Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.

Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses rep...

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Autores principales:	Josep Sardanyés, Santiago F Elena
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3ca25529eb90420ca40324be0eab3ca9
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spelling	oai:doaj.org-article:3ca25529eb90420ca40324be0eab3ca92021-11-04T06:08:17ZQuasispecies spatial models for RNA viruses with different replication modes and infection strategies.1932-620310.1371/journal.pone.0024884https://doaj.org/article/3ca25529eb90420ca40324be0eab3ca92011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21949777/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and infect cells that are rarely in suspension but spatially organized. Surprisingly, most quasispecies models of virus replication have ignored these two phenomena. In order to study these two viral characteristics, we have developed stochastic cellular automata models that simulate two different modes of replication (geometric vs stamping machine) for quasispecies replicating and spreading on a two-dimensional space. Furthermore, we explored these two replication models considering epistatic fitness landscapes (antagonistic vs synergistic) and different scenarios for cell-to-cell spread, one with free superinfection and another with superinfection inhibition. We found that the master sequences for populations replicating geometrically and with antagonistic fitness effects vanished at low critical mutation rates. By contrast, the highest critical mutation rate was observed for populations replicating geometrically but with a synergistic fitness landscape. Our simulations also showed that for stamping machine replication and antagonistic epistasis, a combination that appears to be common among plant viruses, populations further increased their robustness by inhibiting superinfection. We have also shown that the mode of replication strongly influenced the linkage between viral loci, which rapidly reached linkage equilibrium at increasing mutations for geometric replication. We also found that the strategy that minimized the time required to spread over the whole space was the stamping machine with antagonistic epistasis among mutations. Finally, our simulations revealed that the multiplicity of infection fluctuated but generically increased along time.Josep SardanyésSantiago F ElenaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e24884 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Josep Sardanyés Santiago F Elena Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
description	Empirical observations and theoretical studies suggest that viruses may use different replication strategies to amplify their genomes, which impact the dynamics of mutation accumulation in viral populations and therefore, their fitness and virulence. Similarly, during natural infections, viruses replicate and infect cells that are rarely in suspension but spatially organized. Surprisingly, most quasispecies models of virus replication have ignored these two phenomena. In order to study these two viral characteristics, we have developed stochastic cellular automata models that simulate two different modes of replication (geometric vs stamping machine) for quasispecies replicating and spreading on a two-dimensional space. Furthermore, we explored these two replication models considering epistatic fitness landscapes (antagonistic vs synergistic) and different scenarios for cell-to-cell spread, one with free superinfection and another with superinfection inhibition. We found that the master sequences for populations replicating geometrically and with antagonistic fitness effects vanished at low critical mutation rates. By contrast, the highest critical mutation rate was observed for populations replicating geometrically but with a synergistic fitness landscape. Our simulations also showed that for stamping machine replication and antagonistic epistasis, a combination that appears to be common among plant viruses, populations further increased their robustness by inhibiting superinfection. We have also shown that the mode of replication strongly influenced the linkage between viral loci, which rapidly reached linkage equilibrium at increasing mutations for geometric replication. We also found that the strategy that minimized the time required to spread over the whole space was the stamping machine with antagonistic epistasis among mutations. Finally, our simulations revealed that the multiplicity of infection fluctuated but generically increased along time.
format	article
author	Josep Sardanyés Santiago F Elena
author_facet	Josep Sardanyés Santiago F Elena
author_sort	Josep Sardanyés
title	Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
title_short	Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
title_full	Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
title_fullStr	Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
title_full_unstemmed	Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.
title_sort	quasispecies spatial models for rna viruses with different replication modes and infection strategies.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/3ca25529eb90420ca40324be0eab3ca9
work_keys_str_mv	AT josepsardanyes quasispeciesspatialmodelsforrnaviruseswithdifferentreplicationmodesandinfectionstrategies AT santiagofelena quasispeciesspatialmodelsforrnaviruseswithdifferentreplicationmodesandinfectionstrategies
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Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.

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