Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic.
RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA.
Int J Environ Res Public Health. 2023 Apr 13;20(8):5503. doi: 10.3390/ijerph20085503.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10 (95% HPD: 1.2358 × 10, 1.8635 × 10) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 是一种 RNA 病毒，随着时间的推移会发生进化，导致新的变种。在本研究中，我们评估了多米尼加共和国 SARS-CoV-2 的基因组流行病学。从全球流感数据共享倡议 (GISAID) 数据库中获取了 2020 年 3 月至 2022 年 2 月中旬在多米尼加共和国采集的 1149 份 SARS-CoV-2 全基因组核苷酸序列。使用最大似然法和贝叶斯马尔可夫链蒙特卡罗 (MCMC) 方法分析了系统发育关系和进化率。使用 Pangolin 网络应用程序获得基因型详细信息（谱系）。此外，还使用了 Coronapp、Genome Detective Viral Tools 等网络工具来监测流行病学特征。我们的研究结果表明，研究期间最常见的非同义突变是 D614G。在 1149 个样本中，根据 Pangolin/Scorpio，870 个（75.74%）被分为 8 个相关变种。首个监测变种（VBM）于 2020 年 12 月被发现。同时，在 2021 年，发现了令人关注的变异株德尔塔和奥密克戎。估计平均突变率为每个位点 1.5523×10（95%HPD：1.2358×10，1.8635×10）核苷酸取代。我们还报告了一种源自多米尼加共和国的 SARS-CoV-2 谱系 B.1.575.2 的出现，该谱系于 2021 年 10 月至 2022 年 1 月与令人关注的变异株德尔塔和奥密克戎共同流行。B.1.575.2 在多米尼加共和国的影响很小，但随后在西班牙迅速扩大。更好地了解病毒进化和基因组监测数据将有助于制定减轻对公共卫生影响的策略。
