Influenza and other respiratory viruses
Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance
By Fatawou MA, Pierre C, Arnaud L and 7 others.
Abstract
Background
In Cameroon, national influenza surveillance identifies influenza-positive cases, but the causes of non-influenza ARIs remain poorly characterized. We applied metagenomic next-generation sequencing (mNGS) to investigate respiratory pathogens in influenza-negative nasopharyngeal swabs collected through national influenza surveillance.
Methods
We analyzed 199 influenza-negative nasopharyngeal swabs collected between September and December 2023 from patients with influenza-like illness or severe acute respiratory infection. Mixed DNA/RNA libraries were prepared and sequenced on an Illumina NovaSeq platform. Taxonomic classification was performed using METAMIC (v2.0) and SPAdes (V3.15.5) bioinformatic pipelines.