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Howell LM, Gracie NP, Newsome TP. Single-cell analysis of VACV infection reveals pathogen-driven timing of early and late phases and host-limited dynamics of virus production. PLoS Pathog 2024; 20:e1012423. [PMID: 39093901 PMCID: PMC11347022 DOI: 10.1371/journal.ppat.1012423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 08/26/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The extent and origin of variation in the replication dynamics of complex DNA viruses is not well-defined. Here, we investigate the vaccinia virus (VACV) infection cycle at the single-cell level, quantifying the temporal dynamics of early and post(dna)-replicative phase gene expression across thousands of infections. We found that viral factors determine the initiation time of these phases, and this is influenced by the multiplicity of infection (MOI). In contrast, virus production dynamics are largely constrained by the host cell. Additionally, between-cell variability in infection start time and virus production rate were strongly influenced by MOI, providing evidence for cooperativity between infecting virions. Blocking programmed cell death by pan-caspase inhibition increased infection frequency but not virus production at the population level due to a concurrent attenuation of per-cell virus yield, suggesting a dual role for caspase signaling in VACV infection. Our findings provide key insights into the pivotal factors influencing heterogeneity in the infection cycle of a large DNA virus at the single-cell level.
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Affiliation(s)
- Liam Michael Howell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Nicholas Peter Gracie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Timothy Peter Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
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2
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Velusamy T, Singh N, Croft S, Smith S, Tscharke DC. The expression and function of HSV ICP47 and its promoter in mice. J Virol 2023; 97:e0110723. [PMID: 37902400 PMCID: PMC10688380 DOI: 10.1128/jvi.01107-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Immune evasion and latency are key mechanisms that underlie the success of herpesviruses. In each case, interactions between viral and host proteins are required and due to co-evolution, not all mechanisms are preserved across host species, even if infection is possible. This is highlighted by the herpes simplex virus (HSV) protein immediate early-infected cell protein (ICP)47, which inhibits the detection of infected cells by killer T cells and acts with high efficiency in humans, but poorly, if at all in mouse cells. Here, we show that ICP47 retains modest but detectable function in mouse cells, but in an in vivo model we found no role during acute infection or latency. We also explored the activity of the ICP47 promoter, finding that it could be active during latency, but this was dependent on genome location. These results are important to interpret HSV pathogenesis work done in mice.
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Affiliation(s)
- Thilaga Velusamy
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Navneet Singh
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Sarah Croft
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Stewart Smith
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
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Tavukcuoglu E, Yanik H, Parveen M, Uluturk S, Durusu-Tanriover M, Inkaya AC, Akova M, Unal S, Esendagli G. Human memory T cell dynamics after aluminum-adjuvanted inactivated whole-virion SARS-CoV-2 vaccination. Sci Rep 2023; 13:4610. [PMID: 36944716 PMCID: PMC10028771 DOI: 10.1038/s41598-023-31347-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
This study evaluates the functional capacity of CD4+ and CD8+ terminally-differentiated effector (TEMRA), central memory (TCM), and effector memory (TEM) cells obtained from the volunteers vaccinated with an aluminum-adjuvanted inactivated whole-virion SARS-CoV-2 vaccine (CoronaVac). The volunteers were followed for T cell immune responses following the termination of a randomized phase III clinical trial. Seven days and four months after the second dose of the vaccine, the memory T cell subsets were collected and stimulated by autologous monocyte-derived dendritic cells (mDCs) loaded with SARS-CoV-2 spike glycoprotein S1. Compared to the placebo group, memory T cells from the vaccinated individuals significantly proliferated in response to S1-loaded mDCs. CD4+ and CD8+ memory T cell proliferation was detected in 86% and 78% of the vaccinated individuals, respectively. More than 73% (after a short-term) and 62% (after an intermediate-term) of the vaccinated individuals harbored TCM and/or TEM cells that responded to S1-loaded mDCs by secreting IFN-γ. The expression of CD25, CD38, 4-1BB, PD-1, and CD107a indicated a modulation in the memory T cell subsets. Especially on day 120, PD-1 was upregulated on CD4+ TEMRA and TCM, and on CD8+ TEM and TCM cells; accordingly, proliferation and IFN-γ secretion capacities tended to decline after 4 months. In conclusion, the combination of inactivated whole-virion particles with aluminum adjuvants possesses capacities to induce functional T cell responses.
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Affiliation(s)
- Ece Tavukcuoglu
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Hamdullah Yanik
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Mubaida Parveen
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Sila Uluturk
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Mine Durusu-Tanriover
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Ahmet Cagkan Inkaya
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Murat Akova
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gunes Esendagli
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey.
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Monticelli SR, Bryk P, Brewer MG, Aguilar HC, Norbury CC, Ward BM. An increase in glycoprotein concentration on extracellular virions dramatically alters vaccinia virus infectivity and pathogenesis without impacting immunogenicity. PLoS Pathog 2021; 17:e1010177. [PMID: 34962975 PMCID: PMC8746760 DOI: 10.1371/journal.ppat.1010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/10/2022] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The extracellular virion (EV) form of Orthopoxviruses is required for cell-to-cell spread and pathogenesis, and is the target of neutralizing antibodies in the protective immune response. EV have a double envelope that contains several unique proteins that are involved in its intracellular envelopment and/or subsequent infectivity. One of these, F13, is involved in both EV formation and infectivity. Here, we report that replacement of vaccinia virus F13L with the molluscum contagiosum virus homolog, MC021L, results in the production of EV particles with significantly increased levels of EV glycoproteins, which correlate with a small plaque phenotype. Using a novel fluorescence-activated virion sorting assay to isolate EV populations based on glycoprotein content we determine that EV containing either higher or lower levels of glycoproteins are less infectious, suggesting that there is an optimal concentration of glycoproteins in the outer envelope that is required for maximal infectivity of EV. This optimal glycoprotein concentration was required for lethality and induction of pathology in a cutaneous model of animal infection, but was not required for induction of a protective immune response. Therefore, our results demonstrate that there is a sensitive balance between glycoprotein incorporation, infectivity, and pathogenesis, and that manipulation of EV glycoprotein levels can produce vaccine vectors in which pathologic side effects are attenuated without a marked diminution in induction of protective immunity. Viral glycoproteins are critical determinants of host cell tropism, immunity, and pathogenesis. Vaccinia virus was used for the most successful immunization program in history, and poxviruses continue to be used as vaccine vectors. Here, we report that vaccinia virus extracellular virion (EV) protein F13 plays an important, previously unappreciated, role in controlling glycoprotein incorporation, and that there is a direct relationship between glycoprotein concentrations and subsequent infectivity. Crucially, manipulation of the EV glycoprotein concentrations altered pathogenesis and lethality in an in vivo infection model, but did not markedly alter the induced immune response. These results have important implications that inform the design of safer and more efficacious poxvirus-based vaccine vectors by altering glycoprotein content.
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Affiliation(s)
- Stephanie R. Monticelli
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Peter Bryk
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Matthew G. Brewer
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, United States of America
| | - Christopher C. Norbury
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Brian M. Ward
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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Lin LCW, Croft SN, Croft NP, Wong YC, Smith SA, Tang SS, Purcell AW, Tscharke DC. Direct Priming of CD8 + T Cells Persists in the Face of Cowpox Virus Inhibitors of Antigen Presentation. J Virol 2021; 95:JVI.00186-21. [PMID: 33692206 PMCID: PMC8139650 DOI: 10.1128/jvi.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/27/2021] [Indexed: 11/30/2022] Open
Abstract
Vaccinia virus (VACV) was the vaccine used to eradicate smallpox and is being repurposed as a vaccine vector. CD8+ T cells are key anti-viral mediators, but require priming to become effector or memory cells. Priming requires an interaction with dendritic cells that are either infected (direct priming), or that have acquired virus proteins but remain uninfected (cross priming). To investigate CD8+ T cell priming pathways for VACV, we engineered the virus to express CPXV12 and CPXV203, two inhibitors of antigen presentation encoded by cowpox virus. These intracellular proteins would be expected to block direct but not cross priming. The inhibitors had diverse impacts on the size of anti-VACV CD8+ T cell responses across epitopes and by different infection routes in mice, superficially suggesting variable use of direct and cross priming. However, when we then tested a form of antigen that requires direct priming, we found surprisingly that CD8+ T cell responses were not diminished by co-expression with CPXV12 and CPXV203. We then directly quantified the impact of CPXV12 and CPXV203 on viral antigen presentation using mass spectrometry, which revealed strong, but incomplete inhibition of antigen presentation by the CPXV proteins. Therefore, direct priming of CD8+ T cells by poxviruses is robust enough to withstand highly potent viral inhibitors of antigen presentation. This is a reminder of the limits of viral immune evasion and shows that viral inhibitors of antigen presentation cannot be assumed to dissect cleanly direct and cross priming of anti-viral CD8+ T cells.ImportanceCD8+ T cells are key to anti-viral immunity, so it is important to understand how they are activated. Many viruses have proteins that protect infected cells from T cell attack by interfering with the process that allows virus infection to be recognised by CD8+ T cells. It is thought that these proteins would also stop infected cells from activating T cells in the first place. However, we show here that this is not the case for two very powerful inhibitory proteins from cowpox virus. This demonstrates the flexibility and robustness of immune processes that turn on the immune responses required to fight infection.
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Affiliation(s)
- Leon C. W. Lin
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sarah N. Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Nathan P. Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Stewart A. Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Swee-Seong Tang
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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Rapid poxvirus engineering using CRISPR/Cas9 as a selection tool. Commun Biol 2020; 3:643. [PMID: 33144673 PMCID: PMC7641209 DOI: 10.1038/s42003-020-01374-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023] Open
Abstract
In standard uses of CRISPR/Cas9 technology, the cutting of genomes and their efficient repair are considered to go hand-in-hand to achieve desired genetic changes. This includes the current approach for engineering genomes of large dsDNA viruses. However, for poxviruses we show that Cas9-guide RNA complexes cut viral genomes soon after their entry into cells, but repair of these breaks is inefficient. As a result, Cas9 targeting makes only modest, if any, improvements to basal rates of homologous recombination between repair constructs and poxvirus genomes. Instead, Cas9 cleavage leads to inhibition of poxvirus DNA replication thereby suppressing virus spread in culture. This unexpected outcome allows Cas9 to be used as a powerful tool for selecting conventionally generated poxvirus recombinants, which are otherwise impossible to separate from a large background of parental virus without the use of marker genes. This application of CRISPR/Cas9 greatly speeds up the generation of poxvirus-based vaccines, making this platform considerably more attractive in the context of personalised cancer vaccines and emerging disease outbreaks. Gowripalan, Smith et al. use CRISPR/Cas9 technology to rapidly select recombinant poxviruses without using selectable marker genes. They find that Cas9 cleavage inhibits poxvirus DNA replication, suppressing virus spread in culture. This application makes poxviruses more attractive vector platforms for fighting cancer and emerging disease outbreaks.
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