Tropism of avian influenza A (H5N1) in the upper and lower respiratory tract

Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures.

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Lower respiratory tract hemorrhage associated with 2009 pandemic influenza A (H1N1) virus infection

Influenza and Other Respiratory Viruses ◽

10.1111/irv.12026 ◽

2012 ◽

Vol 7 (5) ◽

pp. 761-765 ◽

Cited By ~ 8

Author(s):

Erin D. Kennedy ◽

Monika Roy ◽

Jeffrey Norris ◽

Alicia M. Fry ◽

Mitul Kanzaria ◽

...

Keyword(s):

Virus Infection ◽

Respiratory Tract ◽

Pandemic Influenza ◽

Lower Respiratory Tract ◽

Influenza A ◽

H1n1 Virus ◽

Influenza A H1n1 ◽

H1n1 Virus Infection

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Exogenous IFN-alpha Administration Reduces Influenza A Virus Replication in the Lower Respiratory Tract of Rhesus Macaques

PLoS ONE ◽

10.1371/journal.pone.0029255 ◽

2011 ◽

Vol 6 (12) ◽

pp. e29255 ◽

Cited By ~ 14

Author(s):

Shannon R. Matzinger ◽

Timothy D. Carroll ◽

Linda Fritts ◽

Michael B. McChesney ◽

Christopher J. Miller

Keyword(s):

Respiratory Tract ◽

Influenza A Virus ◽

Virus Replication ◽

Lower Respiratory Tract ◽

Influenza A ◽

Rhesus Macaques ◽

Ifn Alpha

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Frequency of respiratory virus infections and next-generation analysis of influenza A/H1N1pdm09 dynamics in the lower respiratory tract of patients admitted to the ICU

PLoS ONE ◽

10.1371/journal.pone.0178926 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0178926 ◽

Cited By ~ 6

Author(s):

Antonio Piralla ◽

Francesca Rovida ◽

Alessia Girello ◽

Marta Premoli ◽

Francesco Mojoli ◽

...

Keyword(s):

Respiratory Tract ◽

Lower Respiratory Tract ◽

Influenza A ◽

Respiratory Virus ◽

Next Generation ◽

Virus Infections ◽

Respiratory Virus Infections

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Segregation of Virulent Influenza A(H1N1) Variants in the Lower Respiratory Tract of Critically Ill Patients during the 2010–2011 Seasonal Epidemic

PLoS ONE ◽

10.1371/journal.pone.0028332 ◽

2011 ◽

Vol 6 (12) ◽

pp. e28332 ◽

Cited By ~ 26

Author(s):

Antonio Piralla ◽

Elena Pariani ◽

Francesca Rovida ◽

Giulia Campanini ◽

Alba Muzzi ◽

...

Keyword(s):

Respiratory Tract ◽

Critically Ill ◽

Critically Ill Patients ◽

Lower Respiratory Tract ◽

Influenza A ◽

Influenza A H1n1 ◽

Seasonal Epidemic

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Ozonated Air Therapy for the Treatment of Upper and Lower Respiratory Tract Infections as a Potential Therapy for Prevention and Treatment of Covid 19 Infection

Global Journal of Medical Research ◽

10.34257/gjmrfvol20is6pg39 ◽

2020 ◽

pp. 39-45

Author(s):

Sagar A. Jawale

Keyword(s):

Respiratory Tract ◽

Lower Respiratory Tract ◽

Influenza A ◽

Respiratory Tract Infections ◽

Respiratory Infections ◽

Inhalation Therapy ◽

Lower Respiratory Tract Infections ◽

Influenza A H1n1 ◽

Novel Coronavirus ◽

Tract Infections

Introduction: In India and worldwide, there are millions of cases of acute respiratory infections annually killing hundreds of thousand people. It also has billions of dollars of losses worldwide. There are frequent outbreaks of deadly infections such as severe acute respiratory syndrome (SARS) in 2003, caused by a novel coronavirus (SARS-CoV), the novel swine-origin influenza A (H1N1) virus in Mexico in March 2009, Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 and the current pandemic with Novel CoronaVirus -Covid19. I did my research to find a common effective, safe, and cheap therapynamed as Ozonated air inhalation therapy (OAIT) for respiratory infections. Materials and methods: In the last one year, I treated 21 patients (group A) with upper and lower respiratory tract infections (URTI and LRTI) with 0.1 ppm Ozonated air inhalation therapy (OAIT). OAIT was given as a monotherapy. In the same time period, 36 patients (group B) were given conventional treatment in the form of antibiotics, anti-histaminic and analgesics kept as control.

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Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens

Journal of Clinical Microbiology ◽

10.1128/jcm.00787-18 ◽

2018 ◽

Vol 56 (8) ◽

Cited By ~ 10

Author(s):

Soya S. Sam ◽

Angela M. Caliendo ◽

Jessica Ingersoll ◽

Deborah Abdul-Ali ◽

Charles E. Hill ◽

...

Keyword(s):

Respiratory Tract ◽

Positive Result ◽

Lower Respiratory Tract ◽

Influenza A ◽

Performance Characteristics ◽

Influenza B Virus ◽

Influenza B ◽

Respiratory Pathogens ◽

Percent Agreement ◽

Syncytial Virus

ABSTRACT Accurate and rapid diagnosis is needed for timely intervention and clinical management of acute respiratory infections. This study evaluated performance characteristics of the Panther Fusion assay for the detection of influenza A virus (Flu A), influenza B virus (Flu B), respiratory syncytial virus (RSV), parainfluenza viruses 1 to 3 (Para 1 to 3), human metapneumovirus (hMPV), rhinovirus (RV), and adenovirus (Adeno) targets in comparison to those of the eSensor and Lyra assays using 395 nasopharyngeal (NP) and 104 lower respiratory tract (LRT) specimens. Based on the consensus positive result established (positive result in 2 of the 3 assays), the NP specimens for the Fusion and eSensor assays had 100% positive percent agreement (PPA) for all the analytes and the Lyra assays had 100% PPA for Flu A and Adeno analytes. A 100% negative percent agreement (NPA) was observed for all the Lyra analytes, whereas those for the Fusion targets ranged from 98.4 to 100% and those for the eSensor ranged from 99.4 to 100% for all the analytes except RV. For the LRT specimens, Fusion had 100% PPA and 100% NPA for all the targets except hMPV. There was a 100% PPA for eSensor analytes; the NPA ranged from 98 to 100%, except for RV. For the Lyra assays, the PPA ranged between 50 and 100%, while the NPA was 100% for all the targets except Adeno. The Fusion assay performed similarly to the eSensor assay for majority of the targets tested and provides laboratories with a fully automated random-access system to test for a broad array of viral respiratory pathogens.

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Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community

10.1101/2021.10.27.21265424 ◽

2021 ◽

Author(s):

Nicolae Sapoval ◽

P. Jacob Bueno de Mesquita ◽

Yunxi Liu ◽

Roger Wang ◽

Tian Rui Liu ◽

...

Keyword(s):

Influenza Virus ◽

Respiratory Tract ◽

Lower Respiratory Tract ◽

Influenza A ◽

Nucleotide Polymorphisms ◽

Single Patient ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Site Specific ◽

College Community

Motivation. Influenza is a rapidly mutating RNA virus responsible for annual epidemics causing substantial morbidity, mortality, and economic loss. Characterizing influenza virus mutational diversity and evolutionary processes within and between human hosts can provide tools to help track and understand transmission events. In this study we investigated possible differences between the intrahost genomic content of influenza virus in upper respiratory swabs and exhaled aerosols thought to be enriched for virus from the lower respiratory tract. Results. We examined the sequences of specimens collected from influenza A virus (IAV) infected college community members from December 2012 through May 2013. We analyzed four types of IAV samples μm aerosols (N=38), coarse >5μm aerosols (N=27), nasopharyngeal (N=53), and oropharyngeal swabs (N=47)) collected from 42 study participants with 60 sampling instances. Eighteen (42.9%) participants had data from four sample types (nasopharyngeal swab, oropharyngeal swab, coarse aerosol, fine aerosol) included in the analysis, 10 (23.8%) had data from 3 sample types, 10 (23.8%) had data from 2 sample types, and 4 (9.5%) had data from one type of sample included in the analysis. We found that 481 (53.3%) consensus single nucleotide polymorphisms are shared by all sample types and 600 (66.5%) are shared by at least three different sample types. We observed that within a single patient consensus and non-consensus single nucleotide variants are shared across all sample types. Finally, we inferred a phylogenetic tree using consensus sequences and found that samples derived from a single patient are monophyletic. Conclusions. Single nucleotide polymorphisms did not differentiate between samples with varying origin along the respiratory tree. We found that signatures of variation in non-consensus intrahost single nucleotide variants are host and sample, but not site-specific. We conclude that the genomic information available does not allow us to discern a transmission route. Future investigation into whether any site-specific mutational signatures emerge over a longer period of infection, for example in immunocompromised hosts, can be interesting from the virus evolution perspective.

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