The importance of epistasis in the evolution of viral pathogens.
| Title: | The importance of epistasis in the evolution of viral pathogens. |
|---|---|
| Authors: | Manivannan SN; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, United States.; Diaz Arenas C; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, United States.; Grubaugh ND; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, United States.; Yale School of Public Health, 60 College Street, New Haven, CT 06510, United States.; Public Health Modeling Unit, Yale School of Public Health, 60 College Street, New Haven, CT 06510, United States.; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven, Belgium.; Ogbunugafor CB; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, United States.; Public Health Modeling Unit, Yale School of Public Health, 60 College Street, New Haven, CT 06510, United States.; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, United States. |
| Source: | Virus evolution [Virus Evol] 2025 Nov 24; Vol. 11 (1), pp. veaf091. Date of Electronic Publication: 2025 Nov 24 (Print Publication: 2025). |
| Publication Type: | Journal Article; Review |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: England NLM ID: 101664675 Publication Model: eCollection Cited Medium: Print ISSN: 2057-1577 (Print) Linking ISSN: 20571577 NLM ISO Abbreviation: Virus Evol Subsets: PubMed not MEDLINE |
| Imprint Name(s): | Original Publication: Oxford : Oxford University Press, [2015]- |
| Abstract: | Understanding the genetic and genomic underpinnings of infectious disease outbreaks has emerged as a frontier of epidemiology. Here, we argue that epistasis-where the phenotypic effects of mutations or gene variants are dictated by the presence of other mutations or genes-should become a focus of genomic epidemiology. To demonstrate this, we present the results of a systematic review of the literature on epistasis in viruses, focusing on three major human viral systems: (i) influenza, (ii) SARS-CoV-2, and (iii) human immunodeficiency virus, as well as two other bodies of the literature mainly focusing on nonhuman viruses: (iv) tobacco etch virus and (v) experimental evolution of viruses. Our systematic review of these five bodies of the literature highlights that epistasis is prevalent in host-virus systems of various kinds, manifesting within and between different loci, with effects of different magnitudes and directions, and shaping various phenotypic traits of epidemiological interest. At the same time, our systematic review demonstrates that our ability to draw general conclusions about the direction and magnitude of epistasis in viral evolution is constrained by several factors: the idiosyncrasies of virus-host systems, biases in the underlying data collection exercises, and the limitations of existing methods. Moving forward, we encourage collaborations between genomic epidemiologists and evolutionary biologists to identify and measure epistasis in studying the evolution of viral pathogens.; (© The Author(s) 2025. Published by Oxford University Press.) |
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| Grant Information: | R01 AI168166 United States AI NIAID NIH HHS |
| Contributed Indexing: | Keywords: HIV; SARS-CoV-2; epistasis; genomic epidemiology; influenza; tobacco etch virus; virus evolution |
| Entry Date(s): | Date Created: 20251212 Date Completed: 20251212 Latest Revision: 20260122 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC12694738 |
| DOI: | 10.1093/ve/veaf091 |
| PMID: | 41383811 |
| Database: | MEDLINE |
Journal Article; Review