{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T01:19:34Z","timestamp":1789607974359,"version":"build-2803163510"},"reference-count":73,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T00:00:00Z","timestamp":1737072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The study of mutational processes in somatic genomes has gained recent momentum, uncovering a wide array of endogenous and exogenous factors associated with somatic changes. However, the overall landscape of mutational processes in germline mutations across the tree of life and associated evolutionary driving forces are rather unclear. In this study, we analyzed mutational processes in single-stranded RNA (ssRNA) viruses which are known to jump between different hosts with divergent exogenous environments. We found that mutational spectra in different ssRNA viruses differ significantly and are mainly associated with their genetic divergence. Surprisingly, host environments contribute much less significantly to the mutational spectrum, challenging the prevailing view that the exogenous cellular environment is a major determinant of the mutational spectrum in viruses. To dissect the evolutionary forces shaping viral spectra, we selected two important scenarios, namely the inter-host evolution between different viral strains as well as the intra-host evolution. In both scenarios, we found mutational spectra change significantly through space and time, strongly correlating with levels of natural selection. Combining the mutations across all ssRNA viruses, we identified a suite of mutational signatures with varying degrees of similarity to somatic signatures in humans, indicating universal and divergent mutational processes across the tree of life. Taken together, we unraveled an unprecedented dynamic landscape of mutational processes in ssRNA viruses, pinpointing important evolutionary forces shaping fast evolution of mutational spectra in different species.<\/jats:p>","DOI":"10.1093\/molbev\/msaf009","type":"journal-article","created":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T18:42:52Z","timestamp":1737139372000},"source":"Crossref","is-referenced-by-count":5,"title":["An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-7284-114X","authenticated-orcid":false,"given":"Yue","family":"Yang","sequence":"first","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5850-7299","authenticated-orcid":false,"given":"Xinyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2527-9733","authenticated-orcid":false,"given":"Tingting","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2621-5330","authenticated-orcid":false,"given":"Fengyuan","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5967-4948","authenticated-orcid":false,"given":"Yu S","family":"Huang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica , Chinese Academy of Sciences, Shanghai 201203 ,","place":["China"]},{"name":"Genecast Biotechnology Co., Ltd. , Wuxi 214105 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4590-7787","authenticated-orcid":false,"given":"Yanhua","family":"Qu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7091-4199","authenticated-orcid":false,"given":"Miao","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center , Guangzhou 510060 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1428-8426","authenticated-orcid":false,"given":"Liang","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5990-6585","authenticated-orcid":false,"given":"Mo","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Sino-French Hoffmann Institute, Guangzhou Medical University , Guangzhou 511436 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7938-0226","authenticated-orcid":false,"given":"Weiwei","family":"Zhai","sequence":"additional","affiliation":[{"name":"Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,17]]},"reference":[{"issue":"12","key":"2025022411262693000_msaf009-B1","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1038\/ng.3441","article-title":"Clock-like mutational processes in human somatic cells","volume":"47","author":"Alexandrov","year":"2015","journal-title":"Nat Genet"},{"issue":"7793","key":"2025022411262693000_msaf009-B2","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","article-title":"The repertoire of mutational signatures in human cancer","volume":"578","author":"Alexandrov","year":"2020","journal-title":"Nature"},{"issue":"7463","key":"2025022411262693000_msaf009-B3","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"issue":"10","key":"2025022411262693000_msaf009-B4","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad213","article-title":"Evolution of the mutation spectrum across a mammalian phylogeny","volume":"40","author":"Beichman","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2025022411262693000_msaf009-B5","doi-asserted-by":"publisher","first-page":"msad085","DOI":"10.1093\/molbev\/msad085","article-title":"Evolution of the SARS-CoV-2 mutational spectrum","volume":"40","author":"Bloom","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"9","key":"2025022411262693000_msaf009-B6","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1038\/ng.3378","article-title":"An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers","volume":"47","author":"Chan","year":"2015","journal-title":"Nat Genet"},{"issue":"7","key":"2025022411262693000_msaf009-B7","doi-asserted-by":"publisher","first-page":"1430","DOI":"10.1093\/molbev\/msz075","article-title":"Tumorigenesis as the paradigm of quasi-neutral molecular evolution","volume":"36","author":"Chen","year":"2019","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2025022411262693000_msaf009-B8","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1038\/s41559-020-1124-7","article-title":"Dissimilation of synonymous codon usage bias in virus\u2013host coevolution due to translational selection","volume":"4","author":"Chen","year":"2020","journal-title":"Nat Ecol Evol."},{"issue":"7","key":"2025022411262693000_msaf009-B9","doi-asserted-by":"publisher","first-page":"1198","DOI":"10.1093\/cid\/ciy1065","article-title":"Passage adaptation correlates with the reduced efficacy of the influenza vaccine","volume":"69","author":"Chen","year":"2019","journal-title":"Clin Infect Dis"},{"issue":"12","key":"2025022411262693000_msaf009-B10","doi-asserted-by":"publisher","first-page":"3133","DOI":"10.1093\/molbev\/msw190","article-title":"Dynamic convergent evolution drives the passage adaptation across 48 years\u2019 history of H3N2 influenza evolution","volume":"33","author":"Chen","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"8004","key":"2025022411262693000_msaf009-B11","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1038\/s41586-024-07054-3","article-title":"Deep whole-genome analysis of 494 hepatocellular carcinomas","volume":"627","author":"Chen","year":"2024","journal-title":"Nature"},{"issue":"5","key":"2025022411262693000_msaf009-B12","doi-asserted-by":"publisher","first-page":"e1005646","DOI":"10.1371\/journal.ppat.1005646","article-title":"Minimal contribution of APOBEC3-induced G-to-A hypermutation to HIV-1 recombination and genetic variation","volume":"12","author":"Delviks-Frankenberry","year":"2016","journal-title":"PLoS Pathog"},{"issue":"2","key":"2025022411262693000_msaf009-B13","doi-asserted-by":"publisher","first-page":"nwab220","DOI":"10.1093\/nsr\/nwab220","article-title":"Mutation signatures inform the natural host of SARS-CoV-2","volume":"9","author":"Deng","year":"2022","journal-title":"Natl Sci Rev"},{"issue":"21","key":"2025022411262693000_msaf009-B14","doi-asserted-by":"publisher","first-page":"e2013798118","DOI":"10.1073\/pnas.2013798118","article-title":"Nonparametric coalescent inference of mutation spectrum history and demography","volume":"118","author":"DeWitt","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"2025022411262693000_msaf009-B15","doi-asserted-by":"publisher","first-page":"btad756","DOI":"10.1093\/bioinformatics\/btad756","article-title":"Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment","volume":"39","author":"Diaz-Gay","year":"2023","journal-title":"Bioinformatics"},{"issue":"5663","key":"2025022411262693000_msaf009-B16","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1126\/science.1093616","article-title":"Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA","volume":"303","author":"Diebold","year":"2004","journal-title":"Science"},{"issue":"25","key":"2025022411262693000_msaf009-B17","doi-asserted-by":"publisher","first-page":"eabb5813","DOI":"10.1126\/sciadv.abb5813","article-title":"Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2","volume":"6","author":"Di Giorgio","year":"2020","journal-title":"Sci Adv."},{"issue":"3","key":"2025022411262693000_msaf009-B18","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1093\/sysbio\/22.3.240","article-title":"Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters","volume":"22","author":"Felsenstein","year":"1973","journal-title":"Syst Biol."},{"key":"2025022411262693000_msaf009-B19","volume-title":"An R companion to applied regression","author":"Fox","year":"2018"},{"issue":"1","key":"2025022411262693000_msaf009-B20","doi-asserted-by":"publisher","first-page":"evab104","DOI":"10.1093\/gbe\/evab104","article-title":"Mutational signatures of replication timing and epigenetic modification persist through the global divergence of mutation Spectra across the great ape phylogeny","volume":"14","author":"Goldberg","year":"2022","journal-title":"Genome Biol Evol."},{"issue":"2","key":"2025022411262693000_msaf009-B21","doi-asserted-by":"publisher","first-page":"102116","DOI":"10.1016\/j.isci.2021.102116","article-title":"Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity","volume":"24","author":"Graudenzi","year":"2021","journal-title":"iScience"},{"issue":"23","key":"2025022411262693000_msaf009-B22","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"issue":"11","key":"2025022411262693000_msaf009-B23","doi-asserted-by":"publisher","first-page":"3439","DOI":"10.1073\/pnas.1418652112","article-title":"Evidence for recent, population-specific evolution of the human mutation rate","volume":"112","author":"Harris","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025022411262693000_msaf009-B24","volume-title":"Principles of population genetics","author":"Hartl","year":"1997"},{"issue":"9","key":"2025022411262693000_msaf009-B25","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/nrg3729","article-title":"Mechanisms underlying mutational signatures in human cancers","volume":"15","author":"Helleday","year":"2014","journal-title":"Nat Rev Genet"},{"issue":"9","key":"2025022411262693000_msaf009-B26","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad204","article-title":"Intra- vs. interhost evolution of SARS-CoV-2 driven by uncorrelated selection \u2013 the evolution thwarted","volume":"40","author":"Hou","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"11","key":"2025022411262693000_msaf009-B27","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100179","article-title":"Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor","volume":"2","author":"Islam","year":"2022","journal-title":"Cell Genom"},{"issue":"5","key":"2025022411262693000_msaf009-B28","doi-asserted-by":"publisher","first-page":"669","DOI":"10.2105\/AJPH.2019.305557","article-title":"Fifty years of influenza A(H3N2) following the pandemic of 1968","volume":"110","author":"Jester","year":"2020","journal-title":"Am J Public Health"},{"issue":"4","key":"2025022411262693000_msaf009-B29","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/s41579-020-00449-9","article-title":"Viral and host heterogeneity and their effects on the viral life cycle","volume":"19","author":"Jones","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"2025022411262693000_msaf009-B30","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1093\/genetics\/61.3.763","article-title":"The average number of generations until fixation of a mutant gene in a finite population","volume":"61","author":"Kimura","year":"1969","journal-title":"Genetics"},{"issue":"11","key":"2025022411262693000_msaf009-B31","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.1007\/s00018-010-0277-y","article-title":"Oxidative damage to RNA: mechanisms, consequences, and diseases","volume":"67","author":"Kong","year":"2010","journal-title":"Cell Mol Life Sci"},{"issue":"2","key":"2025022411262693000_msaf009-B32","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/molbev\/msaa247","article-title":"Biased mutation and selection in RNA viruses","volume":"38","author":"Kustin","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2025022411262693000_msaf009-B33","doi-asserted-by":"publisher","first-page":"e1011795","DOI":"10.1371\/journal.pcbi.1011795","article-title":"Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules","volume":"20","author":"Lamb","year":"2024","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"2025022411262693000_msaf009-B34","doi-asserted-by":"publisher","first-page":"110205","DOI":"10.1016\/j.celrep.2021.110205","article-title":"Two-step fitness selection for intra-host variations in SARS-CoV-2","volume":"38","author":"Li","year":"2022","journal-title":"Cell Rep"},{"issue":"1","key":"2025022411262693000_msaf009-B35","doi-asserted-by":"publisher","first-page":"lqad005","DOI":"10.1093\/nargab\/lqad005","article-title":"mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery","volume":"5","author":"Liu","year":"2023","journal-title":"NAR Genom Bioinform"},{"issue":"1","key":"2025022411262693000_msaf009-B36","doi-asserted-by":"publisher","first-page":"1948","DOI":"10.1038\/s41467-018-04273-x","article-title":"AID\/APOBEC-like cytidine deaminases are ancient innate immune mediators in invertebrates","volume":"9","author":"Liu","year":"2018","journal-title":"Nat Commun"},{"issue":"8","key":"2025022411262693000_msaf009-B37","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1016\/j.tig.2010.05.003","article-title":"Evolution of the mutation rate","volume":"26","author":"Lynch","year":"2010","journal-title":"Trends Genet"},{"issue":"11","key":"2025022411262693000_msaf009-B38","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1038\/nrg.2016.104","article-title":"Genetic drift, selection and the evolution of the mutation rate","volume":"17","author":"Lynch","year":"2016","journal-title":"Nat Rev Genet"},{"issue":"5","key":"2025022411262693000_msaf009-B39","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1016\/j.cell.2017.09.042","article-title":"Universal patterns of selection in cancer and somatic tissues","volume":"171","author":"Martincorena","year":"2017","journal-title":"Cell"},{"issue":"5","key":"2025022411262693000_msaf009-B40","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol."},{"issue":"14","key":"2025022411262693000_msaf009-B41","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1093\/bioinformatics\/bty121","article-title":"Parallelization of MAFFT for large-scale multiple sequence alignments","volume":"34","author":"Nakamura","year":"2018","journal-title":"Bioinformatics"},{"issue":"2","key":"2025022411262693000_msaf009-B42","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1093\/nar\/gkac1238","article-title":"Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome","volume":"51","author":"Nakata","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2025022411262693000_msaf009-B43","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1080\/10635150290102393","article-title":"Mapping mutations on phylogenies","volume":"51","author":"Nielsen","year":"2002","journal-title":"Syst Biol"},{"issue":"D1","key":"2025022411262693000_msaf009-B44","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"6670","key":"2025022411262693000_msaf009-B45","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1126\/science.adg8116","article-title":"APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016","volume":"382","author":"O\u2019Toole","year":"2023","journal-title":"Science"},{"issue":"3","key":"2025022411262693000_msaf009-B46","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1128\/MMBR.00004-08","article-title":"Cross-species virus transmission and the emergence of new epidemic diseases","volume":"72","author":"Parrish","year":"2008","journal-title":"Microbiol Mol Biol Rev"},{"issue":"4","key":"2025022411262693000_msaf009-B47","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1111\/j.1745-9125.1998.tb01268.x","article-title":"Using the correct statistical test for the equality of regression coefficients","volume":"36","author":"Paternoster","year":"1998","journal-title":"Criminology"},{"issue":"10","key":"2025022411262693000_msaf009-B48","doi-asserted-by":"publisher","first-page":"e1008080","DOI":"10.1371\/journal.ppat.1008080","article-title":"Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies","volume":"15","author":"Perelygina","year":"2019","journal-title":"PLoS Pathog"},{"issue":"9","key":"2025022411262693000_msaf009-B49","doi-asserted-by":"publisher","first-page":"e238","DOI":"10.1016\/S1473-3099(20)30484-9","article-title":"Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics","volume":"20","author":"Petersen","year":"2020","journal-title":"Lancet Infect Dis"},{"issue":"12","key":"2025022411262693000_msaf009-B50","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1038\/s41564-022-01268-9","article-title":"Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission","volume":"7","author":"Pickering","year":"2022","journal-title":"Nat Microbiol"},{"issue":"11","key":"2025022411262693000_msaf009-B51","doi-asserted-by":"publisher","first-page":"evab240","DOI":"10.1093\/gbe\/evab240","article-title":"ADAR editing in viruses: an evolutionary force to reckon with","volume":"13","author":"Piontkivska","year":"2021","journal-title":"Genome Biol Evol"},{"issue":"573","key":"2025022411262693000_msaf009-B52","doi-asserted-by":"publisher","first-page":"eabe2555","DOI":"10.1126\/scitranslmed.abe2555","article-title":"Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2","volume":"12","author":"Popa","year":"2020","journal-title":"Sci Transl Med."},{"issue":"W1","key":"2025022411262693000_msaf009-B53","doi-asserted-by":"publisher","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2025022411262693000_msaf009-B54","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1093\/molbev\/msaa188","article-title":"Evidence for strong mutation bias toward, and selection against, U content in SARS-CoV-2: implications for vaccine design","volume":"38","author":"Rice","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"6","key":"2025022411262693000_msaf009-B55","doi-asserted-by":"publisher","first-page":"e2112663119","DOI":"10.1073\/pnas.2112663119","article-title":"Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2","volume":"119","author":"Ringlander","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"2025022411262693000_msaf009-B56","doi-asserted-by":"publisher","first-page":"mgen001018","DOI":"10.1099\/mgen.0.001018","article-title":"A lung-specific mutational signature enables inference of viral and bacterial respiratory niche","volume":"9","author":"Ruis","year":"2023","journal-title":"Microb Genom"},{"issue":"1","key":"2025022411262693000_msaf009-B57","doi-asserted-by":"publisher","first-page":"7091","DOI":"10.1038\/s41467-023-42916-w","article-title":"Mutational spectra are associated with bacterial niche","volume":"14","author":"Ruis","year":"2023","journal-title":"Nat Commun"},{"issue":"7987","key":"2025022411262693000_msaf009-B58","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/s41586-023-06649-6","article-title":"A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes","volume":"623","author":"Sanderson","year":"2023","journal-title":"Nature"},{"issue":"10","key":"2025022411262693000_msaf009-B59","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1038\/ng.3659","article-title":"Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance","volume":"48","author":"Secrier","year":"2016","journal-title":"Nat Genet"},{"issue":"4","key":"2025022411262693000_msaf009-B60","doi-asserted-by":"publisher","first-page":"100159","DOI":"10.1016\/j.xinn.2021.100159","article-title":"Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process","volume":"2","author":"Shan","year":"2021","journal-title":"Innovation (Camb)"},{"issue":"13","key":"2025022411262693000_msaf009-B61","doi-asserted-by":"publisher","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data\u2014from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveill"},{"issue":"7239","key":"2025022411262693000_msaf009-B62","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1038\/nature07943","article-title":"The cancer genome","volume":"458","author":"Stratton","year":"2009","journal-title":"Nature"},{"issue":"5","key":"2025022411262693000_msaf009-B63","doi-asserted-by":"publisher","first-page":"2458","DOI":"10.1128\/JVI.02138-10","article-title":"Double-stranded RNA adenosine deaminase ADAR-1-induced hypermutated genomes among inactivated seasonal influenza and live attenuated measles virus vaccines","volume":"85","author":"Suspene","year":"2011","journal-title":"J Virol"},{"issue":"7674","key":"2025022411262693000_msaf009-B64","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/nature24039","article-title":"CG dinucleotide suppression enables antiviral defence targeting non-self RNA","volume":"550","author":"Takata","year":"2017","journal-title":"Nature"},{"issue":"5","key":"2025022411262693000_msaf009-B65","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1099\/vir.0.19462-0","article-title":"Conserved RNA secondary structures in Flaviviridae genomes","volume":"85","author":"Thurner","year":"2004","journal-title":"J Gen Virol."},{"key":"2025022411262693000_msaf009-B66","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.meegid.2018.05.034","article-title":"The adaptation of codon usage of +ssRNA viruses to their hosts","volume":"63","author":"Tian","year":"2018","journal-title":"Infect Genet Evol."},{"issue":"2","key":"2025022411262693000_msaf009-B67","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/s41588-022-01296-5","article-title":"APOBEC mutagenesis is a common process in normal human small intestine","volume":"55","author":"Wang","year":"2023","journal-title":"Nat Genet"},{"issue":"12","key":"2025022411262693000_msaf009-B68","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1016\/j.jgg.2021.12.003","article-title":"Evidence for a mouse origin of the SARS-CoV-2 Omicron variant","volume":"48","author":"Wei","year":"2021","journal-title":"J Genet Genomics"},{"issue":"3","key":"2025022411262693000_msaf009-B69","doi-asserted-by":"publisher","first-page":"100221","DOI":"10.1016\/j.xcrm.2021.100221","article-title":"Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2","volume":"2","author":"Wilson","year":"2021","journal-title":"Cell Rep Med"},{"issue":"21","key":"2025022411262693000_msaf009-B70","doi-asserted-by":"publisher","first-page":"8176","DOI":"10.3390\/ijms21218176","article-title":"The roles of host 5-methylcytosine RNA methyltransferases during viral infections","volume":"21","author":"Wnuk","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"8","key":"2025022411262693000_msaf009-B71","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1038\/s12276-021-00658-z","article-title":"Mutational spectrum of SARS-CoV-2 during the global pandemic","volume":"53","author":"Yi","year":"2021","journal-title":"Exp Mol Med"},{"key":"2025022411262693000_msaf009-B72","first-page":"7110","article-title":"Methylated CpG dinucleotides are the preferential targets for G-to-T transversion mutations induced by benzo[a]pyrene diol epoxide in mammalian cells: similarities with the p53 mutation Spectrum in smoking-associated lung cancers","volume":"61","author":"Yoon","year":"2001","journal-title":"Cancer Res"},{"issue":"4","key":"2025022411262693000_msaf009-B73","doi-asserted-by":"publisher","first-page":"e2300109","DOI":"10.1002\/bies.202300109","article-title":"NLRC5\/MHC class I transactivator: a key target for immune escape by SARS-CoV-2","volume":"46","author":"Zhu","year":"2024","journal-title":"Bioessays"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msaf009\/61489298\/msaf009.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/2\/msaf009\/61489298\/msaf009.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/2\/msaf009\/61489298\/msaf009.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T11:27:13Z","timestamp":1740396433000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msaf009\/7959759"}},"subtitle":[],"editor":[{"given":"Kelley","family":"Harris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,1,17]]},"references-count":73,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,2,3]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msaf009","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,2]]},"published":{"date-parts":[[2025,1,17]]},"article-number":"msaf009"}}