{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:21:49Z","timestamp":1767176509200,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007656","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,2,21]],"date-time":"2020-02-21T00:00:00Z","timestamp":1582243200000}}],"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2020,2,10]],"date-time":"2020-02-10T00:00:00Z","timestamp":1581292800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["724519 Vis-a-Vis"],"award-info":[{"award-number":["724519 Vis-a-Vis"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007656","type":"journal-article","created":{"date-parts":[[2020,2,10]],"date-time":"2020-02-10T13:34:56Z","timestamp":1581341696000},"page":"e1007656","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["The role of spatial structure in the evolution of viral innate immunity evasion: A\u00a0diffusion-reaction cellular automaton model"],"prefix":"10.1371","volume":"16","author":[{"given":"Ernesto","family":"Segredo-Otero","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1844-545X","authenticated-orcid":true,"given":"Rafael","family":"Sanju\u00e1n","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,2,10]]},"reference":[{"key":"pcbi.1007656.ref001","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nri3581","article-title":"Regulation of type I interferon responses","volume":"14","author":"LB Ivashkiv","year":"2014","journal-title":"Nat Rev Immunol"},{"key":"pcbi.1007656.ref002","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1146\/annurev-virology-100114-055249","article-title":"No love lost between viruses and interferons","volume":"2","author":"V Fensterl","year":"2015","journal-title":"Annu Rev Virol"},{"key":"pcbi.1007656.ref003","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.chom.2017.07.012","article-title":"Ten strategies of interferon evasion by viruses","volume":"22","author":"A Garc\u00eda-Sastre","year":"2017","journal-title":"Cell Host Microbe"},{"key":"pcbi.1007656.ref004","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.smim.2015.03.005","article-title":"Early IFN type I response: Learning from microbial evasion strategies","volume":"27","author":"EM Coccia","year":"2015","journal-title":"Semin Immunol"},{"key":"pcbi.1007656.ref005","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1038\/s41564-019-0379-8","article-title":"Social evolution of innate immunity evasion in a virus","volume":"4","author":"P Domingo-Calap","year":"2019","journal-title":"Nat Microbiol"},{"key":"pcbi.1007656.ref006","doi-asserted-by":"crossref","first-page":"e1002929","DOI":"10.1371\/journal.ppat.1002929","article-title":"Complexes of vesicular stomatitis virus matrix protein with host Rae1 and Nup98 involved in inhibition of host transcription","volume":"8","author":"KR Rajani","year":"2012","journal-title":"PLoS Pathog"},{"key":"pcbi.1007656.ref007","doi-asserted-by":"crossref","first-page":"R545","DOI":"10.1016\/j.cub.2019.03.068","article-title":"Drivers of spatial structure in social microbial communities","volume":"29","author":"D Yanni","year":"2019","journal-title":"Curr Biol"},{"key":"pcbi.1007656.ref008","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1016\/S0006-3495(92)81958-6","article-title":"Replication of viruses in a growing plaque: a reaction-diffusion model","volume":"61","author":"J Yin","year":"1992","journal-title":"Biophys J"},{"key":"pcbi.1007656.ref009","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1006\/jtbi.1999.1001","article-title":"Amplification and spread of viruses in a growing plaque","volume":"200","author":"L You","year":"1999","journal-title":"J Theor Biol"},{"key":"pcbi.1007656.ref010","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1007\/s00285-011-0434-4","article-title":"Persistence of bacteria and phages in a chemostat","volume":"64","author":"HL Smith","year":"2012","journal-title":"J Math Biol"},{"key":"pcbi.1007656.ref011","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.physa.2014.08.023","article-title":"Cohabitation reaction-diffusion model for virus focal infections","volume":"416","author":"D Amor","year":"2014","journal-title":"Physica A"},{"key":"pcbi.1007656.ref012","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.immuni.2017.03.011","article-title":"A tunable diffusion-consumption mechanism of cytokine propagation enables plasticity in cell-to-cell communication in the immune system","volume":"46","author":"A Oyler-Yaniv","year":"2017","journal-title":"Immunity"},{"key":"pcbi.1007656.ref013","doi-asserted-by":"crossref","first-page":"e32035","DOI":"10.7554\/eLife.32035","article-title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","volume":"7","author":"P Payne","year":"2018","journal-title":"Elife"},{"key":"pcbi.1007656.ref014","doi-asserted-by":"crossref","first-page":"e1004615","DOI":"10.1371\/journal.pcbi.1004615","article-title":"How obstacles perturb population fronts and alter their genetic structure","volume":"11","author":"W Mobius","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007656.ref015","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/BF00163881","article-title":"Pathogen invasion and host extinction in lattice structured populations","volume":"32","author":"K Sato","year":"1994","journal-title":"J Math Biol"},{"key":"pcbi.1007656.ref016","doi-asserted-by":"crossref","first-page":"e1002547","DOI":"10.1371\/journal.pcbi.1002547","article-title":"Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches","volume":"8","author":"D Wodarz","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007656.ref017","doi-asserted-by":"crossref","first-page":"7552","DOI":"10.1128\/JVI.00807-16","article-title":"Spatial-temporal patterns of viral amplification and interference initiated by a single infected cell","volume":"90","author":"F Akpinar","year":"2016","journal-title":"J Virol"},{"key":"pcbi.1007656.ref018","doi-asserted-by":"crossref","first-page":"e23358","DOI":"10.1371\/journal.pone.0023358","article-title":"Severe hindrance of viral infection propagation in spatially extended hosts","volume":"6","author":"JA Capit\u00e1n","year":"2011","journal-title":"PLoS One"},{"key":"pcbi.1007656.ref019","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1098\/rsif.2010.0266","article-title":"Effect of different modes of viral spread on the dynamics of multiply infected cells in human immunodeficiency virus infection","volume":"8","author":"D Wodarz","year":"2011","journal-title":"J R Soc Interface"},{"key":"pcbi.1007656.ref020","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.bbrc.2006.01.166","article-title":"A probability cellular automaton model for hepatitis B viral infections","volume":"342","author":"X Xiao","year":"2006","journal-title":"Biochem Biophys Res Commun"},{"key":"pcbi.1007656.ref021","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1006\/jtbi.2002.3055","article-title":"Spatiotemporal dynamics of HIV propagation","volume":"218","author":"MC Strain","year":"2002","journal-title":"J Theor Biol"},{"key":"pcbi.1007656.ref022","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2014.0289","article-title":"How is the effectiveness of immune surveillance impacted by the spatial distribution of spreading infections?","volume":"370","author":"UD Kadolsky","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pcbi.1007656.ref023","doi-asserted-by":"crossref","first-page":"e1003656","DOI":"10.1371\/journal.ppat.1003656","article-title":"Can non-lytic CD8+ T cells drive HIV-1 escape?","volume":"9","author":"NK Seich Al Basatena","year":"2013","journal-title":"PLoS Pathog"},{"key":"pcbi.1007656.ref024","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.virol.2016.05.019","article-title":"Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells","volume":"496","author":"EA Voigt","year":"2016","journal-title":"Virology"},{"key":"pcbi.1007656.ref025","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1098\/rsif.2006.0136","article-title":"Modelling dynamics of the type I interferon response to in vitro viral infection","volume":"3","author":"TJ Howat","year":"2006","journal-title":"J R Soc Interface"},{"key":"pcbi.1007656.ref026","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1089\/jir.2015.0008","article-title":"Kinetic differences and synergistic antiviral effects between type I and type III interferon signaling indicate pathway independence","volume":"35","author":"EA Voigt","year":"2015","journal-title":"J Interferon Cytokine Res"},{"key":"pcbi.1007656.ref027","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1073\/pnas.1614623114","article-title":"Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein","volume":"114","author":"H Qi","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007656.ref028","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1089\/107999002753452692","article-title":"Enhancement and diversification of IFN induction by IRF-7-mediated positive feedback","volume":"22","author":"DE Levy","year":"2002","journal-title":"J Interferon Cytokine Res"},{"key":"pcbi.1007656.ref029","doi-asserted-by":"crossref","first-page":"4433","DOI":"10.1007\/s00018-016-2299-6","article-title":"Mechanisms of viral mutation","volume":"73","author":"R Sanju\u00e1n","year":"2016","journal-title":"Cell Mol Life Sci"},{"key":"pcbi.1007656.ref030","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.3389\/fimmu.2018.01135","article-title":"A positive feedback amplifier circuit that regulates interferon (IFN)-stimulated gene expression and controls type I and type II IFN responses","volume":"9","author":"A Michalska","year":"2018","journal-title":"Front Immunol"},{"key":"pcbi.1007656.ref031","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1111\/j.1420-9101.2011.02236.x","article-title":"The genetical theory of kin selection","volume":"24","author":"A Gardner","year":"2011","journal-title":"J Evol Biol"},{"key":"pcbi.1007656.ref032","doi-asserted-by":"crossref","first-page":"e1001127","DOI":"10.1371\/journal.ppat.1001127","article-title":"The length of vesicular stomatitis virus particles dictates a need for actin assembly during clathrin-dependent endocytosis","volume":"6","author":"DK Cureton","year":"2010","journal-title":"PLoS Pathog"},{"key":"pcbi.1007656.ref033","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1128\/JB.89.2.462-469.1965","article-title":"Physical properties of chick interferon","volume":"89","author":"LE Kreuz","year":"1965","journal-title":"J Bacteriol"},{"key":"pcbi.1007656.ref034","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/bs.pmbts.2014.10.012","article-title":"Molecular determinants of the ratio of inert to infectious virus particles","volume":"129","author":"PJ Klasse","year":"2015","journal-title":"Prog Mol Biol Transl Sci"},{"key":"pcbi.1007656.ref035","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.vetmic.2012.08.023","article-title":"Stability and inactivation of vesicular stomatitis virus, a prototype rhabdovirus","volume":"162","author":"B Zimmer","year":"2013","journal-title":"Vet Microbiol"},{"key":"pcbi.1007656.ref036","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1126\/science.1133755","article-title":"Five rules for the evolution of cooperation","volume":"314","author":"MA Nowak","year":"2006","journal-title":"Science"},{"key":"pcbi.1007656.ref037","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1098\/rspb.2008.0829","article-title":"A simple and general explanation for the evolution of altruism","volume":"276","author":"JA Fletcher","year":"2009","journal-title":"Proc Biol Sci"},{"key":"pcbi.1007656.ref038","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/nrmicro1461","article-title":"Social evolution theory for microorganisms","volume":"4","author":"SA West","year":"2006","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1007656.ref039","doi-asserted-by":"crossref","first-page":"20130362","DOI":"10.1098\/rstb.2013.0362","article-title":"Hamilton's rule and the causes of social evolution","volume":"369","author":"AF Bourke","year":"2014","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pcbi.1007656.ref040","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.jtbi.2011.03.008","article-title":"Understanding microbial cooperation","volume":"299","author":"JA Damore","year":"2012","journal-title":"J Theor Biol"},{"key":"pcbi.1007656.ref041","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/359826a0","article-title":"Evolutionary games and spatial chaos","volume":"359","author":"MA Nowak","year":"1992","journal-title":"Nature"},{"key":"pcbi.1007656.ref042","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1098\/rstb.2009.0215","article-title":"Evolutionary dynamics in structured populations","volume":"365","author":"MA Nowak","year":"2010","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pcbi.1007656.ref043","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1038\/nrmicro.2016.84","article-title":"Spatial structure, cooperation and competition in biofilms","volume":"14","author":"CD Nadell","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1007656.ref044","doi-asserted-by":"crossref","first-page":"e00960","DOI":"10.7554\/eLife.00960","article-title":"Spatial self-organization favors heterotypic cooperation over cheating","volume":"2","author":"B Momeni","year":"2013","journal-title":"Elife"},{"key":"pcbi.1007656.ref045","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1146\/annurev-virology-100114-055135","article-title":"Matters of size: genetic bottlenecks in virus infection and their potential impact on evolution","volume":"2","author":"MP Zwart","year":"2015","journal-title":"Annu Rev Virol"},{"key":"pcbi.1007656.ref046","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.coviro.2012.08.001","article-title":"Virus population bottlenecks during within-host progression and host-to-host transmission","volume":"2","author":"S Gutierrez","year":"2012","journal-title":"Curr Opin Virol"},{"key":"pcbi.1007656.ref047","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.coviro.2017.10.008","article-title":"Genetic bottlenecks in intraspecies virus transmission","volume":"28","author":"JT McCrone","year":"2018","journal-title":"Curr Opin Virol"},{"key":"pcbi.1007656.ref048","doi-asserted-by":"crossref","first-page":"5520","DOI":"10.1073\/pnas.0600834103","article-title":"Bottleneck-mediated quasispecies restriction during spread of an RNA virus from inoculation site to brain","volume":"103","author":"JK Pfeiffer","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007656.ref049","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nature11398","article-title":"HIV-infected T cells are migratory vehicles for viral dissemination","volume":"490","author":"TT Murooka","year":"2012","journal-title":"Nature"},{"key":"pcbi.1007656.ref050","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1126\/science.1183173","article-title":"Repulsion of superinfecting virions: a mechanism for rapid virus spread","volume":"327","author":"V Doceul","year":"2010","journal-title":"Science"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007656","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,2,21]],"date-time":"2020-02-21T00:00:00Z","timestamp":1582243200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007656","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,21]],"date-time":"2020-02-21T14:01:20Z","timestamp":1582293680000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007656"}},"subtitle":[],"editor":[{"given":"Roland R.","family":"Regoes","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,10]]},"references-count":50,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2020,2,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007656","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,10]]}}}