Cecchetto Riccardo, Tonon Emil, Medaina Nicoletta, Turri Giona, Diani Erica, Piccaluga Pier Paolo, Salomoni Angela, Conti Michela, Tacconelli Evelina, Lagni Anna, Lotti Virginia, Favarato Mosé, Gibellini Davide
Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy.
UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy.
Microorganisms. 2023 Sep 23;11(10):2378. doi: 10.3390/microorganisms11102378.
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.
对2022年最后几个月采集的新冠病毒（SARS-CoV-2）阳性拭子进行的下一代测序（NGS）显示，在6名感染BA.5.1奥密克戎变种的患者中，出现了一个跨越开放阅读框7b（ORF7b）和开放阅读框8（ORF8）的大片段缺失（426个核苷酸）。这种广泛的基因组缺失去除了这两个基因的很大一部分，使ORF7b的前22个氨基酸和ORF8的最后三个氨基酸保持读码框。有趣的是，缺失区域两侧有两个小重复序列，它们可能参与了发夹结构的形成。在NCBI数据库的15个序列中也发现了大小和位置与该缺失相当的类似重排。在这一组中，来自美国和瑞士的15个病例中有7个同时呈现BA.5.1变种和相同的426个核苷酸缺失。值得注意的是，6例中有3例是在免疫缺陷患者中检测到的，可以想象这种临床状况可能会促进这些突变的复制和选择。
