{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T04:32:05Z","timestamp":1772253125804,"version":"3.50.1"},"reference-count":34,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T00:00:00Z","timestamp":1631232000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004809","name":"Financiadora de Estudos e Projetos","doi-asserted-by":"publisher","award":["01.20.0029.000462\/20"],"award-info":[{"award-number":["01.20.0029.000462\/20"]}],"id":[{"id":"10.13039\/501100004809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["404096\/2020-4"],"award-info":[{"award-number":["404096\/2020-4"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5\u2032 and two in 3\u2032 UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough \u201cspace\u201d for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the \u201chotspots\u201d in the generation of new variants.<\/jats:p>","DOI":"10.3390\/v13091806","type":"journal-article","created":{"date-parts":[[2021,9,12]],"date-time":"2021-09-12T21:48:01Z","timestamp":1631483281000},"page":"1806","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1442-4771","authenticated-orcid":false,"given":"Ueric Jos\u00e9 Borges","family":"de Souza","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio de Bioinform\u00e1tica e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Gurupi 77402-970, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3388-890X","authenticated-orcid":false,"given":"Ra\u00edssa Nunes","family":"dos Santos","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Bioinform\u00e1tica e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Gurupi 77402-970, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5948-472X","authenticated-orcid":false,"given":"Fabr\u00edcio Souza","family":"Campos","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Bioinform\u00e1tica e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Gurupi 77402-970, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karine Lima","family":"Louren\u00e7o","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Virologia B\u00e1sica e Aplicada, Departamento de Microbiologia, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1416-8694","authenticated-orcid":false,"given":"Flavio Guimar\u00e3es","family":"da Fonseca","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Virologia B\u00e1sica e Aplicada, Departamento de Microbiologia, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5804-7045","authenticated-orcid":false,"given":"Fernando Rosado","family":"Spilki","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Sa\u00fade \u00danica, Feevale Techpark, Universidade Feevale, Av. Edgar Hoffmeister, 600, Zona Industrial Norte, Campo Bom 93700-000, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Corona-\u00f4mica.BR\/MCTI Network","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/s41591-020-0820-9","article-title":"The proximal origin of SARS-CoV-2","volume":"26","author":"Andersen","year":"2020","journal-title":"Nat. Med."},{"key":"ref_2","unstructured":"World Health Organization (2021, July 08). WHO Coronavirus (COVID-19) Dashboard. Available online: https:\/\/covid19.who.int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1126\/science.abc5343","article-title":"Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques","volume":"369","author":"Deng","year":"2020","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1098\/rstb.2004.1478","article-title":"Viral evolution and the emergence of SARS coronavirus","volume":"359","author":"Holmes","year":"2004","journal-title":"Philos. Trans. R. Soc. Lond. B. Biol. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/nrmicro.2017.45","article-title":"Pathways to zoonotic spillover","volume":"15","author":"Plowright","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"104773","DOI":"10.1016\/j.meegid.2021.104773","article-title":"Variants in ACE2; potential influences on virus infection and COVID-19 severity","volume":"90","author":"Bakhshandeh","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ijbiomac.2021.02.203","article-title":"The human pandemic coronaviruses on the show: The spike glycoprotein as the main actor in the coronaviruses play","volume":"179","author":"Souza","year":"2021","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_8","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"},{"key":"ref_9","first-page":"707","article-title":"Spread of a SARS-CoV-2 variant through Europe in the summer of 2020","volume":"595","author":"Hodcroft","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2332","DOI":"10.1016\/j.cell.2021.03.028","article-title":"N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2","volume":"184","author":"McCallum","year":"2021","journal-title":"Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e27","DOI":"10.1016\/j.jinf.2020.12.024","article-title":"Emergence of a new SARS-CoV-2 variant in the UK","volume":"82","author":"Tang","year":"2021","journal-title":"J. Infect."},{"key":"ref_12","first-page":"438","article-title":"Detection of a SARS-CoV-2 variant of concern in South Africa","volume":"592","author":"Tegally","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1146\/annurev.micro.51.1.151","article-title":"RNA virus mutations and fitness for survival","volume":"51","author":"Domingo","year":"1997","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"9436","DOI":"10.1073\/pnas.1508686112","article-title":"Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex","volume":"112","author":"Ma","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.pbiomolbio.2020.10.006","article-title":"Human coronavirus spike protein-host receptor recognition","volume":"161","author":"Guruprasad","year":"2021","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Yurkovetskiy, L., Wang, X., Pascal, K.E., Tomkins-Tinch, C., Nyalile, T., Wang, Y., Baum, A., Diehl, W.E., Dauphin, A., and Carbone, C. (2020). Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. bioRxiv, Available online: https:\/\/pubmed.ncbi.nlm.nih.gov\/32637944\/.","DOI":"10.1101\/2020.07.04.187757"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID:The cr Global initiative on sharing all influenza data-from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Eur. Surveill."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl Variant Effect Predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"ref_21","doi-asserted-by":"crossref","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"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.21105\/joss.02906","article-title":"Augur: A bioinformatics toolkit for phylogenetic analyses of human pathogens","volume":"6","author":"Huddleston","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"8435","DOI":"10.1038\/s41598-021-87713-x","article-title":"Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology","volume":"11","author":"Hamed","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/s41649-020-00118-2","article-title":"COVID-19 Super-spreaders: Definitional Quandaries and Implications","volume":"12","author":"Cave","year":"2020","journal-title":"Asian Bioeth. Rev."},{"key":"ref_26","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":"ref_27","doi-asserted-by":"crossref","unstructured":"Rouchka, E.C., Chariker, J.H., and Chung, D. (2020). Variant analysis of 1,040 SARS-CoV-2 genomes. PLoS ONE, 15.","DOI":"10.20944\/preprints202005.0396.v1"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/s41586-020-2895-3","article-title":"Spike mutation D614G alters SARS-CoV-2 fitness","volume":"592","author":"Plante","year":"2021","journal-title":"Nature"},{"key":"ref_29","unstructured":"Resende, P.C., Bezerra, J.F., de Vasconcelos, R.H.T., Arantes, I., Appolinario, L., Mendon\u00e7a, A.C., Paixao, A.C., Rodrigues, A.C.D., Silva, T., and Rocha, A.S. (2021, July 07). Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020-SARS-CoV-2 coronavirus. Virol. org., Available online: https:\/\/virological.org\/t\/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020\/584."},{"key":"ref_30","unstructured":"Naveca, F., Nascimento, V., Souza, V., Corado, A., Nascimento, F., Silva, G., Costa, \u00c1., Duarte, D., Pessoa, K., and Gon\u00e7alves, L. (2021, July 07). Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein-SARS-CoV-2 coronavirus\/nCoV-2019. Virol. Org., Available online: https:\/\/virological.org\/t\/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein\/585."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.ijid.2020.11.190","article-title":"Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences","volume":"103","author":"Motayo","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.3201\/eid2705.210191","article-title":"Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil","volume":"27","author":"Nonaka","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Hou, Y., Zhao, J., Martin, W., Kallianpur, A., Chung, M.K., Jehi, L., Sharifi, N., Erzurum, S., Eng, C., and Cheng, F. (2020). New insights into genetic susceptibility of COVID-19: An ACE2 and TMPRSS2 polymorphism analysis. BMC Med., 18.","DOI":"10.1186\/s12916-020-01673-z"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cell.2020.02.058","article-title":"Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein","volume":"181","author":"Walls","year":"2020","journal-title":"Cell"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/9\/1806\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:00:44Z","timestamp":1760166044000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/9\/1806"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,10]]},"references-count":34,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2021,9]]}},"alternative-id":["v13091806"],"URL":"https:\/\/doi.org\/10.3390\/v13091806","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.07.10.451922","asserted-by":"object"}]},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,10]]}}}