Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.

Autor:	Pyöriä L; Department of Virology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland., Pratas D; Department of Virology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland.; IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.; Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal., Toppinen M; Department of Forensic Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland., Simmonds P; Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, OX1 3SY, Oxford, UK., Hedman K; Department of Virology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland., Sajantila A; Department of Forensic Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland.; Forensic Medicine Unit, Finnish Institute for Health and Welfare, Mannerheimintie 166 A, P.O. Box 30, FI-00271, Helsinki, Finland., Perdomo MF; Department of Virology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Oct 21. Date of Electronic Publication: 2024 Oct 21.
DOI:	10.1093/nar/gkae871
Abstrakt:	The viral intra-host genetic diversities and interactions with the human genome during decades of persistence remain poorly characterized. In this study, we analyzed the variability and integration sites of persisting viruses in nine organs from thirteen individuals who died suddenly from non-viral causes. The viruses studied included parvovirus B19, six herpesviruses, Merkel cell (MCPyV) and JC polyomaviruses, totaling 127 genomes. The viral sequences across organs were remarkably conserved within each individual, suggesting that persistence stems from single dominant strains. This indicates that intra-host viral evolution, thus far inferred primarily from immunocompromised patients, is likely overestimated in healthy subjects. Indeed, we detected increased viral subpopulations in two individuals with putative reactivations, suggesting that replication status influences diversity. Furthermore, we identified asymmetrical mutation patterns reflecting selective pressures exerted by the host. Strikingly, our analysis revealed non-clonal viral integrations even in individuals without cancer. These included MCPyV integrations and truncations resembling clonally expanded variants in Merkel cell carcinomas, as well as novel junctions between herpesvirus 6B and mitochondrial sequences, the significance of which remains to be evaluated. Our work systematically characterizes the genomic landscape of the tissue-resident virome, highlighting potential deviations occurring during disease. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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