Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection

{ 'indexed': { 'date-parts': [[2024, 10, 12]], 'date-time': '2024-10-12T16:10:12Z', 'timestamp': 1728749412742}, 'reference-count': 61, 'publisher': 'Oxford University Press (OUP)', 'issue': '1', 'license': [ { 'start': { 'date-parts': [[2024, 8, 31]], 'date-time': '2024-08-31T00:00:00Z', 'timestamp': 1725062400000}, 'content-version': 'vor', 'delay-in-days': 243, 'URL': 'https://creativecommons.org/licenses/by/4.0/'}], 'funder': [ {'name': 'LEAPS', 'award': ['101094685']}, { 'DOI': '10.13039/100010661', 'name': 'Horizon 2020 Framework Programme', 'doi-asserted-by': 'publisher', 'award': ['874850'], 'id': [{'id': '10.13039/100010661', 'id-type': 'DOI', 'asserted-by': 'publisher'}]}, {'name': 'Région Wallone', 'award': ['1710180']}, {'name': 'Fonds De La Recherche Scientifique – FNRS', 'award': ['F.4515.22 H.C.008.20']}, { 'DOI': '10.13039/501100003130', 'name': 'Fonds Wetenschappelijk Onderzoek', 'doi-asserted-by': 'publisher', 'award': ['G098321N'], 'id': [{'id': '10.13039/501100003130', 'id-type': 'DOI', 'asserted-by': 'publisher'}]}, {'name': 'LEAPS', 'award': ['101094685']}, { 'DOI': '10.13039/100010661', 'name': 'Horizon 2020 Framework Programme', 'doi-asserted-by': 'publisher', 'award': ['874850'], 'id': [{'id': '10.13039/100010661', 'id-type': 'DOI', 'asserted-by': 'publisher'}]}, {'name': 'Région Wallone', 'award': ['1710180']}, {'name': 'Fonds De La Recherche Scientifique – FNRS', 'award': ['F.4515.22 H.C.008.20']}, { 'DOI': '10.13039/501100003130', 'name': 'Fonds Wetenschappelijk Onderzoek', 'doi-asserted-by': 'publisher', 'award': ['G098321N'], 'id': [{'id': '10.13039/501100003130', 'id-type': 'DOI', 'asserted-by': 'publisher'}]}], 'content-domain': {'domain': [], 'crossmark-restriction': False}, 'published-print': {'date-parts': [[2024, 10, 12]]}, 'abstract': '<jats:title>Abstract</jats:title>\n' ' <jats:p>Accumulating evidence points to persistent severe acute respiratory ' 'syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source ' 'of novel lineages. While intrahost evolution of the virus in chronically infected patients ' 'has previously been reported, existing knowledge is primarily based on samples from the ' 'nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that ' 'accumulated during a prolonged SARS-CoV-2 infection with the Omicron BF.7 sublineage, which ' 'is estimated to have persisted for &amp;gt;1\u2009year in an immunosuppressed patient. Based ' 'on the sequencing of eight samples collected at six time points, we identified 87 intrahost ' 'single-nucleotide variants, 2 indels, and a 362-bp deletion. Our analysis revealed distinct ' 'viral genotypes in the nasopharyngeal (NP), endotracheal aspirate, and bronchoalveolar lavage ' 'samples. This suggests that NP samples may not offer a comprehensive representation of the ' 'overall intrahost viral diversity. Our findings not only demonstrate that the Omicron BF.7 ' 'sublineage can further diverge from its already exceptionally mutated state but also ' 'highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific ' 'viral populations across distinct anatomic compartments. This provides novel insights into ' 'the intricate nature of viral diversity and evolution dynamics in persistent ' 'infections.</jats:p>', 'DOI': '10.1093/ve/veae073', 'type': 'journal-article', 'created': {'date-parts': [[2024, 8, 30]], 'date-time': '2024-08-30T00:09:16Z', 'timestamp': 1724976556000}, 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts ' 'during SARS-CoV-2 prolonged infection', 'prefix': '10.1093', 'volume': '10', 'author': [ { 'given': 'Majdouline', 'family': 'El Moussaoui', 'sequence': 'first', 'affiliation': [ { 'name': 'Department of Infectious Diseases and General Internal Medicine, ' 'University Hospital of Liège , 1 Avenue de l’Hôpital, Liège ' '4000,', 'place': ['Belgium']}]}, { 'given': 'Sebastien', 'family': 'Bontems', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Microbiology, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'given': 'Cecile', 'family': 'Meex', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Microbiology, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'given': 'Marie-Pierre', 'family': 'Hayette', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Microbiology, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'given': 'Marie', 'family': 'Lejeune', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Hematology, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'ORCID': 'http://orcid.org/0000-0001-6354-4943', 'authenticated-orcid': False, 'given': 'Samuel L', 'family': 'Hong', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Microbiology, Immunology and Transplantation, ' 'Laboratory for Clinical and Epidemiological Virology, Rega ' 'Institute, KU Leuven , 49 Herestraat, Leuven 3000,', 'place': ['Belgium']}]}, { 'ORCID': 'http://orcid.org/0000-0001-9558-1052', 'authenticated-orcid': False, 'given': 'Simon', 'family': 'Dellicour', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Microbiology, Immunology and Transplantation, ' 'Laboratory for Clinical and Epidemiological Virology, Rega ' 'Institute, KU Leuven , 49 Herestraat, Leuven 3000,', 'place': ['Belgium']}, { 'name': 'Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles ' ', 50 Avenue Franklin Roosevelt, Bruxelles 1050,', 'place': ['Belgium']}]}, { 'given': 'Michel', 'family': 'Moutschen', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Infectious Diseases and General Internal Medicine, ' 'University Hospital of Liège , 1 Avenue de l’Hôpital, Liège ' '4000,', 'place': ['Belgium']}]}, { 'given': 'Nadine', 'family': 'Cambisano', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Human Genetics, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}, { 'name': 'Laboratory of Human Genetics, GIGA Institute, University of ' 'Liège , 1 Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'given': 'Nathalie', 'family': 'Renotte', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Human Genetics, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}, { 'name': 'Laboratory of Human Genetics, GIGA Institute, University of ' 'Liège , 1 Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'given': 'Vincent', 'family': 'Bours', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Human Genetics, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}, { 'name': 'Laboratory of Human Genetics, GIGA Institute, University of ' 'Liège , 1 Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'ORCID': 'http://orcid.org/0000-0001-8192-1351', 'authenticated-orcid': False, 'given': 'Gilles', 'family': 'Darcis', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Infectious Diseases and General Internal Medicine, ' 'University Hospital of Liège , 1 Avenue de l’Hôpital, Liège ' '4000,', 'place': ['Belgium']}]}, { 'given': 'Maria', 'family': 'Artesi', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Human Genetics, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}, { 'name': 'Laboratory of Human Genetics, GIGA Institute, University of ' 'Liège , 1 Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}]}, { 'ORCID': 'http://orcid.org/0000-0001-7475-6618', 'authenticated-orcid': False, 'given': 'Keith', 'family': 'Durkin', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Human Genetics, University Hospital of Liège , 1 ' 'Avenue de l’Hôpital, Liège 4000,', 'place': ['Belgium']}, { 'name': 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