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1.
Virus Res ; 345: 199387, 2024 Jul.
Article En | MEDLINE | ID: mdl-38719025

Influenza A virus can infect respiratory tracts and may cause severe illness in humans. Proteins encoded by influenza A virus can interact with cellular factors and dysregulate host biological processes to support viral replication and cause pathogenicity. The influenza viral PA protein is not only a subunit of influenza viral polymerase but also a virulence factor involved in pathogenicity during infection. To explore the role of the influenza virus PA protein in regulating host biological processes, we performed immunoprecipitation and LC‒MS/MS to globally identify cellular factors that interact with the PA proteins of the influenza A H1N1, 2009 pandemic H1N1, and H3N2 viruses. The results demonstrated that proteins located in the mitochondrion, proteasome, and nucleus are associated with the PA protein. We further discovered that the PA protein is partly located in mitochondria by immunofluorescence and mitochondrial fractionation and that overexpression of the PA protein reduces mitochondrial respiration. In addition, our results revealed the interaction between PA and the mitochondrial matrix protein PYCR2 and the antiviral role of PYCR2 during influenza A virus replication. Moreover, we found that the PA protein could also trigger autophagy and disrupt mitochondrial homeostasis. Overall, our research revealed the impacts of the influenza A virus PA protein on mitochondrial function and autophagy.


Mitochondria , Viral Proteins , Virus Replication , Humans , Mitochondria/metabolism , Mitochondria/virology , Viral Proteins/metabolism , Viral Proteins/genetics , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , Influenza A virus/physiology , Influenza A virus/genetics , Influenza A virus/pathogenicity , Influenza A virus/metabolism , Host-Pathogen Interactions , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/physiology , Influenza A Virus, H3N2 Subtype/metabolism , Autophagy , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/physiology , Influenza A Virus, H1N1 Subtype/pathogenicity , HEK293 Cells , Influenza, Human/virology , Influenza, Human/metabolism , A549 Cells , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Tandem Mass Spectrometry
2.
Clin Sci (Lond) ; 138(8): 537-554, 2024 Apr 24.
Article En | MEDLINE | ID: mdl-38577922

Patients with pulmonary fibrosis (PF) often experience exacerbations of their disease, characterised by a rapid, severe deterioration in lung function that is associated with high mortality. Whilst the pathobiology of such exacerbations is poorly understood, virus infection is a trigger. The present study investigated virus-induced injury responses of alveolar and bronchial epithelial cells (AECs and BECs, respectively) from patients with PF and age-matched controls (Ctrls). Air-liquid interface (ALI) cultures of AECs, comprising type I and II pneumocytes or BECs were inoculated with influenza A virus (H1N1) at 0.1 multiplicity of infection (MOI). Levels of interleukin-6 (IL-6), IL-36γ and IL-1ß were elevated in cultures of AECs from PF patients (PF-AECs, n = 8-11), being markedly higher than Ctrl-AECs (n = 5-6), 48 h post inoculation (pi) (P<0.05); despite no difference in H1N1 RNA copy numbers 24 h pi. Furthermore, the virus-induced inflammatory responses of PF-AECs were greater than BECs (from either PF patients or controls), even though viral loads in the BECs were overall 2- to 3-fold higher than AECs. Baseline levels of the senescence and DNA damage markers, nuclear p21, p16 and H2AXγ were also significantly higher in PF-AECs than Ctrl-AECs and further elevated post-infection. Senescence induction using etoposide augmented virus-induced injuries in AECs (but not viral load), whereas selected senotherapeutics (rapamycin and mitoTEMPO) were protective. The present study provides evidence that senescence increases the susceptibility of AECs from PF patients to severe virus-induced injury and suggests targeting senescence may provide an alternative option to prevent or treat the exacerbations that worsen the underlying disease.


Alveolar Epithelial Cells , Influenza A Virus, H1N1 Subtype , Pulmonary Fibrosis , Humans , Influenza A Virus, H1N1 Subtype/pathogenicity , Alveolar Epithelial Cells/virology , Alveolar Epithelial Cells/pathology , Alveolar Epithelial Cells/metabolism , Pulmonary Fibrosis/virology , Pulmonary Fibrosis/pathology , Male , Influenza, Human/virology , Influenza, Human/complications , Influenza, Human/pathology , Middle Aged , Female , Cells, Cultured , Aged , Cellular Senescence , Case-Control Studies , Cytokines/metabolism
3.
Virol Sin ; 39(2): 205-217, 2024 Apr.
Article En | MEDLINE | ID: mdl-38346538

Swine are regarded as "intermediate hosts" or "mixing vessels" of influenza viruses, capable of generating strains with pandemic potential. From 2020 to 2021, we conducted surveillance on swine H1N2 influenza (swH1N2) viruses in swine farms located in Guangdong, Yunnan, and Guizhou provinces in southern China, as well as Henan and Shandong provinces in northern China. We systematically analyzed the evolution and pathogenicity of swH1N2 isolates, and characterized their replication and transmission abilities. The isolated viruses are quadruple reassortant H1N2 viruses containing genes from pdm/09 H1N1 (PB2, PB1, PA and NP genes), triple-reassortant swine (NS gene), Eurasian Avian-like (HA and M genes), and recent human H3N2 (NA gene) lineages. The NA, PB2, and NP of SW/188/20 and SW/198/20 show high gene similarities to A/Guangdong/Yue Fang277/2017 (H3N2). The HA gene of swH1N2 exhibits a high evolutionary rate. The five swH1N2 isolates replicate efficiently in human, canine, and swine cells, as well as in the turbinate, trachea, and lungs of mice. A/swine/Shandong/198/2020 strain efficiently replicates in the respiratory tract of pigs and effectively transmitted among them. Collectively, these current swH1N2 viruses possess zoonotic potential, highlighting the need for strengthened surveillance of swH1N2 viruses.


Evolution, Molecular , Influenza A Virus, H1N2 Subtype , Orthomyxoviridae Infections , Reassortant Viruses , Swine Diseases , Animals , Swine , Reassortant Viruses/genetics , Reassortant Viruses/pathogenicity , Reassortant Viruses/isolation & purification , China/epidemiology , Orthomyxoviridae Infections/virology , Orthomyxoviridae Infections/transmission , Orthomyxoviridae Infections/veterinary , Swine Diseases/virology , Swine Diseases/transmission , Influenza A Virus, H1N2 Subtype/genetics , Influenza A Virus, H1N2 Subtype/pathogenicity , Influenza A Virus, H1N2 Subtype/isolation & purification , Humans , Mice , Dogs , Phylogeny , Virus Replication , Public Health , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/virology , Influenza, Human/transmission , Mice, Inbred BALB C , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/isolation & purification , Virulence , Female
4.
Proc Natl Acad Sci U S A ; 119(34): e2203919119, 2022 08 23.
Article En | MEDLINE | ID: mdl-35969783

Previous studies have shown that the Eurasian avian-like H1N1 (EA H1N1) swine influenza viruses circulated widely in pigs around the world and formed multiple genotypes by acquiring non-hemagglutinin and neuraminidase segments derived from other swine influenza viruses. Swine influenza control is not a priority for the pig industry in many countries, and it is worrisome that some strains may become more pathogenic and/or transmissible during their circulation in nature. Our routine surveillance indicated that the EA H1N1 viruses obtained different internal genes from different swine influenza viruses and formed various new genotypes. In this study, we found that a naturally isolated swine influenza reassortant, A/swine/Liaoning/265/2017 (LN265), a representative strain of one of the predominant genotypes in recent years, is lethal in mice and transmissible in ferrets. LN265 contains the hemagglutinin, neuraminidase, and matrix of the EA H1N1 virus; the basic polymerase 2, basic polymerase 1, acidic polymerase (PA), and nucleoprotein of the 2009 H1N1 pandemic virus; and the nonstructural protein of the North American triple-reassortment H1N2 virus. By generating and testing a series of reassortants and mutants, we found that four gradually accumulated mutations in PA are responsible for the increased pathogenicity and transmissibility of LN265. We further revealed that these mutations increase the messenger RNA transcription of viral proteins by enhancing the endonuclease cleavage activity and viral RNA-binding ability of the PA protein. Our study demonstrates that EA H1N1 swine influenza virus became pathogenic and transmissible in ferrets by acquiring key mutations in PA and provides important insights for monitoring field strains with pandemic potential.


Influenza A Virus, H1N1 Subtype , Orthomyxoviridae Infections , RNA-Dependent RNA Polymerase , Swine Diseases , Animals , Ferrets , Genotype , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Mice , Mutation , Neuraminidase/genetics , Orthomyxoviridae Infections/veterinary , Orthomyxoviridae Infections/virology , Phylogeny , RNA-Dependent RNA Polymerase/genetics , Reassortant Viruses/genetics , Swine , Swine Diseases/virology , Viral Proteins/genetics
5.
Int J Infect Dis ; 121: 195-202, 2022 Aug.
Article En | MEDLINE | ID: mdl-35584743

OBJECTIVES: Because of the spread of the Omicron variant, many countries have experienced COVID-19 case numbers unseen since the start of the pandemic. We aimed to compare the epidemiological characteristics of Omicron with previous variants and different strains of influenza to provide context for public health responses. METHODS: We developed transmission models for SARS-CoV-2 variants and influenza, in which transmission, death, and vaccination rates were taken to be time-varying. We fit our model based on publicly available data in South Africa, the United States, and Canada. We used this model to evaluate the relative transmissibility and mortality of Omicron compared with previous variants and influenza. RESULTS: We found that Omicron is more transmissible and less fatal than both seasonal and 2009 H1N1 influenza and the Delta variant; these characteristics make Omicron epidemiologically more similar to influenza than it is to Delta. We estimate that as of February 7, 2022, booster doses have prevented 4.29×107 and 1.14×106 Omicron infections in the United States and Canada, respectively. CONCLUSION: Our findings indicate that the high infectivity of Omicron will keep COVID-19 endemic, similar to influenza. However, because of Omicron's lower fatality rate, our work suggests that human populations living with SARS-CoV-2 are most likely.


COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza, Human , Mutation , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/virology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza, Human/prevention & control , Influenza, Human/virology , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , United States/epidemiology
6.
Int J Mol Sci ; 23(3)2022 Feb 07.
Article En | MEDLINE | ID: mdl-35163797

H1N1 and H3N2 are the two most common subtypes of swine influenza virus (SIV). They not only endanger the pig industry, but are also a huge risk of zoonotic diseases. However, the molecular mechanism and regulatory network of pigs (hosts) against influenza virus infection are still unclear. In this study, porcine alveolar macrophage cell (3D4/21) models infected by swine influenza virus (H1N1 and H3N2) were constructed. The expression profiles of miRNAs, mRNAs, lncRNAs and circRNAs after H1N1 and H3N2 infected 3D4/21 cells were revealed in this study. Then, two ceRNAs (TCONS_00166432-miR10391-MAN2A1 and novel_circ_0004733-miR10391-MAN2A1) that regulated H1N1 and H3N2 infection in 3D4/21 cells were verified by the methods of bioinformatics analysis, gene overexpression, gene interference, real-time quantitative PCR (qPCR), dual luciferase activity assay and RNA immunoprecipitation (RIP). In addition, the important candidate molecules (miR-10391, TCONS_00166432, and novel_circ_0004733) were identified by qPCR and enzyme linked immunosorbent assay (ELISA). Finally, the regulatory effect and possible molecular mechanism of the target gene MAN2A1 were identified by the methods of gene interference, qPCR, Western blot and ELISA. The results of this study suggested that TCONS_00166432 and novel_circ_0004733 could competitively bind miR-10391 to target the MAN2A1 gene to regulate swine influenza virus infecting 3D4/21 cells. This study reported for the first time the ceRNA networks involved in the regulation of the swine influenza virus infecting 3D4/21 cells, which provided a new insight into the molecular mechanism of 3D4/21 cells against swine influenza virus infection.


Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/pathogenicity , Macrophages, Alveolar/virology , MicroRNAs/genetics , RNA, Circular/genetics , alpha-Mannosidase/genetics , Animals , Cell Line , Computational Biology , Dogs , Gene Expression Profiling , Gene Expression Regulation , Macrophages, Alveolar/chemistry , Macrophages, Alveolar/cytology , Madin Darby Canine Kidney Cells , Models, Biological , Swine
7.
Sci Rep ; 12(1): 163, 2022 01 07.
Article En | MEDLINE | ID: mdl-34997090

Influenza A virus infection causes a series of diseases, but the factors associated with disease severity are not fully understood. Disruption of the endothelial glycocalyx contributes to acute lung injury in sepsis, but has not been well studied in H1N1 influenza. We aim to determine whether the plasma glycocalyx components levels are predictive of disease severity in H1N1 influenza. This prospective observational study included 53 patients with influenza A (H1N1) during the influenza season, and 30 healthy controls in our hospital. Patients were grouped by severity and survival. We collected clinical data and blood samples at admission. Inflammatory factors (tumor necrosis factor-α, interleukin-6, interleukin-10) and endothelial glycocalyx components (syndecan-1, hyaluronan, heparan sulfate) were measured. The plasma levels of syndecan-1, hyaluronan, and heparan sulfate were significantly higher in patients with severe influenza A (H1N1) than in mild cases. Syndecan-1 and hyaluronan were positively correlated with disease severity, which was indicated by the APACHE II and SOFA scores and lactate levels, and negatively correlated with albumin levels. At a cutoff point ≥ 173.9 ng/mL, syndecan-1 had a 81.3% sensitivity and 70.3% specificity for predicting of 28-day mortality. Kaplan-Meier analysis demonstrated a strong association between syndecan-1 levels and 28-day mortality (log-rank 11.04, P = 0.001). Elevated plasma levels of syndecan-1 has a potential role in systemic organ dysfunction and may be indicative of disease severity in patients with influenza A (H1N1).


Endothelial Cells/metabolism , Glycocalyx/metabolism , Influenza A Virus, H1N1 Subtype/pathogenicity , Syndecan-1/blood , Adult , Aged , Biomarkers/blood , Endothelial Cells/virology , Female , Glycocalyx/virology , Heparitin Sulfate/blood , Humans , Hyaluronic Acid/blood , Influenza, Human/blood , Influenza, Human/diagnosis , Influenza, Human/mortality , Influenza, Human/virology , Male , Middle Aged , Predictive Value of Tests , Prognosis , Prospective Studies , Severity of Illness Index , Time Factors
8.
STAR Protoc ; 3(1): 101045, 2022 03 18.
Article En | MEDLINE | ID: mdl-34870243

In this protocol, we describe global proteome profiling for the respiratory specimen of COVID-19 patients, patients suspected with COVID-19, and H1N1 patients. In this protocol, details for identifying host, viral, or bacterial proteome (Meta-proteome) are provided. Major steps of the protocol include virus inactivation, protein quantification and digestion, desalting of peptides, high-resolution mass spectrometry (HRMS)-based analysis, and downstream bioinformatics analysis. For complete details on the use and execution of this profile, please refer to Maras et al. (2021).


COVID-19/diagnosis , Genomics/methods , Proteomics/methods , COVID-19/metabolism , Chromatography, Liquid/methods , Computational Biology , Diagnostic Tests, Routine , Gene Expression Profiling , Genetic Techniques , Genome, Viral/genetics , Humans , Influenza A Virus, H1N1 Subtype/metabolism , Influenza A Virus, H1N1 Subtype/pathogenicity , Peptides , Proteome , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Specimen Handling/methods , Tandem Mass Spectrometry/methods , Virome/genetics , Virome/physiology
9.
STAR Protoc ; 3(1): 101051, 2022 03 18.
Article En | MEDLINE | ID: mdl-34877545

Here we describe a protocol for identifying metabolites in respiratory specimens of patients that are SARS-CoV-2 positive, SARS-CoV-2 negative, or H1N1 positive. This protocol provides step-by-step instructions on sample collection from patients, followed by metabolite extraction. We use ultra-high-pressure liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS) for data acquisition and describe the steps for data analysis. The protocol was standardized with specific customization for SARS-CoV-2-containing respiratory specimens. For complete details on the use and execution of this protocol, please refer to Maras et al. (2021).


COVID-19/diagnosis , Chromatography, High Pressure Liquid/methods , Metabolomics/methods , COVID-19/metabolism , Computational Biology , Diagnostic Tests, Routine , Gene Expression Profiling , Genetic Techniques , Humans , Influenza A Virus, H1N1 Subtype/metabolism , Influenza A Virus, H1N1 Subtype/pathogenicity , Mass Spectrometry/methods , Metabolome , Reference Standards , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Specimen Handling/methods
10.
Virology ; 566: 89-97, 2022 01.
Article En | MEDLINE | ID: mdl-34894525

Virus-like particles (VLPs) modified through different molecular technologies are employed as delivery vehicles or platforms for heterologous antigen display. We have recently created a norovirus (NoV) VLP platform, where two influenza antigens, the extracellular domain of matrix protein M2 (M2e) or the stem domain of the major envelope glycoprotein hemagglutinin (HA2) are displayed on the surface of the NoV VLPs by SpyTag/SpyCatcher conjugation. To demonstrate the feasibility of the platform to deliver foreign antigens, this study examined potential interference of the conjugation with induction of antibodies against conjugated M2e peptide, HA2, and NoV VLP carrier. High antibody response was induced by HA2 but not M2e decorated VLPs. Furthermore, HA2-elicited antibodies did not neutralize the homologous influenza virus in vitro. Conjugated NoV VLPs retained intact receptor binding capacity and self-immunogenicity. The results demonstrate that NoV VLPs could be simultaneously used as a platform to deliver foreign antigens and a NoV vaccine.


Antibodies, Viral/biosynthesis , Hemagglutinins, Viral/genetics , Immunoglobulin G/biosynthesis , Influenza Vaccines/genetics , Influenza, Human/prevention & control , Orthomyxoviridae Infections/prevention & control , Vaccines, Virus-Like Particle/genetics , Animals , Antigens, Viral/genetics , Antigens, Viral/immunology , Capsid Proteins/genetics , Capsid Proteins/immunology , Female , Hemagglutinins, Viral/immunology , Humans , Immunoconjugates/genetics , Immunoconjugates/immunology , Immunogenicity, Vaccine , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza Vaccines/administration & dosage , Influenza Vaccines/biosynthesis , Influenza, Human/immunology , Influenza, Human/virology , Mice , Mice, Inbred BALB C , Norovirus/genetics , Norovirus/immunology , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/virology , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Vaccination/methods , Vaccines, Virus-Like Particle/administration & dosage , Vaccines, Virus-Like Particle/biosynthesis , Viral Matrix Proteins/genetics , Viral Matrix Proteins/immunology
11.
Virology ; 566: 143-152, 2022 01.
Article En | MEDLINE | ID: mdl-34929590

Annual repeat influenza vaccination raises concerns about protective efficacy against mismatched viruses. We investigated the impact of heterologous prime-boost vaccination on inducing cross protection by designing recombinant influenza viruses with chimeric hemagglutinin (HA) carrying M2 extracellular domains (M2e-HA). Heterologous prime-boost vaccination of C57BL/6 mice with M2e-HA chimeric virus more effectively induced M2e and HA stalk specific IgG antibodies correlating with cross protection than homologous prime-boost vaccination. Induction of M2e and HA stalk specific IgG antibodies was compromised in 1-year old mice, indicating significant aging effects on priming subdominant M2e and HA stalk IgG antibody responses. This study demonstrates that a heterologous prime-boost strategy with recombinant influenza virus expressing extra M2e epitopes provides more effective cross protection than homologous vaccination.


Aging/immunology , Antibodies, Viral/biosynthesis , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Immunoglobulin G/biosynthesis , Influenza Vaccines/genetics , Influenza, Human/prevention & control , Orthomyxoviridae Infections/prevention & control , Age Factors , Aging/genetics , Animals , Antigens, Viral/genetics , Antigens, Viral/immunology , Cross Protection , Female , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Humans , Immunization, Secondary/methods , Immunogenicity, Vaccine , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza Vaccines/administration & dosage , Influenza Vaccines/biosynthesis , Influenza, Human/immunology , Influenza, Human/virology , Mice , Mice, Inbred C57BL , Models, Molecular , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/virology , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Vaccination/methods , Vaccines, Synthetic , Viral Matrix Proteins/genetics , Viral Matrix Proteins/immunology
12.
Int J Mol Sci ; 22(22)2021 Nov 09.
Article En | MEDLINE | ID: mdl-34829979

Influenza is a respiratory virus that alone or in combination with secondary bacterial pathogens can contribute to the development of acute pneumonia in persons >65 years of age. Host innate immune antiviral signaling early in response to influenza is essential to inhibit early viral replication and guide the initiation of adaptive immune responses. Using young adult (3 months) and aged adult mice infected with mouse adapted H1N1 or H3N2, the results of our study illustrate dysregulated and/or diminished activation of key signaling pathways in aged lung contribute to increased lung inflammation and morbidity. Specifically, within the first seven days of infection, there were significant changes in genes associated with TLR and RIG-I signaling detected in aged murine lung in response to H1N1 or H3N2. Taken together, the results of our study expand our current understanding of age-associated changes in antiviral signaling in the lung.


Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/genetics , Pneumonia/genetics , A549 Cells , Animals , DEAD Box Protein 58/genetics , Disease Models, Animal , Gene Expression Regulation, Viral/genetics , Humans , Immunity, Innate/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza, Human/microbiology , Influenza, Human/virology , Lung/metabolism , Lung/microbiology , Lung/pathology , Mice , Orthomyxoviridae Infections/genetics , Orthomyxoviridae Infections/microbiology , Orthomyxoviridae Infections/virology , Pneumonia/microbiology , Pneumonia/virology , Toll-Like Receptors/genetics , Virus Replication/genetics
13.
Sci Rep ; 11(1): 20609, 2021 10 18.
Article En | MEDLINE | ID: mdl-34663857

Seasonal Influenza A virus (IAV) infections can promote dissemination of upper respiratory tract commensals such as Streptococcus pneumoniae to the lower respiratory tract resulting in severe life-threatening pneumonia. Here, we aimed to compare innate immune responses in the lungs of healthy colonized and non-colonized mice after IAV challenge at the initial asymptomatic stage of infection. Responses during a severe bacterial pneumonia were profiled for comparison. Cytokine and innate immune cell imprints of the lungs were analyzed. Irrespective of the colonization status, mild H1N1 IAV infection was characterized by a bi-phasic disease progression resulting in full recovery of the animals. Already at the asymptomatic stage of viral infection, the pro-inflammatory cytokine response was as high as in pneumococcal pneumonia. Flow cytometry analyses revealed an early influx of inflammatory monocytes into the lungs. Neutrophil influx was mostly limited to bacterial infections. The majority of cells, except monocytes, displayed an activated phenotype characterized by elevated CCR2 and MHCII expression. In conclusion, we show that IAV challenge of colonized healthy mice does not automatically result in severe co-infection. However, a general local inflammatory response was noted at the asymptomatic stage of infection irrespective of the infection type.


Immunity, Innate/immunology , Orthomyxoviridae Infections/immunology , Pneumococcal Infections/immunology , Animals , Carrier State/immunology , Coinfection/virology , Cytokines/metabolism , Disease Models, Animal , Female , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A virus/immunology , Influenza A virus/pathogenicity , Lung/immunology , Macrophages/immunology , Mice , Mice, Inbred C57BL , Neutrophils/metabolism , Orthomyxoviridae Infections/virology , Pneumococcal Infections/complications , Pneumonia, Bacterial , Pneumonia, Pneumococcal/immunology , Primary Cell Culture , Respiratory Tract Infections/immunology , Respiratory Tract Infections/virology , Streptococcus pneumoniae/pathogenicity
14.
Viruses ; 13(10)2021 09 29.
Article En | MEDLINE | ID: mdl-34696386

The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.


Epidemics , Genome, Viral , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza, Human/epidemiology , Genetic Variation , Hemagglutinin Glycoproteins, Influenza Virus/genetics , High-Throughput Nucleotide Sequencing , Humans , Kenya/epidemiology , Phylogeny , RNA, Viral/genetics , Seasons
15.
Viruses ; 13(10)2021 10 16.
Article En | MEDLINE | ID: mdl-34696517

Influenza viruses represent a continuous threat to both animal and human health. The 2009 H1N1 A influenza pandemic highlighted the importance of a swine host in the adaptation of influenza viruses to humans. Nowadays, one of the most extended strategies used to control swine influenza viruses (SIVs) is the trivalent vaccine application, whose formulation contains the most frequently circulating SIV subtypes H1N1, H1N2, and H3N2. These vaccines do not provide full protection against the virus, allowing its replication, evolution, and adaptation. To better understand the main mechanisms that shape viral evolution, here, the SIV intra-host diversity was analyzed in samples collected from both vaccinated and nonvaccinated animals challenged with the H1N1 influenza A virus. Twenty-eight whole SIV genomes were obtained by next-generation sequencing, and differences in nucleotide variants between groups were established. Substitutions were allocated along all influenza genetic segments, while the most relevant nonsynonymous substitutions were allocated in the NS1 protein on samples collected from vaccinated animals, suggesting that SIV is continuously evolving despite vaccine application. Moreover, new viral variants were found in both vaccinated and nonvaccinated pigs, showing relevant substitutions in the HA, NA, and NP proteins, which may increase viral fitness under field conditions.


Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Orthomyxoviridae Infections/epidemiology , Animals , Disease Outbreaks/veterinary , Influenza A Virus, H5N2 Subtype/genetics , Influenza A Virus, H5N2 Subtype/pathogenicity , Influenza A virus/genetics , Influenza A virus/pathogenicity , Influenza Vaccines/immunology , Phylogeny , Swine/virology , Swine Diseases/virology
16.
Pediatr Infect Dis J ; 40(12): e466-e471, 2021 Dec 01.
Article En | MEDLINE | ID: mdl-34609108

BACKGROUND: The rates of influenza-associated neurologic complications are variable among studies, and a difference has been observed between the Western and Asian countries. The study aims to evaluate the frequency and characteristics of influenza-associated neurologic complications. METHODS: We performed a retrospective review of hospitalized cases of influenza infection from October 2010 to April 2017 from 3 referral hospitals. RESULTS: A total of 1988 influenza cases were identified. Influenza-associated neurologic complications were 161 cases (8.1%); influenza virus A was detected in 113 (70.2%) cases, B in 47 (29.2%) cases and both A and B in 1 case (0.6%). Twenty-four patients (15%) had underlying neurologic diseases. The most common diagnosis was a simple febrile convulsion (44%), followed by complex febrile convulsion (29%), fever-provoked seizure under pre-existing neurologic disease or afebrile seizure (14%), encephalopathy/encephalitis (8%) and meningitis (5%). Most of the patients fully recovered (96%). Three patients (1.9%) died of myocarditis (n = 1), encephalopathy (n = 1), and simultaneous encephalitis and myocarditis (n = 1). Pre-existing neurologic disease, age groups of 6 months to 6 years and 6-12 years were a risk factor of influenza-associated neurologic complications with an adjusted odds ratio of 5.41 (95% confidence interval [CI] 3.23-9.06, P < 0.001), 12.99 (95% CI 1.77-95.19, P = 0.01) and 8.54 (95% CI 1.14-64.79, P = 0.04), respectively. There was no association between neuropsychiatric adverse events and oseltamivir prescription (P = 0.17). CONCLUSIONS: Influenza-associated neurologic complications are not uncommon, and most patients fully recovered. The frequency of influenza-associated neurologic complications in Korean children was not significantly different from that of children in Western countries.


Brain Diseases/virology , Hospitalization/statistics & numerical data , Influenza, Human/complications , Adolescent , Antiviral Agents/therapeutic use , Child , Child, Preschool , Female , Humans , Infant , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza, Human/drug therapy , Male , Oseltamivir/therapeutic use , Republic of Korea , Retrospective Studies , Risk Factors , Seizures, Febrile/virology
17.
Microbiol Spectr ; 9(2): e0018221, 2021 10 31.
Article En | MEDLINE | ID: mdl-34612695

Seasonal influenza outbreaks represent a large burden for the health care system as well as the economy. While the role of the microbiome has been elucidated in the context of various diseases, the impact of respiratory viral infections on the human microbiome is largely unknown. In this study, swine was used as an animal model to characterize the temporal dynamics of the respiratory and gastrointestinal microbiome in response to an influenza A virus (IAV) infection. A multi-omics approach was applied on fecal samples to identify alterations in microbiome composition and function during IAV infection. We observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, increased abundances of Prevotellaceae were detected, while Clostridiaceae and Lachnospiraceae decreased. Moreover, our metaproteomics data indicated that the functional composition of the microbiome was heavily affected by the influenza infection. For instance, we identified decreased amounts of flagellin, correlating with reduced abundances of Lachnospiraceae and Clostridiaceae, possibly indicating involvement of a direct immune response toward flagellated Clostridia during IAV infection. Furthermore, enzymes involved in short-chain fatty acid (SCFA) synthesis were identified in higher abundances, while metabolome analyses revealed rather stable concentrations of SCFAs. In addition, 16S rRNA gene sequencing was used to characterize effects on the composition and natural development of the upper respiratory tract microbiome. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae in the upper respiratory tract. Surprisingly, temporal development of the respiratory microbiome structure was not affected. IMPORTANCE Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.


Bacteria/classification , Bacteria/isolation & purification , Gastrointestinal Microbiome/physiology , Orthomyxoviridae Infections/pathology , Respiratory System/microbiology , Animals , Bacteria/genetics , Disease Models, Animal , Fatty Acids, Volatile/biosynthesis , Feces/microbiology , Female , Gene Expression Profiling , Influenza A Virus, H1N1 Subtype/pathogenicity , Male , Proteomics , RNA, Ribosomal, 16S/genetics , Swine
18.
mBio ; 12(5): e0148421, 2021 10 26.
Article En | MEDLINE | ID: mdl-34517760

Membrane-associated RING-CH8 (MARCH8) impairs the cell surface expression of envelope glycoproteins from different viruses, reducing their incorporation into virions. Using stable cell lines with inducible MARCH8 expression, we show that MARCH8 did not alter susceptibility to influenza A virus (IAV) infection, but virions released from infected cells were markedly less infectious. Knockdown of endogenous MARCH8 confirmed its effect on IAV infectivity. The expression of MARCH8 impaired the infectivity of both H3N2 and H1N1 strains and was dependent on its E3 ligase activity. Although virions released in the presence of MARCH8 expressed smaller amounts of viral hemagglutinin (HA) and neuraminidase (NA) proteins, there was no impact on levels of the viral HA, NA, or matrix 2 (M2) proteins detected on the surface of infected cells. Moreover, mutation of lysine residues in the cytoplasmic tails of HA, NA, and/or M2, or in the viral M1 protein, did not abrogate MARCH8-mediated restriction. While MARCH1 and -8 target similar immunological ligands and both restrict HIV-1, only MARCH8 inhibited IAV infectivity. Deletion of the N-terminal cytoplasmic (N-CT) domain of MARCH8 confirmed it to be a critical determinant of IAV inhibition. Of interest, deletion of the MARCH1 N-CT or its replacement with the MARCH8 N-CT resulted in acquisition of IAV restriction. Together, these data demonstrate that MARCH8 restricts a late stage in IAV replication by a mechanism distinct to its reported activity against other viruses. Moreover, we show that the N-CT of MARCH8 is essential for anti-IAV activity, whereas the MARCH1 N-CT inhibits its ability to restrict IAV. IMPORTANCE The antiviral activity of MARCH8 has been associated with the downregulation of envelope glycoproteins from a range of different viruses, resulting in reduced incorporation into nascent virions. Here, we show that MARCH8 restricts IAV at a late stage in virus replication, but this was not associated with reduced expression of IAV envelope glycoproteins on the surface of infected cells, pointing to a distinct mechanism of antiviral activity. Our studies also demonstrate the differential ability of MARCH1 and -8 to restrict IAV infectivity, highlighting the critical role of the N-CT domain of each protein in modulating IAV restriction. Overall, these studies provide novel insights regarding the mechanisms by which MARCH proteins contribute to cell-intrinsic immunity against IAV.


Gene Expression , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Ubiquitin-Protein Ligases/genetics , Virus Replication/genetics , Animals , Dogs , Down-Regulation , HEK293 Cells , Humans , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/pathogenicity , Madin Darby Canine Kidney Cells
19.
Viruses ; 13(9)2021 08 27.
Article En | MEDLINE | ID: mdl-34578289

Influenza hemagglutinin (HA) is considered a major protective antigen of seasonal influenza vaccine but antigenic drift of HA necessitates annual immunizations using new circulating HA versions. Low variation found within conserved non-HA influenza virus (INFV) antigens may maintain protection with less frequent immunizations. Conserved antigens of influenza A virus (INFV A) that can generate cross protection against multiple INFV strains were evaluated in BALB/c mice using modified Vaccinia virus Ankara (MVA)-vectored vaccines that expressed INFV A antigens hemagglutinin (HA), matrix protein 1 (M1), nucleoprotein (NP), matrix protein 2 (M2), repeats of the external portion of M2 (M2e) or as tandem repeats (METR), and M2e with transmembrane region and cytoplasmic loop (M2eTML). Protection by combinations of non-HA antigens was equivalent to that of subtype-matched HA. Combinations of NP and forms of M2e generated serum antibody responses and protected mice against lethal INFV A challenge using PR8, pandemic H1N1 A/Mexico/4108/2009 (pH1N1) or H5N1 A/Vietnam/1203/2004 (H5N1) viruses, as demonstrated by reduced lung viral burden and protection against weight loss. The highest levels of protection were obtained with NP and M2e antigens delivered as MVA inserts, resulting in broadly protective immunity in mice and enhancement of previous natural immunity to INFV A.


Antibodies, Viral/blood , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H5N1 Subtype/immunology , Influenza Vaccines/immunology , Nucleocapsid Proteins/immunology , Orthomyxoviridae Infections/prevention & control , Viral Matrix Proteins/immunology , Viroporin Proteins/immunology , Animals , Antigens, Viral/immunology , Cross Protection , Female , Genetic Vectors , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H5N1 Subtype/pathogenicity , Influenza Vaccines/administration & dosage , Mice, Inbred BALB C , Nucleocapsid Proteins/administration & dosage , Orthomyxoviridae Infections/immunology , Pandemics , Vaccination , Viral Matrix Proteins/administration & dosage , Viral Matrix Proteins/genetics , Viroporin Proteins/administration & dosage
20.
Curr Med Sci ; 41(4): 815-820, 2021 Aug.
Article En | MEDLINE | ID: mdl-34403107

OBJECTIVE: Mild encephalopathy with reversible splenial lesion (MERS) is associated with a variety of infections and anti-epileptic drug withdrawal. Here we report the clinical characteristics of H1N1 influenza A-associated MERS based on our experience of four pediatric cases. METHODS: A detailed retrospective analysis of four patients with H1N1 influenza A-associated MERS was performed at Guangzhou Women and Children's Medical Center. RESULTS: All patients exhibited mild influenza-like illness and seizures. Three patients presented with a new-onset seizure with fever after 5 years of age. 75% patients had altered mental status. For all four patients, influenza A (H1N1) viral RNA was detected in throat swab specimens at least twice. Brain magnetic resonance images revealed similar ovoid lesions in the corpus callosum, mainly in the splenium and for one patient in the splenium and genu of the corpus callosum. Only one patient had an abnormal electroencephalogram tracing. Cells and protein in the cerebrospinal fluid were normal in all patients. All patients received oseltamivir and one patient received intravenous immunoglobulin. As a result, all patients fully recovered after 2 months and showed no neurologic sequelae at discharge. CONCLUSION: This case series provides insight towards clinical features of H1N1 influenza A-associated MERS.


Brain Diseases/diagnosis , Brain/diagnostic imaging , Corpus Callosum/diagnostic imaging , Influenza A Virus, H1N1 Subtype/pathogenicity , Brain/physiopathology , Brain Diseases/diagnostic imaging , Brain Diseases/physiopathology , Brain Diseases/virology , Child , Child, Preschool , Corpus Callosum/physiopathology , Female , Humans , Influenza, Human/complications , Influenza, Human/diagnosis , Influenza, Human/physiopathology , Influenza, Human/virology , Magnetic Resonance Imaging , Male
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