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1.
Nat Commun ; 11(1): 2750, 2020 06 02.
Article in English | MEDLINE | ID: covidwho-680538

ABSTRACT

Influenza viruses annually kill 290,000-650,000 people worldwide. Antivirals can reduce death tolls. Baloxavir, the recently approved influenza antiviral, inhibits initiation of viral mRNA synthesis, whereas oseltamivir, an older drug, inhibits release of virus progeny. Baloxavir blocks virus replication more rapidly and completely than oseltamivir, reducing the duration of infectiousness. Hence, early baloxavir treatment may indirectly prevent transmission. Here, we estimate impacts of ramping up and accelerating baloxavir treatment on population-level incidence using a new model that links viral load dynamics from clinical trial data to between-host transmission. We estimate that ~22 million infections and >6,000 deaths would have been averted in the 2017-2018 epidemic season by administering baloxavir to 30% of infected cases within 48 h after symptom onset. Treatment within 24 h would almost double the impact. Consequently, scaling up early baloxavir treatment would substantially reduce influenza morbidity and mortality every year. The development of antivirals against the SARS-CoV2 virus that function like baloxavir might similarly curtail transmission and save lives.


Subject(s)
Antiviral Agents/therapeutic use , Epidemics , Influenza, Human/drug therapy , Orthomyxoviridae/drug effects , Oxazines/therapeutic use , Pyridines/therapeutic use , Thiepins/therapeutic use , Triazines/therapeutic use , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Cell Proliferation , Coronavirus Infections/drug therapy , Humans , Influenza, Human/virology , Oseltamivir/pharmacology , Oseltamivir/therapeutic use , Oxazines/pharmacology , Pandemics , Pneumonia, Viral/drug therapy , Public Health , Pyridines/pharmacology , RNA, Messenger/metabolism , Seasons , Thiepins/pharmacology , Triazines/pharmacology , Viral Load , Virus Replication/drug effects
2.
Blood Adv ; 4(13): 2967-2978, 2020 07 14.
Article in English | MEDLINE | ID: covidwho-625455

ABSTRACT

Thrombocytopenia is a common complication of influenza virus infection, and its severity predicts the clinical outcome of critically ill patients. The underlying cause(s) remain incompletely understood. In this study, in patients with an influenza A/H1N1 virus infection, viral load and platelet count correlated inversely during the acute infection phase. We confirmed this finding in a ferret model of influenza virus infection. In these animals, platelet count decreased with the degree of virus pathogenicity varying from 0% in animals infected with the influenza A/H3N2 virus, to 22% in those with the pandemic influenza A/H1N1 virus, up to 62% in animals with a highly pathogenic A/H5N1 virus infection. This thrombocytopenia is associated with virus-containing platelets that circulate in the blood. Uptake of influenza virus particles by platelets requires binding to sialoglycans and results in the removal of sialic acids by the virus neuraminidase, a trigger for hepatic clearance of platelets. We propose the clearance of influenza virus by platelets as a paradigm. These insights clarify the pathophysiology of influenza virus infection and show how severe respiratory infections, including COVID-19, may propagate thrombocytopenia and/or thromboembolic complications.


Subject(s)
Blood Platelets/virology , Influenza A virus/pathogenicity , Influenza, Human/complications , N-Acetylneuraminic Acid/metabolism , Polysaccharides/metabolism , Thrombocytopenia/etiology , Animals , Blood Platelets/metabolism , Blood Platelets/pathology , Disease Models, Animal , Ferrets , Host-Pathogen Interactions , Humans , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H1N1 Subtype/physiology , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/physiology , Influenza A Virus, H5N1 Subtype/pathogenicity , Influenza A Virus, H5N1 Subtype/physiology , Influenza A virus/physiology , Influenza, Human/metabolism , Influenza, Human/pathology , Influenza, Human/virology , Orthomyxoviridae Infections/complications , Orthomyxoviridae Infections/metabolism , Orthomyxoviridae Infections/pathology , Orthomyxoviridae Infections/virology , Thrombocytopenia/metabolism , Thrombocytopenia/pathology , Thrombocytopenia/virology , Virus Internalization
3.
Viruses ; 12(6)2020 06 24.
Article in English | MEDLINE | ID: covidwho-620517

ABSTRACT

The respiratory Influenza A Viruses (IAVs) and emerging zoonotic viruses such as Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) pose a significant threat to human health. To accelerate our understanding of the host-pathogen response to respiratory viruses, the use of more complex in vitro systems such as normal human bronchial epithelial (NHBE) cell culture models has gained prominence as an alternative to animal models. NHBE cells were differentiated under air-liquid interface (ALI) conditions to form an in vitro pseudostratified epithelium. The responses of well-differentiated (wd) NHBE cells were examined following infection with the 2009 pandemic Influenza A/H1N1pdm09 strain or following challenge with the dsRNA mimic, poly(I:C). At 30 h postinfection with H1N1pdm09, the integrity of the airway epithelium was severely impaired and apical junction complex damage was exhibited by the disassembly of zona occludens-1 (ZO-1) from the cell cytoskeleton. wdNHBE cells produced an innate immune response to IAV-infection with increased transcription of pro- and anti-inflammatory cytokines and chemokines and the antiviral viperin but reduced expression of the mucin-encoding MUC5B, which may impair mucociliary clearance. Poly(I:C) produced similar responses to IAV, with the exception of MUC5B expression which was more than 3-fold higher than for control cells. This study demonstrates that wdNHBE cells are an appropriate ex-vivo model system to investigate the pathogenesis of respiratory viruses.


Subject(s)
Influenza A Virus, H1N1 Subtype/physiology , Influenza, Human/virology , Respiratory Mucosa/cytology , Respiratory Mucosa/virology , Animals , Bronchi/cytology , Bronchi/virology , Cells, Cultured , Chemokines/metabolism , Cytokines/metabolism , Dogs , Host-Pathogen Interactions , Humans , Immunity, Innate , Influenza A Virus, H1N1 Subtype/immunology , Influenza, Human/epidemiology , Intercellular Junctions , Madin Darby Canine Kidney Cells , Models, Biological , Mucin 5AC/metabolism , Pandemics , Virus Cultivation
6.
mBio ; 11(4)2020 08 07.
Article in English | MEDLINE | ID: covidwho-705638

ABSTRACT

Proponents of the use of gain-of-function (GOF) experiments with pathogens with pandemic potential (PPP) have argued that such experiments are necessary because they reveal important facets of pathogenesis and can be performed safely. Opponents of GOF experiments with PPP have argued that the risks outweigh the knowledge gained. The COVID-19 pandemic demonstrates the vulnerability of human societies to a new PPP, while also validating some arguments of both camps, questioning others, and suggesting the need to rethink how we approach this class of experiments.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Gain of Function Mutation , Pneumonia, Viral/virology , Biomedical Research/ethics , Biomedical Research/standards , Bioterrorism , Containment of Biohazards/ethics , Containment of Biohazards/standards , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Humans , Influenza A Virus, H5N1 Subtype/genetics , Influenza, Human/epidemiology , Influenza, Human/virology , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control
7.
Nat Hum Behav ; 4(8): 856-865, 2020 08.
Article in English | MEDLINE | ID: covidwho-690410

ABSTRACT

The first case of COVID-19 was detected in Brazil on 25 February 2020. We report and contextualize epidemiological, demographic and clinical findings for COVID-19 cases during the first 3 months of the epidemic. By 31 May 2020, 514,200 COVID-19 cases, including 29,314 deaths, had been reported in 75.3% (4,196 of 5,570) of municipalities across all five administrative regions of Brazil. The R0 value for Brazil was estimated at 3.1 (95% Bayesian credible interval = 2.4-5.5), with a higher median but overlapping credible intervals compared with some other seriously affected countries. A positive association between higher per-capita income and COVID-19 diagnosis was identified. Furthermore, the severe acute respiratory infection cases with unknown aetiology were associated with lower per-capita income. Co-circulation of six respiratory viruses was detected but at very low levels. These findings provide a comprehensive description of the ongoing COVID-19 epidemic in Brazil and may help to guide subsequent measures to control virus transmission.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections , Disease Transmission, Infectious , Influenza, Human , Pandemics , Pneumonia, Viral , Adult , Aged , Brazil/epidemiology , Child , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/statistics & numerical data , Coinfection/epidemiology , Coronavirus Infections/diagnosis , Coronavirus Infections/drug therapy , Coronavirus Infections/mortality , Coronavirus Infections/therapy , Coronavirus Infections/transmission , Disease Transmission, Infectious/prevention & control , Disease Transmission, Infectious/statistics & numerical data , Female , Hospitalization/statistics & numerical data , Humans , Infant , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/virology , Male , Mortality , Pneumonia, Viral/diagnosis , Pneumonia, Viral/mortality , Pneumonia, Viral/therapy , Pneumonia, Viral/transmission , Socioeconomic Factors
9.
Sci Immunol ; 5(49)2020 07 10.
Article in English | MEDLINE | ID: covidwho-639363

ABSTRACT

Although most SARS-CoV-2-infected individuals experience mild coronavirus disease 2019 (COVID-19), some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly up-regulation of the TNF/IL-1ß-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1ß-driven inflammation, and this was not seen in patients with milder COVID-19. Interestingly, we documented type I IFN-driven inflammatory features in patients with severe influenza as well. Based on this, we propose that the type I IFN response plays a pivotal role in exacerbating inflammation in severe COVID-19.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/immunology , Coronavirus Infections/immunology , Immunophenotyping , Influenza A virus/immunology , Influenza, Human/immunology , Interferon Type I/metabolism , Pneumonia, Viral/immunology , Severity of Illness Index , Adult , Aged , Aged, 80 and over , CD8-Positive T-Lymphocytes/immunology , Cells, Cultured , Coronavirus Infections/blood , Coronavirus Infections/virology , Female , Healthy Volunteers , Humans , Inflammation/immunology , Influenza, Human/blood , Influenza, Human/virology , Interleukin-1beta/metabolism , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/virology , RNA-Seq , Single-Cell Analysis , Transcriptome , Tumor Necrosis Factor-alpha/metabolism
10.
Lancet Infect Dis ; 20(9): e238-e244, 2020 09.
Article in English | MEDLINE | ID: covidwho-622690

ABSTRACT

The objective of this Personal View is to compare transmissibility, hospitalisation, and mortality rates for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with those of other epidemic coronaviruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and pandemic influenza viruses. The basic reproductive rate (R0) for SARS-CoV-2 is estimated to be 2·5 (range 1·8-3·6) compared with 2·0-3·0 for SARS-CoV and the 1918 influenza pandemic, 0·9 for MERS-CoV, and 1·5 for the 2009 influenza pandemic. SARS-CoV-2 causes mild or asymptomatic disease in most cases; however, severe to critical illness occurs in a small proportion of infected individuals, with the highest rate seen in people older than 70 years. The measured case fatality rate varies between countries, probably because of differences in testing strategies. Population-based mortality estimates vary widely across Europe, ranging from zero to high. Numbers from the first affected region in Italy, Lombardy, show an all age mortality rate of 154 per 100 000 population. Differences are most likely due to varying demographic structures, among other factors. However, this new virus has a focal dissemination; therefore, some areas have a higher disease burden and are affected more than others for reasons that are still not understood. Nevertheless, early introduction of strict physical distancing and hygiene measures have proven effective in sharply reducing R0 and associated mortality and could in part explain the geographical differences.


Subject(s)
Betacoronavirus/physiology , Coronavirus Infections/epidemiology , Influenza, Human/epidemiology , Pandemics , Pneumonia, Viral/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Age Factors , Coronavirus Infections/mortality , Coronavirus Infections/transmission , Coronavirus Infections/virology , Epidemics , Hospitalization/statistics & numerical data , Humans , Hygiene , Influenza, Human/mortality , Influenza, Human/transmission , Influenza, Human/virology , Pneumonia, Viral/mortality , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Severe Acute Respiratory Syndrome/mortality , Severe Acute Respiratory Syndrome/transmission , Severe Acute Respiratory Syndrome/virology , Social Distance
11.
Rev Invest Clin ; 72(3): 144-150, 2020.
Article in English | MEDLINE | ID: covidwho-617020

ABSTRACT

The emergence of coronavirus disease 19 pandemic and novel research on the high transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised controversies over the use of face masks to prevent community transmission. Specific regulations need to be fulfilled to use a face mask as part of the personal protective equipment and high quality of evidence supporting its use to prevent respiratory viral infections, including SARS-CoV-2, is lacking. However, its widespread use is becoming a standard practice in some countries and discrepancies between health authorities on their policy have led to controversy. The aim of this review is to provide an outlook on recent research in this matter and areas of opportunity.


Subject(s)
Betacoronavirus , Communicable Disease Control/instrumentation , Coronavirus Infections/prevention & control , Masks , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Aerosols , Air Microbiology , Betacoronavirus/isolation & purification , Communicable Disease Control/legislation & jurisprudence , Communicable Disease Control/methods , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Disease Outbreaks , Disease Transmission, Infectious/prevention & control , Equipment Design , Equipment Failure , Humans , Influenza A Virus, H1N1 Subtype , Influenza, Human/epidemiology , Influenza, Human/virology , Particle Size , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Procedures and Techniques Utilization , Program Evaluation , Respiratory Protective Devices , Severe Acute Respiratory Syndrome/epidemiology , Survival Rate
12.
Trends Biotechnol ; 38(9): 943-947, 2020 09.
Article in English | MEDLINE | ID: covidwho-597298

ABSTRACT

Vaccine solutions rarely reach the public until after an outbreak abates; an Ebola vaccine was approved 5 years after peak outbreak and SARS, MERS, and Zika vaccines are still in clinical development. Despite massive leaps forward in rapid science, other regulatory bottlenecks are hamstringing the global effort for pandemic vaccines.


Subject(s)
Coronavirus Infections/prevention & control , Drug Approval/organization & administration , Hemorrhagic Fever, Ebola/prevention & control , Influenza, Human/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Viral Vaccines/biosynthesis , Betacoronavirus/drug effects , Betacoronavirus/immunology , Betacoronavirus/pathogenicity , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Ebola Vaccines/administration & dosage , Ebola Vaccines/biosynthesis , Ebolavirus/drug effects , Ebolavirus/immunology , Ebolavirus/pathogenicity , Europe/epidemiology , Global Health/trends , Government Regulation , Hemorrhagic Fever, Ebola/epidemiology , Hemorrhagic Fever, Ebola/immunology , Hemorrhagic Fever, Ebola/virology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/administration & dosage , Influenza Vaccines/biosynthesis , Influenza, Human/epidemiology , Influenza, Human/immunology , Influenza, Human/virology , Middle East Respiratory Syndrome Coronavirus/drug effects , Middle East Respiratory Syndrome Coronavirus/immunology , Middle East Respiratory Syndrome Coronavirus/pathogenicity , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , SARS Virus/drug effects , SARS Virus/immunology , SARS Virus/pathogenicity , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/immunology , Severe Acute Respiratory Syndrome/prevention & control , Severe Acute Respiratory Syndrome/virology , United States/epidemiology , Viral Vaccines/administration & dosage , Zika Virus/drug effects , Zika Virus/immunology , Zika Virus/pathogenicity , Zika Virus Infection/epidemiology , Zika Virus Infection/immunology , Zika Virus Infection/prevention & control , Zika Virus Infection/virology
13.
J Clin Virol ; 129: 104470, 2020 08.
Article in English | MEDLINE | ID: covidwho-478301

ABSTRACT

In Italy, the first SARS-CoV-2 infections were diagnosed in Rome, Lazio region, at the end of January 2020, but sustained transmission occurred later, since the end of February. From 1 February to 12 April 2020, 17,164 nasopharyngeal swabs were tested by real time PCR for the presence of SARS-CoV-2 at the Laboratory of Virology of National Institute for Infectious Diseases "Lazzaro Spallanzani" (INMI) in Rome. In the same period, coincident with the winter peak of influenza and other respiratory illnesses, 847 samples were analyzed by multiplex PCR assay for the presence of common respiratory pathogens. In our study the time trend of SARS-CoV-2 and that of other respiratory pathogens in the same observation period were analysed. Overall, results obtained suggest that the spread of the pandemic SARS-CoV-2 virus did not substantially affect the time trend of other respiratory infections in our region, highlighting no significant difference in rates of SARS-CoV-2 infection in patients with or without other respiratory pathogens. Therefore, in the present scenario of COVID-19 pandemic, differential diagnosis resulting positive for common respiratory pathogen(s) should not exclude testing of SARS-CoV-2.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus/isolation & purification , Influenza, Human/epidemiology , Nasopharynx/virology , Orthomyxoviridae/isolation & purification , Respiratory Tract Infections/epidemiology , Coronavirus/classification , Coronavirus Infections/virology , Humans , Influenza, Human/virology , Multiplex Polymerase Chain Reaction , Orthomyxoviridae/classification , Respiratory Tract Infections/virology , Rome/epidemiology
14.
HLA ; 96(3): 277-298, 2020 09.
Article in English | MEDLINE | ID: covidwho-437381

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 , 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 , Severe Acute Respiratory Syndrome/immunology , Severe Acute Respiratory Syndrome/virology , Viral Proteins/genetics , Viral Proteins/immunology
15.
Pediatr Infect Dis J ; 39(8): 653-657, 2020 08.
Article in English | MEDLINE | ID: covidwho-388714

ABSTRACT

BACKGROUND: Human coronaviruses (HCoVs) have been recognized as causative agents of respiratory tract infections.Our aim was to describe HCoV infections in hospitalized children in a prospective surveillance study for 14 years and compare them with other respiratory viruses. METHODS: As a part of an ongoing prospective study to identify the etiology of viral respiratory infections in Spain, we performed the analysis of HCoV infections in children hospitalized in a secondary hospital in Madrid, between October 2005 and June 2018. Clinical data of HCoV patients were compared with those infected by rhinovirus, respiratory syncytial virus and influenza. RESULTS: The study population consisted of 5131 hospitalizations for respiratory causes in children. A total of 3901 cases (75.9%) had a positive viral identification and 205 cases (4.1%) were positive for HCoV. Only 41 cases (20%) of HCoV infection were detected as single infections. Episodes of recurrent wheezing were the most common diagnosis, and 112 children (54%) had hypoxia. Clinical data in HCoV cases were similar to those associated with rhinovirus; however, patients with HCoV were younger. Other viruses were associated with hypoxia more frequently than cases with HCoV; high fever was more common in influenza infections and bronchiolitis in respiratory syncytial virus group. Although a slight peak of circulation appears mostly in winter, HCoV has been detected throughout the year as well. CONCLUSIONS: HCoV infections represent a small fraction of respiratory infections that require hospitalization in children and their characteristics do not differ greatly from other respiratory viral infections.


Subject(s)
Bronchiolitis, Viral/epidemiology , Coronavirus Infections/epidemiology , Hospitalization , Pneumonia, Viral/epidemiology , Adolescent , Age Distribution , Betacoronavirus , Bronchiolitis, Viral/physiopathology , Bronchiolitis, Viral/virology , Child , Child, Preschool , Coronavirus Infections/physiopathology , Coronavirus Infections/virology , Coronavirus NL63, Human , Coronavirus OC43, Human , Female , Fever/physiopathology , Humans , Hypoxia/physiopathology , Infant , Infant, Newborn , Influenza, Human/epidemiology , Influenza, Human/physiopathology , Influenza, Human/virology , Male , Middle East Respiratory Syndrome Coronavirus , Pandemics , Picornaviridae Infections/epidemiology , Picornaviridae Infections/physiopathology , Picornaviridae Infections/virology , Pneumonia, Viral/physiopathology , Pneumonia, Viral/virology , Prospective Studies , Respiratory Sounds/physiopathology , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/physiopathology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/physiopathology , Respiratory Tract Infections/virology , Rhinovirus , SARS Virus , Seasons , Severe Acute Respiratory Syndrome , Severity of Illness Index , Spain/epidemiology
16.
BMC Infect Dis ; 20(1): 369, 2020 May 24.
Article in English | MEDLINE | ID: covidwho-343360

ABSTRACT

BACKGROUND: Previous studies have proven that the closure of live poultry markets (LPMs) was an effective intervention to reduce human risk of avian influenza A (H7N9) infection, but evidence is limited on the impact of scale and duration of LPMs closure on the transmission of H7N9. METHOD: Five cities (i.e., Shanghai, Suzhou, Shenzhen, Guangzhou and Hangzhou) with the largest number of H7N9 cases in mainland China from 2013 to 2017 were selected in this study. Data on laboratory-confirmed H7N9 human cases in those five cities were obtained from the Chinese National Influenza Centre. The detailed information of LPMs closure (i.e., area and duration) was obtained from the Ministry of Agriculture. We used a generalized linear model with a Poisson link to estimate the effect of LPMs closure, reported as relative risk reduction (RRR). We used classification and regression trees (CARTs) model to select and quantify the dominant factor of H7N9 infection. RESULTS: All five cities implemented the LPMs closure, and the risk of H7N9 infection decreased significantly after LPMs closure with RRR ranging from 0.80 to 0.93. Respectively, a long-term LPMs closure for 10-13 weeks elicited a sustained and highly significant risk reduction of H7N9 infection (RRR = 0.98). Short-time LPMs closure with 2 weeks in every epidemic did not reduce the risk of H7N9 infection (p > 0.05). Partially closed LPMs in some suburbs contributed only 35% for reduction rate (RRR = 0.35). Shenzhen implemented partial closure for first 3 epidemics (p > 0.05) and all closure in the latest 2 epidemic waves (RRR = 0.64). CONCLUSION: Our findings suggest that LPMs all closure in whole city can be a highly effective measure comparing with partial closure (i.e. only urban closure, suburb and rural remain open). Extend the duration of closure and consider permanently closing the LPMs will help improve the control effect. The effect of LPMs closure seems greater than that of meteorology on H7N9 transmission.


Subject(s)
Epidemics/prevention & control , Influenza A Virus, H7N9 Subtype , Influenza in Birds/epidemiology , Influenza in Birds/transmission , Influenza, Human/epidemiology , Poultry/virology , Animals , China/epidemiology , Cities/epidemiology , Humans , Humidity , Incidence , Influenza in Birds/virology , Influenza, Human/virology , Linear Models , Poisson Distribution , Risk Factors , Temperature , Urban Population
18.
PLoS One ; 15(5): e0233117, 2020.
Article in English | MEDLINE | ID: covidwho-244945

ABSTRACT

Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017-2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2-3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7-22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.


Subject(s)
Pneumonia/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/virology , Adolescent , Adult , Coronavirus/isolation & purification , Enterovirus/isolation & purification , Female , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/epidemiology , Influenza, Human/virology , Male , Middle Aged , Military Facilities/statistics & numerical data , Pneumonia/virology , Vietnam/epidemiology , Young Adult
19.
NTM ; 28(2): 211-217, 2020 06.
Article in German | MEDLINE | ID: covidwho-232269

ABSTRACT

This paper is part of Forum COVID-19: Perspectives in the Humanities and Social Sciences. The Spanish Flu 1918-1920 caused between 50 and 100 million deaths. Despite this, West German officials ignored the pandemics of 1957/1958 and 1968-1970. Patient perseverance seems to be an appropriate label for the lack of any action. The appearance of new viruses had a massive impact on the discourse concerning pandemics: "patient perseverance" became "omnipresent prevention." The actual measures against SARS-CoV­2 exceed the "omnipresent prevention" used during the 2009 swine flu pandemic by far.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Influenza, Human/history , Pandemics/history , Pneumonia, Viral/epidemiology , Germany, West , History, 20th Century , History, 21st Century , Humans , Influenza A Virus, H5N1 Subtype , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Influenza, Human/virology , Vaccination/history
20.
NTM ; 28(2): 211-217, 2020 06.
Article in German | MEDLINE | ID: covidwho-197842

ABSTRACT

This paper is part of Forum COVID-19: Perspectives in the Humanities and Social Sciences. The Spanish Flu 1918-1920 caused between 50 and 100 million deaths. Despite this, West German officials ignored the pandemics of 1957/1958 and 1968-1970. Patient perseverance seems to be an appropriate label for the lack of any action. The appearance of new viruses had a massive impact on the discourse concerning pandemics: "patient perseverance" became "omnipresent prevention." The actual measures against SARS-CoV­2 exceed the "omnipresent prevention" used during the 2009 swine flu pandemic by far.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Influenza, Human/history , Pandemics/history , Pneumonia, Viral/epidemiology , Germany, West , History, 20th Century , History, 21st Century , Humans , Influenza A Virus, H5N1 Subtype , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Influenza, Human/virology , Vaccination/history
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