{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T06:41:05Z","timestamp":1782369665068,"version":"3.54.5"},"reference-count":47,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,4,30]],"date-time":"2020-04-30T00:00:00Z","timestamp":1588204800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first occurred in Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a high mortality rate, and has spread around the world. To gain an understanding of the evolution of the newly emerging SARS-CoV-2, we herein analyzed the codon usage pattern of SARS-CoV-2. For this purpose, we compared the codon usage of SARS-CoV-2 with that of other viruses belonging to the subfamily of Orthocoronavirinae. We found that SARS-CoV-2 has a high AU content that strongly influences its codon usage, which appears to be better adapted to the human host. We also studied the evolutionary pressures that influence the codon usage of five conserved coronavirus genes encoding the viral replicase, spike, envelope, membrane and nucleocapsid proteins. We found different patterns of both mutational bias and natural selection that affect the codon usage of these genes. Moreover, we show here that the two integral membrane proteins (matrix and envelope) tend to evolve slowly by accumulating nucleotide mutations on their corresponding genes. Conversely, genes encoding nucleocapsid (N), viral replicase and spike proteins (S), although they are regarded as are important targets for the development of vaccines and antiviral drugs, tend to evolve faster in comparison to the two genes mentioned above. Overall, our results suggest that the higher divergence observed for the latter three genes could represent a significant barrier in the development of antiviral therapeutics against SARS-CoV-2.<\/jats:p>","DOI":"10.3390\/v12050498","type":"journal-article","created":{"date-parts":[[2020,5,4]],"date-time":"2020-05-04T03:29:39Z","timestamp":1588562979000},"page":"498","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":81,"title":["Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2179-4677","authenticated-orcid":false,"given":"Maddalena","family":"Dilucca","sequence":"first","affiliation":[{"name":"Physics Department, Sapienza University of Rome, 00185 Rome, Italy"},{"name":"Liceo Scientifico Statale Augusto Righi, 00187 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Forcelloni","sequence":"additional","affiliation":[{"name":"Physics Department, Sapienza University of Rome, 00185 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5971-0010","authenticated-orcid":false,"given":"Alexandros G.","family":"Georgakilas","sequence":"additional","affiliation":[{"name":"DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campous, 15780 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Giansanti","sequence":"additional","affiliation":[{"name":"Physics Department, Sapienza University of Rome, 00185 Rome, Italy"},{"name":"INFN Roma1 Unit, 00185 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0815-3808","authenticated-orcid":false,"given":"Athanasia","family":"Pavlopoulou","sequence":"additional","affiliation":[{"name":"Izmir Biomedicine and Genome Center (IBG), 35340 Balcova, Izmir, Turkey"},{"name":"Izmir International Biomedicine and Genome Institute, Dokuz Eyl\u00fcl University, 35340 Balcova, Izmir, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1146\/annurev.mi.44.100190.001511","article-title":"Coronavirus: Organization, replication and expression of genome","volume":"44","author":"Lai","year":"1990","journal-title":"Annu. Vet. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.virusres.2006.01.017","article-title":"Nidovirales: Evolving the largest RNA virus genome","volume":"117","author":"Gorbalenya","year":"2006","journal-title":"Virus Res."},{"key":"ref_3","unstructured":"Siddell, S.G., Ziebuhr, J., and Snijder, E.J. (2005). Coronaviruses, Toroviruses, and Arteriviruses. Topley Wilson\u2019s Microbiol. Microb. Infect."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1804","DOI":"10.3390\/v2081803","article-title":"Coronavirus genomics and bioinformatics analysis","volume":"2","author":"Woo","year":"2010","journal-title":"Viruses"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/423240a","article-title":"Aetiology: Koch\u2019s postulates fulfilled for SARS virus","volume":"423","author":"Fouchier","year":"2003","journal-title":"Nature"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nm1024","article-title":"Identification of a new human coronavirus","volume":"10","author":"Pyrc","year":"2004","journal-title":"Nat. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1128\/JVI.79.2.884-895.2005","article-title":"Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia","volume":"79","author":"Woo","year":"2005","journal-title":"J. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1056\/NEJMoa1211721","article-title":"Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia","volume":"367","author":"Zaki","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Andersen, K.G., Rambaut, A., Lipkin, W.I., Holmes, E., and Garry, R.F. (2020). The proximal origin of SARS-CoV-2. Nat. Med.","DOI":"10.1038\/s41591-020-0820-9"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41564-020-0695-z","article-title":"The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2","volume":"5","author":"Gorbalenya","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_11","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":"ref_12","doi-asserted-by":"crossref","first-page":"113806","DOI":"10.1016\/j.jviromet.2019.113806","article-title":"Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design","volume":"277","author":"Sheikh","year":"2020","journal-title":"J. Virol. Methods"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Belalov, I.S., and Lukashev, A.N. (2013). Causes and Implications of Codon Usage Bias in RNA Viruses. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0056642"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.gene.2018.04.017","article-title":"Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes","volume":"663","author":"Dilucca","year":"2018","journal-title":"Gene"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1007\/s00239-019-09921-4","article-title":"Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome","volume":"88","author":"Forcelloni","year":"2020","journal-title":"J. Mol. Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"r49","DOI":"10.1093\/nar\/8.1.197-c","article-title":"Codon catalog usage and the genome hypothesis","volume":"8","author":"Grantham","year":"1980","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0168-1702(02)00309-X","article-title":"The extent of codon usage bias in human RNA viruses and its evolutionary origin","volume":"92","author":"Jenkins","year":"2003","journal-title":"Virus Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"110337","DOI":"10.18632\/oncotarget.22738","article-title":"Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus","volume":"8","author":"Chen","year":"2017","journal-title":"Oncotarget"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1007\/BF02099948","article-title":"An evolutionary perspective on synonymous codon usage in unicellular organisms","volume":"24","author":"Sharp","year":"1986","journal-title":"J. Mol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1126\/science.275.5298.343","article-title":"An information-intensive approach to the molecular pharmacology of cancer","volume":"275","author":"Weinstein","year":"1997","journal-title":"Science"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1093\/molbev\/mst064","article-title":"DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution","volume":"30","author":"Xia","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/nar\/15.3.1281","article-title":"The codon adaptation index\u2014A measure of directional synonymous codon usage bias, and its potential applications","volume":"15","author":"Sharp","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1080\/21505594.2018.1492863","article-title":"Insights into the genetic and host adaptability of emerging porcine circovirus","volume":"9","author":"Lia","year":"2018","journal-title":"Virulence"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/0378-1119(90)90491-9","article-title":"The \u2019effective number of codons\u2019 used in a gene","volume":"87","author":"Wright","year":"1990","journal-title":"Gene"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2653","DOI":"10.1073\/pnas.85.8.2653","article-title":"Directional mutation pressure and neutral molecular evolution","volume":"85","author":"Sueoka","year":"1988","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"4467","DOI":"10.1038\/s41598-020-61466-5","article-title":"Mutations in disordered proteins as early indicators of nucleic acid changes triggering speciation","volume":"10","author":"Forcelloni","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1002\/0471250953.bi0313s48","article-title":"Clustal omega","volume":"48","author":"Sievers","year":"2014","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/978-1-62703-646-7_6","article-title":"Clustal Omega, accurate alignment of very large numbers of sequences","volume":"1079","author":"Sievers","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/molbev\/msz189","article-title":"ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models","volume":"37","author":"Darriba","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.virusres.2014.11.031","article-title":"On the biased nucleotide composition of the human coronavirus RNA genome","volume":"202","author":"Berkhout","year":"2015","journal-title":"Virus Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.virol.2007.08.010","article-title":"Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses","volume":"369","author":"Woo","year":"2007","journal-title":"Virology"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Ji, W., Wang, W., Zhao, X., Zai, J., and Li, X. (2020). Cross-species transmission of the newly identified coronavirus 2019-nCoV. J. Med. Virol.","DOI":"10.1002\/jmv.25682"},{"key":"ref_34","first-page":"1","article-title":"Why snakes probably aren\u2019t spreading the new China virus","volume":"577","author":"Callaway","year":"2020","journal-title":"Nature"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1021\/acs.jproteome.0c00129","article-title":"Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1","volume":"19","author":"Zhang","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lam, T.T.Y., Shum, M.H.H., Zhu, H.C., Tong, Y.G., Ni, X.B., Liao, Y.S., Wei, W., Cheung, W.Y.M., Li, W.J., and Li, L.F. (2020). Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature.","DOI":"10.1101\/2020.02.13.945485"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ceraolo, C., and Giorgi, F.M. (2020). Genomic variance of the 2019-nCoV coronavirus. J. Med. Virol.","DOI":"10.1101\/2020.02.02.931162"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.3181\/0903-MR-94","article-title":"Coronavirus Diversity, Phylogeny and Interspecies Jumping","volume":"234","author":"Woo","year":"2009","journal-title":"Exp. Biol. Med."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Cavanagh, D. (1995). The Coronavirus Surface Glycoprotein. The Coronaviridae, Springer.","DOI":"10.1007\/978-1-4899-1531-3_5"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"363","DOI":"10.3390\/v4030363","article-title":"The coronavirus E protein: assembly and beyond","volume":"4","author":"Ruch","year":"2012","journal-title":"Viruses"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jsb.2010.11.021","article-title":"A structural analysis of M protein in coronavirus assembly and morphology","volume":"174","author":"Neuman","year":"2011","journal-title":"J. Struct. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.jcv.2004.01.001","article-title":"Cloning, sequencing, expression, and purification of SARS-associated coronavirus nucleocapsid protein for serodiagnosis of SARS","volume":"30","author":"Timani","year":"2004","journal-title":"J. Clin. Virol."},{"key":"ref_43","first-page":"241","article-title":"COVID-19 Tragic Pandemic: Concerns over Unintentional \u201cDirected Accelerated Evolution\u201d of Novel Coronavirus (SARS-CoV-2) and Introducing a Modified Treatment Method for ARDS","volume":"10","author":"Haghani","year":"2020","journal-title":"J. Biomed. Phys. Eng."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"855","DOI":"10.4049\/jimmunol.1402513","article-title":"The acute respiratory distress syndrome: from mechanism to translation","volume":"194","author":"SeungHye","year":"2015","journal-title":"J. Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Zhang, W., Zhao, Y., Zhang, F., Wang, Q., Li, T., Liu, Z., Wang, J., Qin, Y., Zhang, X., and Yan, X. (2020). The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The experience of clinical immunologists from China. Clin Immunol., 108393.","DOI":"10.1016\/j.clim.2020.108393"},{"key":"ref_46","first-page":"555","article-title":"How radiotherapy was historically used to treat pneumonia: Could it be useful today?","volume":"86","author":"Calabrese","year":"2013","journal-title":"Yale J. Biol. Med."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Kirby, C., and Mackenzie, M. (2020). Is low dose radiation herapy a potential treatment for COVID-19 pneumonia?. Radiother. Oncol.","DOI":"10.1016\/j.radonc.2020.04.004"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/498\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:25:04Z","timestamp":1760361904000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/5\/498"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,30]]},"references-count":47,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5]]}},"alternative-id":["v12050498"],"URL":"https:\/\/doi.org\/10.3390\/v12050498","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,30]]}}}