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

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 BA.5.1 Omicron variant. This extensive genome loss removed part these two genes, maintaining frame first 22 aminoacids three ORF8. Interestingly, deleted region was flanked by small repeats, which were likely involved formation hairpin structure. Similar rearrangements, comparable size location to deletion, also identified 15 sequences NCBI database. In this group, seven out cases USA Switzerland presented both variant same 426 nucleotides deletion. It is noteworthy that detected immunodeficiency, it conceivable clinical condition could promote replication selection mutations.