{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:11:21Z","timestamp":1792059081070,"version":"4.4.0"},"reference-count":42,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,7,25]],"date-time":"2025-07-25T00:00:00Z","timestamp":1753401600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The COVID-19 pandemic significantly impacted the circulation, seasonality, and disease burden of viral respiratory infections. This study aimed to evaluate the impact of SARS-CoV-2 on the frequency of viral respiratory infections at a teaching hospital in Southern Italy by comparing data from before, during, and after the COVID-19 pandemic and by investigating how the emergence of SARS-CoV-2 affected the circulation and seasonality of other respiratory viruses. This retrospective and prospective study was performed on de-identified nasopharyngeal specimens classified as pre-COVID-19 (before 15 March 2020), during-COVID-19 (from 16 March 2020 to 5 May 2023), and post-COVID-19 (from 6 May 2023 to 31 December 2024). Overall, 790 out of 3930 (20%) patient samples tested positive for at least one respiratory virus. The mean age of patients was 60 \u00b1 19 years, with significant positivity rates observed in the 65\u201398 age group (p \u2264 0.05) across all periods. In the pre-COVID-19 period, the most prevalent virus was influenza A (47.5%, 47\/99), followed by the human rhinovirus (19.2%, 19\/99). During the COVID-19 pandemic, SARS-CoV-2 was the most prevalent (64.9%, 290\/447), before decreasing to 38% (92\/244) after the pandemic, while influenza A\u2019s positivity prevalence increased to 14.3% (35\/244). Rhinovirus\/enterovirus remained relatively stable throughout all periods. The pandemic notably altered viral co-infection dynamics, with its effects lasting into the post-COVID-19 period. Specifically, a marked decrease in influenza A circulation was observed, while respiratory syncytial virus (RSV) epidemiology remained stable and significant co-circulation of rhinovirus\/enterovirus with SARS-CoV-2 persisted. Therefore, since COVID-19 and influenza affect the same high-risk groups, those individuals must be vaccinated against both viruses.<\/jats:p>","DOI":"10.3390\/v17081040","type":"journal-article","created":{"date-parts":[[2025,7,25]],"date-time":"2025-07-25T08:13:31Z","timestamp":1753431211000},"page":"1040","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Respiratory Virus Prevalence Across Pre-, During-, and Post-SARS-CoV-2 Pandemic Periods"],"prefix":"10.3390","volume":"17","author":[{"given":"Michele","family":"Manno","sequence":"first","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7685-3419","authenticated-orcid":false,"given":"Grazia","family":"Pavia","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simona","family":"Gigliotti","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Pantanella","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2120-8084","authenticated-orcid":false,"given":"Giorgio Settimo","family":"Barreca","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cinzia","family":"Peronace","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luigia","family":"Gallo","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Trimboli","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Colosimo","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5934-8322","authenticated-orcid":false,"given":"Angelo Giuseppe","family":"Lamberti","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0880-8955","authenticated-orcid":false,"given":"Nadia","family":"Marascio","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Matera","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Quirino","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences, \u201cMagna Gr\u00e6cia\u201d University, A.O.U. \u201cR. Dulbecco\u201d, 88100 Catanzaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,25]]},"reference":[{"key":"ref_1","unstructured":"(2025, April 01). Respiratory Infectious Diseases on the Rise Across WHO European Region. Available online: https:\/\/www.who.int\/europe\/news\/item\/15-12-2023-respiratory-infectious-diseases-on-the-rise-across-who-european-region."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Trifonova, I., Christova, I., Madzharova, I., Angelova, S., Voleva, S., Yordanova, R., Tcherveniakova, T., Krumova, S., and Korsun, N. (2022). Clinical Significance and Role of Coinfections with Respiratory Pathogens among Individuals with Confirmed Severe Acute Respiratory Syndrome Coronavirus-2 Infection. Front. Public Health, 10.","DOI":"10.3389\/fpubh.2022.959319"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1159\/000538382","article-title":"Changing and Evolution of Influenza Virus: Is It a Trivial Flu?","volume":"69","author":"Pavia","year":"2024","journal-title":"Chemotherapy"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e29708","DOI":"10.1002\/jmv.29708","article-title":"Persistence of SARS-CoV-2 Infection and Viral Intra- and Inter- host Evolution in COVID-19 Hospitalized Patients","volume":"96","author":"Pavia","year":"2024","journal-title":"J. Med. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Branda, F., Pavia, G., Ciccozzi, A., Quirino, A., Marascio, N., Matera, G., Romano, C., Locci, C., Azzena, I., and Pascale, N. (2024). Zoonotic Paramyxoviruses: Evolution, Ecology, and Public Health Strategies in a Changing World. Viruses, 16.","DOI":"10.3390\/v16111688"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"De Marco, C., Veneziano, C., Massacci, A., Pallocca, M., Marascio, N., Quirino, A., Barreca, G.S., Giancotti, A., Gallo, L., and Lamberti, A.G. (2022). Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.934993"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Cui, C., Timbrook, T.T., Polacek, C., Heins, Z., and Rosenthal, N.A. (2024). Disease Burden and High-Risk Populations for Complications in Patients with Acute Respiratory Infections: A Scoping Review. Front. Med., 11.","DOI":"10.3389\/fmed.2024.1325236"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e01161-24","DOI":"10.1128\/spectrum.01161-24","article-title":"Epidemiology of Respiratory Pathogens in Patients with Acute Respiratory Infections during the COVID-19 Pandemic and after Easing of COVID-19 Restrictions","volume":"12","author":"Zhao","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.jcv.2017.07.019","article-title":"Systematic Review of Respiratory Viral Pathogens Identified in Adults with Community-Acquired Pneumonia in Europe","volume":"95","author":"Alimi","year":"2017","journal-title":"J. Clin. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/s41586-022-05522-2","article-title":"The WHO Estimates of Excess Mortality Associated with the COVID-19 Pandemic","volume":"613","author":"Msemburi","year":"2023","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.virol.2018.10.019","article-title":"Historical and Clinical Aspects of the 1918 H1N1 Pandemic in the United States","volume":"527","author":"Jester","year":"2019","journal-title":"Virology"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S577","DOI":"10.1093\/infdis\/jiz059","article-title":"Global Disease Burden Estimates of Respiratory Syncytial Virus-Associated Acute Respiratory Infection in Older Adults in 2015: A Systematic Review and Meta-Analysis","volume":"222","author":"Shi","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1016\/S0140-6736(22)00478-0","article-title":"Global, Regional, and National Disease Burden Estimates of Acute Lower Respiratory Infections Due to Respiratory Syncytial Virus in Children Younger than 5 Years in 2019: A Systematic Analysis","volume":"399","author":"Li","year":"2022","journal-title":"Lancet Lond. Engl."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"100112","DOI":"10.1016\/j.lanepe.2021.100112","article-title":"Trends in Respiratory Virus Circulation Following COVID-19-Targeted Nonpharmaceutical Interventions in Germany, January\u2013September 2020: Analysis of National Surveillance Data","volume":"6","author":"Oh","year":"2021","journal-title":"Lancet Reg. Health Eur."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e13291","DOI":"10.1111\/irv.13291","article-title":"Impact of COVID-19 Nonpharmaceutical Interventions on Respiratory Syncytial Virus Infections in Hospitalized Children","volume":"18","author":"Lu","year":"2024","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.idnow.2021.05.004","article-title":"Pediatric Infectious Disease Group (GPIP) Position Paper on the Immune Debt of the COVID-19 Pandemic in Childhood, How Can We Fill the Immunity Gap?","volume":"51","author":"Cohen","year":"2021","journal-title":"Infect. Dis. Now"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"30547","DOI":"10.1073\/pnas.2013182117","article-title":"The Impact of COVID-19 Nonpharmaceutical Interventions on the Future Dynamics of Endemic Infections","volume":"117","author":"Baker","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"198005","DOI":"10.1016\/j.virusres.2020.198005","article-title":"Co-Infection with Respiratory Pathogens among COVID-2019 Cases","volume":"285","author":"Zhu","year":"2020","journal-title":"Virus Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"106474","DOI":"10.1016\/j.jinf.2025.106474","article-title":"Co-Infection Dynamics of SARS-CoV-2 and Respiratory Viruses in the 2022\/2023 Respiratory Season in the Netherlands","volume":"90","author":"Carstens","year":"2025","journal-title":"J. Infect."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.ijid.2023.08.021","article-title":"Prevalence and Associated Outcomes of Coinfection between SARS-CoV-2 and Influenza: A Systematic Review and Meta-Analysis","volume":"136","author":"Yan","year":"2023","journal-title":"Int. J. Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Wong, A., Barrero Guevara, L.A., Goult, E., Briga, M., Kramer, S.C., Kovacevic, A., Opatowski, L., and Domenech de Cell\u00e8s, M. (2023). The Interactions of SARS-CoV-2 with Cocirculating Pathogens: Epidemiological Implications and Current Knowledge Gaps. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1011167"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.jinf.2023.03.005","article-title":"Rapid Multiplex PCR for Respiratory Viruses Reduces Time to Result and Improves Clinical Care: Results of a Systematic Review and Meta-Analysis","volume":"86","author":"Clark","year":"2023","journal-title":"J. Infect."},{"key":"ref_23","unstructured":"(2025, April 29). The BioFire\u00ae FilmArray\u00ae Respiratory Panels (RP & RP2). Available online: https:\/\/www.biofiredx.com\/products\/the-filmarray-panels\/rp-2-1-plus-panel\/."},{"key":"ref_24","unstructured":"(2025, April 29). QIAstat-Dx SARS-CoV-2. Available online: https:\/\/www.qiagen.com\/ca\/products\/diagnostics-and-clinical-research\/infectious-disease\/qiastat-dx-syndromic-testing\/qiastat-dx-ca."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1128\/JCM.01117-07","article-title":"Evidence from Multiplex Molecular Assays for Complex Multipathogen Interactions in Acute Respiratory Infections","volume":"46","author":"Brunstein","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1743-422X-6-155","article-title":"Multipathogen Infections in Hospitalized Children with Acute Respiratory Infections","volume":"6","author":"Peng","year":"2009","journal-title":"Virol. J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1111\/irv.12858","article-title":"Differentiating Impacts of Non-Pharmaceutical Interventions on Non-Coronavirus Disease-2019 Respiratory Viral Infections: Hospital-Based Retrospective Observational Study in Taiwan","volume":"15","author":"Chen","year":"2021","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1111\/jpc.14076","article-title":"Respiratory Virus Detection and Co-Infection in Children and Adults in a Large Australian Hospital in 2009-2015","volume":"54","author":"Ching","year":"2018","journal-title":"J. Paediatr. Child Health"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Chong, Y.M., Chan, Y.F., Jamaluddin, M.F.H., Hasan, M.S., Pang, Y.K., Ponnampalavanar, S., Syed Omar, S.F., and Sam, I.-C. (2022). Rhinovirus\/Enterovirus Was the Most Common Respiratory Virus Detected in Adults with Severe Acute Respiratory Infections Pre-COVID-19 in Kuala Lumpur, Malaysia. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0273697"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/j.jmii.2022.03.005","article-title":"Circulating Pediatric Respiratory Pathogens in Taiwan during 2020: Dynamic Change under Low COVID-19 Incidence","volume":"55","author":"Sim","year":"2022","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2281","DOI":"10.21037\/tp-21-150","article-title":"Rotavirus and Adenovirus Infections in Children during COVID-19 Outbreak in Hangzhou, China","volume":"10","author":"Li","year":"2021","journal-title":"Transl. Pediatr."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/S1473-3099(22)00525-4","article-title":"Epidemiology of Respiratory Syncytial Virus in Children Younger than 5 Years in England during the COVID-19 Pandemic, Measured by Laboratory, Clinical, and Syndromic Surveillance: A Retrospective Observational Study","volume":"23","author":"Bardsley","year":"2023","journal-title":"Lancet Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1093\/infdis\/jiab606","article-title":"Understanding the Potential Drivers for Respiratory Syncytial Virus Rebound During the Coronavirus Disease 2019 Pandemic","volume":"225","author":"Li","year":"2022","journal-title":"J. Infect. Dis."},{"key":"ref_34","first-page":"34","article-title":"SARS-CoV-2 and Rhinovirus\/Enterovirus Co-Infection in a Critically Ill Young Adult Patient in Colombia","volume":"40","year":"2020","journal-title":"Biomedica"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Le Glass, E., Hoang, V.T., Boschi, C., Ninove, L., Zandotti, C., Boutin, A., Bremond, V., Dubourg, G., Ranque, S., and Lagier, J.-C. (2021). Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus. Viruses, 13.","DOI":"10.3390\/v13122528"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lade, H., Kim, J.-M., Chung, Y., Han, M., Mo, E.-K., and Kim, J.-S. (2021). Comparative Evaluation of Allplex Respiratory Panels 1, 2, 3, and BioFire FilmArray Respiratory Panel for the Detection of Respiratory Infections. Diagnostics, 12.","DOI":"10.3390\/diagnostics12010009"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1016\/j.jinf.2022.01.034","article-title":"Routine Molecular Point-of-Care Testing for SARS-CoV-2 Reduces Hospital-Acquired COVID-19","volume":"84","author":"Livingstone","year":"2022","journal-title":"J. Infect."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1002\/jmv.26817","article-title":"Co-Infection of Influenza A Virus and SARS-CoV-2: A Retrospective Cohort Study","volume":"93","author":"Cheng","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/infdis\/jiab587","article-title":"SARS-CoV-2 Interference of Influenza Virus Replication in Syrian Hamsters","volume":"225","author":"Halfmann","year":"2022","journal-title":"J. Infect. Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e0076522","DOI":"10.1128\/jvi.00765-22","article-title":"The Host Response to Influenza A Virus Interferes with SARS-CoV-2 Replication during Coinfection","volume":"96","author":"Oishi","year":"2022","journal-title":"J. Virol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1093\/infdis\/jiac494","article-title":"Influenza A and Respiratory Syncytial Virus Trigger a Cellular Response That Blocks Severe Acute Respiratory Syndrome Virus 2 Infection in the Respiratory Tract","volume":"227","author":"Dee","year":"2023","journal-title":"J. Infect. Dis."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Berry, G.J., Zhen, W., Smith, E., Manji, R., Silbert, S., Lima, A., Harington, A., McKinley, K., Kensinger, B., and Neff, C. (2022). Multicenter Evaluation of the BioFire Respiratory Panel 2.1 (RP2.1) for Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. J. Clin. Microbiol., 60.","DOI":"10.1128\/jcm.00066-22"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/8\/1040\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:15:46Z","timestamp":1760033746000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/8\/1040"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,25]]},"references-count":42,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["v17081040"],"URL":"https:\/\/doi.org\/10.3390\/v17081040","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,25]]}}}