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1.
J Virol ; 96(5): e0179121, 2022 03 09.
Article in English | MEDLINE | ID: covidwho-1799229

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal influenza viruses are cocirculating in the human population. However, only a few cases of viral coinfection with these two viruses have been documented in humans with some people having severe disease and others mild disease. To examine this phenomenon, ferrets were coinfected with SARS-CoV-2 and human seasonal influenza A viruses (IAVs; H1N1 or H3N2) and were compared to animals that received each virus alone. Ferrets were either immunologically naive to both viruses or vaccinated with the 2019 to 2020 split-inactivated influenza virus vaccine. Coinfected naive ferrets lost significantly more body weight than ferrets infected with each virus alone and had more severe inflammation in both the nose and lungs compared to that of ferrets that were single infected with each virus. Coinfected, naive animals had predominantly higher IAV titers than SARS-CoV-2 titers, and IAVs were efficiently transmitted by direct contact to the cohoused ferrets. Comparatively, SARS-CoV-2 failed to transmit to the ferrets that cohoused with coinfected ferrets by direct contact. Moreover, vaccination significantly reduced IAV titers and shortened the viral shedding but did not completely block direct contact transmission of the influenza virus. Notably, vaccination significantly ameliorated influenza-associated disease by protecting vaccinated animals from severe morbidity after IAV single infection or IAV and SARS-CoV-2 coinfection, suggesting that seasonal influenza virus vaccination is pivotal to prevent severe disease induced by IAV and SARS-CoV-2 coinfection during the COVID-19 pandemic. IMPORTANCE Influenza A viruses cause severe morbidity and mortality during each influenza virus season. The emergence of SARS-CoV-2 infection in the human population offers the opportunity to potential coinfections of both viruses. The development of useful animal models to assess the pathogenesis, transmission, and viral evolution of these viruses as they coinfect a host is of critical importance for the development of vaccines and therapeutics. The ability to prevent the most severe effects of viral coinfections can be studied using effect coinfection ferret models described in this report.


Subject(s)
Antibodies, Viral/blood , COVID-19/prevention & control , Coinfection/prevention & control , Influenza Vaccines/immunology , Orthomyxoviridae Infections/prevention & control , Animals , COVID-19/immunology , Female , Ferrets/immunology , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/immunology , Orthomyxoviridae Infections/immunology , Vaccination , Virus Shedding
2.
Viruses ; 14(2)2022 02 21.
Article in English | MEDLINE | ID: covidwho-1744920

ABSTRACT

Involvement of macrophages in the SARS-CoV-2-associated cytokine storm, the excessive secretion of inflammatory/anti-viral factors leading to the acute respiratory distress syndrome (ARDS) in COVID-19 patients, is unclear. In this study, we sought to characterize the interplay between the virus and primary human monocyte-derived macrophages (MDM). MDM were stimulated with recombinant IFN-α and/or infected with either live or UV-inactivated SARS-CoV-2 or with two reassortant influenza viruses containing external genes from the H1N1 PR8 strain and heterologous internal genes from a highly pathogenic avian H5N1 or a low pathogenic human seasonal H1N1 strain. Virus replication was monitored by qRT-PCR for the E viral gene for SARS-CoV-2 or M gene for influenza and TCID50 or plaque assay, and cytokine levels were assessed semiquantitatively with qRT-PCR and a proteome cytokine array. We report that MDM are not susceptible to SARS-CoV-2 whereas both influenza viruses replicated in MDM, albeit abortively. We observed a modest cytokine response in SARS-CoV-2 exposed MDM with notable absence of IFN-ß induction, which was instead strongly induced by the influenza viruses. Pre-treatment of MDM with IFN-α enhanced proinflammatory cytokine expression upon exposure to virus. Together, the findings concur that the hyperinflammation observed in SARS-CoV-2 infection is not driven by macrophages.


Subject(s)
Inflammation/virology , Macrophages/immunology , Macrophages/virology , SARS-CoV-2/immunology , Virus Replication/genetics , Cell Line , Cell Line, Tumor , Cells, Cultured , Cytokines/analysis , Cytokines/immunology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H5N1 Subtype/genetics , Influenza A Virus, H5N1 Subtype/immunology , Interferon-alpha/pharmacology , Macrophages/drug effects , Male , SARS-CoV-2/genetics , SARS-CoV-2/physiology
3.
Science ; 374(6571): 1127-1133, 2021 Nov 26.
Article in English | MEDLINE | ID: covidwho-1723460

ABSTRACT

Humans differ in their susceptibility to infectious disease, partly owing to variation in the immune response after infection. We used single-cell RNA sequencing to quantify variation in the response to influenza infection in peripheral blood mononuclear cells from European- and African-ancestry males. Genetic ancestry effects are common but highly cell type specific. Higher levels of European ancestry are associated with increased type I interferon pathway activity in early infection, which predicts reduced viral titers at later time points. Substantial population-associated variation is explained by cis-expression quantitative trait loci that are differentiated by genetic ancestry. Furthermore, genetic ancestry­associated genes are enriched among genes correlated with COVID-19 disease severity, suggesting that the early immune response contributes to ancestry-associated differences for multiple viral infection outcomes.


Subject(s)
African Americans/genetics , COVID-19/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza, Human/genetics , Influenza, Human/immunology , Leukocytes, Mononuclear/virology , /genetics , Adult , Aged , COVID-19/immunology , COVID-19/physiopathology , Disease Susceptibility , Gene Expression Regulation , Genetic Variation , Humans , Influenza A Virus, H1N1 Subtype/physiology , Interferon Type I/immunology , Interferon Type I/metabolism , Leukocytes, Mononuclear/immunology , Male , Middle Aged , Quantitative Trait Loci , Severity of Illness Index , Single-Cell Analysis , Transcription, Genetic , Viral Load , Young Adult
4.
Front Immunol ; 13: 782198, 2022.
Article in English | MEDLINE | ID: covidwho-1699887

ABSTRACT

Misunderstanding temporal coincidence of adverse events during mass vaccination and invalid assessment of possible safety concerns have negative effects on immunization programs, leading to low immunization coverage. We conducted this systematic review and meta-analysis to identify the incidence rates of GBS that are temporally associated with viral vaccine administration but might not be attributable to the vaccines. By literature search in Embase and PubMed, we included 48 publications and 2,110,441,600 participants. The pooled incidence rate of GBS was 3.09 per million persons (95% confidence interval [CI]: 2.67 to 3.51) within six weeks of vaccination, equally 2.47 per 100,000 person-year (95%CI: 2.14 to 2.81). Subgroup analyses illustrated that the pooled rates were 2.77 per million persons (95%CI: 2.47 to 3.07) for individuals who received the influenza vaccine and 2.44 per million persons (95%CI: 0.97 to 3.91) for human papillomavirus (HPV) vaccines, respectively. Our findings evidence the GBS-associated safety of virus vaccines. We present a reference for the evaluation of post-vaccination GBS rates in mass immunization campaigns, including the SARS-CoV-2 vaccine.


Subject(s)
COVID-19 Vaccines/adverse effects , Guillain-Barre Syndrome/epidemiology , Influenza Vaccines/adverse effects , Mass Vaccination/adverse effects , Papillomavirus Vaccines/adverse effects , Alphapapillomavirus/immunology , COVID-19/prevention & control , COVID-19 Vaccines/immunology , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/immunology , Influenza, Human/prevention & control , Papillomavirus Infections/prevention & control , Papillomavirus Vaccines/immunology , Population Surveillance , SARS-CoV-2/immunology
5.
Sci Rep ; 12(1): 2594, 2022 02 16.
Article in English | MEDLINE | ID: covidwho-1692553

ABSTRACT

Complex glycans decorate viral surface proteins and play a critical role in virus-host interactions. Viral surface glycans shield vulnerable protein epitopes from host immunity yet can also present distinct "glycoepitopes" that can be targeted by host antibodies such as the potent anti-HIV antibody 2G12 that binds high-mannose glycans on gp120. Two recent publications demonstrate 2G12 binding to high mannose glycans on SARS-CoV-2 and select Influenza A (Flu) H3N2 viruses. Previously, our lab observed 2G12 binding and functional inhibition of a range of Flu viruses that include H3N2 and H1N1 lineages. In this manuscript, we present these data alongside structural analyses to offer an expanded picture of 2G12-Flu interactions. Further, based on the remarkable breadth of 2G12 N-glycan recognition and the structural factors promoting glycoprotein oligomannosylation, we hypothesize that 2G12 glycoepitopes can be defined from protein structure alone according to N-glycan site topology. We develop a model describing 2G12 glycoepitopes based on N-glycan site topology, and apply the model to identify viruses within the Protein Data Bank presenting putative 2G12 glycoepitopes for 2G12 repurposing toward analytical, diagnostic, and therapeutic applications.


Subject(s)
Antibodies, Monoclonal/metabolism , Broadly Neutralizing Antibodies/metabolism , HIV Antibodies/metabolism , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/immunology , Models, Immunological , SARS-CoV-2/immunology , Animals , Dogs , Drug Repositioning , Epitopes , Hemagglutinin Glycoproteins, Influenza Virus/metabolism , Humans , Influenza A Virus, H1N1 Subtype/metabolism , Influenza A Virus, H3N2 Subtype/metabolism , Madin Darby Canine Kidney Cells , Molecular Targeted Therapy , Neutralization Tests , Polysaccharides/metabolism
6.
PLoS One ; 17(2): e0263419, 2022.
Article in English | MEDLINE | ID: covidwho-1674014

ABSTRACT

Mucosal immunity plays a crucial role in controlling upper respiratory infections, including influenza. We established a quantitative ELISA to measure the amount of influenza virus-specific salivery IgA (sIgA) and salivary IgG (sIgG) antibodies using a standard antibody broadly reactive to the influenza A virus. We then analyzed saliva and serum samples from seven individuals infected with the A(H1N1)pdm09 influenza virus during the 2019-2020 flu seasons. We detected an early (6-10 days post-infection) increase of sIgA in five of the seven samples and a later (3-5 weeks) increase of sIgG in six of the seven saliva samples. Although the conventional parenteral influenza vaccine did not induce IgA production in saliva, vaccinated individuals with a history of influenza infection had higher basal levels of sIgA than those without a history. Interestingly, we observed sIgA and sIgG in an asymptomatic individual who had close contact with two influenza cases. Both early mucosal sIgA secretion and late systemically induced sIgG in the mucosal surface may protect against virus infection. Despite the small sample size, our results indicate that the saliva test system can be useful for analyzing upper mucosal immunity in influenza.


Subject(s)
Immunity, Mucosal/physiology , Influenza, Human/immunology , Saliva/immunology , Adult , Aged , Antibodies, Viral/analysis , Antibodies, Viral/metabolism , Antibody Formation , Cohort Studies , Female , History, 21st Century , Humans , Immunoglobulin A/analysis , Immunoglobulin A/metabolism , Immunoglobulin A, Secretory/analysis , Immunoglobulin A, Secretory/metabolism , Immunoglobulin G/analysis , Immunoglobulin G/metabolism , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/therapeutic use , Influenza, Human/diagnosis , Influenza, Human/prevention & control , Japan , Longitudinal Studies , Male , Predictive Value of Tests , Prognosis , Saliva/chemistry , Saliva/metabolism , Young Adult
7.
Cells ; 11(3)2022 01 30.
Article in English | MEDLINE | ID: covidwho-1667057

ABSTRACT

The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still ongoing, as is research on the molecular mechanisms underlying cellular infection by coronaviruses, with the hope of developing therapeutic agents against this pandemic. Other important respiratory viruses such as 2009 pandemic H1N1 and H7N9 avian influenza virus (AIV), influenza A viruses, are also responsible for a possible outbreak due to their respiratory susceptibility. However, the interaction of these viruses with host cells and the regulation of post-transcriptional genes remains unclear. In this study, we detected and analyzed the comparative transcriptome profiling of SARS-CoV-2, panH1N1 (A/California/07/2009), and H7N9 (A/Shanghai/1/2013) infected cells. The results showed that the commonly upregulated genes among the three groups were mainly involved in autophagy, pertussis, and tuberculosis, which indicated that autophagy plays an important role in viral pathogenicity. There are three groups of commonly downregulated genes involved in metabolic pathways. Notably, unlike panH1N1 and H7N9, SARS-CoV-2 infection can inhibit the m-TOR pathway and activate the p53 signaling pathway, which may be responsible for unique autophagy induction and cell apoptosis. Particularly, upregulated expression of IRF1 was found in SARS-CoV-2, panH1N1, and H7N9 infection. Further analysis showed SARS-CoV-2, panH1N1, and H7N9 infection-induced upregulation of lncRNA-34087.27 could serve as a competitive endogenous RNA to stabilize IRF1 mRNA by competitively binding with miR-302b-3p. This study provides new insights into the molecular mechanisms of influenza A virus and SARS-CoV-2 infection.


Subject(s)
COVID-19/immunology , Immunity/immunology , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H7N9 Subtype/immunology , Influenza, Human/immunology , RNA/immunology , Transcriptome/immunology , A549 Cells , Animals , COVID-19/genetics , COVID-19/virology , HEK293 Cells , Host-Pathogen Interactions/immunology , Humans , Immunity/genetics , Influenza A Virus, H1N1 Subtype/physiology , Influenza A Virus, H7N9 Subtype/physiology , Influenza, Human/genetics , Influenza, Human/virology , Interferon Regulatory Factor-1/genetics , Interferon Regulatory Factor-1/immunology , Interferon Regulatory Factor-1/metabolism , MicroRNAs/genetics , MicroRNAs/immunology , MicroRNAs/metabolism , Pandemics/prevention & control , RNA/genetics , RNA/metabolism , RNA, Long Noncoding/genetics , RNA, Long Noncoding/immunology , RNA, Long Noncoding/metabolism , RNA, Messenger/genetics , RNA, Messenger/immunology , RNA, Messenger/metabolism , RNA-Seq/methods , SARS-CoV-2/physiology , Signal Transduction/genetics , Signal Transduction/immunology , Transcriptome/genetics
8.
J Nippon Med Sch ; 88(6): 524-532, 2021 Dec 29.
Article in English | MEDLINE | ID: covidwho-1581928

ABSTRACT

BACKGROUND: Behavioral changes among Japanese, along with the coronavirus disease 2019 (COVID-19) epidemic, may affect the seasonal influenza epidemic in Japan and change influenza vaccine effectiveness (VE). METHODS: This single-center, test-negative case-control (TNCC) study estimated influenza VE in children for the first influenza season (2019/20) to overlap the COVID-19 epidemic in. Effects of prior influenza infection and vaccination in children were assessed for the 2019-2020 season. RESULTS: Among 386 children, adjusted VE was significant for influenza A/H1N1 (45.5%; 95% confidence interval [CI]: 2.0-69.7) and influenza B (66.7%; 95% CI: 35.9-82.7). Among patients aged 0-6 years, adjusted VE was significant for influenza A (total: A/H1N1+A/H3N2) (65.0%; 95% CI: 22.2-84.3), influenza A/H1N1 (64.8%; 95% CI: 16.9-85.1) and influenza B (87.4%; 95% CI: 50.5-96.8). No VE was observed in patients aged 7-15 years. Administration of two vaccine doses tended to decrease incidences of influenza A (total) and influenza A/H1N1 in patients aged 0-6 years. The adjusted odds ratios (ORs) of influenza B infection in patients, who had influenza during the previous season, were significantly lower among all participants (0.29; 95% CI: 0.11-0.78) and patients aged 7-15 years (0.34; 95% CI: 0.12-0.94). The adjusted ORs of influenza infections were not significant in patients vaccinated during the previous season. CONCLUSIONS: TNCC-based estimates of influenza VE were consistent despite the overlapping COVID-19 epidemic.


Subject(s)
COVID-19 , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , COVID-19/epidemiology , Case-Control Studies , Child , Female , Humans , Infant , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/immunology , Influenza Vaccines/adverse effects , Influenza, Human/epidemiology , Male , SARS-CoV-2 , Seasons , Vaccination
9.
PLoS Comput Biol ; 17(12): e1009664, 2021 12.
Article in English | MEDLINE | ID: covidwho-1571973

ABSTRACT

The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the viral spike. Because of the high density of spikes on the viral surface, not all antigenic sites are targeted equally by antibodies. We offer here a geometry-based approach to predict and rank the probability of surface residues of SARS spike (S protein) and influenza H1N1 spike (hemagglutinin) to acquire antibody-escaping mutations utilizing in-silico models of viral structure. We used coarse-grained MD simulations to estimate the on-rate (targeting) of an antibody model to surface residues of the spike protein. Analyzing publicly available sequences, we found that spike surface sequence diversity of the pre-pandemic seasonal influenza H1N1 and the sarbecovirus subgenus highly correlates with our model prediction of antibody targeting. In particular, we identified an antibody-targeting gradient, which matches a mutability gradient along the main axis of the spike. This identifies the role of viral surface geometry in shaping the evolution of circulating viruses. For the 2009 H1N1 and SARS-CoV-2 pandemics, a mutability gradient along the main axis of the spike was not observed. Our model further allowed us to identify key residues of the SARS-CoV-2 spike at which antibody escape mutations have now occurred. Therefore, it can inform of the likely functional role of observed mutations and predict at which residues antibody-escaping mutation might arise.


Subject(s)
Evolution, Molecular , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Viral Envelope Proteins/genetics , Viral Envelope Proteins/immunology , Animals , Antibodies, Viral/biosynthesis , Antigens, Viral/chemistry , Antigens, Viral/genetics , COVID-19/epidemiology , COVID-19/immunology , COVID-19/virology , Computational Biology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/genetics , Hemagglutinin Glycoproteins, Influenza Virus/chemistry , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Host Microbial Interactions/genetics , Host Microbial Interactions/immunology , Humans , Immune Evasion/genetics , Influenza, Human/immunology , Influenza, Human/virology , Models, Immunological , Molecular Dynamics Simulation , Mutation , Pandemics , Spike Glycoprotein, Coronavirus/chemistry , Viral Envelope Proteins/chemistry
10.
J Clin Invest ; 131(13)2021 07 01.
Article in English | MEDLINE | ID: covidwho-1556620

ABSTRACT

Seasonal influenza vaccination elicits a diminished adaptive immune response in the elderly, and the mechanisms of immunosenescence are not fully understood. Using Ig-Seq, we found a marked increase with age in the prevalence of cross-reactive (CR) serum antibodies that recognize both the H1N1 (vaccine-H1) and H3N2 (vaccine-H3) components of an egg-produced split influenza vaccine. CR antibodies accounted for 73% ± 18% of the serum vaccine responses in a cohort of elderly donors, 65% ± 15% in late middle-aged donors, and only 13% ± 5% in persons under 35 years of age. The antibody response to non-HA antigens was boosted by vaccination. Recombinant expression of 19 vaccine-H1+H3 CR serum monoclonal antibodies (s-mAbs) revealed that they predominantly bound to non-HA influenza proteins. A sizable fraction of vaccine-H1+H3 CR s-mAbs recognized with high affinity the sulfated glycans, in particular sulfated type 2 N-acetyllactosamine (Galß1-4GalNAcß), which is found on egg-produced proteins and thus unlikely to contribute to protection against influenza infection in humans. Antibodies against sulfated glycans in egg-produced vaccine had been identified in animals but were not previously characterized in humans. Collectively, our results provide a quantitative basis for how repeated exposure to split influenza vaccine correlates with unintended focusing of serum antibody responses to non-HA antigens that may result in suboptimal immunity against influenza.


Subject(s)
Antibodies, Viral/biosynthesis , Influenza Vaccines/immunology , Influenza, Human/immunology , Viral Proteins/immunology , Adult , Age Factors , Aged , Animals , Antibodies, Monoclonal/immunology , Antibodies, Viral/blood , Cohort Studies , Cross Reactions , Eggs/analysis , Humans , Immunoglobulin G/biosynthesis , Immunoglobulin G/blood , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/immunology , Influenza, Human/prevention & control , Influenza, Human/virology , Middle Aged , Polysaccharides/immunology , Vaccination
11.
Influenza Other Respir Viruses ; 14(5): 530-540, 2020 09.
Article in English | MEDLINE | ID: covidwho-1452864

ABSTRACT

BACKGROUND: Influenza is an acute infection affecting all age groups; however, elderly patients are at an increased risk. We aim to describe the clinical characteristics and the circulation of influenza virus types in elderly patients admitted for severe acute respiratory infection (SARI) to a tertiary care hospital in Bucharest, Romania, part of the I-MOVE+ hospital network. METHODS: We conducted an active surveillance study at the National Institute for Infectious Diseases "Prof. Dr Matei Balș," Bucharest, Romania, during three consecutive influenza seasons: 2015/16, 2016/17, and 2017/18. All patients aged 65 and older admitted to our hospital for SARI were tested for influenza by PCR. RESULTS: A total of 349 eligible patients were tested during the study period, and 149 (42.7%) were confirmed with influenza. Most patients, 321 (92.5%) presented at least one underlying condition at the time of hospital admission, the most frequent being cardiovascular disease, 270 (78.3%). The main influenza viral subtype circulating in 2015/16 was A(H1N1)pdm09, followed by A(H3N2) in 2016/17 and B influenza in 2017/18. Case fatality was highest in the 2015/16 season (3.7%), 0% in 2016/17, and 1.0% in 2017/18. Vaccination coverage in elderly patients with SARI from our study population was 22 (6.3%) over the three seasons. CONCLUSIONS: Our study has highlighted a high burden of comorbidities in elderly patients presenting with SARI during winter season in Romania. The influenza vaccine coverage rate needs to be substantially increased in the elderly population, through targeted interventions.


Subject(s)
Influenza, Human/epidemiology , Sentinel Surveillance , Age Factors , Aged , Aged, 80 and over , Female , Hospitalization/statistics & numerical data , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/immunology , Influenza B virus/genetics , Influenza B virus/immunology , Influenza Vaccines/immunology , Male , Romania/epidemiology , Seasons , Tertiary Healthcare
12.
Infect Genet Evol ; 81: 104270, 2020 07.
Article in English | MEDLINE | ID: covidwho-1452334

ABSTRACT

In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.


Subject(s)
Antigenic Variation/genetics , Antigenic Variation/immunology , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/immunology , Influenza, Human/immunology , Adolescent , Adult , Amino Acid Substitution/genetics , Amino Acid Substitution/immunology , Child , Child, Preschool , Drug Resistance, Viral/genetics , Female , Humans , India , Influenza, Human/virology , Male , Middle Aged , Neuraminidase/genetics , Oseltamivir/therapeutic use , Phylogeny , Viral Proteins/genetics , Young Adult
13.
Sci Rep ; 11(1): 20143, 2021 10 11.
Article in English | MEDLINE | ID: covidwho-1462040

ABSTRACT

Rapid, high-throughput diagnostic tests are essential to decelerate the spread of the novel coronavirus disease 2019 (COVID-19) pandemic. While RT-PCR tests performed in centralized laboratories remain the gold standard, rapid point-of-care antigen tests might provide faster results. However, they are associated with markedly reduced sensitivity. Bedside breath gas analysis of volatile organic compounds detected by ion mobility spectrometry (IMS) may enable a quick and sensitive point-of-care testing alternative. In this proof-of-concept study, we investigated whether gas analysis by IMS can discriminate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from other respiratory viruses in an experimental set-up. Repeated gas analyses of air samples collected from the headspace of virus-infected in vitro cultures were performed for 5 days. A three-step decision tree using the intensities of four spectrometry peaks correlating to unidentified volatile organic compounds allowed the correct classification of SARS-CoV-2, human coronavirus-NL63, and influenza A virus H1N1 without misassignment when the calculation was performed with data 3 days post infection. The forward selection assignment model allowed the identification of SARS-CoV-2 with high sensitivity and specificity, with only one of 231 measurements (0.43%) being misclassified. Thus, volatile organic compound analysis by IMS allows highly accurate differentiation of SARS-CoV-2 from other respiratory viruses in an experimental set-up, supporting further research and evaluation in clinical studies.


Subject(s)
Antigens, Viral/isolation & purification , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Point-of-Care Testing , SARS-CoV-2/isolation & purification , Animals , COVID-19/immunology , COVID-19/virology , COVID-19 Serological Testing/instrumentation , Chlorocebus aethiops , Coronavirus NL63, Human/immunology , Coronavirus NL63, Human/isolation & purification , Diagnosis, Differential , High-Throughput Screening Assays/instrumentation , High-Throughput Screening Assays/methods , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/isolation & purification , Ion Mobility Spectrometry , Proof of Concept Study , SARS-CoV-2/immunology , Vero Cells
15.
HLA ; 96(3): 277-298, 2020 09.
Article in English | MEDLINE | ID: covidwho-1388402

ABSTRACT

We report detailed peptide-binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide-binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.


Subject(s)
Coronavirus Infections/epidemiology , HIV Infections/epidemiology , HLA Antigens/chemistry , Influenza, Human/epidemiology , Pandemics , Peptides/chemistry , Pneumonia, Viral/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Viral Proteins/chemistry , Africa/epidemiology , Americas/epidemiology , Amino Acid Sequence , Asia/epidemiology , Australia/epidemiology , Betacoronavirus/genetics , Betacoronavirus/immunology , COVID-19 , Computational Biology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Europe/epidemiology , HIV Infections/immunology , HIV Infections/virology , HIV-1/genetics , HIV-1/immunology , HLA Antigens/classification , HLA Antigens/genetics , HLA Antigens/immunology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H7N9 Subtype/genetics , Influenza A Virus, H7N9 Subtype/immunology , Influenza, Human/immunology , Influenza, Human/virology , Kinetics , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/immunology , Peptides/genetics , Peptides/immunology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Binding , SARS Virus/genetics , SARS Virus/immunology , SARS-CoV-2 , Severe Acute Respiratory Syndrome/immunology , Severe Acute Respiratory Syndrome/virology , Viral Proteins/genetics , Viral Proteins/immunology
16.
mBio ; 12(4): e0159821, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1360544

ABSTRACT

The gut microbiota plays a critical role in the induction of adaptive immune responses to influenza virus infection. However, the role of nasal bacteria in the induction of the virus-specific adaptive immunity is less clear. Here, we found that disruption of nasal bacteria by intranasal application of antibiotics before influenza virus infection enhanced the virus-specific antibody response in a MyD88-dependent manner. Similarly, disruption of nasal bacteria by lysozyme enhanced antibody responses to intranasally administered influenza virus hemagglutinin (HA) vaccine in a MyD88-dependent manner, suggesting that intranasal application of antibiotics or lysozyme could release bacterial pathogen-associated molecular patterns (PAMPs) from disrupted nasal bacteria that act as mucosal adjuvants by activating the MyD88 signaling pathway. Since commensal bacteria in the nasal mucosal surface were significantly lower than those in the oral cavity, intranasal administration of HA vaccine alone was insufficient to induce the vaccine-specific antibody response. However, intranasal supplementation of cultured oral bacteria from a healthy human volunteer enhanced antibody responses to an intranasally administered HA vaccine. Finally, we demonstrated that oral bacteria combined with an intranasal vaccine protect from influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our results reveal the role of nasal bacteria in the induction of the virus-specific adaptive immunity and provide clues for developing better intranasal vaccines. IMPORTANCE Intranasal vaccination induces the nasal IgA antibody which is protective against respiratory viruses, such as influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, understanding how mucosal immune responses are elicited following viral infection is important for developing better vaccines. Here, we focused on the role of nasal commensal bacteria in the induction of immune responses following influenza virus infection. To deplete nasal bacteria, we intranasally administered antibiotics to mice before influenza virus infection and found that antibiotic-induced disruption of nasal bacteria could release bacterial components which stimulate the virus-specific antibody responses. Since commensal bacteria in nasal mucosa were significantly lower than those in the oral cavity, intranasal administration of split virus vaccine alone was insufficient to induce the vaccine-specific antibody response. However, intranasal supplementation of cultured oral bacteria from a healthy human volunteer enhanced antibody responses to the intranasally administered vaccine. Therefore, both integrity and amounts of nasal bacteria may be critical for an effective intranasal vaccine.


Subject(s)
Bacteria/immunology , COVID-19 Vaccines/immunology , COVID-19/prevention & control , Influenza Vaccines/immunology , Nasal Mucosa/microbiology , Orthomyxoviridae Infections/prevention & control , Adaptive Immunity/immunology , Adjuvants, Immunologic , Administration, Intranasal , Animals , Antibodies, Viral/immunology , Cell Line , Chlorocebus aethiops , Dogs , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Immunity, Mucosal/immunology , Influenza A Virus, H1N1 Subtype/immunology , Madin Darby Canine Kidney Cells , Mice , Mice, Inbred BALB C , Myeloid Differentiation Factor 88/metabolism , Nasal Mucosa/immunology , Pathogen-Associated Molecular Pattern Molecules/immunology , SARS-CoV-2/immunology , Vaccination/methods , Vero Cells
17.
Therapie ; 76(4): 305-309, 2021.
Article in English | MEDLINE | ID: covidwho-1265885

ABSTRACT

The marketing authorization granted to SARS-Cov-2 vaccines was accompanied by reinforced safety monitoring plans. These plans' implementation was part of the usual logic of post-marketing surveillance of new and innovative health products. It was especially adapted to the context of post-marketing monitoring of drugs developed according to the usual scientific quality standards but in an accelerated schedule. In Europe, the reinforced surveillance system relies on the complementary strengths of pharmacovigilance and pharmacoepidemiology. If the performances of pharmacovigilance monitoring are incomparable for the detection of safety signals relating to rare events of atypical presentation, it needs to be completed with pharmacoepidemiology activities for more common events, either multifactorial or frequently classified as idiopathic. The pharmacoepidemiological monitoring developed in Europe was elaborated before the first SARS-Cov-2 vaccines where marketed, taking into account the lessons learned from the vaccination campaign against 2009 A (H1N1) influenza. It includes numerous academic studies as well as studies performed within vaccines risk management plans. In terms of safety, those defined a priori mostly concerns a list of pre-established health events of specific interest. Aside of these planned activities, ad-hoc studies will be latter developed on purpose to investigate safety signals or potential signals that could be identified as the result of pharmacovigilance activities. Aside of these regulated activities, as for today, very few studies have been published regarding SARS-Cov-2 vaccines; most of the existing consist in preprints that should be considered with caution. Pharmacoepidemiology of vaccines is thought to allow near-real time monitoring that needs sufficient time to provide with valid results. In the constant urge for information that accompanies COVID-related science, it is important not to make haste the enemy of speed and to let pharmacoepidemiology provides with what it is expected to do: rock-solid scientific information contributing to evidence-based decision-making.


Subject(s)
COVID-19 Vaccines , COVID-19/epidemiology , COVID-19/prevention & control , Immunization Programs , Pharmacoepidemiology , COVID-19/immunology , COVID-19 Vaccines/adverse effects , COVID-19 Vaccines/immunology , Europe/epidemiology , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/adverse effects , Influenza Vaccines/immunology , SARS-CoV-2/immunology
18.
Cytokine ; 144: 155593, 2021 08.
Article in English | MEDLINE | ID: covidwho-1242912

ABSTRACT

An analysis of published data appertaining to the cytokine storms of COVID-19, H1N1 influenza, cytokine release syndrome (CRS), and macrophage activation syndrome (MAS) reveals many common immunological and biochemical abnormalities. These include evidence of a hyperactive coagulation system with elevated D-dimer and ferritin levels, disseminated intravascular coagulopathy (DIC) and microthrombi coupled with an activated and highly permeable vascular endothelium. Common immune abnormalities include progressive hypercytokinemia with elevated levels of TNF-α, interleukin (IL)-6, and IL-1ß, proinflammatory chemokines, activated macrophages and increased levels of nuclear factor kappa beta (NFκB). Inflammasome activation and release of damage associated molecular patterns (DAMPs) is common to COVID-19, H1N1, and MAS but does not appear to be a feature of CRS. Elevated levels of IL-18 are detected in patients with COVID-19 and MAS but have not been reported in patients with H1N1 influenza and CRS. Elevated interferon-γ is common to H1N1, MAS, and CRS but levels of this molecule appear to be depressed in patients with COVID-19. CD4+ T, CD8+ and NK lymphocytes are involved in the pathophysiology of CRS, MAS, and possibly H1N1 but are reduced in number and dysfunctional in COVID-19. Additional elements underpinning the pathophysiology of cytokine storms include Inflammasome activity and DAMPs. Treatment with anakinra may theoretically offer an avenue to positively manipulate the range of biochemical and immune abnormalities reported in COVID-19 and thought to underpin the pathophysiology of cytokine storms beyond those manipulated via the use of, canakinumab, Jak inhibitors or tocilizumab. Thus, despite the relative success of tocilizumab in reducing mortality in COVID-19 patients already on dexamethasone and promising results with Baricitinib, the combination of anakinra in combination with dexamethasone offers the theoretical prospect of further improvements in patient survival. However, there is currently an absence of trial of evidence in favour or contravening this proposition. Accordingly, a large well powered blinded prospective randomised controlled trial (RCT) to test this hypothesis is recommended.


Subject(s)
Anti-Inflammatory Agents/therapeutic use , Antiviral Agents/therapeutic use , COVID-19 , Cytokine Release Syndrome , Influenza A Virus, H1N1 Subtype/immunology , SARS-CoV-2/immunology , COVID-19/drug therapy , COVID-19/immunology , COVID-19/mortality , COVID-19/pathology , Cytokine Release Syndrome/drug therapy , Cytokine Release Syndrome/immunology , Cytokine Release Syndrome/mortality , Cytokine Release Syndrome/pathology , Disease-Free Survival , Humans , Influenza, Human/drug therapy , Influenza, Human/immunology , Influenza, Human/mortality , Influenza, Human/pathology , Janus Kinases/antagonists & inhibitors , Janus Kinases/metabolism , Lymphocytes/immunology , Lymphocytes/pathology , Survival Rate
19.
Signal Transduct Target Ther ; 6(1): 200, 2021 05 20.
Article in English | MEDLINE | ID: covidwho-1237988

ABSTRACT

Influenza A virus may circulate simultaneously with the SARS-CoV-2 virus, leading to more serious respiratory diseases during this winter. However, the influence of these viruses on disease outcome when both influenza A and SARS-CoV-2 are present in the host remains unclear. Using a mammalian model, sequential infection was performed in ferrets and in K18-hACE2 mice, with SARS-CoV-2 infection following H1N1. We found that co-infection with H1N1 and SARS-CoV-2 extended the duration of clinical manifestation of COVID-19, and enhanced pulmonary damage, but reduced viral shedding of throat swabs and viral loads in the lungs of ferrets. Moreover, mortality was increased in sequentially infected mice compared with single-infection mice. Compared with single-vaccine inoculation, co-inoculation of PiCoVacc (a SARS-CoV-2 vaccine) and the flu vaccine showed no significant differences in neutralizing antibody titers or virus-specific immune responses. Combined immunization effectively protected K18-hACE2 mice against both H1N1 and SARS-CoV-2 infection. Our findings indicated the development of systematic models of co-infection of H1N1 and SARS-CoV-2, which together notably enhanced pneumonia in ferrets and mice, as well as demonstrated that simultaneous vaccination against H1N1 and SARS-CoV-2 may be an effective prevention strategy for the coming winter.


Subject(s)
COVID-19 , Coinfection , Influenza A Virus, H1N1 Subtype/immunology , Orthomyxoviridae Infections , SARS-CoV-2/immunology , Animals , COVID-19/immunology , COVID-19/pathology , COVID-19/virology , Coinfection/immunology , Coinfection/pathology , Coinfection/virology , Disease Models, Animal , Ferrets , Humans , Male , Mice , Mice, Transgenic , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/pathology , Orthomyxoviridae Infections/virology
20.
Front Immunol ; 12: 593595, 2021.
Article in English | MEDLINE | ID: covidwho-1229174

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is a global health threat with the potential to cause severe disease manifestations in the lungs. Although COVID-19 has been extensively characterized clinically, the factors distinguishing SARS-CoV-2 from other respiratory viruses are unknown. Here, we compared the clinical, histopathological, and immunological characteristics of patients with COVID-19 and pandemic influenza A(H1N1). We observed a higher frequency of respiratory symptoms, increased tissue injury markers, and a histological pattern of alveolar pneumonia in pandemic influenza A(H1N1) patients. Conversely, dry cough, gastrointestinal symptoms and interstitial lung pathology were observed in COVID-19 cases. Pandemic influenza A(H1N1) was characterized by higher levels of IL-1RA, TNF-α, CCL3, G-CSF, APRIL, sTNF-R1, sTNF-R2, sCD30, and sCD163. Meanwhile, COVID-19 displayed an immune profile distinguished by increased Th1 (IL-12, IFN-γ) and Th2 (IL-4, IL-5, IL-10, IL-13) cytokine levels, along with IL-1ß, IL-6, CCL11, VEGF, TWEAK, TSLP, MMP-1, and MMP-3. Our data suggest that SARS-CoV-2 induces a dysbalanced polyfunctional inflammatory response that is different from the immune response against pandemic influenza A(H1N1). Furthermore, we demonstrated the diagnostic potential of some clinical and immune factors to differentiate both diseases. These findings might be relevant for the ongoing and future influenza seasons in the Northern Hemisphere, which are historically unique due to their convergence with the COVID-19 pandemic.


Subject(s)
COVID-19 , Cytokines , Influenza A Virus, H1N1 Subtype , Influenza, Human , Matrix Metalloproteinase 1 , Matrix Metalloproteinase 3 , Receptors, Immunologic , Adult , Aged , COVID-19/blood , COVID-19/epidemiology , COVID-19/immunology , Cytokines/blood , Cytokines/immunology , Female , Humans , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/metabolism , Influenza, Human/blood , Influenza, Human/epidemiology , Influenza, Human/immunology , Male , Matrix Metalloproteinase 1/blood , Matrix Metalloproteinase 1/immunology , Matrix Metalloproteinase 3/blood , Matrix Metalloproteinase 3/immunology , Middle Aged , Prospective Studies , Receptors, Immunologic/blood , Receptors, Immunologic/immunology , Th1 Cells/immunology , Th2 Cells/immunology
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