{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T08:43:21Z","timestamp":1765961001097,"version":"3.48.0"},"reference-count":73,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Brazil Family Foundation, Australia"},{"name":"National Health and Medical Research Council (NHMRC) of Australia","award":["APP1173880"],"award-info":[{"award-number":["APP1173880"]}]},{"name":"Faculty of Health, Medicine and Behavioral Sciences, University of Queensland, Brisbane, Australia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>We describe RNA-Seq analyses conducted on nasopharyngeal swabs collected from 37 patients admitted to an Australian intensive care unit from October 2022 to August 2023. During this time, the dominant omicron sublineage infections broadly progressed from BA.5 to BA.2-like, to XBB-like, then XBC, consistent with global trends. Viral load and patient metadata correlations indicated this cohort was broadly representative of severe COVID-19 patients. Human gene expression analyses were complicated by the large range (&gt;5 log) and variability in viral reads. Nevertheless, the comparison of XBC and BA.5 samples that had comparable viral read counts, revealed differentially expressed genes and a cellular deconvolution signature that indicated increased targeting of ciliated epithelial cells by XBC. To obtain more evidence for increased targeting of ciliated epithelial cells by the later omicron sublineage viruses, a series of mouse strains were infected with a BA.5 or a XBB isolate. Increased infection of the nasal turbinates and ciliated epithelial cells by XBB was demonstrated by viral titrations and immunohistochemistry, respectively. Compared with previous lineages, the omicron lineage showed increased targeting of ciliated epithelia in the upper respiratory tract, with the data presented herein suggesting this trend continued for the omicron sublineages.<\/jats:p>","DOI":"10.3390\/v17121631","type":"journal-article","created":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T08:32:27Z","timestamp":1765960347000},"page":"1631","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evidence from COVID-19 Patients and Murine Studies for a Continuing Trend Towards Targeting of Nasopharyngeal Ciliated Epithelial Cells by SARS-CoV-2 Omicron Sublineages"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5201-9682","authenticated-orcid":false,"given":"Agnes","family":"Carolin","sequence":"first","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"},{"name":"Faculty of Health, Medicine and Behavioural Sciences, University of Queensland, St. Lucia, QLD 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5710-9942","authenticated-orcid":false,"given":"Cameron R.","family":"Bishop","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kexin","family":"Yan","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4642-105X","authenticated-orcid":false,"given":"Branka","family":"Grubor-Bauk","sequence":"additional","affiliation":[{"name":"Viral Immunology Group, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9640-1911","authenticated-orcid":false,"given":"Mark P.","family":"Plummer","sequence":"additional","affiliation":[{"name":"Viral Immunology Group, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia"},{"name":"Intensive Care Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bing","family":"Tang","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2332-6305","authenticated-orcid":false,"given":"Michael","family":"Leitner","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7060-2283","authenticated-orcid":false,"given":"Eamon","family":"Raith","sequence":"additional","affiliation":[{"name":"Viral Immunology Group, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia"},{"name":"Intensive Care Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon C.","family":"Barry","sequence":"additional","affiliation":[{"name":"Viral Immunology Group, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8206-1939","authenticated-orcid":false,"given":"Christopher M.","family":"Hope","sequence":"additional","affiliation":[{"name":"Viral Immunology Group, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5789-4928","authenticated-orcid":false,"given":"Wilson","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel J.","family":"Rawle","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"},{"name":"GVN Center of Excellence, Australian Infectious Disease Research Centre, Brisbane, QLD 4029 and 4072, Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Suhrbier","sequence":"additional","affiliation":[{"name":"Infection and Inflammation Department, QIMR Berghofer, Brisbane, QLD 4029, Australia"},{"name":"GVN Center of Excellence, Australian Infectious Disease Research Centre, Brisbane, QLD 4029 and 4072, Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41579-023-00878-2","article-title":"The evolution of SARS-CoV-2","volume":"21","author":"Markov","year":"2023","journal-title":"Nat. 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