DOI: 10.1101/509901Jan 2, 2019Paper

Disparate evolution of virus populations in upper and lower airways of mechanically ventilated patients

BioRxiv : the Preprint Server for Biology
Bjorn F. KoelMenno D. de Jong


In routine surveillance and diagnostic testing, influenza virus samples are typically collected only from the upper respiratory tract (URT) due to the invasiveness of sample collection from the lower airways. Very little is known about virus variation in the lower respiratory tract (LRT) and it remains unclear if the virus populations at different sites of the human airways may develop to have divergent genetic signatures. We used deep sequencing of serially obtained matched nasopharyngeal swabs and endotracheal aspirates from four mechanically ventilated patients with influenza A/H3N2 infections. A physical barrier separating both compartments of the respiratory tract introduced as part of the medical procedures enabled us to track and compare the genetic composition of the virus populations during isolated evolution in the same host. Amino acid variants reaching majority proportions emerged during the course of infection in both nasopharyngeal swabs and endotracheal aspirates, and amino acid variation was observed in all influenza virus proteins. Genetic variation of the virus populations differed between the URT and LRT and variants were frequently uniquely present in either URT or LRT virus populations of a patient. These o...Continue Reading

Related Concepts

Biological Evolution
Influenza A virus
Respiratory Tract Diseases
Medical Procedure
Infection Surveillance
Diagnostic Procedure
Upper Respiratory Tract

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