{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T04:28:16Z","timestamp":1776400096403,"version":"3.51.2"},"reference-count":36,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,1,23]],"date-time":"2025-01-23T00:00:00Z","timestamp":1737590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"WISE Program (Doctoral Program for World-leading Innovative &amp; Smart Education) of Ministry of Education, Culture, Sports, Science and Technology","award":["JP223fa627004"],"award-info":[{"award-number":["JP223fa627004"]}]},{"name":"Japan Agency for Medical Research and Development (AMED)","award":["JP223fa627004"],"award-info":[{"award-number":["JP223fa627004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Numerous studies have documented the evidence of virus\u2013virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012\/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A\/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV\u2013RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups\u2014elderly individuals (&gt;64 years old) and school-aged children (6\u201318 years old)\u2014were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09\u20133.06) and 1.38 (95% CI: 1.01\u20131.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available in this study may not be exhaustive, warranting further, more in-depth investigations to conclusively determine the impact of virus\u2013virus interactions on influenza virus genetic diversity.<\/jats:p>","DOI":"10.3390\/v17020152","type":"journal-article","created":{"date-parts":[[2025,1,23]],"date-time":"2025-01-23T09:01:13Z","timestamp":1737622873000},"page":"152","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1052-2219","authenticated-orcid":false,"given":"Su Myat","family":"Han","sequence":"first","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6592-8035","authenticated-orcid":false,"given":"Yoshiano","family":"Kubo","sequence":"additional","affiliation":[{"name":"Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8520, Japan"},{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8102, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexis","family":"Robert","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"},{"name":"Infectious Disease Epidemiology and Dynamics, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8102, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Baguelin","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"},{"name":"MRC Centre for Global Infectious Disease Analysis, and the Abdul Latif Jameel Institute for Disease, Imperial College London, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koya","family":"Ariyoshi","sequence":"additional","affiliation":[{"name":"School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8102, Japan"},{"name":"Infectious Disease Epidemiology and Dynamics, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8102, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41572-018-0002-y","article-title":"Influenza","volume":"4","author":"Krammer","year":"2018","journal-title":"Nat. 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