Olivero Nadia B, Zappia Victoria E, Gargantini Pablo, Human-Gonzalez Candela, Raya-Plasencia Luciana, Marquez Judith, Ortiz-Batsche Lucia, Hernandez-Morfa Mirelys, Cortes Paulo R, Ceschin Danilo, Nuñez-Fernandez Mariana, Perez Daniel R, Echenique José
Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, Argentina.
Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina.
Viruses. 2024 Dec 3;16(12):1877. doi: 10.3390/v16121877.
Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines.
了解严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体，尤其是奥密克戎变体的进化模式和地理传播情况，对于有效的公共卫生应对措施至关重要。本研究聚焦于2021年至2022年阿根廷科尔多瓦省奥密克戎变体的基因组分析。系统发育分析显示，BA.1和BA.2谱系占主导地位，BA.5比BA.4出现得更早，这与其他地区的观察结果一致。单倍型网络分析表明，奥密克戎样本内存在显著的基因差异，形成了不同的簇。与全球数据集相比，我们在刺突蛋白NTD区域的奥密克戎基因组中发现了突变（A27S、Y145D和L212I）。这些突变虽然在全球范围内并不普遍，但在我们地区的发生率更高。特别值得关注的是Y145D和L212I替代，此前在阿根廷未曾报道过。计算机模拟分析表明，这两种突变都会影响T细胞表位与I类和II类HLA等位基因的结合亲和力。值得注意的是，这些等位基因在阿根廷人群中最为常见，其中一些与对SARS-CoV-2感染的保护作用有关，另一些则与易感性有关。这些发现有力地表明，这些普遍存在的突变可能会影响刺突蛋白的免疫原性，并有助于免疫逃逸机制。本研究为阿根廷科尔多瓦省奥密克戎变体的基因组动态提供了有价值的见解，并突出了对新冠疫苗具有潜在影响的独特突变。
