背景:在塞内加尔,分子诊断被广泛用于COVID-19患者的检测和管理。然而,公共部门的基因组监测非常有限.这项研究旨在分享塞内加尔公共部门实验室应对COVID-19大流行的经验,并描述2020年和2021年流通的变体分布。
方法:从2020年7月至2021年12月,在AristideleDantec大学教学医院的细菌学和病毒学实验室(LBV)对旅行者和有症状患者的鼻咽样本进行了SARS-CoV-2qRT-PCR。使用纳米孔技术选择循环阈值(Ct)≤30的样品用于全基因组测序(WGS)。开发了内部脚本以研究塞内加尔SARS-CoV-2变体的时空分布,使用我们的序列和从GISAID数据库检索的序列。
结果:在接受SARS-CoV-2筛查的8,207例患者或旅行者中,970例(11.8%)为阳性,386例Ct≤30。对133个样品进行WGS。同时,在2020年和2021年,在覆盖塞内加尔九个城市的GISAID数据库中保存了高质量序列(n=1,539),我们在2020年观察到20A(B.1,B.1.416和B.1.620)和20B(B.1.1.420)谱系的高循环,而大多数样本在2021年属于Delta变体(AY34和AY.34.1,22%)。
结论:尽管参与较晚,COVID-19诊断是在LBV中常规进行的,但基因组表征仍然具有挑战性。塞内加尔SARS-CoV-2菌株的基因组多样性反映了在大流行的第一波浪潮中在全球范围内观察到的情况。
BACKGROUND: In Senegal, molecular diagnosis was widely used for the detection and management of COVID-19 patients. However, genomic surveillance was very limited in the public sector. This study aimed to share the experience of a Senegalese public sector laboratory in response to the COVID-19 pandemic, and to describe the distribution of variants circulating in 2020 and 2021.
METHODS: From July 2020 to December 2021, SARS-CoV-2 qRT-PCR was performed on nasopharyngeal samples from travelers and symptomatic patients at the Bacteriology and Virology Laboratory (LBV) of the Aristide le Dantec University Teaching Hospital. Samples with a cycle threshold (Ct) ≤ 30 were selected for whole-genome sequencing (WGS) using the Nanopore technology. In-house scripts were developed to study the spatial and temporal distribution of SARS-CoV-2 variants in Senegal, using our sequences and those retrieved from the GISAID database.
RESULTS: Of 8,207 patients or travelers screened for SARS-CoV-2, 970 (11.8%) were positive and 386 had a Ct ≤ 30. WGS was performed on 133 samples. Concomitantly with high-quality sequences deposited in the GISAID database covering nine cities in Senegal in 2020 and 2021 (n = 1,539), we observed a high circulation of the 20A (B.1, B.1.416 and B.1.620) and 20B (B.1.1.420) lineages in 2020, while most of the samples belonged to Delta variants (AY34 and AY.34.1, 22%) in 2021.
CONCLUSIONS: Despite its late involvement, COVID-19 diagnosis was routinely performed in LBV, but genomic characterization remained challenging. The genomic diversity of SARS-CoV-2 strains in Senegal reflected that observed worldwide during the first waves of the pandemic.