Analysis of influenza a genomes and bacterial microbiota in upper respiratory tracts of influenza patients

Abstract

Seasonal influenza is a contagious respiratory illness caused by influenza viruses that infect the upper respiratory tract (URT) of humans and represent a major burden for public health. Furthermore, the URT is colonized by a diverse microbial community which is a key factor protective from pathogens and may directly or indirectly affect viral infection. Therefore, the first aim of this study focuses on influenza A genome characterization and mutation analysis based on NGS technology. The phylogenetic analysis based on the deduced amino acid sequences revealed that the recommended vaccine (A/H1N1) strain might be less effective, whereas the recommended vaccine (A/H3N2) was more effective against the circulating influenza viruses in Thailand during 2017-2018. In addition, several nonsynonymous mutations occurred across eight segmented genes of both viruses, particularly in HA and NA genes. Indeed, nucleotide diversity analysis was observed negative selection in the PB1, PA, HA, and NA genes of A/H1N1 viruses. Then, the second aim of this study is to compare the bacterial microbiota profile in the URT with influenza (Flu A or Flu B groups) and non-influenza (COVID-19 or Non-Flu & COVID-19) patients by 16S rDNA sequencing. The Shannon diversity for the influenza group was significantly lower than Non-Flu & COVID-19 group. The beta diversity revealed that microbial compositions were significantly different among groups. The relative abundance showed that the family of Enterobacteriaceae was increased the in influenza group, whereas Streptococcus, Prevotella, Veillonella, and Fusobacterium were predominated in Non-Flu & COVID-19. In summary, our data provide fundamental knowledge to investigate the association host-microbe interaction that might be useful for predicting health status and applied for microbiome engineering to enhance immunity system to future infections.