Steinhauer DA, Domingo E, Holland JJ. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene. 1992;122:281–8.
Article
CAS
PubMed
Google Scholar
Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. J Virol. 2010;84:9733–48.
Article
PubMed
PubMed Central
Google Scholar
Domingo E. Viruses at the edge of adaptation. Virology. 2000;270:251–3.
Article
CAS
PubMed
Google Scholar
Chao L. Fitness of RNA virus decreased by muller ratchet. Nature. 1990;348:454–5.
Article
CAS
PubMed
Google Scholar
Duarte E, Clarke D, Moya A, Domingo E, Holland J. Rapid fitness losses in mammalian RNA virus clones due to Muller ratchet. Proc Natl Acad Sci U S A. 1992;89:6015–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
De la Iglesia F, Elena SF. Fitness declines in Tobacco etch virus upon serial bottleneck transfers. J Virol. 2007;81:4941–7.
Article
PubMed
PubMed Central
Google Scholar
Elena SF, Carrasco P, Daròs JA, Sanjuán R. Mechanisms of genetic robustness in RNA viruses. EMBO Rep. 2006;7:168–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elena SF, Moya A. Rate of deleterious mutation and the distribution of its effects on fitness in Vesicular stomatitis virus. J Evol Biol. 1999;12:1078–88.
Article
Google Scholar
Sanjuán R, Moya A, Elena SF. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A. 2004;101:8396–401.
Article
PubMed
PubMed Central
Google Scholar
Acevedo A, Brodsky L, Andino R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature. 2014;505:686–90.
Article
CAS
PubMed
Google Scholar
Visher E, Whitefield SE, McCrone JT, Fitzsimmons W, Lauring AS. The mutational robustness of Influenza A virus. PLoS Pathog. 2016;12, e1005856.
Article
PubMed
PubMed Central
Google Scholar
Carrasco P, de la Iglesia F, Elena SF. Distribution of fitness and virulence effects caused by single-nucleotide substitutions in Tobacco etch virus. J Virol. 2007;81:12979–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernet GP, Elena SF. Distribution of mutational fitness effects and of epistasis in the 5′ untranslated region of a plant RNA virus. BMC Evol Biol. 2015;15:274.
Article
PubMed
PubMed Central
Google Scholar
Domingo-Calap P, Cuevas JM, Sanjuán R. The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages. PLoS Genet. 2009;5, e1000742.
Article
PubMed
PubMed Central
Google Scholar
Peris JB, Davis P, Cuevas JM, Nebot MR, Sanjuán R. Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1. Genetics. 2010;185:603–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keightley PD, Ohnishi O. EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster. Genetics. 1998;148:753–66.
CAS
PubMed
PubMed Central
Google Scholar
Keightley PD, Davies EK, Peters AD, Shaw RG. Properties of ethylmethane sulfonate-induced mutations affecting life-history traits in Caenorhabditis elegans and inferences about bivariate distributions of mutation effects. Genetics. 2000;156:143–54.
CAS
PubMed
PubMed Central
Google Scholar
Koufopanou V, Lomas S, Tsai IJ, Burt A. Estimating the fitness effects of new mutations in the wild yeast Saccharomyces paradoxus. Genome Biol Evol. 2015;7:1887–95.
CAS
PubMed
PubMed Central
Google Scholar
Sanjuán R. Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis. Philos Trans R Soc B. 2010;365:1975–82.
Article
Google Scholar
Keightley PD, Lynch M. Toward a realistic model of mutations affecting fitness. Evolution. 2003;57:683–5.
Article
PubMed
Google Scholar
Orr HA. The distribution of fitness effects among beneficial mutations. Genetics. 2003;163:1519–26.
CAS
PubMed
PubMed Central
Google Scholar
Miralles R, Gerrish PJ, Moya A, Elena SF. Clonal interference and the evolution of RNA viruses. Science. 1999;285:1745–7.
Article
CAS
PubMed
Google Scholar
Escarmís C, Dávila M, Charpentier N, Bracho A, Moya A, Domingo E. Genetic lesions associated with Muller’s ratchet in an RNA virus. J Mol Biol. 1996;264:255–67.
Article
PubMed
Google Scholar
Phillips PC. Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 2008;9:855–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Visser JAGM, Krug J. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet. 2014;15:480–90.
Article
PubMed
Google Scholar
Lalić J, Elena SF. Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus. Heredity. 2012;109:71–7.
Lalić J, Elena SF. The impact of higher-order epistasis in the within-host fitness of a positive-sense plant RNA virus. J Evol Biol. 2015;28:2236–47.
Article
PubMed
Google Scholar
Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc B. 2015;370:20140292.
Article
Google Scholar
Cervera H, Lalić J, Elena SF. Effect of host species on the topography of the fitness landscape for a plant RNA virus. J Virol. 2016;90:10160–9.
Article
Google Scholar
Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc R Soc B. 2016;283:20160984.
Article
PubMed
Google Scholar
Blystad DR, van der Vlugt R, Alfaro-Fernandez A, Cordoba MD, Bese G, Hristova D, Pospieszny H, Mehle N, Ravnikar M, Tomassoli L, Varveri C, Nielsen SL. Host range and symptomatology of Pepino mosaic virus strains occurring in Europe. Eur J Plant Pathol. 2015;143:43–56.
Article
Google Scholar
Mumford RA, Metcalfe EJ. The partial sequencing of the genomic RNA of a UK isolate of Pepino mosaic virus and the comparison of the coat protein sequence with other isolates from Europe and Peru. Arch Virol. 2001;146:2455–60.
Article
CAS
PubMed
Google Scholar
Roggero P, Masenga V, Lenzi R, Coghe F, Ena S, Winter S. First report of Pepino mosaic virus in tomato in Italy. Plant Dis. 2001;3:8.
Google Scholar
Cotillon AC, Girard M, Ducouret S. Complete nucleotide sequence of the genomic RNA of a French isolate of Pepino mosaic virus (PepMV). Arch Virol. 2002;147:2231–8.
Article
CAS
PubMed
Google Scholar
Maroon-Lango CJ, Guaragna MA, Jordan RL, Hammond J, Bandla M, Marquardt SK. Two unique US isolates of Pepino mosaic virus from a limited source of pooled tomato tissue are distinct from a third (European-like) US isolate. Arch Virol. 2005;150:1187–201.
Article
CAS
PubMed
Google Scholar
Pagán I, Córdoba-Selles MD, Martínez-Priego L, Fraile A, Malpica JM, Jorda C, García-Arenal F. Genetic structure of the population of Pepino mosaic virus infecting tomato crops in Spain. Phytopathology. 2006;96:274–9.
Article
PubMed
Google Scholar
Ling KS. Molecular characterization of two Pepino mosaic virus variants from imported tomato seed reveals high levels of sequence identity between Chilean and US isolates. Virus Genes. 2007;34:1–8.
Article
CAS
PubMed
Google Scholar
Hanssen IM, Paeleman A, Wittemans L, Goen K, Lievens B, Bragard C, Vanachter A, Thomma B. Genetic characterization of Pepino mosaic virus isolates from Belgian greenhouse tomatoes reveals genetic recombination. Eur J Plant Pathol. 2008;121:131–46.
Article
Google Scholar
Hasiów B, Borodynko N, Pospieszny H. Complete genomic RNA sequence of the Polish Pepino mosaic virus isolate belonging to the US2 strain. Virus Genes. 2008;36:209–14.
Article
PubMed
Google Scholar
Hanssen IM, Paeleman A, Vandewoestijne E, Van Bergen L, Bragard C, Lievens B, Vanacher ACRC, Thomma BPHJ. Pepino mosaic virus isolates and differential symptomatology in tomato. Plant Pathol. 2009;58:450–60.
Article
CAS
Google Scholar
Moreno-Pérez MG, Pagán I, Aragón-Caballero L, Cáceres F, Fraile A, García-Arenal F. Ecological and genetic determinants of Pepino mosaic virus emergence. J Virol. 2014;88:3359–68.
Article
PubMed
PubMed Central
Google Scholar
Ling K, Li R, Bledsoe M. Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification. Virol J. 2013;10:117.
Article
PubMed
PubMed Central
Google Scholar
Hasiów-Jaroszewska B, Paeleman A, Ortega-Parra N, Borodynko N, Minicka J, Czerwoniec A, Thomma BP, Hanssen IM. Ratio of mutated versus wild-type coat protein sequences in Pepino mosaic virus determines the nature and severity of yellowing symptoms on tomato plants. Mol Plant Pathol. 2013;14:923–33.
Article
PubMed
Google Scholar
Sempere RN, Gómez-Aix C, Ruiz-Ramon F, Gómez P, Hasiów-Jaroszewska B, Sánchez-Pina MA, Aranda MA. Pepino mosaic virus RNA-dependent RNA polymerase POL domain is a hypersensitive response-like elicitor shared by necrotic and mild isolates. Phytopathology. 2016;106:395–406.
Article
CAS
PubMed
Google Scholar
Hasiów-Jaroszewska B, Borodynko N, Jackowiak P, Figlerowicz M, Pospieszny H. Single mutation converts mild pathotype of the Pepino mosaic virus into necrotic one. Virus Res. 2011;159:57–61.
Article
PubMed
Google Scholar
Minicka J, Rymelska N, Elena SF, Czerwoniec A, Hasiów-Jaroszewska B. Molecular evolution of Pepino mosaic virus during long-term passaging in different hosts and its impact on virus virulence. Ann Appl Biol. 2015;166:389–401.
Article
CAS
Google Scholar
Hasiów-Jaroszewska B, Jackowiak P, Borodynko N, Figlerowicz M, Pospieszny H. Quasispecies nature of Pepino mosaic virus and its evolutionary dynamics. Virus Genes. 2010;41:260–7.
Article
PubMed
Google Scholar
Eigen M, McCaskill J, Schuster P. Molecular quasi-species. J Phys Chem. 1988;92(24):6881–91.
Article
CAS
Google Scholar
Schneider WL, Roossinck MJ. Evolutionarily related Sindbis-like plant viruses maintain different levels of population diversity in a common host. J Virol. 2000;74:3130–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Legg JP, Thresh JM. Cassava mosaic virus disease in East Africa: a dynamic disease in a changing environment. Virus Res. 2000;71:135–49.
Article
CAS
PubMed
Google Scholar
Hasiów-Jaroszewska B, Borodynko N, Pospieszny H. Infectious RNA transcripts derived from cloned cDNA of a Pepino mosaic virus isolate. Arch Virol. 2009;154:853–6.
Article
PubMed
Google Scholar
Hasiów-Jaroszewska B, Komorowska B. A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3. J Virol Methods. 2013;193:1–5.
Article
PubMed
Google Scholar
Poelwijk FJ, Tanase-Nicola S, Kiviet DJ, Tans SJ. Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes. J Theor Biol. 2011;272:141–4.
Article
PubMed
Google Scholar
Dean AM, Thornton JW. Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet. 2007;8:675–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lalić J, Cuevas JM, Elena SF. Effect of host species on the distribution of mutational fitness effects for an RNA virus. PLoS Genet. 2011;7, e1002378.
Article
PubMed
PubMed Central
Google Scholar
Vale PF, Choisy M, Froissart R, Sanjuán R, Gandon S. The distribution of mutational fitness effects of phage ϕX174 on different hosts. Evolution. 2012;66:3495–507.
Article
CAS
PubMed
Google Scholar
Hasiów-Jaroszewska B, Minicka J, Pospieszny H. Cross-protection between different pathotypes of Pepino mosaic virus representing chilean 2 genotype. Acta Sci Pol Hortoru. 2014;13:177–85.
Google Scholar
Minicka J, Otulak K, Garbaczewska G, Pospieszny H, Hasiów-Jaroszewska B. Ultrastructural insights into tomato infections caused by three different pathotypes of Pepino mosaic virus and immunolocalization of viral coat proteins. Micron. 2015;79:84–92.
Article
CAS
PubMed
Google Scholar
Gómez P, Sempere RN, Aranda MA, Elena SF. Phylodynamics of Pepino mosaic virus in Spain. Eur J Plant Pathol. 2012;134:445–9.
Article
Google Scholar
Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature. 2006;439:344–8.
Article
CAS
PubMed
Google Scholar
Domingo E, Martíb V, Perales C, Grande-Pérez A, García-Arriaza Arias J. Viruses as quasispecies: biological implications. Curr Top Microbiol Immunol. 2006;299:51–82.
CAS
PubMed
Google Scholar
Jones RAC, Koenig R, Lesemann DE. Pepino mosaic virus, a new potexvirus from pepino (Solanum muricatum). Ann Appl Biol. 1980;94:61–8.
Article
CAS
Google Scholar
Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76:159–216.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lough TJ, Emerson SJ, Lucas WJ, Forster RLS. Trans-complementation of long-distance movement of White clover mosaic virus triple gene block (TGB) mutants: Phloem-associated movement of TGBp1. Virology. 2001;288:18–28.
Article
CAS
PubMed
Google Scholar
Pospieszny H, Hasiów B, Borodynko N. Characterization of two distinct Polish isolates of Pepino mosaic virus. Eur J Plant Pathol. 2008;122:443–5.
Article
CAS
Google Scholar
Gómez P, Sempere RN, Elena SF, Aranda MA. Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus. J Virol. 2009;83:12378–87.
Article
PubMed
PubMed Central
Google Scholar
Elena SF, Solé RV, Sardanyés J. Simple genomes, complex interactions: epistasis in RNA virus. Chaos. 2010;20:026106.
Article
PubMed
Google Scholar
Sanjuán R, Moya A, Elena SF. The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci USA. 2004;101:15376–9.
Elena SF. RNA virus genetic robustness: possible causes and some consequences. Curr Opin Virol. 2012;2:525–30.
Article
CAS
PubMed
Google Scholar
Stern A, Bianco S, Yeh MT, Wright CF, Butcher K, Tang C, Nielsen R, Andino R. Costs and benefits of mutational robustness in RNA viruses. Cell Rep. 2014;8:1–11.
Article
Google Scholar
Elena SF, Lalić J. Plant RNA virus fitness predictability: contribution of genetic and environmental factors. Plant Pathol. 2013;62:10–8.
Article
CAS
Google Scholar