RNA to RNA: Natural incorporation of exogenous sequences in mammalian positive-sense RNA virus genomes
Abstract
The incorporation of exogenous sequences into viral genomes is well documented among many positive-sense single-stranded RNA viruses. This review provides an overview of exogenous inserts detected in mammalian viruses: accessory genes of coronavirus of cellular or other viral origin, cellular RNA insertions in the genomes of bovine viral diarrhoea virus and hepatitis E virus, the sequence of a viral enzyme within enterovirus genomes, etc. Such inserts have also been described in defective viral genomes, which may contribute to their persistence within viral populations. The mechanisms underlying these insertions remain unclear: are they driven by viral polymerase-mediated template switching, or do they arise from polymerase-independent events? The fact that genomes harbouring such inserts are rarely detected in nature does not prove that insertion events are uncommon; rather, most genomes containing inserts are likely subjected to counter-selection, for instance because their functions are disrupted or because they exceed the packaging constraints of the viral capsid. This likely explains why certain contexts (in vitro culture, replication in immunocompromised patients) favour their detection. Thus, genomes containing exogenous inserts may be more common than usually assumed. They could continuously contribute to the viral quasispecies, emerging at detectable frequencies only when an abrupt environmental shift reveals their selective advantage. For this reason, studies investigating the diversity of these atypical genomes, their frequency within the viral quasispecies, and the phenotypic traits they confer could deepen our understanding of the genetic plasticity of positive-sense RNA viruses and their capacity to adapt to new environments.
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BibTeX
@article{jouvenet2026natural,
title = {{RNA to RNA: Natural incorporation of exogenous sequences in mammalian positive-sense RNA virus genomes}},
author = {Nolwenn Jouvenet and Sébastien Lhomme and Maël Bessaud},
journal = {Virologie},
year = {2026},
month = nov,
doi = {10.1684/vir.2026.1162},
url = {https://pasteur.hal.science/pasteur-05855112v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - RNA to RNA: Natural incorporation of exogenous sequences in mammalian positive-sense RNA virus genomes
AU - Nolwenn Jouvenet
AU - Sébastien Lhomme
AU - Maël Bessaud
PY - 2026
DA - 2026/11/06
JO - Virologie
DO - 10.1684/vir.2026.1162
UR - https://pasteur.hal.science/pasteur-05855112v1
AB - The incorporation of exogenous sequences into viral genomes is well documented among many positive-sense single-stranded RNA viruses. This review provides an overview of exogenous inserts detected in mammalian viruses: accessory genes of coronavirus of cellular or other viral origin, cellular RNA insertions in the genomes of bovine viral diarrhoea virus and hepatitis E virus, the sequence of a viral enzyme within enterovirus genomes, etc. Such inserts have also been described in defective viral genomes, which may contribute to their persistence within viral populations. The mechanisms underlying these insertions remain unclear: are they driven by viral polymerase-mediated template switching, or do they arise from polymerase-independent events? The fact that genomes harbouring such inserts are rarely detected in nature does not prove that insertion events are uncommon; rather, most genomes containing inserts are likely subjected to counter-selection, for instance because their functions are disrupted or because they exceed the packaging constraints of the viral capsid. This likely explains why certain contexts (in vitro culture, replication in immunocompromised patients) favour their detection. Thus, genomes containing exogenous inserts may be more common than usually assumed. They could continuously contribute to the viral quasispecies, emerging at detectable frequencies only when an abrupt environmental shift reveals their selective advantage. For this reason, studies investigating the diversity of these atypical genomes, their frequency within the viral quasispecies, and the phenotypic traits they confer could deepen our understanding of the genetic plasticity of positive-sense RNA viruses and their capacity to adapt to new environments.
SN - 1267-8694
SN - 1950-6961
ER -