Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance.
- 1Virology Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon.
- 2Plateforme GenoBioMICS, Laboratoire de Virologie, Hôpitaux Universitaires Henri Mondor, Créteil, France.
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.Results
Viral sequences were detected in 120/199 samples (60.3%, 95% CI: 53.5%, 67.1%), representing 15 viral species. The most frequent viruses were rhinovirus (43/131), respiratory syncytial virus (33/131), influenza virus, parainfluenza virus and enterovirus. Two non-respiratory viruses (Rotavirus and Papillomavirus) were also detected. Sequencing generated an average of 26.1 million reads per sample, with a mean depth of 870.3 per sample and an average genomic coverage of 82%. Eleven viral co-infections were identified. Several bacterial and fungal genera were also detected.Conclusion
Our study shows that mNGS provides a powerful, unbiased approach for characterizing respiratory pathogens in Cameroon, revealing substantial viral diversity among influenza-negative ARI cases. However, cost and bioinformatics capacity remain major barriers to routine implementation. Longitudinal studies and clinical correlation are needed to strengthen interpretation and guide integration of mNGS into national surveillance.
Related
- Metagenomic next-generation sequencing for the detection of viruses from respiratory samples: a systematized review on current methods and future directions.
- Comparative evaluation of metagenomic and targeted next-generation sequencing for pathogen detection in bronchoalveolar lavage fluid from patients with lower respiratory tract infections: a retrospective cohort study.
- A nationwide study of pathogens in hospitalized patients with lower respiratory tract infections by metagenomic next-generation sequencing
- Reporting and interpretation of respiratory metagenomic results in clinical practice: a systematic review and consensus guidelines from the UK NHS Respiratory Metagenomics Network
- Case Report: Necrotizing fasciitis caused by Vibrio vulnificus without recalled seafood or seawater exposure diagnosed by metagenomic next-generation sequencing
BibTeX
@article{fatawou2026metagenomic,
title = {{Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance.}},
author = {Modiyinji Abdou Fatawou and Cappy Pierre and Ly Arnaud and Cheval Justine and Moumbeket-Yifomnjou Moise Henri and Tsafack Desmon Toutou and Touoyem Ibrahim and Njankouo Ripa and Monamele Chavely Gwladys and Njouom Richard},
journal = {Influenza and other respiratory viruses},
year = {2026},
month = oct,
doi = {10.1111/irv.70336},
url = {https://europepmc.org/article/MED/42899356},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance.
AU - Modiyinji Abdou Fatawou
AU - Cappy Pierre
AU - Ly Arnaud
AU - Cheval Justine
AU - Moumbeket-Yifomnjou Moise Henri
AU - Tsafack Desmon Toutou
AU - Touoyem Ibrahim
AU - Njankouo Ripa
AU - Monamele Chavely Gwladys
AU - Njouom Richard
PY - 2026
DA - 2026/10/01
JO - Influenza and other respiratory viruses
DO - 10.1111/irv.70336
UR - https://europepmc.org/article/MED/42899356
AB - 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.Results Viral sequences were detected in 120/199 samples (60.3%, 95% CI: 53.5%, 67.1%), representing 15 viral species. The most frequent viruses were rhinovirus (43/131), respiratory syncytial virus (33/131), influenza virus, parainfluenza virus and enterovirus. Two non-respiratory viruses (Rotavirus and Papillomavirus) were also detected. Sequencing generated an average of 26.1 million reads per sample, with a mean depth of 870.3 per sample and an average genomic coverage of 82%. Eleven viral co-infections were identified. Several bacterial and fungal genera were also detected.Conclusion Our study shows that mNGS provides a powerful, unbiased approach for characterizing respiratory pathogens in Cameroon, revealing substantial viral diversity among influenza-negative ARI cases. However, cost and bioinformatics capacity remain major barriers to routine implementation. Longitudinal studies and clinical correlation are needed to strengthen interpretation and guide integration of mNGS into national surveillance.
SN - 1750-2640
SN - 1750-2659
ER -