tetano
Editor, Senior Moderator
Mem Inst Oswaldo Cruz
. 2022 Jan 10;116:e210275.
doi: 10.1590/0074-02760210275. eCollection 2022.
Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion
Yanina Panzera[SUP] 1 [/SUP], Natalia Ramos[SUP] 2 [/SUP], Lucía Calleros[SUP] 1 [/SUP], Ana Marandino[SUP] 1 [/SUP], Gonzalo Tomás[SUP] 1 [/SUP], Claudia Techera[SUP] 1 [/SUP], Sofía Grecco[SUP] 1 [/SUP], Sandra Frabasile[SUP] 2 [/SUP], Eddie Fuques[SUP] 1 [/SUP], Leticia Coppola[SUP] 3 [/SUP], Natalia Goñi[SUP] 3 [/SUP], Viviana Ramas[SUP] 3 [/SUP], Cecilia Sorhouet[SUP] 3 [/SUP], Victoria Bormida[SUP] 3 [/SUP], Analía Burgueño[SUP] 3 [/SUP], María Brasesco[SUP] 3 [/SUP], Maria Rosa Garland[SUP] 3 [/SUP], Sylvia Molinari[SUP] 3 [/SUP], Maria Teresa Perez[SUP] 3 [/SUP], Rosina Somma[SUP] 3 [/SUP], Silvana Somma[SUP] 3 [/SUP], Maria Noelia Morel[SUP] 3 [/SUP], Cristina Mogdasy[SUP] 3 [/SUP], Héctor Chiparelli[SUP] 3 [/SUP], Juan Arbiza[SUP] 2 [/SUP], Adriana Delfraro[SUP] 2 [/SUP], Ruben Pérez[SUP] 1 [/SUP]
Affiliations
Abstract
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.
. 2022 Jan 10;116:e210275.
doi: 10.1590/0074-02760210275. eCollection 2022.
Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion
Yanina Panzera[SUP] 1 [/SUP], Natalia Ramos[SUP] 2 [/SUP], Lucía Calleros[SUP] 1 [/SUP], Ana Marandino[SUP] 1 [/SUP], Gonzalo Tomás[SUP] 1 [/SUP], Claudia Techera[SUP] 1 [/SUP], Sofía Grecco[SUP] 1 [/SUP], Sandra Frabasile[SUP] 2 [/SUP], Eddie Fuques[SUP] 1 [/SUP], Leticia Coppola[SUP] 3 [/SUP], Natalia Goñi[SUP] 3 [/SUP], Viviana Ramas[SUP] 3 [/SUP], Cecilia Sorhouet[SUP] 3 [/SUP], Victoria Bormida[SUP] 3 [/SUP], Analía Burgueño[SUP] 3 [/SUP], María Brasesco[SUP] 3 [/SUP], Maria Rosa Garland[SUP] 3 [/SUP], Sylvia Molinari[SUP] 3 [/SUP], Maria Teresa Perez[SUP] 3 [/SUP], Rosina Somma[SUP] 3 [/SUP], Silvana Somma[SUP] 3 [/SUP], Maria Noelia Morel[SUP] 3 [/SUP], Cristina Mogdasy[SUP] 3 [/SUP], Héctor Chiparelli[SUP] 3 [/SUP], Juan Arbiza[SUP] 2 [/SUP], Adriana Delfraro[SUP] 2 [/SUP], Ruben Pérez[SUP] 1 [/SUP]
Affiliations
- PMID: 35019072
- DOI: 10.1590/0074-02760210275
Abstract
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.