Use of metagenomic next-generation sequencing to investigate respiratory pathogens in nasopharyngeal swabs from children tested negative as part of influenza surveillance in Cameroon

The Centre Pasteur du Cameroun (CPC) is the national influenza centre in Cameroon and has been running a national influenza surveillance programme since 2007. Each year, approximately 1,000 samples are collected from Cameroonians presenting with influenza-like illness (ILI) or severe acute respiratory infection (SARI), with fewer than 30% testing positive for the influenza virus. However, no etiological research is carried out on patients with negative results, representing a significant shortcoming in the control and management of infectious diseases in our country. This study investigated influenza-negative samples using shotgun metagenomics to determine which viruses co-circulate with influenza viruses in Cameroon.