Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

Mazur-Panasiuk, Natalia; Rąbalski, Łukasz; Gromowski, Tomasz; Nowicki, Grzegorz; Kowalski, Michał; Wydmański, Witold; Szulc, Piotr; Kosinski, Maciej; Gackowska, Karolina; Drweska-Matelska, Natalia; Grabowski, Jakub; Piotrowska-Mietelska, Anna; Szewczyk, Bogusław; Bieńkowska-Szewczyk, Krystyna; Swadźba, Jakub; Łabaj, Paweł P.; Grzybek, Maciej; Pyrć, Krzysztof

doi:10.2807/1560-7917.es.2021.26.39.2100902

Cited by 31 publications

(26 citation statements)

References 17 publications

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“…Although highly variable in position and length, frameshift deletions that induce truncation of accessory protein 7a are not unique. There are numerous independent occurrences of such a mutation across both A and B lineages of SARS-CoV-2, including among VOCs [31][32][33][34][35][36][37][38] . Global genomic surveillance of SARS-CoV-2 has shown that mutations frequently occur at the downstream regions of ORF7a with such changes often leading to premature stop codons resulting in protein products with reduced functional activity.…”

Section: Discussionmentioning

confidence: 99%

Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

et al. 2022

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New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

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Section: Discussionmentioning

confidence: 99%

Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

et al. 2022

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“…The second analysis covered the period between September 1, 2021 and January 15, 2022 after completion of basic immunizations at dialysis centers in willing patients. This period corresponded to the fourth wave of the pandemic, dominated by the delta virus variant (B.1.617.2) ( 7 ). Two subgroups of patients were analyzed during the second period: patients fully vaccinated with at least two doses of mRNA vaccine (vaccinated subgroup) and patients who had not been vaccinated (unvaccinated subgroup).…”

Section: Methodsmentioning

confidence: 99%

COVID-19 vaccination reduces mortality in patients on maintenance hemodialysis

et al. 2022

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Patients with chronic kidney disease on maintenance hemodialysis (HD) have a very high risk of death in the course of COVID-19. The aim of the study was to assess the effectiveness of COVID-19 vaccination to reduce the incidence of COVID-19 and the fatality rate in HD patients. A retrospective registry-based cohort study was performed in all HD adult patients in the Pomeranian Voivodeship. Vaccinations were carried out from January to April 2021 with mRNA vaccines, either BNT162b2 or mRNA-1273 with two-dose schedule. In the first analysis (2nd pandemic wave), 1,160 unvaccinated patients were included (59.7% males, 25.7% diabetic). In the second analysis (4th pandemic wave), 1,131 (59.4% male, 30.7% diabetic) individuals were included, 1,042 (92.13%) were fully vaccinated. Three hundred and fifteen HD patients (27.2%) were COVID-19 positive during the 2nd wave, and 6.9% (78/1,131) during the 4th wave. Within the fully vaccinated patients of the 4th wave, 60 were COVID-19 positive, 5.8 vs. 20.2% of unvaccinated COVID-19 positive patients in 2nd wave, respectively. COVID-19 incidence rate ratio (IRR) was 0.21 (4th wave-vaccinated vs. 2nd wave-unvaccinated) indicating a 79% reduction. The IRR between vaccinated and unvaccinated patients of the 4th wave was 0.28 in favor of vaccinated patients with 72% reduction. In the 2nd wave, 93 patients died as a result of COVID-19 (fatality rate: 29.5%). The fatality rate of fully vaccinated patients during the 4th wave was 6.7% (p = 0.004), while the fatality rate in the 4th wave within unvaccinated patients accounted for 11.1%. Significant clinical effectiveness of COVID-19 vaccination was demonstrated in a multicenter study in HD patients.

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“…Remarkably, certain deletions could be so extensive that they eliminate entire accessory ORFs. For example, in Europe and Asia, two phylogenetically unrelated deletions completely removed the 7a, 7b, and 8 consecutive accessory ORFs [ 25 , 26 ]. These extreme deletions pose an interesting question about the role of accessory ORFs in virus viability and reinforce the relevance of deletions in increasing SARS-CoV-2 variability during expansion in the human population.…”

Section: Discussionmentioning

confidence: 99%

“…Based on previous studies, some degree of indels variability was expected in coronavirus infecting human populations. Still, the current global scenario shows that the deletion potential in SARS-CoV-2 was initially sub-estimated and underdiagnosed before it gained full attention by the scientific community [ 7 , 13 , 25 , 26 , 39 , 40 ]. In this sense, our study constitutes an example of the impact of deletion in SARS-CoV-2 evolution and underscores the importance of indel variation in providing new insights into the genome variability and dynamics of accessory ORFs within SARS-CoV-2 lineages.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.

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Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

Cited by 31 publications

References 17 publications

Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

COVID-19 vaccination reduces mortality in patients on maintenance hemodialysis

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

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