Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain.
Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Palermo, Italy.
Front Public Health. 2023 Jan 26;11:1098965. doi: 10.3389/fpubh.2023.1098965. eCollection 2023.
To investigate the influence of geographic constrains to mobility on SARS-CoV-2 circulation before the advent of vaccination, we recently characterized the occurrence in Sicily of viral lineages in the second pandemic wave (September to December 2020). Our data revealed wide prevalence of the then widespread through Europe B.1.177 variant, although some viral samples could not be classified with the limited Sanger sequencing tools used. A particularly interesting sample could not be fitted to a major variant then circulating in Europe and has been subjected here to full genome sequencing in an attempt to clarify its origin, lineage and relations with the seven full genome sequences deposited for that period in Sicily, hoping to provide clues on viral evolution. The obtained genome is unique (not present in databases). It hosts 20 single-base substitutions relative to the original Wuhan-Hu-1 sequence, 8 of them synonymous and the other 12 encoding 11 amino acid substitutions, all of them already reported one by one. They include four highly prevalent substitutions, NSP12:P323L, S:D614G, and N:R203K/G204R; the much less prevalent S:G181V, ORF3a:G49V and N:R209I changes; and the very rare mutations NSP3:L761I, NSP6:S106F, NSP8:S41F and NSP14:Y447H. GISAID labeled this genome as B.1.1 lineage, a lineage that appeared early on in the pandemic. Phylogenetic analysis also confirmed this lineage diagnosis. Comparison with the seven genome sequences deposited in late 2020 from Sicily revealed branching leading to B.1.177 in one branch and to Alpha in the other branch, and suggested a local origin for the S:G118V mutation.
为了研究地理限制对疫苗接种前 SARS-CoV-2 传播的影响，我们最近对西西里岛在第二波大流行期间（2020 年 9 月至 12 月）发生的病毒谱系进行了特征描述。我们的数据显示，当时在欧洲广泛传播的 B.1.177 变体广泛流行，尽管一些病毒样本无法使用有限的 Sanger 测序工具进行分类。一个特别有趣的样本无法与当时在欧洲流行的主要变体相匹配，因此在这里对其进行了全基因组测序，试图阐明其起源、谱系及其与西西里岛同期七个全基因组序列的关系，希望能提供有关病毒进化的线索。获得的基因组是独特的（不在数据库中）。它相对于原始的武汉-Hu-1 序列有 20 个单碱基替换，其中 8 个是同义的，其余 12 个编码 11 个氨基酸替换，所有这些替换都已逐个报道过。它们包括四个高度流行的替换，NSP12:P323L、S:D614G 和 N:R203K/G204R；较少流行的 S:G181V、ORF3a:G49V 和 N:R209I 变化；以及非常罕见的突变 NSP3:L761I、NSP6:S106F、NSP8:S41F 和 NSP14:Y447H。GISAID 将该基因组标记为 B.1.1 谱系，这是一种在大流行早期出现的谱系。系统发育分析也证实了这一谱系诊断。与 2020 年底西西里岛七组基因组序列的比较显示，在一个分支中导致 B.1.177 的分支，在另一个分支中导致 Alpha 的分支，并表明 S:G118V 突变的起源是本地的。
