Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening.

Autor: Cecchetto R; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy.; UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy., Tonon E; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy.; UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy., Medaina N; UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy., Turri G; UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy., Diani E; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy., Piccaluga PP; Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, Bologna University, 40126 Bologna, Italy., Salomoni A; Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, 35020 Padua, Italy., Conti M; Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy., Tacconelli E; Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy., Lagni A; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy., Lotti V; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy., Favarato M; Molecular Diagnostics and Genetics, AULSS 3 Serenissima, 30174 Venice, Italy., Gibellini D; Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy.; UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy.
Jazyk: angličtina
Zdroj: Microorganisms [Microorganisms] 2023 Sep 23; Vol. 11 (10). Date of Electronic Publication: 2023 Sep 23.
DOI: 10.3390/microorganisms11102378
Abstrakt: Next-generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion spanning ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last three aminoacids of ORF8. Interestingly, the deleted region was flanked by two small repeats, which were likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, seven out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nucleotides deletion. It is noteworthy that three out of six cases were detected in patients with immunodeficiency, and it is conceivable that this clinical condition could promote the replication and selection of these mutations.
Databáze: MEDLINE
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