{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T11:42:40Z","timestamp":1788262960150,"version":"build-2803163510"},"reference-count":49,"publisher":"FapUNIFESP (SciELO)","license":[{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Mem. Inst. Oswaldo Cruz"],"DOI":"10.1590\/0074-02760210275","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T13:32:40Z","timestamp":1641821560000},"source":"Crossref","is-referenced-by-count":5,"title":["Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion"],"prefix":"10.1590","volume":"116","author":[{"given":"Yanina","family":"Panzera","sequence":"first","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Ramos","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc\u00eda","family":"Calleros","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Marandino","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Tom\u00e1s","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Techera","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sof\u00eda","family":"Grecco","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Frabasile","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eddie","family":"Fuques","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leticia","family":"Coppola","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Go\u00f1i","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viviana","family":"Ramas","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecilia","family":"Sorhouet","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Bormida","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anal\u00eda","family":"Burgue\u00f1o","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda","family":"Brasesco","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Rosa","family":"Garland","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvia","family":"Molinari","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Teresa","family":"Perez","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosina","family":"Somma","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvana","family":"Somma","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Noelia","family":"Morel","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Mogdasy","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor","family":"Chiparelli","sequence":"additional","affiliation":[{"name":"Ministerio de Salud P\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Arbiza","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3701-9621","authenticated-orcid":false,"given":"Adriana","family":"Delfraro","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4961-4743","authenticated-orcid":false,"given":"Ruben","family":"P\u00e9rez","sequence":"additional","affiliation":[{"name":"Universidad de la Rep\u00fablica,  Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"530","published-online":{"date-parts":[[2021]]},"reference":[{"issue":"7798","key":"ref1","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou P","year":"2020","journal-title":"Nature"},{"issue":"1","key":"ref2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.virusres.2007.10.009","article-title":"SARS coronavirus accessory proteins","volume":"133","author":"Narayanan K","year":"2008","journal-title":"Virus Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"198074","DOI":"10.1016\/j.virusres.2020.198074","article-title":"The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway","volume":"286","author":"Li JY","year":"2020","journal-title":"Virus Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"104353","DOI":"10.1016\/j.meegid.2020.104353","article-title":"Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses","volume":"83","author":"Cagliani R","year":"2020","journal-title":"Infect Genet Evol"},{"issue":"10273","key":"ref5","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/S0140-6736(21)00183-5","article-title":"Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence","volume":"397","author":"Sabino EC","year":"2021","journal-title":"Lancet"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"veab069","DOI":"10.1093\/ve\/veab069","article-title":"The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein","volume":"7","author":"Resende PC","year":"2021","journal-title":"Virus Evol"},{"issue":"4","key":"ref7","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1038\/s41591-021-01285-x","article-title":"SARS-CoV-2 501Y V2 escapes neutralization by South African COVID-19 donor plasma","volume":"27","author":"Wibmer CK","year":"2021","journal-title":"Nat Med"},{"issue":"3","key":"ref8","first-page":"1","article-title":"Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012\/01 and other variants with spike deletion H69-V70, France, August to December 2020","volume":"26","author":"Bal A","year":"2021","journal-title":"Eurosurveillance"},{"key":"ref9","article-title":"Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa","author":"Tegally H","year":"2020","journal-title":"medRxiv"},{"key":"ref10","first-page":"1","article-title":"Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus preliminary findings","author":"Faria NR","year":"2021","journal-title":"Virological"},{"key":"ref11","article-title":"Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data","author":"Volz E","year":"2021","journal-title":"medRxiv"},{"key":"ref12","article-title":"Genomic and proteomic mutation landscapes of SARS-CoV-2","author":"Badua CLDC","year":"2020","journal-title":"J Med Virol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"104557","DOI":"10.1016\/j.meegid.2020.104557","article-title":"Substitutions in spike and nucleocapsid proteins of SARS-CoV-2 circulating in South America","volume":"85","author":"Franco-Mu\u00f1oz C","year":"2020","journal-title":"Infect Genet Evol"},{"issue":"6534","key":"ref14","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1126\/science.abf6950","article-title":"Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape","volume":"371","author":"McCarthy KR","year":"2021","journal-title":"Science"},{"issue":"5","key":"ref15","article-title":"Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)","volume":"16","author":"Liu P","year":"2020","journal-title":"PLoS Pathog"},{"issue":"7","key":"ref16","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1016\/j.cmi.2020.03.020","article-title":"Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)","volume":"26","author":"Bal A","year":"2020","journal-title":"Clin Microbiol Infect"},{"issue":"1","key":"ref17","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1186\/s12967-020-02507-5","article-title":"Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1","volume":"18","author":"Benedetti F","year":"2020","journal-title":"J Transl Med"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"198222","DOI":"10.1016\/j.virusres.2020.198222","article-title":"Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome","volume":"291","author":"Kumar BK","year":"2020","journal-title":"Virus Res"},{"issue":"14","key":"ref19","doi-asserted-by":"crossref","first-page":"e00711","DOI":"10.1128\/JVI.00711-20","article-title":"An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)","volume":"94","author":"Holland LA","year":"2020","journal-title":"J Virol"},{"key":"ref20","article-title":"Discovery and genomic characterization of a 382-nucleotide deletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2","volume":"11","author":"Su YCF","year":"2020","journal-title":"MBio"},{"issue":"1","key":"ref21","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1080\/22221751.2020.1782271","article-title":"SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East","volume":"9","author":"Gong Y-N","year":"2020","journal-title":"Emerg Microbes Infect"},{"key":"ref22","doi-asserted-by":"crossref","DOI":"10.1111\/tbed.14002","article-title":"A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay","author":"Panzera Y","year":"2021","journal-title":"Transbound Emerg Dis"},{"issue":"1","key":"ref23","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1080\/22221751.2021.1872351","article-title":"Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France","volume":"10","author":"Qu\u00e9rom\u00e8s G","year":"2021","journal-title":"Emerg Microbes Infect"},{"issue":"5-6","key":"ref24","first-page":"251","article-title":"Lost in deletion the enigmatic ORF8 protein of SARS-CoV-2","volume":"54","author":"Zinzula L","year":"2020","journal-title":"Biochem Biophys Res Commun"},{"issue":"1","key":"ref25","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1080\/22221751.2020.1756700","article-title":"Attenuated SARS-CoV-2 variants with deletions at the S1\/S2 junction","volume":"9","author":"Lau S-Y","year":"2020","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"ref26","doi-asserted-by":"crossref","first-page":"3810","DOI":"10.1038\/s41467-020-17665-9","article-title":"Activation and evasion of type I interferon responses by SARS-CoV-2","volume":"11","author":"Lei X","year":"2020","journal-title":"Nat Commun"},{"issue":"1","key":"ref27","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1080\/22221751.2020.1780953","article-title":"SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists","volume":"9","author":"Yuen CK","year":"2020","journal-title":"Emerg Microbes Infect"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","first-page":"2000045","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","article-title":"Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR","volume":"25","author":"Corman VM","year":"2020","journal-title":"Euro Surveill"},{"key":"ref29","article-title":"CoV-GLUE: a web application for tracking SARS-CoV-2 genomic variation","author":"Singer J","year":"2020","journal-title":"preprints.org"},{"issue":"11","key":"ref30","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 A","year":"2020","journal-title":"Nat Microbiol"},{"issue":"13","key":"ref31","first-page":"2","article-title":"GISAID global initiative on sharing all influenza data - from vision to reality","volume":"22","author":"Shu Y","year":"2017","journal-title":"Euro Surveill"},{"issue":"4","key":"ref32","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 K","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"7","key":"ref33","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"Price MN","year":"2009","journal-title":"Mol Biol Evol"},{"issue":"2","key":"ref34","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.virusres.2010.08.017","article-title":"SARS-coronavirus protein 6 conformations required to impede protein import into the nucleus","volume":"153","author":"Hussain S","year":"2010","journal-title":"Virus Res"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"4108","DOI":"10.1038\/s41598-021-83595-1","article-title":"Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects","volume":"11","author":"Maldonado LL","year":"2021","journal-title":"Sci Rep"},{"issue":"7","key":"ref36","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s00239-020-09957-x","article-title":"Selection shapes synonymous stop codon use in mammals","volume":"88","author":"Seoighe C","year":"2020","journal-title":"J Mol Evol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/msb.2009.71","article-title":"Viral adaptation to host a proteome-based analysis of codon usage and amino acid preferences","volume":"5","author":"Bahir I","year":"2009","journal-title":"Mol Syst Biol"},{"issue":"21","key":"ref38","doi-asserted-by":"crossref","first-page":"7898","DOI":"10.3390\/ijms21217898","article-title":"Evolution of transmissible gastroenteritis virus (TGEV) a codon usage perspective","volume":"21","author":"Cheng S","year":"2020","journal-title":"Int J Mol Sci"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"104471","DOI":"10.1016\/j.meegid.2020.104471","article-title":"Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19","volume":"85","author":"Nambou K","year":"2020","journal-title":"Infect Genet Evol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"104736","DOI":"10.1016\/j.meegid.2021.104736","article-title":"Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2","volume":"89","author":"Huang W","year":"2021","journal-title":"Infect Genet Evol"},{"key":"ref41","article-title":"A rare deletion in SARS-CoV-2 ORF6 dramatically alters the predicted three-dimensional structure of the resultant protein","author":"Riojas M","year":"2020","journal-title":"bioRxiv"},{"key":"ref42","article-title":"Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)","volume":"11","author":"Nguyen TT","year":"2021","journal-title":"Sci Rep"},{"issue":"45","key":"ref43","doi-asserted-by":"crossref","first-page":"28344","DOI":"10.1073\/pnas.2016650117","article-title":"SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling","volume":"117","author":"Miorin L","year":"2020","journal-title":"Proc Natl Acad Sci"},{"issue":"12","key":"ref44","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1038\/s41418-020-00633-7","article-title":"An aberrant STAT pathway is central to COVID-19","volume":"27","author":"Matsuyama T","year":"2020","journal-title":"Cell Death Differ"},{"issue":"18","key":"ref45","doi-asserted-by":"crossref","first-page":"9812","DOI":"10.1128\/JVI.01012-07","article-title":"Severe acute respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear import factors on the rough endoplasmic eeticulum\/Golgi membrane","volume":"81","author":"Frieman M","year":"2007","journal-title":"J Virol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"615280","DOI":"10.3389\/fmicb.2020.615280","article-title":"Evolutionary dynamics and dissemination pattern of the SARS-CoV-2 lineage B 1.1.33 during the early pandemic phase in Brazil","volume":"11","author":"Resende PC","year":"2020","journal-title":"Front Microbiol"},{"issue":"6508","key":"ref47","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1126\/science.abd2161","article-title":"Evolution and epidemic spread of SARS-CoV-2 in Brazil","volume":"369","author":"Candido DS","year":"2020","journal-title":"Science"},{"key":"ref48","article-title":"Molecular basis of genetic variation of viruses","author":"Domingo E","year":"2020","journal-title":"Elsevier"},{"key":"ref49","year":"2020"}],"container-title":["Mem\u00f3rias do Instituto Oswaldo Cruz"],"original-title":[],"link":[{"URL":"http:\/\/www.scielo.br\/pdf\/mioc\/v116\/1678-8060-mioc-116-e210275.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T13:33:28Z","timestamp":1641821608000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.scielo.br\/scielo.php?script=sci_arttext&pid=S0074-02762021000101107&tlng=en"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"references-count":49,"alternative-id":["S0074-02762021000101107"],"URL":"https:\/\/doi.org\/10.1590\/0074-02760210275","relation":{},"ISSN":["1678-8060","0074-0276"],"issn-type":[{"value":"1678-8060","type":"electronic"},{"value":"0074-0276","type":"print"}],"subject":[],"published":{"date-parts":[[2021]]},"article-number":"e210275"}}