Upper respiratory tract microbiome of infants infected with Respiratory Syncytial Virus (RSV) in USA. human lung metagenome

Infants at risk for Respiratory Syncytial Virus (RSV) infection and subsequent asthma have been frequently found to have bacterial super-infections and there are high incidences of pulmonary bacterial coinfection in children with severe respiratory syncytial virus (RSV) bronchiolitis. As part of another project (PRJNA225816), that is focused to sequence full genome, we are sequencing around 100 genomes from a patient cohort infected with RSV from the USA. This project aims to complement the results from that sequencing project, by taking advantage of the same nasopharyngeal samples to study the effects of RSV infection on the lungs and upper respiratory tract microbiome. As part of this project, we will characterize the microbial communities of the nasopharyngeal wash by sequencing 16S of the bacterial community. Sequencing the microbiome will address if there are changes in microbial dynamics in patients with high disease severity compared to those with low disease severity and allow us to evaluate the impact of RSV infection on the microbiome structure.