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 non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological lin...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Fundação Oswaldo Cruz (FIOCRUZ)
2022-01-01
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| Series: | Memorias do Instituto Oswaldo Cruz |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762021000101107&lng=en&tlng=en |
| _version_ | 1827879944633450496 |
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| author | Yanina Panzera Natalia Ramos Lucía Calleros Ana Marandino Gonzalo Tomás Claudia Techera Sofía Grecco Sandra Frabasile Eddie Fuques Leticia Coppola Natalia Goñi Viviana Ramas Cecilia Sorhouet Victoria Bormida Analía Burgueño María Brasesco Maria Rosa Garland Sylvia Molinari Maria Teresa Perez Rosina Somma Silvana Somma Maria Noelia Morel Cristina Mogdasy Héctor Chiparelli Juan Arbiza Adriana Delfraro Ruben Pérez |
| author_facet | Yanina Panzera Natalia Ramos Lucía Calleros Ana Marandino Gonzalo Tomás Claudia Techera Sofía Grecco Sandra Frabasile Eddie Fuques Leticia Coppola Natalia Goñi Viviana Ramas Cecilia Sorhouet Victoria Bormida Analía Burgueño María Brasesco Maria Rosa Garland Sylvia Molinari Maria Teresa Perez Rosina Somma Silvana Somma Maria Noelia Morel Cristina Mogdasy Héctor Chiparelli Juan Arbiza Adriana Delfraro Ruben Pérez |
| author_sort | Yanina Panzera |
| collection | DOAJ |
| description | BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, 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. |
| first_indexed | 2024-03-12T18:13:08Z |
| format | Article |
| id | doaj.art-3b80af2b80074a079f5c5695162211f5 |
| institution | Directory Open Access Journal |
| issn | 1678-8060 |
| language | English |
| last_indexed | 2024-03-12T18:13:08Z |
| publishDate | 2022-01-01 |
| publisher | Fundação Oswaldo Cruz (FIOCRUZ) |
| record_format | Article |
| series | Memorias do Instituto Oswaldo Cruz |
| spelling | doaj.art-3b80af2b80074a079f5c5695162211f52023-08-02T09:14:05ZengFundação Oswaldo Cruz (FIOCRUZ)Memorias do Instituto Oswaldo Cruz1678-80602022-01-0111610.1590/0074-02760210275Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletionYanina PanzeraNatalia RamosLucía CallerosAna MarandinoGonzalo TomásClaudia TecheraSofía GreccoSandra FrabasileEddie FuquesLeticia CoppolaNatalia GoñiViviana RamasCecilia SorhouetVictoria BormidaAnalía BurgueñoMaría BrasescoMaria Rosa GarlandSylvia MolinariMaria Teresa PerezRosina SommaSilvana SommaMaria Noelia MorelCristina MogdasyHéctor ChiparelliJuan ArbizaAdriana Delfrarohttps://orcid.org/0000-0003-3701-9621Ruben Pérezhttps://orcid.org/0000-0003-4961-4743BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, 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.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762021000101107&lng=en&tlng=engeneticsindelsaccessory generepetitive sequencecoronavirus |
| spellingShingle | Yanina Panzera Natalia Ramos Lucía Calleros Ana Marandino Gonzalo Tomás Claudia Techera Sofía Grecco Sandra Frabasile Eddie Fuques Leticia Coppola Natalia Goñi Viviana Ramas Cecilia Sorhouet Victoria Bormida Analía Burgueño María Brasesco Maria Rosa Garland Sylvia Molinari Maria Teresa Perez Rosina Somma Silvana Somma Maria Noelia Morel Cristina Mogdasy Héctor Chiparelli Juan Arbiza Adriana Delfraro Ruben Pérez Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion Memorias do Instituto Oswaldo Cruz genetics indels accessory gene repetitive sequence coronavirus |
| 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 | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762021000101107&lng=en&tlng=en |
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