Laboratorio Departamental de Salud Pública de Antioquia, Secretaría Seccional de Salud y Protección Social de Antioquia, Medellín, Colombia.
Corporación para Investigaciones Biológicas, Medellín, Colombia.
Biomedica. 2024 Mar 31;44(1):54-66. doi: 10.7705/biomedica.6862.
Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, ɣ, β, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation. Objective. To characterize the genetic diversity of the different SARS-CoV-2 δ sublineages in Antioquia and to describe its prevalence. Materials and methods. We collected sociodemographic information from 2,675 samples, and obtained 1,115 genomes from the GISAID database between July 12th, 2021, and January 18th, 2022. From the analyzed genomes, 515 were selected because of their high coverage values (>90%) to perform phylogenetic analysis and to infer allele frequencies of mutations of interest. Results. We characterized 24 sublineages. The most prevalent was AY.25. Mutations of interest as L452R, P681R, and P681H were identified in this sublineage, comprising a frequency close to 0.99. Conclusions. This study identified that the AY.25 sublineage has a transmission advantage compared to the other δ sublineages. This attribute may be related to the presence of the L452R and P681R mutations associated in other studies with higher evasion of the immune system and less efficacy of drugs against SARS-CoV-2.
简介。在安蒂奥基亚省 SARS-CoV-2 大流行期间，我们经历了与 α、ɣ、β、ƛ 和 δ 变体相关的流行病学高峰。δ 变体的发病率和患病率最高。由于其临床表现和流行病学特征，该谱系引起了关注。PANGOLIN 数据库中已经报告了 253 种 δ 亚谱系。通过基因组分析进行的亚谱系鉴定使追踪其进化和传播成为可能。目的。描述安蒂奥基亚不同 SARS-CoV-2 δ 亚谱系的遗传多样性并描述其流行情况。材料和方法。我们从 2675 个样本中收集了社会人口学信息，并在 2021 年 7 月 12 日至 2022 年 1 月 18 日期间从 GISAID 数据库中获得了 1115 个基因组。从分析的基因组中，选择了 515 个基因组，因为它们的高覆盖率值（>90%）来进行系统发育分析，并推断感兴趣突变的等位基因频率。结果。我们描述了 24 个亚谱系。最流行的是 AY.25。在这个亚谱系中发现了 L452R、P681R 和 P681H 等感兴趣的突变，其频率接近 0.99。结论。本研究表明，与其他 δ 亚谱系相比，AY.25 亚谱系具有传播优势。这种属性可能与其他研究中与免疫系统逃逸能力更高和针对 SARS-CoV-2 的药物疗效降低相关的 L452R 和 P681R 突变的存在有关。
