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Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 DOI: 10.1128/jvi.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
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Affiliation(s)
- Sophia K Adams
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Grace E Ducharme
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Emma K Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
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Zath GK, Thomas MM, Loveday EK, Bikos DA, Sanche S, Ke R, Brooke CB, Chang CB. Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR). PLoS Pathog 2024; 20:e1012257. [PMID: 38950082 PMCID: PMC11244780 DOI: 10.1371/journal.ppat.1012257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 07/12/2024] [Accepted: 05/13/2024] [Indexed: 07/03/2024] Open
Abstract
An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 101 to 104 viruses per cell, and H1N1 ranging from 101 to 103 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.
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Affiliation(s)
- Geoffrey K. Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Emma K. Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Dimitri A. Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Steven Sanche
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Connie B. Chang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
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Fredrikson JP, Domanico LF, Pratt SL, Loveday EK, Taylor MP, Chang CB. Single-cell herpes simplex virus type 1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics. SCIENCE ADVANCES 2024; 10:eadk9185. [PMID: 38416818 PMCID: PMC10901367 DOI: 10.1126/sciadv.adk9185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Single-cell analyses of viral infections reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of herpes simplex virus type 1 (HSV-1) infection of neurons at the single-cell level. We used micrometer-scale Matrigel beads, termed microgels, to culture individual murine superior cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are encapsulated in individual media-in-oil droplets with a dual-fluorescent reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. These techniques for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
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Affiliation(s)
- Jacob P. Fredrikson
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Luke F. Domanico
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Shawna L. Pratt
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Emma K. Loveday
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Connie B. Chang
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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Fredrikson JP, Domanico LF, Pratt SL, Loveday EK, Taylor MP, Chang CB. Single-cell Herpes Simplex Virus type-1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558333. [PMID: 37790515 PMCID: PMC10542126 DOI: 10.1101/2023.09.18.558333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Single-cell analyses of viral infections often reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of HSV-1 infection of neurons at the single-cell level. We used micron-scale Matrigel beads, termed microgels, to culture individual murine Superior Cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are subsequently enclosed in individual media-in-oil droplets with a dual fluorescent-reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. The innovative techniques presented here for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
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Affiliation(s)
- Jacob P. Fredrikson
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Luke F. Domanico
- Department of Microbiology & Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Shawna L. Pratt
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Emma K. Loveday
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology & Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Connie B. Chang
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
- Department of Physiology & Biomedical Engineering, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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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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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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