{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T09:33:36Z","timestamp":1761989616818,"version":"3.41.2"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,9,14]],"date-time":"2021-09-14T00:00:00Z","timestamp":1631577600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002803","name":"Fondazione Cariplo","doi-asserted-by":"publisher","award":["2020-1353"],"award-info":[{"award-number":["2020-1353"]}],"id":[{"id":"10.13039\/501100002803","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bando Progetti Ricerca Covid 19","award":["CUP H44I20000470002"],"award-info":[{"award-number":["CUP H44I20000470002"]}]},{"name":"Italian Ministry of Health"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has triggered an unprecedented international effort to sequence complete viral genomes. We leveraged this wealth of information to characterize the substitution spectrum of SARS-CoV-2 and to compare it with those of other human and animal coronaviruses.<\/jats:p>\n               <jats:p>We show that, once nucleotide composition is taken into account, human and most animal coronaviruses display a mutation spectrum dominated by C to U and G to U substitutions, a feature that is not shared by other positive-sense RNA viruses. However, the proportions of C to U and G to U substitutions tend to decrease as divergence increases, suggesting that, whatever their origin, a proportion of these changes is subsequently eliminated by purifying selection. Analysis of the sequence context of C to U substitutions showed little evidence of apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-mediated editing and such contexts were similar for SARS-CoV-2 and Middle East respiratory syndrome coronavirus sampled from different hosts, despite different repertoires of APOBEC3 proteins in distinct species. Conversely, we found evidence that C to U and G to U changes affect CpG dinucleotides at a frequency higher than expected. Whereas this suggests ongoing selective reduction of CpGs, this effect alone cannot account for the substitution spectra. Finally, we show that, during the first months of SARS-CoV-2 pandemic spread, the frequency of both G to U and C to U substitutions increased. Our data suggest that the substitution spectrum of SARS-CoV-2 is determined by an interplay of factors, including intrinsic biases of the replication process, avoidance of CpG dinucleotides and other constraints exerted by the new host.<\/jats:p>","DOI":"10.1093\/bib\/bbab382","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T11:20:51Z","timestamp":1631100051000},"source":"Crossref","is-referenced-by-count":24,"title":["The substitution spectra of coronavirus genomes"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9291-5352","authenticated-orcid":false,"given":"Diego","family":"Forni","sequence":"first","affiliation":[{"name":"Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy"}]},{"given":"Rachele","family":"Cagliani","sequence":"additional","affiliation":[{"name":"Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy"}]},{"given":"Chiara","family":"Pontremoli","sequence":"additional","affiliation":[{"name":"Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy"}]},{"given":"Mario","family":"Clerici","sequence":"additional","affiliation":[{"name":"Department of Physiopathology and Transplantation, University of Milan, Milan, Italy"},{"name":"Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy"}]},{"given":"Manuela","family":"Sironi","sequence":"additional","affiliation":[{"name":"Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy"}]}],"member":"286","published-online":{"date-parts":[[2021,9,13]]},"reference":[{"key":"2022011921013082500_ref1","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1016\/j.cell.2020.04.026","article-title":"Imbalanced host response to SARS-CoV-2 drives development of COVID-19","volume":"181","author":"Blanco-Melo","year":"2020","journal-title":"Cell"},{"key":"2022011921013082500_ref2","doi-asserted-by":"crossref","first-page":"109126","DOI":"10.1016\/j.celrep.2021.109126","article-title":"Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities","volume":"35","author":"Hayn","year":"2021","journal-title":"Cell Rep"},{"key":"2022011921013082500_ref3","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1016\/j.chom.2021.05.004","article-title":"Innate immune and inflammatory responses to SARS-CoV-2: implications for COVID-19","volume":"29","author":"Lowery","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2022011921013082500_ref4","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab115","article-title":"Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients","author":"Mahmud","year":"2021","journal-title":"Brief Bioinform"},{"key":"2022011921013082500_ref5","doi-asserted-by":"crossref","first-page":"e1008737","DOI":"10.1371\/journal.ppat.1008737","article-title":"Interplay between SARS-CoV-2 and the type I interferon response","volume":"16","author":"Sa Ribero","year":"2020","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref6","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1016\/j.cell.2021.02.029","article-title":"COVID-19 and the human innate immune system","volume":"184","author":"Schultze","year":"2021","journal-title":"Cell"},{"key":"2022011921013082500_ref7","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1093\/bib\/bbaa235","article-title":"Network-based identification genetic effect of SARS-CoV-2 infections to idiopathic pulmonary fibrosis (IPF) patients","volume":"22","author":"Taz","year":"2021","journal-title":"Brief Bioinform"},{"key":"2022011921013082500_ref8","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1016\/j.chom.2020.04.017","article-title":"Heightened innate immune responses in the respiratory tract of COVID-19 patients","volume":"27","author":"Zhou","year":"2020","journal-title":"Cell Host Microbe"},{"issue":"12","key":"2022011921013082500_ref9","doi-asserted-by":"crossref","first-page":"e00411","DOI":"10.1128\/JVI.00411-20","article-title":"Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2","volume":"94","author":"Cagliani","year":"2020","journal-title":"J Virol"},{"key":"2022011921013082500_ref10","doi-asserted-by":"crossref","first-page":"e3001115","DOI":"10.1371\/journal.pbio.3001115","article-title":"Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen","volume":"19","author":"MacLean","year":"2021","journal-title":"PLoS Biol"},{"key":"2022011921013082500_ref11","doi-asserted-by":"crossref","first-page":"e1000896","DOI":"10.1371\/journal.ppat.1000896","article-title":"Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing","volume":"6","author":"Eckerle","year":"2010","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref12","doi-asserted-by":"crossref","first-page":"12135","DOI":"10.1128\/JVI.01296-07","article-title":"High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants","volume":"81","author":"Eckerle","year":"2007","journal-title":"J Virol"},{"key":"2022011921013082500_ref13","doi-asserted-by":"crossref","first-page":"e1003565","DOI":"10.1371\/journal.ppat.1003565","article-title":"Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics","volume":"9","author":"Smith","year":"2013","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref14","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.tim.2016.09.001","article-title":"Molecular evolution of human coronavirus genomes","volume":"25","author":"Forni","year":"2017","journal-title":"Trends Microbiol"},{"key":"2022011921013082500_ref15","doi-asserted-by":"crossref","first-page":"104351","DOI":"10.1016\/j.meegid.2020.104351","article-title":"Emergence of genomic diversity and recurrent mutations in SARS-CoV-2","volume":"83","author":"Dorp","year":"2020","journal-title":"Infect Genet Evol"},{"key":"2022011921013082500_ref16","doi-asserted-by":"crossref","first-page":"veaa061","DOI":"10.1093\/ve\/veaa061","article-title":"Temporal signal and the phylodynamic threshold of SARS-CoV-2","volume":"6","author":"Duchene","year":"2020","journal-title":"Virus Evol"},{"author":"Ghafari","key":"2022011921013082500_ref17"},{"key":"2022011921013082500_ref18","doi-asserted-by":"crossref","first-page":"104869","DOI":"10.1016\/j.meegid.2021.104869","article-title":"One year into the pandemic: short-term evolution of SARS-CoV-2 and emergence of new lineages","volume":"92","author":"Gonz\u00e1lez-Candelas","year":"2021","journal-title":"Infect Genet Evol"},{"key":"2022011921013082500_ref19","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1126\/science.abh2644","article-title":"Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil","volume":"372","author":"Faria","year":"2021","journal-title":"Science"},{"author":"Graf","key":"2022011921013082500_ref20"},{"author":"Rambaut","key":"2022011921013082500_ref21"},{"key":"2022011921013082500_ref22","doi-asserted-by":"crossref","first-page":"evab087","DOI":"10.1093\/gbe\/evab087","article-title":"Mutation rates and selection on synonymous mutations in SARS-CoV-2","volume":"13","author":"De Maio","year":"2021","journal-title":"Genome Biol Evol"},{"key":"2022011921013082500_ref23","doi-asserted-by":"crossref","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"},{"key":"2022011921013082500_ref24","doi-asserted-by":"crossref","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"},{"key":"2022011921013082500_ref25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0237689","article-title":"Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic","volume":"15","author":"Klimczak","year":"2020","journal-title":"PLoS One"},{"key":"2022011921013082500_ref26","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-74843-x","article-title":"Point mutation bias in SARS-CoV-2 variants results in increased ability to stimulate inflammatory responses","volume":"10","author":"Kosuge","year":"2020","journal-title":"Sci Rep"},{"key":"2022011921013082500_ref27","doi-asserted-by":"crossref","first-page":"761","DOI":"10.3390\/genes11070761","article-title":"Mutation patterns of human SARS-CoV-2 and bat RaTG13 coronavirus genomes are strongly biased towards C&gt;U transitions, indicating rapid evolution in their hosts","volume":"11","author":"Maty\u00e1\u0161ek","year":"2020","journal-title":"Genes (Basel)"},{"key":"2022011921013082500_ref28","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.bbrc.2020.10.092","article-title":"Host-directed editing of the SARS-CoV-2 genome","volume":"538","author":"Mourier","year":"2021","journal-title":"Biochem Biophys Res Commun"},{"key":"2022011921013082500_ref29","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1101\/gr.268961.120","article-title":"SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission","volume":"31","author":"Sapoval","year":"2021","journal-title":"Genome Res"},{"key":"2022011921013082500_ref30","doi-asserted-by":"crossref","first-page":"e00408","DOI":"10.1128\/mSphere.00408-20","article-title":"Rampant C\u2192U Hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: causes and consequences for their short- and long-term evolutionary trajectories","volume":"5","author":"Simmonds","year":"2020","journal-title":"mSphere"},{"key":"2022011921013082500_ref31","doi-asserted-by":"crossref","first-page":"e9648","DOI":"10.7717\/peerj.9648","article-title":"Excessive G-U transversions in novel allele variants in SARS-CoV-2 genomes","volume":"8","author":"Panchin","year":"2020","journal-title":"PeerJ"},{"key":"2022011921013082500_ref32","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.virol.2020.12.018","article-title":"Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution","volume":"556","author":"Ratcliff","year":"2021","journal-title":"Virology"},{"key":"2022011921013082500_ref33","doi-asserted-by":"crossref","first-page":"E3201","DOI":"10.1073\/pnas.1720897115","article-title":"Diversification of AID\/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity","volume":"115","author":"Krishnan","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022011921013082500_ref34","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/molbev\/msq338","article-title":"Analysis of reptilian APOBEC1 suggests that RNA editing may not be its ancestral function","volume":"28","author":"Severi","year":"2011","journal-title":"Mol Biol Evol"},{"key":"2022011921013082500_ref35","doi-asserted-by":"crossref","first-page":"e01930","DOI":"10.1128\/mBio.01930-20","article-title":"SARS-CoV-2 is restricted by zinc finger antiviral protein despite preadaptation to the low-CpG environment in humans","volume":"11","author":"Nchioua","year":"2020","journal-title":"MBio"},{"key":"2022011921013082500_ref36","doi-asserted-by":"crossref","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"},{"key":"2022011921013082500_ref37","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1073\/pnas.0607063104","article-title":"The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA","volume":"104","author":"Guo","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022011921013082500_ref38","doi-asserted-by":"crossref","first-page":"e0244025","DOI":"10.1371\/journal.pone.0244025","article-title":"Coronavirus genomes carry the signatures of their habitats","volume":"15","author":"Wei","year":"2020","journal-title":"PLoS One"},{"key":"2022011921013082500_ref39","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/molbev\/msaa094","article-title":"Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral Defense","volume":"37","author":"Xia","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2022011921013082500_ref40","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2022011921013082500_ref41","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"2022011921013082500_ref42","doi-asserted-by":"crossref","first-page":"e02381","DOI":"10.1128\/JVI.02381-16","article-title":"Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species","volume":"91","author":"Di Giallonardo","year":"2017","journal-title":"J Virol"},{"key":"2022011921013082500_ref43","doi-asserted-by":"crossref","first-page":"vez038","DOI":"10.1093\/ve\/vez038","article-title":"Dinucleotide evolutionary dynamics in influenza A virus","volume":"5","author":"Gu","year":"2019","journal-title":"Virus Evol"},{"key":"2022011921013082500_ref44","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1111\/j.1462-2920.2009.01901.x","article-title":"Metagenomic signatures of 86 microbial and viral metagenomes","volume":"11","author":"Willner","year":"2009","journal-title":"Environ Microbiol"},{"key":"2022011921013082500_ref45","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1126\/science.abe5901","article-title":"Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans","volume":"371","author":"Oude Munnink","year":"2020","journal-title":"Science"},{"key":"2022011921013082500_ref46","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"Cui","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2022011921013082500_ref47","doi-asserted-by":"crossref","first-page":"7","DOI":"10.2807\/1560-7917.ES2015.20.25.21163","article-title":"Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2015","volume":"20","author":"Cowling","year":"2015","journal-title":"Euro Surveill"},{"key":"2022011921013082500_ref48","doi-asserted-by":"crossref","first-page":"798","DOI":"10.3390\/v11090798","article-title":"Updated phylogeny of chikungunya virus suggests lineage-specific RNA architecture","volume":"11","author":"Schneider","year":"2019","journal-title":"Viruses"},{"key":"2022011921013082500_ref49","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1126\/science.aat7115","article-title":"Genomic and epidemiological monitoring of yellow fever virus transmission potential","volume":"361","author":"Faria","year":"2018","journal-title":"Science"},{"key":"2022011921013082500_ref50","doi-asserted-by":"crossref","first-page":"3842","DOI":"10.1128\/JVI.01880-10","article-title":"Restriction of porcine endogenous retrovirus by porcine APOBEC3 cytidine deaminases","volume":"85","author":"D\u00f6rrschuck","year":"2011","journal-title":"J Virol"},{"issue":"4","key":"2022011921013082500_ref51","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.cell.2020.06.043","article-title":"Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus","volume":"182","author":"Korber","year":"2020","journal-title":"Cell"},{"key":"2022011921013082500_ref52","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1186\/s12967-020-02344-6","article-title":"Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant","volume":"18","author":"Pachetti","year":"2020","journal-title":"J Transl Med"},{"key":"2022011921013082500_ref53","doi-asserted-by":"crossref","first-page":"vey004","DOI":"10.1093\/ve\/vey004","article-title":"Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy","volume":"4","author":"Kautz","year":"2018","journal-title":"Virus Evol"},{"key":"2022011921013082500_ref54","doi-asserted-by":"crossref","first-page":"e00834","DOI":"10.1128\/JVI.00834-19","article-title":"Tyr82 amino acid mutation in PB1 polymerase induces an influenza virus mutator phenotype","volume":"93","author":"Naito","year":"2019","journal-title":"J Virol"},{"key":"2022011921013082500_ref55","doi-asserted-by":"crossref","first-page":"e1005009","DOI":"10.1371\/journal.ppat.1005009","article-title":"Sequence-specific fidelity alterations associated with West Nile virus attenuation in mosquitoes","volume":"11","author":"Van Slyke","year":"2015","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref56","doi-asserted-by":"crossref","first-page":"e1007610","DOI":"10.1371\/journal.ppat.1007610","article-title":"Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts","volume":"15","author":"Warmbrod","year":"2019","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref57","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/molbev\/msm001","article-title":"Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution","volume":"24","author":"Pybus","year":"2007","journal-title":"Mol Biol Evol"},{"key":"2022011921013082500_ref58","doi-asserted-by":"crossref","first-page":"5972","DOI":"10.1111\/mec.12524","article-title":"On the accumulation of deleterious mutations during range expansions","volume":"22","author":"Peischl","year":"2013","journal-title":"Mol Ecol"},{"key":"2022011921013082500_ref59","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1001\/jama.2020.0757","article-title":"Coronavirus infections-more than just the common cold","volume":"323","author":"Paules","year":"2020","journal-title":"JAMA"},{"key":"2022011921013082500_ref60","first-page":"1","article-title":"Porcine coronaviruses: overview of the state of the art","author":"Turlewicz-Podbielska","year":"2021","journal-title":"Virol Sin"},{"key":"2022011921013082500_ref61","doi-asserted-by":"crossref","first-page":"643220","DOI":"10.3389\/fvets.2021.643220","article-title":"Bovine coronavirus and the associated diseases","volume":"8","author":"Vlasova","year":"2021","journal-title":"Front Vet Sci"},{"key":"2022011921013082500_ref62","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"V'kovski","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2022011921013082500_ref63","doi-asserted-by":"crossref","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"},{"key":"2022011921013082500_ref64","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1073\/pnas.1914183116","article-title":"Retroviruses drive the rapid evolution of mammalian APOBEC3 genes","volume":"117","author":"Ito","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022011921013082500_ref65","doi-asserted-by":"crossref","first-page":"5960","DOI":"10.1038\/s41598-018-24448-2","article-title":"APOBEC3-mediated restriction of RNA virus replication","volume":"8","author":"Milewska","year":"2018","journal-title":"Sci Rep"},{"key":"2022011921013082500_ref66","doi-asserted-by":"crossref","first-page":"14762","DOI":"10.1074\/jbc.270.24.14762","article-title":"Apobec-1, the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme, is a novel RNA-binding protein","volume":"270","author":"Anant","year":"1995","journal-title":"J Biol Chem"},{"key":"2022011921013082500_ref67","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1093\/nar\/22.10.1874","article-title":"Molecular cloning of a human small intestinal apolipoprotein B mRNA editing protein","volume":"22","author":"Hadjiagapiou","year":"1994","journal-title":"Nucl Acids Res"},{"key":"2022011921013082500_ref68","doi-asserted-by":"crossref","first-page":"9887","DOI":"10.1074\/jbc.271.17.9887","article-title":"Targeted disruption of the mouse apobec-1 gene abolishes apolipoprotein B mRNA editing and eliminates apolipoprotein B48","volume":"271","author":"Hirano","year":"1996","journal-title":"J Biol Chem"},{"key":"2022011921013082500_ref69","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/nsmb.1975","article-title":"Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs","volume":"18","author":"Rosenberg","year":"2011","journal-title":"Nat Struct Mol Biol"},{"key":"2022011921013082500_ref70","doi-asserted-by":"crossref","first-page":"e5969","DOI":"10.1371\/journal.pone.0005969","article-title":"Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system","volume":"4","author":"Greenbaum","year":"2009","journal-title":"PLoS One"},{"key":"2022011921013082500_ref71","doi-asserted-by":"crossref","first-page":"2428","DOI":"10.1093\/molbev\/msab036","article-title":"The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2","volume":"38","author":"Di Gioacchino","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2022011921013082500_ref72","doi-asserted-by":"crossref","first-page":"veaa057","DOI":"10.1093\/ve\/veaa057","article-title":"Intra-genome variability in the dinucleotide composition of SARS-CoV-2","volume":"6","author":"Digard","year":"2020","journal-title":"Virus Evol"},{"key":"2022011921013082500_ref73","doi-asserted-by":"crossref","first-page":"e1000079","DOI":"10.1371\/journal.ppat.1000079","article-title":"Patterns of evolution and host gene mimicry in influenza and other RNA viruses","volume":"4","author":"Greenbaum","year":"2008","journal-title":"PLoS Pathog"},{"key":"2022011921013082500_ref74","doi-asserted-by":"crossref","first-page":"e3001201","DOI":"10.1371\/journal.pbio.3001201","article-title":"The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors","volume":"19","author":"Fros","year":"2021","journal-title":"PLoS Biol"},{"key":"2022011921013082500_ref75","doi-asserted-by":"crossref","first-page":"1610","DOI":"10.1038\/s41590-019-0527-6","article-title":"RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions","volume":"20","author":"Schwerk","year":"2019","journal-title":"Nat Immunol"},{"key":"2022011921013082500_ref76","doi-asserted-by":"crossref","first-page":"9372","DOI":"10.1073\/pnas.1201130109","article-title":"RNA 3\u2032-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10\/nsp14 exoribonuclease complex","volume":"109","author":"Bouvet","year":"2012","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/1\/bbab382\/42229475\/bbab382.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/1\/bbab382\/42229475\/bbab382.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,19]],"date-time":"2022-01-19T21:03:02Z","timestamp":1642626182000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbab382\/6369601"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,13]]},"references-count":76,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,1,17]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab382","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2022,1]]},"published":{"date-parts":[[2021,9,13]]},"article-number":"bbab382"}}