2020-2021 年塞内加尔 SARS-CoV-2 基因组流行病学。

IF 1.4 4区 医学 Q4 INFECTIOUS DISEASES Journal of Infection in Developing Countries Pub Date : 2024-06-30 DOI:10.3855/jidc.17796
Adjiratou Aissatou Ba, Romain Coppée, Assane Dieng, Jarra Manneh, Mengue Fall, Khadim Gueye, Pauline Yacine Sene, Samba Ndiour, Dianké Samaté, Pascaline Manga, Oumy Diop Diongue, Abdoulaye Camara, Abdou Padane, Sada Diallo, Sokhna Bousso Gueye, Makhtar Camara, Abdul Karim Sesay, Coumba Toure-Kane, Souleymane Mboup, Charlotte Charpentier, Halimatou Diop-Ndiaye
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引用次数: 0

摘要

导言: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却非常有限。本研究旨在分享塞内加尔公共部门实验室在应对 COVID-19 大流行方面的经验,并描述 2020 年和 2021 年流行变异体的分布情况:从 2020 年 7 月到 2021 年 12 月,阿里斯蒂德-勒丹泰克大学教学医院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-2 qRT-PCR 检测。选取周期阈值(Ct)≤ 30 的样本,使用 Nanopore 技术进行全基因组测序(WGS)。利用我们的序列和从 GISAID 数据库中检索到的序列,开发了内部脚本来研究塞内加尔 SARS-CoV-2 变异体的时空分布:在接受 SARS-CoV-2 筛查的 8207 名患者或旅行者中,970 人(11.8%)呈阳性,386 人的 Ct 值小于 30。对 133 份样本进行了 WGS 检测。与 2020 年和 2021 年塞内加尔九个城市(n = 1,539)存入 GISAID 数据库的高质量序列一致,我们观察到 2020 年 20A (B.1、B.1.416 和 B.1.620)和 20B (B.1.1.420)系的高流通率,而 2021 年大多数样本属于 Delta 变种(AY34 和 AY.34.1,22%):尽管 COVID-19 参与时间较晚,但在枸杞多糖中已被常规诊断,但基因组特征描述仍具有挑战性。塞内加尔 SARS-CoV-2 株系的基因组多样性反映了该流行病第一波期间在全球范围内观察到的多样性。
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Genomic epidemiology of SARS-CoV-2 in Senegal in 2020-2021.

Introduction: 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.

Methodology: 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.

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来源期刊
CiteScore
3.70
自引率
5.30%
发文量
239
审稿时长
4-8 weeks
期刊介绍: The Journal of Infection in Developing Countries (JIDC) is an international journal, intended for the publication of scientific articles from Developing Countries by scientists from Developing Countries. JIDC is an independent, on-line publication with an international editorial board. JIDC is open access with no cost to view or download articles and reasonable cost for publication of research artcles, making JIDC easily availiable to scientists from resource restricted regions.
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