SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations.

Autor:	Lustig G; Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa., Ganga Y; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Rodel HE; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK., Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa.; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa., Khairallah A; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Jackson L; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Cele S; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa., Khan K; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa., Jule Z; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Reedoy K; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Karim F; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa., Bernstein M; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa., Ndung'u T; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK.; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.; HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.; Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA., Moosa MS; Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa., Archary D; Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa., de Oliveira T; KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa.; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa.; Department of Global Health, University of Washington, 3980 15th Avenue NE, Seattle, WA 98105, USA., Lessells R; KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa., Neher RA; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland.; Biozentrum, University of Basel, Spitalstrasse 41 4056, Basel, Switzerland., Abdool Karim SS; Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa.; Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States., Sigal A; Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa.; Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa.; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.
Jazyk:	angličtina
Zdroj:	Virus evolution [Virus Evol] 2023 Dec 28; Vol. 10 (1), pp. vead075. Date of Electronic Publication: 2023 Dec 28 (Print Publication: 2024).
DOI:	10.1093/ve/vead075
Abstrakt:	One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu