{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T03:34:27Z","timestamp":1790220867605,"version":"4.1.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,7,29]],"date-time":"2020-07-29T00:00:00Z","timestamp":1595980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Clinical Virology Division"},{"name":"Clinical Bacteriology and Mycology Division, Laboratory Medicine, University Hospital Basel"},{"name":"Department of Biomedicine, University of Basel"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)\u2013recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Nasopharyngeal\/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus\/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiaa464","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T15:13:01Z","timestamp":1595517181000},"page":"1270-1279","source":"Crossref","is-referenced-by-count":73,"title":["Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses"],"prefix":"10.1093","volume":"222","author":[{"given":"Karoline","family":"Leuzinger","sequence":"first","affiliation":[{"name":"Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland"},{"name":"Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, 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Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans","family":"Pargger","sequence":"additional","affiliation":[{"name":"Intensive Care Unit, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Bassetti","sequence":"additional","affiliation":[{"name":"Internal Medicine, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Bielicki","sequence":"additional","affiliation":[{"name":"Pediatric Infectious Diseases and Hospital Epidemiology, University Children\u2019s Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2642-419X","authenticated-orcid":false,"given":"Nina","family":"Khanna","sequence":"additional","affiliation":[{"name":"Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Tschudin Sutter","sequence":"additional","affiliation":[{"name":"Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Widmer","sequence":"additional","affiliation":[{"name":"Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimira","family":"Hinic","sequence":"additional","affiliation":[{"name":"Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Battegay","sequence":"additional","affiliation":[{"name":"Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, 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