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

Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In...

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Published in:PloS one 2017-06, Vol.12 (6), p.e0178926-e0178926
Main Authors: Piralla, Antonio, Rovida, Francesca, Girello, Alessia, Premoli, Marta, Mojoli, Francesco, Belliato, Mirko, Braschi, Antonio, Iotti, Giorgio, Pariani, Elena, Bubba, Laura, Zanetti, Alessandro R, Baldanti, Fausto
Format: Article
Language:English
Subjects:
Anesthesiology
Base Sequence
Biology and Life Sciences
Causes of
Codons
Diagnosis
Diagnostic systems
Disease prevention
Dynamics
Evolution
Genetic aspects
High-Throughput Nucleotide Sequencing - methods
Hospitalization
Hospitals
Humans
Infections
Influenza
Influenza A
Influenza A Virus, H1N1 Subtype - genetics
Influenza B
Influenza viruses
Intensive care
Intensive Care Units
Laboratories
Longitudinal Studies
Medicine and Health Sciences
Microbiology
Mutation
Pain
Pandemics
Patients
Pediatrics
Phylogeny
Physiological aspects
Pneumonia
Polymorphism, Genetic
Replication
Research and analysis methods
Respiratory System - virology
Respiratory tract
Respiratory tract infections
Respiratory Tract Infections - epidemiology
Respiratory Tract Infections - virology
Seasons
Sequences
Spring (season)
Surgery
Surveillance
Viral infections
Viral Load
Virology
Viruses
Winter
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creator Piralla, Antonio
Rovida, Francesca
Girello, Alessia
Premoli, Marta
Mojoli, Francesco
Belliato, Mirko
Braschi, Antonio
Iotti, Giorgio
Pariani, Elena
Bubba, Laura
Zanetti, Alessandro R
Baldanti, Fausto
description Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014-2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p
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It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014-2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p&lt;0.05). 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Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Piralla, Antonio</au><au>Rovida, Francesca</au><au>Girello, Alessia</au><au>Premoli, Marta</au><au>Mojoli, Francesco</au><au>Belliato, Mirko</au><au>Braschi, Antonio</au><au>Iotti, Giorgio</au><au>Pariani, Elena</au><au>Bubba, Laura</au><au>Zanetti, Alessandro R</au><au>Baldanti, Fausto</au><au>Schildgen, Oliver</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-06-07</date><risdate>2017</risdate><volume>12</volume><issue>6</issue><spage>e0178926</spage><epage>e0178926</epage><pages>e0178926-e0178926</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014-2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p&lt;0.05). Overall, a greater number of H1N1pdm09 virus variants were observed using next generation sequencing on partial HA sequences (codons 180-286) in clinical samples from the LRT as compared to URT. In addition, 222G/N/A mutations were observed in 30% of LRT samples from ICU patients. Finally, intra-host evolution analysis showed the presence of different dynamics of viral population in LRT of patients hospitalized in ICU with a severe influenza infection.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28591230</pmid><doi>10.1371/journal.pone.0178926</doi><tpages>e0178926</tpages><orcidid>https://orcid.org/0000-0002-3358-8969</orcidid><oa>free_for_read</oa></addata></record>
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subjects Anesthesiology
Base Sequence
Biology and Life Sciences
Causes of
Codons
Diagnosis
Diagnostic systems
Disease prevention
Dynamics
Evolution
Genetic aspects
High-Throughput Nucleotide Sequencing - methods
Hospitalization
Hospitals
Humans
Infections
Influenza
Influenza A
Influenza A Virus, H1N1 Subtype - genetics
Influenza B
Influenza viruses
Intensive care
Intensive Care Units
Laboratories
Longitudinal Studies
Medicine and Health Sciences
Microbiology
Mutation
Pain
Pandemics
Patients
Pediatrics
Phylogeny
Physiological aspects
Pneumonia
Polymorphism, Genetic
Replication
Research and analysis methods
Respiratory System - virology
Respiratory tract
Respiratory tract infections
Respiratory Tract Infections - epidemiology
Respiratory Tract Infections - virology
Seasons
Sequences
Spring (season)
Surgery
Surveillance
Viral infections
Viral Load
Virology
Viruses
Winter
title 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
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