruses, is a community that coexists peacefully with humans most of the time, but with the potential to cause disease under certain conditions. When the environment changes or certain stimuli are received, microbes may interact with each other, causing or increasing the severity of disease in a host. With the appropriate methods, we can make these microbiota work for us, creating new applications for human health. This review discusses the wide range of interactions between microorganisms that result in an increase in susceptibility to, severity of, and mortality of diseases, and also briefly introduces how microorganisms interact with each other directly or indirectly. The study of microbial interactions and their mechanisms has revealed a new world of treatments for infectious disease. The regulation of the balance between intestinal flora, the correct application of probiotics, and the development of effective drugs by symbiosis all demonstrate the great contributions of the microbiota to human health and its powerful potential value. Consequently, the study of interactions between microorganisms plays an essential role in identifying the causes of diseases and the development of treatments.
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Affiliation(s)
- Yejia Zhang
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
| | - Hanchi Zhang
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
- The First Clinical Medical College, Nanchang University, China
| | - Tian Xu
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
| | - Lingbing Zeng
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
- The First Clinical Medical College, Nanchang University, China
| | - Fadi Liu
- The Department of Clinical Laboratory, Children's Hospital of Jiangxi Province, Nanchang, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Jiangxi Medical College, Nanchang University, China
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3
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Eberhardt N, Noval MG, Kaur R, Amadori L, Gildea M, Sajja S, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. NATURE CARDIOVASCULAR RESEARCH 2023; 2:899-916. [PMID: 38076343 PMCID: PMC10702930 DOI: 10.1038/s44161-023-00336-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 12/19/2023]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present increased risk for ischemic cardiovascular complications up to 1 year after infection. Although the systemic inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques remains unknown. Here we report that SARS-CoV-2 viral RNA is detectable and replicates in coronary lesions taken at autopsy from severe COVID-19 cases. SARS-CoV-2 targeted plaque macrophages and exhibited a stronger tropism for arterial lesions than adjacent perivascular fat, correlating with macrophage infiltration levels. SARS-CoV-2 entry was increased in cholesterol-loaded primary macrophages and dependent, in part, on neuropilin-1. SARS-CoV-2 induced a robust inflammatory response in cultured macrophages and human atherosclerotic vascular explants with secretion of cytokines known to trigger cardiovascular events. Our data establish that SARS-CoV-2 infects coronary vessels, inducing plaque inflammation that could trigger acute cardiovascular complications and increase the long-term cardiovascular risk.
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Affiliation(s)
- Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Maria Gabriela Noval
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Michael Gildea
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Dayasagar Das
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Burak Cilhoroz
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - O’Jay Stewart
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Andrea Vasquez Guillen
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Sonia Jangra
- 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
| | - Michael Schotsaert
- 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
| | - Jonathan D. Newman
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Maldonado
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Caron Rockman
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Winthrop Hospital, Long Island School of Medicine, New York, NY, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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4
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Maciel-Fiuza MF, Muller GC, Campos DMS, do Socorro Silva Costa P, Peruzzo J, Bonamigo RR, Veit T, Vianna FSL. Role of gut microbiota in infectious and inflammatory diseases. Front Microbiol 2023; 14:1098386. [PMID: 37051522 PMCID: PMC10083300 DOI: 10.3389/fmicb.2023.1098386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Thousands of microorganisms compose the human gut microbiota, fighting pathogens in infectious diseases and inhibiting or inducing inflammation in different immunological contexts. The gut microbiome is a dynamic and complex ecosystem that helps in the proliferation, growth, and differentiation of epithelial and immune cells to maintain intestinal homeostasis. Disorders that cause alteration of this microbiota lead to an imbalance in the host’s immune regulation. Growing evidence supports that the gut microbial community is associated with the development and progression of different infectious and inflammatory diseases. Therefore, understanding the interaction between intestinal microbiota and the modulation of the host’s immune system is fundamental to understanding the mechanisms involved in different pathologies, as well as for the search of new treatments. Here we review the main gut bacteria capable of impacting the immune response in different pathologies and we discuss the mechanisms by which this interaction between the immune system and the microbiota can alter disease outcomes.
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Affiliation(s)
- Miriãn Ferrão Maciel-Fiuza
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Guilherme Cerutti Muller
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Daniel Marques Stuart Campos
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Perpétua do Socorro Silva Costa
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Department of Nursing, Universidade Federal do Maranhão, Imperatriz, Brazil
| | - Juliano Peruzzo
- Dermatology Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Renan Rangel Bonamigo
- Dermatology Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Pathology, Universidade Federal De Ciências Da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Tiago Veit
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- *Correspondence: Fernanda Sales Luiz Vianna,
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5
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Shirogane Y, Harada H, Hirai Y, Takemoto R, Suzuki T, Hashiguchi T, Yanagi Y. Collective fusion activity determines neurotropism of an en bloc transmitted enveloped virus. SCIENCE ADVANCES 2023; 9:eadf3731. [PMID: 36706187 PMCID: PMC9882980 DOI: 10.1126/sciadv.adf3731] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/29/2022] [Indexed: 06/09/2023]
Abstract
Measles virus (MeV), which is usually non-neurotropic, sometimes persists in the brain and causes subacute sclerosing panencephalitis (SSPE) several years after acute infection, serving as a model for persistent viral infections. The persisting MeVs have hyperfusogenic mutant fusion (F) proteins that likely enable cell-cell fusion at synapses and "en bloc transmission" between neurons. We here show that during persistence, F protein fusogenicity is generally enhanced by cumulative mutations, yet mutations paradoxically reducing the fusogenicity may be selected alongside the wild-type (non-neurotropic) MeV genome. A mutant F protein having SSPE-derived substitutions exhibits lower fusogenicity than the hyperfusogenic F protein containing some of those substitutions, but by the wild-type F protein coexpression, the fusogenicity of the former F protein is enhanced, while that of the latter is nearly abolished. These findings advance the understanding of the long-term process of MeV neuropathogenicity and provide critical insight into the genotype-phenotype relationships of en bloc transmitted viruses.
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Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Hidetaka Harada
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Yuichi Hirai
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ryuichi Takemoto
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Yanagi
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
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6
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Plant Virus Adaptation to New Hosts: A Multi-scale Approach. Curr Top Microbiol Immunol 2023; 439:167-196. [PMID: 36592246 DOI: 10.1007/978-3-031-15640-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Viruses are studied at each level of biological complexity: from within-cells to ecosystems. The same basic evolutionary forces and principles operate at each level: mutation and recombination, selection, genetic drift, migration, and adaptive trade-offs. Great efforts have been put into understanding each level in great detail, hoping to predict the dynamics of viral population, prevent virus emergence, and manage their spread and virulence. Unfortunately, we are still far from this. To achieve these ambitious goals, we advocate for an integrative perspective of virus evolution. Focusing in plant viruses, we illustrate the pervasiveness of the above-mentioned principles. Beginning at the within-cell level, we describe replication modes, infection bottlenecks, and cellular contagion rates. Next, we move up to the colonization of distal tissues, discussing the fundamental role of random events. Then, we jump beyond the individual host and discuss the link between transmission mode and virulence. Finally, at the community level, we discuss properties of virus-plant infection networks. To close this review we propose the multilayer network theory, in which elements at different layers are connected and submit to their own dynamics that feed across layers, resulting in new emerging properties, as a way to integrate information from the different levels.
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7
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Loveday EK, Sanchez HS, Thomas MM, Chang CB. Single-Cell Infection of Influenza A Virus Using Drop-Based Microfluidics. Microbiol Spectr 2022; 10:e0099322. [PMID: 36125315 PMCID: PMC9603537 DOI: 10.1128/spectrum.00993-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Drop-based microfluidics has revolutionized single-cell studies and can be applied toward analyzing tens of thousands to millions of single cells and their products contained within picoliter-sized drops. Drop-based microfluidics can shed insight into single-cell virology, enabling higher-resolution analysis of cellular and viral heterogeneity during viral infection. In this work, individual A549, MDCK, and siat7e cells were infected with influenza A virus (IAV) and encapsulated into 100-μm-size drops. Initial studies of uninfected cells encapsulated in drops demonstrated high cell viability and drop stability. Cell viability of uninfected cells in the drops remained above 75%, and the average drop radii changed by less than 3% following cell encapsulation and incubation over 24 h. Infection parameters were analyzed over 24 h from individually infected cells in drops. The number of IAV viral genomes and infectious viruses released from A549 and MDCK cells in drops was not significantly different from bulk infection as measured by reverse transcriptase quantitative PCR (RT-qPCR) and plaque assay. The application of drop-based microfluidics in this work expands the capacity to propagate IAV viruses and perform high-throughput analyses of individually infected cells. IMPORTANCE Drop-based microfluidics is a cutting-edge tool in single-cell research. Here, we used drop-based microfluidics to encapsulate thousands of individual cells infected with influenza A virus within picoliter-sized drops. Drop stability, cell loading, and cell viability were quantified from three different cell lines that support influenza A virus propagation. Similar levels of viral progeny as determined by RT-qPCR and plaque assay were observed from encapsulated cells in drops compared to bulk culture. This approach enables the ability to propagate influenza A virus from encapsulated cells, allowing for future high-throughput analysis of single host cell interactions in isolated microenvironments over the course of the viral life cycle.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Humberto S. Sanchez
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Connie B. Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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8
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Pires De Souza GA, Le Bideau M, Boschi C, Wurtz N, Colson P, Aherfi S, Devaux C, La Scola B. Choosing a cellular model to study SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:1003608. [PMID: 36339347 PMCID: PMC9634005 DOI: 10.3389/fcimb.2022.1003608] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 08/04/2023] Open
Abstract
As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.
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Affiliation(s)
- Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Céline Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Biological Sciences (INSB), Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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9
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In Depth Viral Diversity Analysis in Atypical Neurological and Neonatal Chikungunya Infections in Rio de Janeiro, Brazil. Viruses 2022; 14:v14092006. [PMID: 36146812 PMCID: PMC9506387 DOI: 10.3390/v14092006] [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: 08/09/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Chikungunya virus (CHIKV) is an arthropod-borne virus (arbovirus) transmitted by Aedes mosquitoes. The human infection usually manifests as a febrile and incapacitating arthritogenic illness, self-limiting and non-lethal. However, since 2013, CHIKV spreading through the tropics and to the Americas was accompanied by an increasing number of cases of atypical disease presentation, namely severe neuropathies and neonatal infection due to intrapartum vertical transmission. The pathophysiological mechanisms underlying these conditions have not been fully elucidated. However, arbovirus intrahost genetic diversity is thought to be linked to viral pathogenesis. To determine whether particular viral variants could be somehow associated, we analyzed the intrahost genetic diversity of CHIKV in three infected patients with neurological manifestations and three mothers infected during the intrapartum period, as well as their babies following vertical transmission. No statistically supported differences were observed for the genetic variability (nucleotide substitutions/gene length) along the genome between the groups. However, the newborn and cerebrospinal fluid samples (corresponding to virus passed through the placenta and/or the blood–brain barrier (BBB)) presented a different composition of their intrahost mutant ensembles compared to maternal or patient serum samples, even when concurrent. This finding could be consistent with the unidirectional virus transmission through these barriers, and the effect of selective bottlenecks during the transmission event. In addition, a higher proportion of defective variants (insertions/deletions and stop codons) was detected in the CSF and maternal samples and those were mainly distributed within the viral non-structural genes. Since defective viral genomes in RNA viruses are known to contribute to the outcome of acute viral infections and influence disease severity, their role in these atypical cases should be further investigated. Finally, with the in silico approach adopted, we detected no relevant non-conservative mutational pattern that could provide any hint of the pathophysiological mechanisms underlying these atypical cases. The present analysis represents a unique contribution to our understanding of the transmission events in these cases and generates hypotheses regarding underlying mechanisms, that can be explored further.
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10
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Manrubia S. The simple emergence of complex molecular function. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200422. [PMID: 35599566 DOI: 10.1098/rsta.2020.0422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Systems Biology Department, National Biotechnology Centre (CSIC), c/Darwin 3, 28049 Madrid, Spain
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11
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Abstract
Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.
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12
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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13
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection. Front Microbiol 2022; 13:839513. [PMID: 35668760 PMCID: PMC9163991 DOI: 10.3389/fmicb.2022.839513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.
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Affiliation(s)
- Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Syun-ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Japan
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14
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Triana S, Stanifer ML, Metz‐Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordoñez‐Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T. Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection. Mol Syst Biol 2021; 17:e9833. [PMID: 34309190 PMCID: PMC8311733 DOI: 10.15252/msb.20209833] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Human intestinal epithelial cells form a primary barrier protecting us from pathogens, yet only limited knowledge is available about individual contribution of each cell type to mounting an immune response against infection. Here, we developed a framework combining single-cell RNA-Seq and highly multiplex RNA FISH and applied it to human intestinal organoids infected with human astrovirus, a model human enteric virus. We found that interferon controls the infection and that astrovirus infects all major cell types and lineages and induces expression of the cell proliferation marker MKI67. Intriguingly, each intestinal epithelial cell lineage exhibits a unique basal expression of interferon-stimulated genes and, upon astrovirus infection, undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes. These findings suggest that in the human intestinal epithelium, each cell lineage plays a unique role in resolving virus infection. Our framework is applicable to other organoids and viruses, opening new avenues to unravel roles of individual cell types in viral pathogenesis.
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Affiliation(s)
- Sergio Triana
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular VirologyHeidelberg UniversityHeidelbergGermany
- Research Group “Cellular Polarity and Viral Infection”German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Camila Metz‐Zumaran
- Department of Infectious Diseases, VirologyHeidelberg UniversityHeidelbergGermany
| | - Mohammed Shahraz
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Markus Mukenhirn
- Department of Infectious Diseases, VirologyHeidelberg UniversityHeidelbergGermany
| | - Carmon Kee
- Research Group “Cellular Polarity and Viral Infection”German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Infectious Diseases, VirologyHeidelberg UniversityHeidelbergGermany
| | - Clara Serger
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Ronald Koschny
- Department of Internal Medicine IVInterdisciplinary Endoscopy CenterUniversity Hospital HeidelbergHeidelbergGermany
| | - Diana Ordoñez‐Rueda
- Flow Cytometry Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Malte Paulsen
- Flow Cytometry Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Vladimir Benes
- Genomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Steeve Boulant
- Research Group “Cellular Polarity and Viral Infection”German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Infectious Diseases, VirologyHeidelberg UniversityHeidelbergGermany
| | - Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCAUSA
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15
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Sexton NR, Bellis ED, Murrieta RA, Spangler MC, Cline PJ, Weger-Lucarelli J, Ebel GD. Genome Number and Size Polymorphism in Zika Virus Infectious Units. J Virol 2021; 95:e00787-20. [PMID: 33328311 PMCID: PMC8094933 DOI: 10.1128/jvi.00787-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Zika virus (ZIKV; Flaviviridae, Flavivirus) is an arthropod-borne infection that can result in severe outcomes, particularly in fetuses infected in utero It has been assumed that infection by ZIKV, as well as other viruses, is largely initiated by individual virus particles binding to and entering a cell. However, recent studies have demonstrated that multiple virus particles are frequently delivered to a cell simultaneously and that this collective particle delivery enhances infection. ZIKV is maintained in nature between Aedes aegypti mosquitos and vertebrate hosts, including humans. Human infection is initiated through the injection of a relatively small initial inoculum comprised of a genetically complex virus population. Since most mutations decrease virus fitness, collective particle transmission could benefit ZIKV and other arthropod-borne diseases by facilitating the maintenance of genetic complexity and adaptability during infection or through other mechanisms. Therefore, we utilized a barcoded ZIKV to quantify the number of virus genomes that initiate a plaque. We found that individual plaques contain a mean of 10 infecting viral genomes (range, 1 to 212). Few plaques contained more than two dominant genomes. To determine whether multigenome infectious units consist of collectively transmitting virions, infectious units of ZIKV were then separated mechanically by centrifugation, and heavier fractions were found to contain more genomes per plaque-forming unit, with larger diameters. Finally, larger/heavier infectious units reformed after removal. These data suggest that ZIKV populations consist of a variety of infectious unit sizes, likely mostly made up of aggregates, and only rarely begin with a single virus genome.IMPORTANCE The arthropod-borne Zika virus (ZIKV) infects humans and can cause severe neurological sequelae, particularly in fetuses infected in utero How this virus has been able to spread across vast geological ranges and evolve in new host populations is not yet understood. This research demonstrates a novel mechanism of ZIKV transmission through multigenome aggregates, providing insight into ZIKV evolution, immunologic evasion, and better future therapeutic design. This study shows that ZIKV plaques result from collections of genomes rather than individual genomes, increasing the potential for interactions between ZIKV genotypes.
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Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Eric D Bellis
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Reyes A Murrieta
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Mark Cole Spangler
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Parker J Cline
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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16
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Wu M, Xia M, Li W, Li H. Single-Cell Sequencing Applications in the Inner Ear. Front Cell Dev Biol 2021; 9:637779. [PMID: 33644075 PMCID: PMC7907461 DOI: 10.3389/fcell.2021.637779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/21/2021] [Indexed: 01/29/2023] Open
Abstract
Genomics studies face specific challenges in the inner ear due to the multiple types and limited amounts of inner ear cells that are arranged in a very delicate structure. However, advances in single-cell sequencing (SCS) technology have made it possible to analyze gene expression variations across different cell types as well as within specific cell groups that were previously considered to be homogeneous. In this review, we summarize recent advances in inner ear research brought about by the use of SCS that have delineated tissue heterogeneity, identified unknown cell subtypes, discovered novel cell markers, and revealed dynamic signaling pathways during development. SCS opens up new avenues for inner ear research, and the potential of the technology is only beginning to be explored.
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Affiliation(s)
- Mingxuan Wu
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Mingyu Xia
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Wenyan Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China.,The Institutes of Brain Science and The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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17
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The Role of Single-Cell Technology in the Study and Control of Infectious Diseases. Cells 2020; 9:cells9061440. [PMID: 32531928 PMCID: PMC7348906 DOI: 10.3390/cells9061440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host-pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.
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18
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Liu W, He H, Zheng SY. Microfluidics in Single-Cell Virology: Technologies and Applications. Trends Biotechnol 2020; 38:1360-1372. [PMID: 32430227 DOI: 10.1016/j.tibtech.2020.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
Abstract
Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has been used in the field of virology. An array of strategies based on microwells, microvalves, and droplets is now available for tracking viral infection dynamics, identifying cell subpopulations with particular phenotypes, as well as high-throughput screening. The insights into the virus-host interactions gained at the single-cell level are unprecedented and usually inaccessible by population-based experiments. Therefore, single-cell microfluidics, which opens new avenues for mechanism elucidation and development of antiviral therapeutics, would be a valuable tool for the study of viral pathogenesis.
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Affiliation(s)
- Wu Liu
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Hongzhang He
- Captis Diagnostics Inc., Pittsburgh, PA 15213, USA
| | - Si-Yang Zheng
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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19
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Plant EP, Manukyan H, Sanchez JL, Laassri M, Ye Z. Immune Pressure on Polymorphous Influenza B Populations Results in Diverse Hemagglutinin Escape Mutants and Lineage Switching. Vaccines (Basel) 2020; 8:vaccines8010125. [PMID: 32168968 PMCID: PMC7157493 DOI: 10.3390/vaccines8010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations arise in the genomes of progeny viruses during infection. Mutations that occur in epitopes targeted by host antibodies allow the progeny virus to escape the host adaptive, B-cell mediated antibody immune response. Major epitopes have been identified in influenza B virus (IBV) hemagglutinin (HA) protein. However, IBV strains maintain a seasonal presence in the human population and changes in IBV genomes in response to immune pressure are not well characterized. There are two lineages of IBV that have circulated in the human population since the 1980s, B-Victoria and B-Yamagata. It is hypothesized that early exposure to one influenza subtype leads to immunodominance. Subsequent seasonal vaccination or exposure to new subtypes may modify subsequent immune responses, which, in turn, results in selection of escape mutations in the viral genome. Here we show that while some mutations do occur in known epitopes suggesting antibody escape, many mutations occur in other parts of the HA protein. Analysis of mutations outside of the known epitopes revealed that these mutations occurred at the same amino acid position in viruses from each of the two IBV lineages. Interestingly, where the amino acid sequence differed between viruses from each lineage, reciprocal amino acid changes were observed. That is, the virus from the Yamagata lineage become more like the Victoria lineage virus and vice versa. Our results suggest that some IBV HA sequences are constrained to specific amino acid codons when viruses are cultured in the presence of antibodies. Some changes to the known antigenic regions may also be restricted in a lineage-dependent manner. Questions remain regarding the mechanisms underlying these results. The presence of amino acid residues that are constrained within the HA may provide a new target for universal vaccines for IBV.
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Affiliation(s)
- Ewan P. Plant
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
- Correspondence: ; Tel.: +1-240-402-7319
| | - Hasmik Manukyan
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Jose L. Sanchez
- Armed Forces Health Surveillance Branch, Public Health Division, Assistant Director for Combat Support (AD-CS), Defense Health Agency, Silver Spring, MD 20904, USA;
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Zhiping Ye
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
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20
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Wang H, Xin X, Zheng C, Shen C. Single-Cell Analysis of Foot-and-Mouth Disease Virus. Front Microbiol 2020; 11:361. [PMID: 32194538 PMCID: PMC7066083 DOI: 10.3389/fmicb.2020.00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/18/2020] [Indexed: 11/25/2022] Open
Abstract
With the rapid development of single-cell technologies, the mechanisms underlying viral infections and the interactions between hosts and viruses are starting to be explored at the single-cell level. The foot-and-mouth-disease (FMD) virus (FMDV) causes an acute and persistent infection that can result in the break-out of FMD, which can have serious effects on animal husbandry. Single-cell techniques have emerged as powerful approaches to analyze virus infection at the resolution of individual cells. In this review, the existing single-cell studies examining FMDV will be systematically summarized, and the central themes of these studies will be presented.
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Affiliation(s)
- Hailong Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiu Xin
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Congyi Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Chao Shen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
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21
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Yasen A, Aini A, Wang H, Li W, Zhang C, Ran B, Tuxun T, Maimaitinijiati Y, Shao Y, Aji T, Wen H. Progress and applications of single-cell sequencing techniques. INFECTION GENETICS AND EVOLUTION 2020; 80:104198. [PMID: 31958516 DOI: 10.1016/j.meegid.2020.104198] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 01/06/2023]
Abstract
Single-cell sequencing (SCS) is a next-generation sequencing method that is mainly used to analyze differences in genetic and protein information between cells, to obtain genetic information on microorganisms that are difficult to cultivate at a single-cell level and to better understand their specific roles in the microenvironment. By sequencing the whole genome, transcriptome and epigenome of a single cell, the complex heterogeneous mechanisms involved in disease occurrence and progression can be revealed, further improving disease diagnosis, prognosis prediction and monitoring of the therapeutic effects of drugs. In this study, we mainly summarized the methods and application fields of SCS, which may provide potential references for its future clinical applications, including the analysis of embryonic and organ development, the immune system, cancer progression, and parasitic and infectious diseases as well as stem cell research, antibody screening, and therapeutic research and development.
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Affiliation(s)
- Aimaiti Yasen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Abudusalamu Aini
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Hui Wang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Wending Li
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Chuanshan Zhang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Bo Ran
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerhongjiang Tuxun
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yusufukadier Maimaitinijiati
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yingmei Shao
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerganaili Aji
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
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22
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Steele EJ, Gorczynski RM, Lindley RA, Tokoro G, Temple R, Wickramasinghe NC. Origin of new emergent Coronavirus and Candida fungal diseases-Terrestrial or cosmic? ADVANCES IN GENETICS 2020; 106:75-100. [PMID: 33081928 PMCID: PMC7358766 DOI: 10.1016/bs.adgen.2020.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The origins and global spread of two recent, yet quite different, pandemic diseases is discussed and reviewed in depth: Candida auris, a eukaryotic fungal disease, and COVID-19 (SARS-CoV-2), a positive strand RNA viral respiratory disease. Both these diseases display highly distinctive patterns of sudden emergence and global spread, which are not easy to understand by conventional epidemiological analysis based on simple infection-driven human- to-human spread of an infectious disease (assumed to jump suddenly and thus genetically, from an animal reservoir). Both these enigmatic diseases make sense however under a Panspermia in-fall model and the evidence consistent with such a model is critically reviewed.
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Affiliation(s)
- Edward J. Steele
- C.Y.O'Connor ERADE Village Foundation, Piara Waters, Perth, WA, Australia,Melville Analytics Pty Ltd, Melbourne, VIC, Australia,Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka,Corresponding authors:
| | - Reginald M. Gorczynski
- University Toronto Health Network, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Robyn A. Lindley
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Melbourne, VIC, Australia,GMDx Group Ltd, Melbourne, VIC, Australia
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astroeconomics, Gifu, Japan
| | - Robert Temple
- The History of Chinese Science and Culture Foundation, Conway Hall, London, United Kingdom
| | - N. Chandra Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka,Institute for the Study of Panspermia and Astroeconomics, Gifu, Japan,University of Buckingham, Buckingham, United Kingdom,National Institute of Fundamental Studies, Kandy, Sri Lanka,Corresponding authors:
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23
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Abortive herpes simplex virus infection of nonneuronal cells results in quiescent viral genomes that can reactivate. Proc Natl Acad Sci U S A 2019; 117:635-640. [PMID: 31871148 DOI: 10.1073/pnas.1910537117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abortive viral infections are usually studied in populations of susceptible but nonpermissive cells. Single-cell studies of viral infections have demonstrated that even in susceptible and permissive cell populations, abortive infections can be detected in subpopulations of the infected cells. We have previously identified abortive infections in HeLa cells infected with herpes simplex virus 1 (HSV-1) at high multiplicity of infection (MOI). Here, we tested 4 additional human-derived nonneuronal cell lines (cancerous or immortalized) and found significant subpopulations that remain abortive. To characterize these abortive cells, we recovered cell populations that survived infection with HSV-1 at high MOI. The surviving cells retained proliferative potential and the ability to be reinfected. These recovered cell populations maintained the viral genomes in a quiescent state for at least 5 wk postinfection. Our results indicate that these viral genomes are maintained inside the nucleus, bound to cellular histones and occasionally reactivated to produce new progeny viruses. We conclude that abortive HSV-1 infection is a common feature during infection of nonneuronal cells and results in a latency-like state in the infected cells. Our findings question the longstanding paradigm that alphaherpesviruses can establish spontaneous latency only in neuronal cells and emphasize the stochastic nature of lytic versus latency decision of HSV-1 in nonneuronal cells.
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24
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Liu W, Caglar MU, Mao Z, Woodman A, Arnold JJ, Wilke CO, Cameron CE. More than efficacy revealed by single-cell analysis of antiviral therapeutics. SCIENCE ADVANCES 2019; 5:eaax4761. [PMID: 31692968 PMCID: PMC6821460 DOI: 10.1126/sciadv.aax4761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/16/2019] [Indexed: 05/11/2023]
Abstract
Because many aspects of viral infection dynamics and inhibition are governed by stochastic processes, single-cell analysis should provide more information than approaches using population averaging. We have developed a microfluidic device composed of ~6000 wells, with each well containing a microstructure to capture single, infected cells replicating an enterovirus expressing a fluorescent reporter protein. We have used this system to characterize enterovirus inhibitors with distinct mechanisms of action. Single-cell analysis reveals that each class of inhibitor interferes with the viral infection cycle in a manner that can be distinguished by principal component analysis. Single-cell analysis of antiviral candidates not only reveals efficacy but also facilitates clustering of drugs with the same mechanism of action and provides some indication of the ease with which resistance will develop.
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Affiliation(s)
- Wu Liu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Mehmet U. Caglar
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Jamie J. Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Claus O. Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Craig E. Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
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25
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Sardanyés J, Arderiu A, Elena SF, Alarcón T. Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes. J R Soc Interface 2019; 15:rsif.2018.0129. [PMID: 29848592 DOI: 10.1098/rsif.2018.0129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/08/2018] [Indexed: 12/14/2022] Open
Abstract
Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called 'stamping machine replication' (SMR) and 'geometric replication' (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasi-neutral coexistence scenario, with a line of fixed points involving different strands' equilibrium ratios depending on the initial conditions. Recent research into the quasi-neutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alter the mean-field scenario, and one of the two species outcompetes the other. In this article, we study this phenomenon for viral RNA replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNAs, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication.
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Affiliation(s)
- Josep Sardanyés
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain .,Barcelona Graduate School of Mathematics (BGSMath), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain
| | - Andreu Arderiu
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 València, Spain.,Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Parc Científic UV, Catedrático José Beltrán 2, Paterna, 46980 València, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Tomás Alarcón
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.,Barcelona Graduate School of Mathematics (BGSMath), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain.,Departament de Matemàtiques, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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26
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Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJW, Bloom JD. Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity. J Virol 2019; 93:e00500-19. [PMID: 31068418 PMCID: PMC6600203 DOI: 10.1128/jvi.00500-19] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
Influenza virus-infected cells vary widely in their expression of viral genes and only occasionally activate innate immunity. Here, we develop a new method to assess how the genetic variation in viral populations contributes to this heterogeneity. We do this by determining the transcriptome and full-length sequences of all viral genes in single cells infected with a nominally "pure" stock of influenza virus. Most cells are infected by virions with defects, some of which increase the frequency of innate-immune activation. These immunostimulatory defects are diverse and include mutations that perturb the function of the viral polymerase protein PB1, large internal deletions in viral genes, and failure to express the virus's interferon antagonist NS1. However, immune activation remains stochastic in cells infected by virions with these defects and occasionally is triggered even by virions that express unmutated copies of all genes. Our work shows that the diverse spectrum of defects in influenza virus populations contributes to-but does not completely explain-the heterogeneity in viral gene expression and immune activation in single infected cells.IMPORTANCE Because influenza virus has a high mutation rate, many cells are infected by mutated virions. But so far, it has been impossible to fully characterize the sequence of the virion infecting any given cell, since conventional techniques such as flow cytometry and single-cell transcriptome sequencing (scRNA-seq) only detect if a protein or transcript is present, not its sequence. Here we develop a new approach that uses long-read PacBio sequencing to determine the sequences of virions infecting single cells. We show that viral genetic variation explains some but not all of the cell-to-cell variability in viral gene expression and innate immune induction. Overall, our study provides the first complete picture of how viral mutations affect the course of infection in single cells.
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Affiliation(s)
- Alistair B Russell
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Elizaveta Elshina
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jacob R Kowalsky
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Aartjan J W Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
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27
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Li N, Ma WT, Pang M, Fan QL, Hua JL. The Commensal Microbiota and Viral Infection: A Comprehensive Review. Front Immunol 2019; 10:1551. [PMID: 31333675 PMCID: PMC6620863 DOI: 10.3389/fimmu.2019.01551] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
The human body is inhabited by a diverse microbial community that is collectively coined as commensal microbiota. Recent research has greatly advanced our understanding of how the commensal microbiota affects host health. Among the various kinds of pathogenic infections of the host, viral infections constitute one of the most serious public health problems worldwide. During the infection process, viruses may have substantial and intimate interactions with the commensal microbiota. A plethora of evidence suggests that the commensal microbiota regulates and is in turn regulated by invading viruses through diverse mechanisms, thereby having stimulatory or suppressive roles in viral infections. Furthermore, the integrity of the commensal microbiota can be disturbed by invading viruses, causing dysbiosis in the host and further influencing virus infectivity. In the present article, we discuss current insights into the regulation of viral infection by the commensal microbiota. We also draw attention to the disruption of microbiota homeostasis by several viruses.
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Affiliation(s)
- Na Li
- College of Veterinary Medicine, Northwest A & F University, Yangling, China
| | - Wen-Tao Ma
- College of Veterinary Medicine, Northwest A & F University, Yangling, China
| | - Ming Pang
- College of Veterinary Medicine, Northwest A & F University, Yangling, China
| | - Qin-Lei Fan
- Animal Health and Epidemiology Center, Qingdao, China
| | - Jin-Lian Hua
- College of Veterinary Medicine, Northwest A & F University, Yangling, China
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28
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Díaz-Muñoz SL. Uncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput Tools. mSystems 2019; 4:e00121-19. [PMID: 31164405 PMCID: PMC6584877 DOI: 10.1128/msystems.00121-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 01/05/2023] Open
Abstract
Virus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion. Coinfection and subsequent social interactions can change viral pathogenicity, host range, and genetic composition, with implications for human health and viral evolution. I propose that this field can be advanced by bringing new perspectives into virology (e.g., social evolution theory) and uniting disciplinary divides within virology (classical, host-focused, and ecoevolutionary). The development of novel high-throughput tools that meld molecular and evolutionary approaches can harness viral diversity as an experimental asset to understand complex viral social interactions. A greater knowledge of virus-virus interactions will lead to the reformulation of basic concepts of virology and advances in applied virology, with new treatments that harness interactions between viruses to fight viral and bacterial infections.
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Affiliation(s)
- Samuel L Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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29
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Drayman N, Patel P, Vistain L, Tay S. HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 2019; 8:e46339. [PMID: 31090537 PMCID: PMC6570482 DOI: 10.7554/elife.46339] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022] Open
Abstract
Viral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous, with most infected cells giving rise to no or few viral progeny while some cells produce thousands. Analysis of Herpes Simplex virus 1 (HSV-1) infection by population-averaged measurements has taught us a lot about the course of viral infection, but has also produced contradictory results, such as the concurrent activation and inhibition of type I interferon signaling during infection. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that these cells cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming involves the recruitment of β-catenin to the host nucleus and viral replication compartments, and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.
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Affiliation(s)
- Nir Drayman
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Parthiv Patel
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Luke Vistain
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Savaş Tay
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
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30
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Aguilera ER, Pfeiffer JK. Strength in numbers: Mechanisms of viral co-infection. Virus Res 2019; 265:43-46. [PMID: 30836113 PMCID: PMC6461475 DOI: 10.1016/j.virusres.2019.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/01/2019] [Indexed: 12/12/2022]
Abstract
RNA virus populations are diverse due to a variety of factors, including lack of proofreading of the viral RNA-dependent RNA polymerase. These diverse viral populations include defective viruses incapable of productive infection. Recent studies have determined the existence of several modes of viral transmission outside of canonical pathways, including en bloc transmission of multiple viruses into a single host cell via membrane vesicles. Additionally, it has recently been determined that viral aggregation and bacteria can facilitate the delivery of multiple viruses to a single cell. Co-infection of RNA viruses is important since it has the potential to enhance viral fitness. Furthermore, through complementation and recombination, co-infection could potentially promote "resurrection" of otherwise defective viral genomes and has the potential to expand viral diversity.
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Affiliation(s)
- Elizabeth R Aguilera
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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31
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Abstract
Host-pathogen interactions, particularly in the context of bacterial infections, are dynamic exchanges where transcriptional heterogeneity from both the host and the pathogen can lead to many diverse outcomes via distinct molecular pathways. Transcriptional profiling at the single-cell level, on a genome-wide scale, has enabled a greater appreciation of the cellular diversity in complex biological organisms and the myriad of host transcriptional states during infection. Here, we highlight recent reports of single-cell RNA sequencing within the context of host-pathogen interactions, describe current limitations for detecting and profiling the transcriptome of invading pathogens at the single-cell level, and suggest exciting future prospects for this technology in the study of infection. We propose that understanding infection as an integrated process between pathogen and host with resolution at the single-cell level will ultimately inform development of vaccines with greater productive and protective host immunity, enable the development of novel therapeutics that harness host mechanisms, and yield more accurate biomarkers to guide better diagnostics.
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Affiliation(s)
- Cristina Penaranda
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Deborah T. Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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32
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Shirogane Y, Watanabe S, Yanagi Y. Cooperation between different variants: A unique potential for virus evolution. Virus Res 2019; 264:68-73. [PMID: 30822430 DOI: 10.1016/j.virusres.2019.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 02/05/2023]
Abstract
RNA viruses exist as quasispecies containing many variants within their populations because of the error prone nature of viral RNA-dependent RNA polymerases. Quasispecies are not a simple collection of individual variants. Instead, internal interactions among variants provide quasispecies with unique evolvability. An example is 'cooperation' between wild-type and defective measles viruses, in which co-existence of a wild-type and a mutant genome produces a new phenotype. Such internal interactions presuppose efficient co-transmission of multiple genomes to the same cell, which is achieved by polyploid virions of some virus families or by a high multiplicity of infection. Recent studies have revealed that multiple viral genomes can also be transmitted simultaneously ('bloc transmission') by other mechanisms, strengthening the concept of internal interactions among viral quasispecies. Elucidation of the mechanisms of virus evolution, including internal interactions and bloc transmission, may provide rational strategies to solve such important problems of virus infections as drug-resistance, immune evasion, and acquisition of the new tropism and host range.
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Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
| | - Shumpei Watanabe
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-0085, Japan
| | - Yusuke Yanagi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
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33
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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34
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Chattopadhyay PK, Roederer M, Bolton DL. A deadly dance: the choreography of host-pathogen interactions, as revealed by single-cell technologies. Nat Commun 2018; 9:4638. [PMID: 30401874 PMCID: PMC6219517 DOI: 10.1038/s41467-018-06214-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023] Open
Abstract
Pathogens have numerous mechanisms by which they replicate within a host, who in turn responds by developing innate and adaptive immune countermeasures to limit disease. The advent of high-content single-cell technologies has facilitated a greater understanding of the properties of host cells harboring infection, the host's pathogen-specific immune responses, and the mechanisms pathogens have evolved to escape host control. Here we review these advances and argue for greater inclusion of higher resolution single-cell technologies into approaches for defining immune evasion mechanisms by pathogens.
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Affiliation(s)
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, 20892, MD, USA
| | - Diane L Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research, Silver Spring, 20910, MD, USA.
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35
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RNA Virus Fidelity Mutants: A Useful Tool for Evolutionary Biology or a Complex Challenge? Viruses 2018; 10:v10110600. [PMID: 30388745 PMCID: PMC6267201 DOI: 10.3390/v10110600] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022] Open
Abstract
RNA viruses replicate with low fidelity due to the error-prone nature of the RNA-dependent RNA polymerase, which generates approximately one mutation per round of genome replication. Due to the large population sizes produced by RNA viruses during replication, this results in a cloud of closely related virus variants during host infection, of which small increases or decreases in replication fidelity have been shown to result in virus attenuation in vivo, but not typically in vitro. Since the discovery of the first RNA virus fidelity mutants during the mid-aughts, the field has exploded with the identification of over 50 virus fidelity mutants distributed amongst 7 RNA virus families. This review summarizes the current RNA virus fidelity mutant literature, with a focus upon the definition of a fidelity mutant as well as methods to confirm any mutational changes associated with the fidelity mutant. Due to the complexity of such a definition, in addition to reports of unstable virus fidelity phenotypes, the future translational utility of these mutants and applications for basic science are examined.
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36
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Fornés J, Tomás Lázaro J, Alarcón T, Elena SF, Sardanyés J. Viral replication modes in single-peak fitness landscapes: A dynamical systems analysis. J Theor Biol 2018; 460:170-183. [PMID: 30300648 DOI: 10.1016/j.jtbi.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/30/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidence from distributions of mutations and from viral RNA amplification suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) mode. Although previous theoretical work has focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, little is known in terms of the bifurcations and transitions involving the so-called error threshold (mutation-induced dominance of mutants) and lethal mutagenesis (extinction of all sequences due to mutation accumulation and demographic stochasticity). Here we analyze a dynamical system describing the intracellular amplification of viral RNA genomes evolving on a single-peak fitness landscape focusing on three cases considering neutral, deleterious, and lethal mutants. We analytically derive the critical mutation rates causing lethal mutagenesis and error threshold, governed by transcritical bifurcations that depend on parameters α (parameter introducing the mode of replication), replicative fitness of mutants (k1), and on the spontaneous degradation rates of the sequences (ϵ). Our results relate the error catastrophe with lethal mutagenesis in a model with continuous populations of viral genomes. The former case involves dominance of the mutant sequences, while the latter, a deterministic extinction of the viral RNAs during replication due to increased mutation. For the lethal case the critical mutation rate involving lethal mutagenesis is μc=1-ɛ/α. Here, the SMR involves lower critical mutation rates, being the system more robust to lethal mutagenesis replicating closer to the GR mode. This result is also found for the neutral and deleterious cases, but for these later cases lethal mutagenesis can shift to the error threshold once the replication mode surpasses a threshold given by α=ϵ/k1.
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Affiliation(s)
- Joan Fornés
- Departament de Matemàtiques, Universitat Politècnica de Catalunya, Av Diagonal, 647, Barcelona 08028, Spain
| | - J Tomás Lázaro
- Departament de Matemàtiques, Universitat Politècnica de Catalunya, Av Diagonal, 647, Barcelona 08028, Spain; Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain
| | - Tomás Alarcón
- Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain; Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain; The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain.
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Single-Cell Analysis of the Impact of Host Cell Heterogeneity on Infection with Foot-and-Mouth Disease Virus. J Virol 2018; 92:JVI.00179-18. [PMID: 29444939 DOI: 10.1128/jvi.00179-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 01/02/2023] Open
Abstract
Viral infection and replication are affected by host cell heterogeneity, but the mechanisms underlying the effects remain unclear. Using single-cell analysis, we investigated the effects of host cell heterogeneity, including cell size, inclusion, and cell cycle, on foot-and-mouth disease virus (FMDV) infection (acute and persistent infections) and replication. We detected various viral genome replication levels in FMDV-infected cells. Large cells and cells with a high number of inclusions generated more viral RNA copies and viral protein and a higher proportion of infectious cells than other cells. Additionally, we found that the viral titer was 10- to 100-fold higher in cells in G2/M than those in other cell cycle phases and identified a strong correlation between cell size, inclusion, and cell cycle heterogeneity, which all affected the infection and replication of FMDV. Furthermore, we demonstrated that host cell heterogeneity influenced the adsorption of FMDV due to differences in the levels of FMDV integrin receptors expression. Collectively, these results further our understanding of the evolution of a virus in a single host cell.IMPORTANCE It is important to understand how host cell heterogeneity affects viral infection and replication. Using single-cell analysis, we found that viral genome replication levels exhibited dramatic variability in foot-and-mouth disease virus (FMDV)-infected cells. We also found a strong correlation between heterogeneity in cell size, inclusion number, and cell cycle status and that all of these characteristics affect the infection and replication of FMDV. Moreover, we found that host cell heterogeneity influenced the viral adsorption as differences in the levels of FMDV integrin receptors' expression. This study provided new ideas for the studies of correlation between FMDV infection mechanisms and host cells.
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38
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Steele EJ, Al-Mufti S, Augustyn KA, Chandrajith R, Coghlan JP, Coulson SG, Ghosh S, Gillman M, Gorczynski RM, Klyce B, Louis G, Mahanama K, Oliver KR, Padron J, Qu J, Schuster JA, Smith WE, Snyder DP, Steele JA, Stewart BJ, Temple R, Tokoro G, Tout CA, Unzicker A, Wainwright M, Wallis J, Wallis DH, Wallis MK, Wetherall J, Wickramasinghe DT, Wickramasinghe JT, Wickramasinghe NC, Liu Y. Cause of Cambrian Explosion - Terrestrial or Cosmic? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:3-23. [PMID: 29544820 DOI: 10.1016/j.pbiomolbio.2018.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.
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Affiliation(s)
- Edward J Steele
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka.
| | - Shirwan Al-Mufti
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Kenneth A Augustyn
- Center for the Physics of Living Organisms, Department of Physics, Michigan Technological University, Michigan, United States
| | | | - John P Coghlan
- University of Melbourne, Office of the Dean, Faculty Medicine, Dentistry and Health Sciences, 3rd Level, Alan Gilbert Building, Australia
| | - S G Coulson
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Sudipto Ghosh
- Metallurgical & Materials Engineering IIT, Kanpur, India
| | - Mark Gillman
- South African Brain Research Institute, 6 Campbell Street, Waverly, Johannesburg, South Africa
| | - Reginald M Gorczynski
- University Toronto Health Network, Toronto General Hospital, University of Toronto, Canada
| | - Brig Klyce
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Godfrey Louis
- Department of Physics, Cochin University of Science and Technology Cochin, India
| | | | - Keith R Oliver
- School of Veterinary and Life Sciences Murdoch University, Perth, WA, Australia
| | - Julio Padron
- Studio Eutropi, Clinical Pathology and Nutrition, Via Pompei 46, Ardea, 00040, Rome, Italy
| | - Jiangwen Qu
- Department of Infectious Disease Control, Tianjin Center for Disease Control and Prevention, China
| | - John A Schuster
- School of History and Philosophy of Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - W E Smith
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Duane P Snyder
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Julian A Steele
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Brent J Stewart
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
| | - Robert Temple
- The History of Chinese Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Christopher A Tout
- Institute of Astronomy, The Observatories, Madingley Road, Cambridge, CB3 0HA, UK
| | | | - Milton Wainwright
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka
| | - Jamie Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Daryl H Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Max K Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - John Wetherall
- School of Biomedical Sciences, Perth, Curtin University, WA, Australia
| | - D T Wickramasinghe
- College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | | | - N Chandra Wickramasinghe
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Russell AB, Trapnell C, Bloom JD. Extreme heterogeneity of influenza virus infection in single cells. eLife 2018; 7:e32303. [PMID: 29451492 PMCID: PMC5826275 DOI: 10.7554/elife.32303] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in the productivity of viral transcription - viral transcripts comprise less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. Some infected cells fail to express at least one viral gene, but this gene absence only partially explains variation in viral transcriptional load. Despite variation in viral load, the relative abundances of viral mRNAs are fairly consistent across infected cells. Activation of innate immune pathways is rare, but some cellular genes co-vary in abundance with the amount of viral mRNA. Overall, our results highlight the complexity of viral infection at the level of single cells.
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Affiliation(s)
- Alistair B Russell
- Basic Sciences Division and Computational Biology ProgramFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology ProgramFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
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40
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Erickson AK, Jesudhasan PR, Mayer MJ, Narbad A, Winter SE, Pfeiffer JK. Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination. Cell Host Microbe 2018; 23:77-88.e5. [PMID: 29290575 PMCID: PMC5764776 DOI: 10.1016/j.chom.2017.11.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 11/15/2017] [Indexed: 01/12/2023]
Abstract
RNA viruses exist in genetically diverse populations due to high levels of mutations, many of which reduce viral fitness. Interestingly, intestinal bacteria can promote infection of several mammalian enteric RNA viruses, but the mechanisms and consequences are unclear. We screened a panel of 41 bacterial strains as a platform to determine how different bacteria impact infection of poliovirus, a model enteric virus. Most bacterial strains, including those extracted from cecal contents of mice, bound poliovirus, with each bacterium binding multiple virions. Certain bacterial strains increased viral co-infection of mammalian cells even at a low virus-to-host cell ratio. Bacteria-mediated viral co-infection correlated with bacterial adherence to cells. Importantly, bacterial strains that induced viral co-infection facilitated genetic recombination between two different viruses, thereby removing deleterious mutations and restoring viral fitness. Thus, bacteria-virus interactions may increase viral fitness through viral recombination at initial sites of infection, potentially limiting abortive infections.
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Affiliation(s)
- Andrea K Erickson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Palmy R Jesudhasan
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Melinda J Mayer
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA.
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41
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Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE. Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. Cell Rep 2017; 21:1692-1704. [PMID: 29117571 PMCID: PMC5689460 DOI: 10.1016/j.celrep.2017.10.051] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 09/05/2017] [Accepted: 10/13/2017] [Indexed: 02/05/2023] Open
Abstract
We have developed a high-throughput, microfluidics-based platform to perform kinetic analysis of viral infections in individual cells. We have analyzed thousands of individual poliovirus infections while varying experimental parameters, including multiplicity of infection, cell cycle, viral genotype, and presence of a drug. We make several unexpected observations masked by population-based experiments: (1) viral and cellular factors contribute uniquely and independently to viral infection kinetics; (2) cellular factors cause wide variation in replication start times; and (3) infections frequently begin later and replication occurs faster than predicted by population measurements. We show that mutational load impairs interaction of the viral population with the host, delaying replication start times and explaining the attenuated phenotype of a mutator virus. We show that an antiviral drug can selectively extinguish the most-fit members of the viral population. Single-cell virology facilitates discovery and characterization of virulence determinants and elucidation of mechanisms of drug action eluded by population methods.
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Affiliation(s)
- Feng Guo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sixing Li
- Molecular Cellular and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mehmet Umut Caglar
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wu Liu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Claus O Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA; Molecular Cellular and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Craig E Cameron
- Molecular Cellular and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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42
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Drayman N, Karin O, Mayo A, Danon T, Shapira L, Rafael D, Zimmer A, Bren A, Kobiler O, Alon U. Dynamic Proteomics of Herpes Simplex Virus Infection. mBio 2017; 8:e01612-17. [PMID: 29114028 PMCID: PMC5676043 DOI: 10.1128/mbio.01612-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 10/06/2017] [Indexed: 12/28/2022] Open
Abstract
The cellular response to viral infection is usually studied at the level of cell populations. Currently, it remains an open question whether and to what extent cell-to-cell variability impacts the course of infection. Here we address this by dynamic proteomics-imaging and tracking 400 yellow fluorescent protein (YFP)-tagged host proteins in individual cells infected by herpes simplex virus 1. By quantifying time-lapse fluorescence imaging, we analyze how cell-to-cell variability impacts gene expression from the viral genome. We identify two proteins, RFX7 and geminin, whose levels at the time of infection correlate with successful initiation of gene expression. These proteins are cell cycle markers, and we find that the position in the cell cycle at the time of infection (along with the cell motility and local cell density) can reasonably predict in which individual cells gene expression from the viral genome will commence. We find that the onset of cell division dramatically impacts the progress of infection, with 70% of dividing cells showing no additional gene expression after mitosis. Last, we identify four host proteins that are specifically modulated in infected cells, of which only one has been previously recognized. SUMO2 and RPAP3 levels are rapidly reduced, while SLTM and YTHDC1 are redistributed to form nuclear foci. These modulations are dependent on the expression of ICP0, as shown by infection with two mutant viruses that lack ICP0. Taken together, our results provide experimental validation for the long-held notion that the success of infection is dependent on the state of the host cell at the time of infection.IMPORTANCE High-throughput assays have revolutionized many fields in biology, both by allowing a more global understanding of biological processes and by deciphering rare events in subpopulations. Here we use such an assay, dynamic proteomics, to study viral infection at the single-cell level. We follow tens of thousands of individual cells infected by herpes simplex virus using fluorescence live imaging. Our results link the state of a cell at the time of virus infection with its probability to successfully initiate gene expression from the viral genome. Further, we identified three cellular proteins that were previously unknown to respond to viral infection. We conclude that dynamic proteomics provides a powerful tool to study single-cell differences during viral infection.
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Affiliation(s)
- Nir Drayman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Karin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Danon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Shapira
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dor Rafael
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anat Zimmer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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43
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Ralph M, Bednarchik M, Tomer E, Rafael D, Zargarian S, Gerlic M, Kobiler O. Promoting Simultaneous Onset of Viral Gene Expression Among Cells Infected with Herpes Simplex Virus-1. Front Microbiol 2017; 8:2152. [PMID: 29163436 PMCID: PMC5671993 DOI: 10.3389/fmicb.2017.02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/20/2017] [Indexed: 11/30/2022] Open
Abstract
Synchronous viral infection facilitates the study of viral gene expression, viral host interactions, and viral replication processes. However, the protocols for achieving synchronous infections were hardly ever tested in proper temporal resolution at the single-cell level. We set up a fluorescence-based, time lapse microscopy assay to study sources of variability in the timing of gene expression during herpes simplex virus-1 (HSV-1) infection. We found that with the common protocol, the onset of gene expression within different cells can vary by more than 3 h. We showed that simultaneous viral genome entry to the nucleus can be achieved with a derivative of the previously characterized temperature sensitive mutant tsB7, however, this did not improve gene expression synchrony. We found that elevating the temperature in which the infection is done and increasing the multiplicity of infection (MOI) significantly promoted simultaneous onset of viral gene expression among infected cells. Further, elevated temperature result in a decrease in the coefficient of variation (a standardized measure of dispersion) of viral replication compartments (RCs) sizes among cells as well as a slight increment of viral late gene expression synchrony. We conclude that simultaneous viral gene expression can be improved by simple modifications to the infection process and may reduce the effect of single-cell variability on population-based assays.
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Affiliation(s)
| | | | | | | | | | | | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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44
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Pauly MD, Procario MC, Lauring AS. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. eLife 2017; 6. [PMID: 28598328 PMCID: PMC5511008 DOI: 10.7554/elife.26437] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza virus’ low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the influenza virus mutation rate is 2.7 × 10–6 - 3.0 × 10–5 substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal fitness impacts and fluctuation tests typically investigate only a subset of all possible single nucleotide mutations. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins, which allowed us to measure the rates of selectively neutral mutations representative of the twelve different mutation types. We measured an overall mutation rate of 1.8 × 10–4 s/n/r for PR8 (H1N1) and 2.5 × 10–4 s/n/r for Hong Kong 2014 (H3N2) and a transitional bias of 2.7–3.6. Our data suggest that each replicated genome will have an average of 2–3 mutations and highlight the importance of mutational load in influenza virus evolution. DOI:http://dx.doi.org/10.7554/eLife.26437.001
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Affiliation(s)
- Matthew D Pauly
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Megan C Procario
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
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45
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Cuevas JM, Durán-Moreno M, Sanjuán R. Multi-virion infectious units arise from free viral particles in an enveloped virus. Nat Microbiol 2017; 2:17078. [PMID: 28530650 PMCID: PMC5447809 DOI: 10.1038/nmicrobiol.2017.78] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 04/11/2017] [Indexed: 12/20/2022]
Abstract
Many animal viruses are enveloped in a lipid bilayer taken up from cellular membranes. Because viral surface proteins bind to these membranes to initiate infection, we hypothesized that free virions may also be capable of interacting with the envelopes of other virions extracellularly. Here, we demonstrate this hypothesis in the vesicular stomatitis virus (VSV), a prototypic negative-strand RNA virus composed of an internal ribonucleocapsid, a matrix protein and an external envelope1. Using microscopy, dynamic light scattering, differential centrifugation and flow cytometry, we show that free viral particles can spontaneously aggregate into multi-virion infectious units. We also show that, following establishment of these contacts, different viral genetic variants are co-transmitted to the same target cell. Furthermore, virion-virion binding can determine key aspects of viral fitness such as antibody escape. In purified virions, this process is driven by protein-lipid interactions probably involving the VSV surface glycoprotein and phosphatidylserine. Whereas we found that multi-virion complexes occurred unfrequently in standard cell cultures, they were abundant in other fluids such as saliva, a natural VSV shedding route2. Our findings contrast with the commonly accepted perception of virions as passive propagules and show the ability of enveloped viruses to establish collective infectious units, which could in turn facilitate the evolution of virus-virus interactions and of social-like traits3.
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Affiliation(s)
- José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de
València, Spain
- Department of Genetics, Universitat de València,
València, Spain
| | - María Durán-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Universitat de
València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de
València, Spain
- Department of Genetics, Universitat de València,
València, Spain
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46
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Ghoul M, Andersen SB, West SA. Sociomics: Using Omic Approaches to Understand Social Evolution. Trends Genet 2017; 33:408-419. [PMID: 28506494 DOI: 10.1016/j.tig.2017.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression. This is especially useful in cases where there is clear variation in the level of sociality, such as the social insects. Major tasks for the future are to apply these approaches to a wider range of non-model organisms, and to move from exploratory analyses to the testing of evolutionary theory.
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Affiliation(s)
- Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| | - Sandra B Andersen
- Langone Medical Center, New York University, 423 East 23rd Street, New York, NY 10010, USA.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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47
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Aguilera ER, Erickson AK, Jesudhasan PR, Robinson CM, Pfeiffer JK. Plaques Formed by Mutagenized Viral Populations Have Elevated Coinfection Frequencies. mBio 2017; 8:e02020-16. [PMID: 28292984 PMCID: PMC5350468 DOI: 10.1128/mbio.02020-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/14/2017] [Indexed: 02/05/2023] Open
Abstract
The plaque assay is a common technique used to measure virus concentrations and is based upon the principle that each plaque represents a single infectious unit. As such, the number of plaques is expected to correlate linearly with the virus dilution plated, and each plaque should be formed by a single founder virus. Here, we examined whether more than one virus can contribute to plaque formation. By using genetic and phenotypic assays with genetically marked polioviruses, we found that multiple parental viruses are present in 5 to 7% of plaques, even at an extremely low multiplicity of infection. We demonstrated through visual and biophysical assays that, like many viral stocks, our viral stocks contain both single particles and aggregates. These data suggest that aggregated virions are capable of inducing coinfection and chimeric plaque formation. In fact, inducing virion aggregation via exposure to low pH increased coinfection in a flow cytometry-based assay. We hypothesized that plaques generated by viruses with high mutation loads may have higher coinfection frequencies due to processes restoring fitness, such as complementation and recombination. Indeed, we found that coinfection frequency correlated with mutation load, with 17% chimeric plaque formation for heavily mutagenized viruses. Importantly, the frequency of chimeric plaques may be underestimated by up to threefold, since coinfection with the same parental virus cannot be scored in our assay. This work indicates that more than one virus can contribute to plaque formation and that coinfection may assist plaque formation in situations where the amount of genome damage is high.IMPORTANCE One of the most common methods to quantify viruses is the plaque assay, where it is generally presumed that each plaque represents a single infectious virus. Using genetically marked polioviruses, we demonstrate that a plaque can contain more than one parental virus, likely due to aggregates within virus stocks that induce coinfection of a cell. A relatively small number of plaques are the products of coinfection for our standard virus stocks. However, mutagenized virus stocks with increased genome damage give rise to a higher amount of plaques that are chimeric. These results suggest that coinfection may aid plaque formation of viruses with genome damage, possibly due to processes such as complementation and recombination. Overall, our results suggest that the relationship between viral dilution and plaque number may not be linear, particularly for mutagenized viral populations.
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Affiliation(s)
- Elizabeth R Aguilera
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andrea K Erickson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Palmy R Jesudhasan
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christopher M Robinson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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48
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Collective Infectious Units in Viruses. Trends Microbiol 2017; 25:402-412. [PMID: 28262512 DOI: 10.1016/j.tim.2017.02.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 01/15/2023]
Abstract
Increasing evidence indicates that viruses do not simply propagate as independent virions among cells, organs, and hosts. Instead, viral spread is often mediated by structures that simultaneously transport groups of viral genomes, such as polyploid virions, aggregates of virions, virion-containing proteinaceous structures, secreted lipid vesicles, and virus-induced cell-cell contacts. These structures increase the multiplicity of infection, independently of viral population density and transmission bottlenecks. Collective infectious units may contribute to the maintenance of viral genetic diversity, and could have implications for the evolution of social-like virus-virus interactions. These may include various forms of cooperation such as immunity evasion, genetic complementation, division of labor, and relaxation of fitness trade-offs, but also noncooperative interactions such as negative dominance and interference, potentially leading to conflict.
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49
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Altan-Bonnet N. Lipid Tales of Viral Replication and Transmission. Trends Cell Biol 2017; 27:201-213. [PMID: 27838086 PMCID: PMC5318230 DOI: 10.1016/j.tcb.2016.09.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/22/2022]
Abstract
Positive-strand RNA viruses are the largest group of RNA viruses on Earth and cellular membranes are critical for all aspects of their life cycle, from entry and replication to exit. In particular, membranes serve as platforms for replication and as carriers to transmit these viruses to other cells, the latter either as an envelope surrounding a single virus or as the vesicle containing a population of viruses. Notably, many animal and human viruses appear to induce and exploit phosphatidylinositol 4-phosphate/cholesterol-enriched membranes for replication, whereas many plant and insect-vectored animal viruses utilize phosphatidylethanolamine/cholesterol-enriched membranes for the same purpose; and phosphatidylserine-enriched membrane carriers are widely used by both single and populations of viruses for transmission. Here I discuss the implications for viral pathogenesis and therapeutic development of this remarkable convergence on specific membrane lipid blueprints for replication and transmission.
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Affiliation(s)
- Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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50
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Alexander HK, Mayer SI, Bonhoeffer S. Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load. Mol Biol Evol 2017; 34:419-436. [PMID: 27836985 PMCID: PMC5850754 DOI: 10.1093/molbev/msw244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic population genetic models to allow an arbitrary distribution of mutation rate among individuals, either with or without inheritance. With this general new framework, we rigorously establish the effects of heterogeneity at various evolutionary timescales. In a single generation, variation of mutation rate about the mean increases the probability of producing zero or many simultaneous mutations on a genome. Over multiple generations of mutation and selection, heterogeneity accelerates the appearance of both deleterious and beneficial multi-point mutants. At mutation-selection balance, higher-order mutant frequencies are likewise boosted, while lower-order mutants exhibit subtler effects; nonetheless, population mean fitness is always enhanced. We quantify the dependencies on moments of the mutation rate distribution and selection coefficients, and clarify the role of mutation rate inheritance. While typical methods of estimating mutation rate will recover only the population mean, analyses assuming mutation rate is fixed to this mean could underestimate the potential for multi-locus adaptation, including medically relevant evolution in pathogenic and cancerous populations. We discuss the potential to empirically parameterize mutation rate distributions, which have to date hardly been quantified.
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Affiliation(s)
- Helen K. Alexander
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Stephanie I. Mayer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
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