Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.
Mem Inst Oswaldo Cruz
; 116: e210275, 2022.
Article
in English
| MEDLINE | ID: covidwho-1622414
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. MAINCONCLUSIONS:
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.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Open Reading Frames
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
Topics:
Variants
Limits:
Humans
Country/Region as subject:
South America
/
Uruguay
Language:
English
Journal:
Mem Inst Oswaldo Cruz
Year:
2022
Document Type:
Article
Affiliation country:
0074-02760210275
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