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

Autor:	El Moussaoui M; Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Bontems S; Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Meex C; Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Hayette MP; Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Lejeune M; Department of Hematology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Hong SL; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium., Dellicour S; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium.; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 50 Avenue Franklin Roosevelt, Bruxelles 1050, Belgium., Moutschen M; Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Cambisano N; Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.; Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Renotte N; Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.; Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Bours V; Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.; Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Darcis G; Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Artesi M; Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.; Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium., Durkin K; Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.; Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium.
Jazyk:	angličtina
Zdroj:	Virus evolution [Virus Evol] 2024 Aug 31; Vol. 10 (1), pp. veae073. Date of Electronic Publication: 2024 Aug 31 (Print Publication: 2024).
DOI:	10.1093/ve/veae073
Abstrakt:	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 >1 year 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. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu