Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion

Abstract

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.

Intragenomic rearrangements involving 5′-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses

“…Some of the intragenomic rearrangements described here in ORF8 and ORF7a and one previously in ORF6 occurred in viruses with deletions that removed or truncated ORFs, such as the deletion in the B.1.36.27 lineage from Hong Kong which lacks ORFs 7a , 7b , and 8 and has the last 12 nucleotides of the ORF6 replaced by ~ 60 nucleotides from the 5′-UTR [ 39 ]. An 872-nucleotide deletion described in the AY.4 lineage (Delta variant) from Southern Poland also eliminated ORFs 7a , 7b and 8 [ 132 ], as did a 872-nucleotide deletion documented in late 2021 in Uruguay in a different Delta lineage (AY.20), with viruses without the deletion coexisting with wild-type AY.20 and AY.43 strains [ 128 , 129 ].…”

“…Most insertion and deletions likely negatively affect viral fitness [122] and duplication of TRS sequences in coronaviruses led to attenuation [123] and when affecting essential genes frequently to viral genetic instability [124]. However, a small number of insertions/ deletions emerge and spread in viral populations, suggesting a positive effect on fitness and adaptive evolution [125][126][127][128][129][130][131]. Thus, analyzing these insertion/deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence.…”

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes

“…Sampling was also affected by the relatively reduced number of sampling sites ( Table 1 ); individuals submitted for the report may not fully reflect the prevalence of infections in the overall population. Despite the above limitations, the deletion frequency in the sample (~25%) is significant in the context of the scenario in Uruguay during 2020, characterized by very few outbreaks and cases with epidemiological connections [ 38 ].…”

Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay

“…Indels in coronaviruses are enhanced by the discontinuous RNA synthesis of the polymerase machinery and remain uncorrected by the proofreading activity of nsp14-exoribonuclease ( Chen et al, 2020 ). Although most indels likely negatively affect viral fitness ( Grubaugh et al, 2020 ), a small number emerge and spread in viral populations, suggesting a positive effect on fitness and adaptive evolution ( Foster and Rawlinson, 2021 ; Kemp et al, 2021 ; Lau et al, 2020 ; McCarthy et al, 2021 ; Panzera et al, 2021a , Panzera et al, 2021b ; Su et al, 2020 ; Young et al, 2020 ). Thus, analyzing these indels may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its recent emergence.…”