Guzmán María G, Pérez Lissette, Tejero Yahisel, Mederos Dailyn, Aguado Mirtha E, Pintos Yanet, Valdes Odalys, Álvarez Mayling, de León Liena de Regla Ponce, Baldoquín Waldemar, Martínez Yenisleidys, Figueredo Claudia, Naranjo Celine, Nuñes Lirialys, López Almaguer Yanaris, Fernández José R de Armas, Portal Miranda José A, Kourí Vivian
Department of Virology, Pedro Kourí Tropical Medicine Institute, Havana, Cuba.
Center of Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba.
J Clin Virol Plus. 2022 Nov;2(4):100104. doi: 10.1016/j.jcvp.2022.100104. Epub 2022 Aug 22.
The SARS CoV-2 D614G variant circulated in Cuba in 2020. New viral variants were detected after the opening of the border in November 2020. We show the results of the genomic surveillance in Cuba from December 28, 2020, to September 28, 2021 and their relationship to the epidemiological situation in the country. A total of 1,406 nasopharyngeal exudates from COVID-19 patients were processed for RNA extraction and the 1836 bp fragment of the spike gene was amplified and sequenced. The mutations present were determined using the GISAID database. Prevalence ratios were estimated by fitting Poisson univariate and multivariate regression models to investigate associations between SARS-CoV-2 variant group (VOC, non-VOC) and disease outcome. Seventeen genetic variants were detected including VOC Alpha, Beta, Gamma and Delta, one variant of interest (VOI) (Lambda) and two previous VOI (A.2.5.1 and Zeta/P.2). Beta (34.77%), Delta (24.89%) and D614G (19%) variants were the most frequently detected. By June, Delta increased in frequency, displacing Beta. Disease severity increased significantly with age and VOC (PR =1.98, IC 95%: 1.33-3.05, <0.05). Genomic surveillance allowed us to identify the upsurge of novel variants. Coinciding with the higher epidemic period, multiple variants were co-circulating. Although we cannot rule out that failure in the transmission containment measures occurred, the increase in the number of cases associated with the circulation of several variants, particularly the Beta and Delta variants is highly suggestive. A greater association of Beta variant with clinical severity and Delta variant with a greater transmissibility was observed.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的D614G变异株于2020年在古巴传播。2020年11月边境开放后检测到了新的病毒变异株。我们展示了2020年12月28日至2021年9月28日古巴基因组监测的结果及其与该国流行病学情况的关系。对1406份来自新冠肺炎患者的鼻咽渗出物进行处理以提取RNA，并对刺突基因的1836 bp片段进行扩增和测序。使用全球共享流感数据倡议组织（GISAID）数据库确定存在的突变。通过拟合泊松单变量和多变量回归模型来估计患病率比，以研究SARS-CoV-2变异株组（变异株、非变异株）与疾病结局之间的关联。检测到17种基因变异，包括变异株阿尔法、贝塔、伽马和德尔塔，1种关注变异株（VOI）（拉姆达）以及2种既往关注变异株（A.2.5.1和泽塔/P.2）。贝塔变异株（34.77%）、德尔塔变异株（24.89%）和D614G变异株（19%）是最常检测到的。到6月，德尔塔变异株的频率增加，取代了贝塔变异株。疾病严重程度随年龄和变异株显著增加（患病率比=1.98，95%置信区间：1.33 - 3.05，P<0.05）。基因组监测使我们能够识别新型变异株的激增。与更高的疫情时期一致，多种变异株同时传播。尽管我们不能排除传播控制措施存在失误，但与几种变异株传播相关的病例数增加，特别是贝塔和德尔塔变异株，具有很强的提示性。观察到贝塔变异株与临床严重程度有更大关联，而德尔塔变异株具有更强的传播性。
