{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T09:41:11Z","timestamp":1792489271246,"version":"4.5.0"},"reference-count":33,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T00:00:00Z","timestamp":1792454400000},"content-version":"vor","delay-in-days":19,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>In Cameroon, national influenza surveillance identifies influenza\u2010positive cases, but the causes of non\u2010influenza ARIs remain poorly characterized. We applied metagenomic next\u2010generation sequencing (mNGS) to investigate respiratory pathogens in influenza\u2010negative nasopharyngeal swabs collected through national influenza surveillance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed 199 influenza\u2010negative nasopharyngeal swabs collected between September and December 2023 from patients with influenza\u2010like 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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\u2010respiratory 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\u2010infections were identified. Several bacterial and fungal genera were also detected.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our study shows that mNGS provides a powerful, unbiased approach for characterizing respiratory pathogens in Cameroon, revealing substantial viral diversity among influenza\u2010negative 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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/irv.70336","type":"journal-article","created":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T09:05:53Z","timestamp":1792487153000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Use of Metagenomic Next\u2010Generation Sequencing to Investigate Respiratory Pathogens in Influenza\u2010Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6706-3012","authenticated-orcid":false,"given":"Modiyinji Abdou","family":"Fatawou","sequence":"first","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cappy","family":"Pierre","sequence":"additional","affiliation":[{"name":"Plateforme GenoBioMICS, Laboratoire de Virologie H\u00f4pitaux Universitaires Henri Mondor  Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9394-9861","authenticated-orcid":false,"given":"Ly","family":"Arnaud","sequence":"additional","affiliation":[{"name":"Plateforme GenoBioMICS, Laboratoire de Virologie H\u00f4pitaux Universitaires Henri Mondor  Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheval","family":"Justine","sequence":"additional","affiliation":[{"name":"Plateforme GenoBioMICS, Laboratoire de Virologie H\u00f4pitaux Universitaires Henri Mondor  Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6691-2884","authenticated-orcid":false,"given":"Moumbeket\u2010Yifomnjou Moise","family":"Henri","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5220-3309","authenticated-orcid":false,"given":"Tsafack Desmon","family":"Toutou","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Touoyem","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Njankouo","family":"Ripa","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monamele Chavely","family":"Gwladys","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3112-6370","authenticated-orcid":false,"given":"Njouom","family":"Richard","sequence":"additional","affiliation":[{"name":"Virology Unit Centre Pasteur du Cameroun  Yaound\u00e9 Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,20]]},"reference":[{"issue":"12","key":"e_1_2_12_2_1","doi-asserted-by":"crossref","DOI":"10.3390\/v17121554","article-title":"Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics\u2010A Review","volume":"17","author":"Dos Santos M. 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