scholarly journals Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chang Wang ◽  
Christian V. Forst ◽  
Tsui-wen Chou ◽  
Adam Geber ◽  
Minghui Wang ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Infection ◽  
Single Cell ◽  
Influenza Virus Infection ◽  
Host Responses ◽  
Viral Transcription ◽  
Single Cell Level ◽  
Cell Level ◽  
Viral Genomes ◽  
Defective Virus

ABSTRACT Virus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single-cell level and how it impacts virus-host interactions at a system level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability in viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show (i) a correlation between DVGs and virus-induced variation of the host transcriptional program and (ii) an association between differential inductions of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single-cell level improve our understanding of the complex virus-host interplay during influenza virus infection. IMPORTANCE Defective influenza virus particles generated during viral replication carry incomplete viral genomes and can interfere with the replication of competent viruses. These defective genomes are thought to modulate the disease severity and pathogenicity of an influenza virus infection. Different defective viral genomes also introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single-cell transcriptional profiling. Here, we characterized virus and host transcriptomes in individual influenza virus-infected cells, including those of defective viruses that arise during influenza A virus infection. We established an association between defective virus transcription and host responses and validated interfering and immunostimulatory functions of identified dominant defective viral genome species in vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level.

scholarly journals Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection

2018 ◽  
Author(s):  
Chang Wang ◽  
Christian V. Forst ◽  
Tsui-wen Chou ◽  
Adam Geber ◽  
Minghui Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Influenza A ◽  
Influenza Infection ◽  
Host Responses ◽  
Viral Transcription ◽  
Single Cell Level ◽  
Cell Level ◽  
Viral Genomes ◽  
Cell Variation ◽  
Defective Virus

ABSTRACTVirus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single cell level and how it impacts virus-host interactions at a systems level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability of viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show a correlation between DVGs and viral-induced variation of the host transcriptional program and an association between differential induction of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single cell level improve our understanding of the complex virus-host interplay during influenza infection.IMPORTANCEDefective influenza virus particles generated during viral replication carry incomplete viral genomes and can interfere with the replication of competent viruses. These defective genomes are thought to modulate disease severity and pathogenicity of the influenza infection. Different defective viral genomes also introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single cell transcriptional profiling. Here we characterized virus and host transcriptomes in individual influenza-infected cells, including that of defective viruses that arise during influenza A virus infection. We established an association between defective virus transcription and host responses and validated interfering and immunostimulatory functions of identified dominant defective virus genome speciesin vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level.

scholarly journals TIV Vaccination Modulates Host Responses to Influenza Virus Infection that Correlate with Protection against Bacterial Superinfection

Vaccines ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 113 ◽  
Author(s):  
Choi ◽  
Christopoulou ◽  
Saelens ◽  
García-Sastre ◽  
Schotsaert
Keyword(s):  
Influenza Virus ◽  
Virus Infection ◽  
Influenza Vaccination ◽  
Neutralizing Antibodies ◽  
Influenza A ◽  
Influenza Virus Infection ◽  
Neutralizing Antibody ◽  
Host Responses ◽  
Host Immune Responses ◽  
Bacterial Superinfection

Background: Influenza virus infection predisposes to secondary bacterial pneumonia. Currently licensed influenza vaccines aim at the induction of neutralizing antibodies and are less effective if the induction of neutralizing antibodies is low and/or the influenza virus changes its antigenic surface. We investigated the effect of suboptimal vaccination on the outcome of post-influenza bacterial superinfection. Methods: We established a mouse vaccination model that allows control of disease severity after influenza virus infection despite inefficient induction of virus-neutralizing antibody titers by vaccination. We investigated the effect of vaccination on virus-induced host immune responses and on the outcome of superinfection with Staphylococcus aureus. Results: Vaccination with trivalent inactivated virus vaccine (TIV) reduced morbidity after influenza A virus infection but did not prevent virus replication completely. Despite the poor induction of influenza-specific antibodies, TIV protected from mortality after bacterial superinfection. Vaccination limited loss of alveolar macrophages and reduced levels of infiltrating pulmonary monocytes after influenza virus infection. Interestingly, TIV vaccination resulted in enhanced levels of eosinophils after influenza virus infection and recruitment of neutrophils in both lungs and mediastinal lymph nodes after bacterial superinfection. Conclusion: These observations highlight the importance of disease modulation by influenza vaccination, even when suboptimal, and suggest that influenza vaccination is still beneficial to protect during bacterial superinfection in the absence of complete virus neutralization.

scholarly journals Adeno-associated virus type 2 (AAV2) uncoating is a stepwise process and is linked to structural reorganization of the nucleolus

2021 ◽  
Author(s):  
Sereina Olivia Sutter ◽  
Anouk Lkharrazi ◽  
Elisabeth Maria Schraner ◽  
Kevin Michaelsen ◽  
Anita Felicitas Meier ◽  
...  
Keyword(s):  
Single Cell ◽  
Virus Type ◽  
Helper Virus ◽  
Single Cell Level ◽  
Cellular Functions ◽  
Cell Level ◽  
Structural Reorganization ◽  
Adeno Associated Virus ◽  
Viral Genomes

Nucleoli are membrane-less structures located within the nucleus and are known to be involved in many cellular functions, including stress response and cell cycle regulation. Besides, many viruses can employ the nucleolus or nucleolar proteins to promote different steps of their life cycle such as replication, transcription and assembly. While adeno-associated virus type 2 (AAV2) capsids have previously been reported to enter the host cell nucleus and accumulate in the nucleolus, both the role of the nucleolus in AAV2 infection, and the viral uncoating mechanism remain elusive. In all prior studies on AAV uncoating, viral capsids and viral genomes were not directly correlated on the single cell level, at least not in absence of a helper virus. To elucidate the properties of the nucleolus during AAV2 infection and to assess viral uncoating on a single cell level, we combined immunofluorescence analysis for detection of intact AAV2 capsids and capsid proteins with fluorescence in situ hybridization for detection of AAV2 genomes. The results of our experiments provide evidence that uncoating of AAV2 particles occurs in a stepwise process that is completed in the nucleolus and supported by alteration of the nucleolar structure.

scholarly journals Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression

2018 ◽  
Author(s):  
Lauren M. Oko ◽  
Abigail K. Kimball ◽  
Rachael E. Kaspar ◽  
Ashley N. Knox ◽  
Carrie B. Coleman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Virus Infection ◽  
Single Cell ◽  
Viral Gene Expression ◽  
Lytic Replication ◽  
Viral Gene ◽  
Single Cell Level ◽  
Cell Level ◽  
Non Coding Rnas ◽  
Cell Variation

ABSTRACTVirus-host interactions are frequently studied in bulk cell populations, obscuring cell-to-cell variation. Here we investigate endogenous herpesvirus gene expression at the single-cell level, combining a sensitive and robust fluorescent in situ hybridization platform with multiparameter flow cytometry, to study the expression of gammaherpesvirus non-coding RNAs (ncRNAs) during lytic replication, latent infection and reactivation in vitro. This method allowed robust detection of viral ncRNAs of murine gammaherpesvirus 68 (γHV68), Kaposi’s sarcoma associated herpesvirus and Epstein-Barr virus, revealing variable expression at the single-cell level. By quantifying the inter-relationship of viral ncRNA, viral mRNA, viral protein and host mRNA regulation during γHV68 infection, we find heterogeneous and asynchronous gene expression during latency and reactivation, with reactivation from latency identified by a distinct gene expression profile within rare cells. Further, during lytic replication with γHV68, we find many cells have limited viral gene expression, with only a fraction of cells showing robust gene expression, dynamic RNA localization, and progressive infection. Lytic viral gene expression was enhanced in primary fibroblasts and by conditions associated with enhanced viral replication, with multiple subpopulations of cells present in even highly permissive infection conditions. These findings, powered by single-cell analysis integrated with automated clustering algorithms, suggest inefficient or abortive γHV infection in many cells, and identify substantial heterogeneity in viral gene expression at the single-cell level.AUTHOR SUMMARYThe gammaherpesviruses are a group of DNA tumor viruses that establish lifelong infection. How these viruses infect and manipulate cells has frequently been studied in bulk populations of cells. While these studies have been incredibly insightful, there is limited understanding of how virus infection proceeds within a single cell. Here we present a new approach to quantify gammaherpesvirus gene expression at the single-cell level. This method allows us to detect cell-to-cell variation in the expression of virus non-coding RNAs, an important and understudied class of RNAs which do not encode for proteins. By examining multiple features of virus gene expression, this method further reveals significant variation in infection between cells across multiple stages of infection, even in conditions generally thought to be highly uniform. These studies emphasize that gammaherpesvirus infection can be surprisingly heterogeneous when viewed at the level of the individual cell. Because this approach can be broadly applied across diverse viruses, this study affords new opportunities to understand the complexity of virus infection within single cells.

scholarly journals Characterization of innate responses to influenza virus infection in a novel lung type I epithelial cell model

2014 ◽  
Vol 95 (2) ◽  
pp. 350-362 ◽  
Author(s):  
Carrie M. Rosenberger ◽  
Rebecca L. Podyminogin ◽  
Peter S. Askovich ◽  
Garnet Navarro ◽  
Shari M. Kaiser ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Epithelial Cell ◽  
Epithelial Cells ◽  
Virus Infection ◽  
Cell Model ◽  
Influenza Virus Infection ◽  
Alveolar Epithelial Cells ◽  
Host Responses ◽  
Type I

Type I alveolar epithelial cells are a replicative niche for influenza in vivo, yet their response to infection is not fully understood. To better characterize their cellular responses, we have created an immortalized murine lung epithelial type I cell line (LET1). These cells support spreading influenza virus infection in the absence of exogenous protease and thus permit simultaneous analysis of viral replication dynamics and host cell responses. LET1 cells can be productively infected with human, swine and mouse-adapted strains of influenza virus and exhibit expression of an antiviral transcriptional programme and robust cytokine secretion. We characterized influenza virus replication dynamics and host responses of lung type I epithelial cells and identified the capacity of epithelial cell-derived type I IFN to regulate specific modules of antiviral effectors to establish an effective antiviral state. Together, our results indicate that the type I epithelial cell can play a major role in restricting influenza virus infection without contribution from the haematopoietic compartment.

scholarly journals Glycomic analysis of host-response reveals high mannose as a key mediator of influenza severity

2020 ◽  
Author(s):  
Daniel W. Heindel ◽  
Sujeethraj Koppolu ◽  
Yue Zhang ◽  
Brian Kasper ◽  
Lawrence Meche ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Virus Infection ◽  
Molecular Mechanisms ◽  
Influenza Virus Infection ◽  
Host Responses ◽  
Differential Host ◽  
Unfolded Protein ◽  
High Mannose ◽  
The Unfolded Protein Response ◽  
Protein Response

ABSTRACTInfluenza virus infections cause a wide variety of outcomes, from mild disease to 3-5 million cases of severe illness and ~290,000-645,000 deaths annually worldwide. The molecular mechanisms underlying these disparate outcomes are currently unknown. Glycosylation within the human host plays a critical role in influenza virus biology. However, the impact these modifications have on the severity of influenza disease has not been examined. Herein, we profile the glycomic host responses to influenza virus infection as a function of disease severity using a ferret model and our lectin microarray technology. We identify the glycan epitope high mannose as a marker of influenza virus-induced pathogenesis and severity of disease outcome. Induction of high mannose is dependent upon the unfolded protein response (UPR) pathway, a pathway previously shown to associate with lung damage and severity of influenza virus infection. Also, the mannan-binding lectin (MBL2), an innate immune lectin that negatively impacts influenza outcomes, recognizes influenza virus-infected cells in a high mannose dependent manner. Together, our data argue that the high mannose motif is an infection-associated molecular pattern on host cells that may guide immune responses leading to the concomitant damage associated with severity.SIGNIFICANCEInfluenza virus infection causes a range of outcomes from mild illness to death. The molecular mechanisms leading to these differential host responses are currently unknown. Herein, we identify the induction of high mannose, a glycan epitope, as a key mediator of severe disease outcome. We propose a mechanism in which activation of the unfolded protein response (UPR) upon influenza virus infection turns on expression of high mannose, which is then recognized by the innate immune lectin MBL2, activating the complement cascade and leading to subsequent inflammation. This work is the first to systematically study host glycomic changes in response to influenza virus infection, identifying high mannose as a key feature of differential host response.

Sign in / Sign up

Export Citation Format

Share Document