Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion
BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in nonstructural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links b...
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| Natura: | article |
| Lingua: | inglese |
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2021
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| Accesso online: | https://hdl.handle.net/20.500.12008/38454 |
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| _version_ | 1868890243846897664 |
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| author | Panzera Crespo, Yanina |
| author2 | Ramos, Natalia Calleros Basilio, Lucía Marandino, Ana Tomás Custodio, Gonzalo Martín Techera, Claudia Grecco Patiño, Sofía Frabasile Giurato, Sandra Alicia Fuques Villalba, Eddie Coppola, Leticia Goñi Mazzitelli, Natalia Ramas, Vivivana Sorhouet, Cecilia Bórmida, Victoria Burgueño, Analía Brasesco, María Garland, Maria Rosa Molinari, Sylvia Pérez, María Teresa Somma, Rosina Somma, Silvana Morel, Noelia Mogdasy, Cristina Chiparelli, Héctor Arbiza, Juan Delfraro Vázquez, Adriana Beatriz Pérez Crossa, Ruben Gustavo |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author author author author |
| author_browse | Arbiza, Juan Brasesco, María Burgueño, Analía Bórmida, Victoria Calleros Basilio, Lucía Chiparelli, Héctor Coppola, Leticia Delfraro Vázquez, Adriana Beatriz Frabasile Giurato, Sandra Alicia Fuques Villalba, Eddie Garland, Maria Rosa Goñi Mazzitelli, Natalia Grecco Patiño, Sofía Marandino, Ana Mogdasy, Cristina Molinari, Sylvia Morel, Noelia Panzera Crespo, Yanina Pérez Crossa, Ruben Gustavo Pérez, María Teresa Ramas, Vivivana Ramos, Natalia Somma, Rosina Somma, Silvana Sorhouet, Cecilia Techera, Claudia Tomás Custodio, Gonzalo Martín |
| author_facet | Panzera Crespo, Yanina Ramos, Natalia Calleros Basilio, Lucía Marandino, Ana Tomás Custodio, Gonzalo Martín Techera, Claudia Grecco Patiño, Sofía Frabasile Giurato, Sandra Alicia Fuques Villalba, Eddie Coppola, Leticia Goñi Mazzitelli, Natalia Ramas, Vivivana Sorhouet, Cecilia Bórmida, Victoria Burgueño, Analía Brasesco, María Garland, Maria Rosa Molinari, Sylvia Pérez, María Teresa Somma, Rosina Somma, Silvana Morel, Noelia Mogdasy, Cristina Chiparelli, Héctor Arbiza, Juan Delfraro Vázquez, Adriana Beatriz Pérez Crossa, Ruben Gustavo |
| author_role | author |
| collection | COLIBRI |
| dc.contributor.none.fl_str_mv | Panzera Crespo Yanina, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Ramos Natalia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Calleros Basilio Lucía, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Marandino Ana, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Tomás Custodio Gonzalo Martín, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Techera Claudia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Grecco Patiño Sofía, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Frabasile Giurato Sandra Alicia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Fuques Villalba Eddie, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Coppola Leticia, MSP Goñi Mazzitelli Natalia, MSP Ramas Vivivana, MSP Sorhouet Cecilia, MSP Bórmida Victoria, MSP Burgueño Analía, MSP Brasesco María, MSP Garland Maria Rosa, MSP Molinari Sylvia, MSP Pérez María Teresa, MSP Somma Rosina, MSP Somma Silvana, MSP Morel Noelia, MSP Mogdasy Cristina, MSP Chiparelli Héctor, MSP Arbiza Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Delfraro Vázquez Adriana Beatriz, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Pérez Crossa Ruben Gustavo, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. |
| dc.creator.none.fl_str_mv | Panzera Crespo, Yanina Ramos, Natalia Calleros Basilio, Lucía Marandino, Ana Tomás Custodio, Gonzalo Martín Techera, Claudia Grecco Patiño, Sofía Frabasile Giurato, Sandra Alicia Fuques Villalba, Eddie Coppola, Leticia Goñi Mazzitelli, Natalia Ramas, Vivivana Sorhouet, Cecilia Bórmida, Victoria Burgueño, Analía Brasesco, María Garland, Maria Rosa Molinari, Sylvia Pérez, María Teresa Somma, Rosina Somma, Silvana Morel, Noelia Mogdasy, Cristina Chiparelli, Héctor Arbiza, Juan Delfraro Vázquez, Adriana Beatriz Pérez Crossa, Ruben Gustavo |
| dc.date.none.fl_str_mv | 2021 2023-07-27T13:00:11Z 2023-07-27T13:00:11Z |
| dc.format.none.fl_str_mv | 8 h application/pdf |
| dc.identifier.none.fl_str_mv | Panzera Crespo, Y, Ramos, N, Calleros Basilio, L, [y otros autores]. "Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion". Memórias do Instituto Oswaldo Cruz. [en línea] 2021, 116: e210275. 8 h. DOI: 10.1590/0074-02760210275 1678-8060 https://hdl.handle.net/20.500.12008/38454 10.1590/0074-02760210275 |
| dc.language.none.fl_str_mv | en eng |
| dc.publisher.none.fl_str_mv | Instituto Oswaldo Cruz |
| dc.relation.none.fl_str_mv | Memórias do Instituto Oswaldo Cruz, 2021, 116: e210275 |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Licencia Creative Commons Atribución (CC - By 4.0) |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.none.fl_str_mv | Genetics Indels Accessory gene Repetitive sequence Coronavirus |
| dc.title.none.fl_str_mv | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| dc.type.none.fl_str_mv | Artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in nonstructural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_faa2e31736584bc251f8a7affbeb8e6c |
| identifier_str_mv | Panzera Crespo, Y, Ramos, N, Calleros Basilio, L, [y otros autores]. "Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion". Memórias do Instituto Oswaldo Cruz. [en línea] 2021, 116: e210275. 8 h. DOI: 10.1590/0074-02760210275 1678-8060 10.1590/0074-02760210275 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/38454 |
| publishDate | 2021 |
| publishDateSort | 2021 |
| publisher.none.fl_str_mv | Instituto Oswaldo Cruz |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| spelling | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletionPanzera Crespo, YaninaRamos, NataliaCalleros Basilio, LucíaMarandino, AnaTomás Custodio, Gonzalo MartínTechera, ClaudiaGrecco Patiño, SofíaFrabasile Giurato, Sandra AliciaFuques Villalba, EddieCoppola, LeticiaGoñi Mazzitelli, NataliaRamas, VivivanaSorhouet, CeciliaBórmida, VictoriaBurgueño, AnalíaBrasesco, MaríaGarland, Maria RosaMolinari, SylviaPérez, María TeresaSomma, RosinaSomma, SilvanaMorel, NoeliaMogdasy, CristinaChiparelli, HéctorArbiza, JuanDelfraro Vázquez, Adriana BeatrizPérez Crossa, Ruben GustavoGeneticsIndelsAccessory geneRepetitive sequenceCoronavirusBACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in nonstructural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.Instituto Oswaldo CruzPanzera Crespo Yanina, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Ramos Natalia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Calleros Basilio Lucía, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Marandino Ana, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Tomás Custodio Gonzalo Martín, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Techera Claudia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Grecco Patiño Sofía, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Frabasile Giurato Sandra Alicia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Fuques Villalba Eddie, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Coppola Leticia, MSPGoñi Mazzitelli Natalia, MSPRamas Vivivana, MSPSorhouet Cecilia, MSPBórmida Victoria, MSPBurgueño Analía, MSPBrasesco María, MSPGarland Maria Rosa, MSPMolinari Sylvia, MSPPérez María Teresa, MSPSomma Rosina, MSPSomma Silvana, MSPMorel Noelia, MSPMogdasy Cristina, MSPChiparelli Héctor, MSPArbiza Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Delfraro Vázquez Adriana Beatriz, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Pérez Crossa Ruben Gustavo, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.2023-07-27T13:00:11Z2023-07-27T13:00:11Z2021Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion8 happlication/pdfPanzera Crespo, Y, Ramos, N, Calleros Basilio, L, [y otros autores]. "Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion". Memórias do Instituto Oswaldo Cruz. [en línea] 2021, 116: e210275. 8 h. DOI: 10.1590/0074-027602102751678-8060https://hdl.handle.net/20.500.12008/3845410.1590/0074-02760210275reponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaenengMemórias do Instituto Oswaldo Cruz, 2021, 116: e210275Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)oai:colibri.udelar.edu.uy:20.500.12008/384542026-04-14T10:10:09Z |
| spellingShingle | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion Panzera Crespo, Yanina Genetics Indels Accessory gene Repetitive sequence Coronavirus |
| status_str | publishedVersion |
| title | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| title_full | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| title_fullStr | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| title_full_unstemmed | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| title_short | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| title_sort | Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion |
| topic | Genetics Indels Accessory gene Repetitive sequence Coronavirus |
| url | https://hdl.handle.net/20.500.12008/38454 |