SARS-CoV-2 基因组监测：2021 年 1 月至 2022 年 2 月突尼斯战略的数据分析与评估

Epidemiologia Pub Date : 2024-02-06 DOI:10.3390/epidemiologia5010005

Arwa Neffati, Mouna Safer, Wissal Kalai, A. Hechaichi, S. Dhaouadi, H. Letaief, Chaima Aichouch, L. Bouabid, Sondes Darouiche, Nawel El Mili, H. Triki, I. Boutiba, Maha Mastouri, Lamia Fki Berrajah, Nissaf Bouafif Ben Alaya

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引用次数: 0

摘要

由于 2020 年英国出现了 SARS-CoV-2 B.1.1.7 (Alpha)变异体及其传播风险的增加，突尼斯卫生部实施了 SARS-CoV-2 测序监测策略。本研究旨在分析突尼斯的 SARS-CoV-2 基因组监测数据（2021 年 1 月至 2022 年 2 月），并根据国家建议和 SARS-CoV-2 基因组监测指南评估 SARS-CoV-2 测序策略的实施情况，以实现公共卫生目标。对所有已测序的 RT-PCR 样本进行描述性研究（2021 年 1 月至 2022 年 2 月）。此外，还进行了一次内部审计，以评估是否符合国家建议的标准和为实现公共卫生目标而进行的 SARS-CoV-2 基因组监测指南。审计标准共包括与以下方面有关的 12 项简单或综合要求：取样（1 项要求）、数据收集/分析（6 项要求）、伙伴关系（1 项要求）和伦理考虑（1 项要求）。共有 4819 份样本被送往实验室，4278 份样本被测序。共对 3648 个样本进行了分类。阳性变异体（VOC）样本占 80.92%，区分如下：α，40.24%；β，0.24%；γ，0.03%；δ，45.26%；Ω，14.19%。每个 ISO 周的挥发性有机化合物显示为三个主要阶段：Alpha 3/2021-25/2021；Delta 26/2021-2/2022；Omicron 3/2022-6/2022。在总共 12 项要求中，7 项被视为 "未达到"，4 项被视为 "部分达到"，1 项被视为 "完全达到"，但包括未完全实现的目标。总之，对国家 SARS-CoV-2 测序战略的内部审计表明，总体上 "未达到 "合规水平。审计结果为与所有利益相关者合作制定监测战略提供了一个触发点，以便及早发现和应对由挥发性有机化合物引起的疾病爆发。

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Genomic Surveillance of SARS-CoV-2: Data Analysis and Assessment of Tunisian Strategy from January 2021 to February 2022

Due to the emergence of the SARS-CoV-2 B.1.1.7 (Alpha) variant in the UK in 2020 and its risk of increased transmission, the Ministry of Health in Tunisia implemented a sequencing surveillance strategy for SARS-CoV-2. The aim of this study was to analyze SARS-CoV-2 genomic surveillance data in Tunisia (January 2021–February 2022) and to assess the implementation of the sequencing strategy for SARS-CoV-2 in accordance with national recommendations and the guidance for SARS-CoV-2 genomic surveillance for public health goals. A descriptive study of all sequenced RT-PCR samples sequenced (January 2021–February2022). An internal audit was also done to assess the compliance against standards covering national recommendations and the Guidance for SARS-CoV-2 genomic surveillance for public health goals. A total of 12 simple or composite requirements related to the following areas were included in the audit standards: sampling (one requirements); data collection/analysis (six requirements); partnership (one requirement); and ethical considerations (one requirement). A total of 4819 samples were sent to laboratories and 4278 samples were sequenced. A total of 3648 samples were classified. Positive variants of concern (VOC) samples were 80.92%, differentiated as follows: Alpha, 40.24%; Beta, 0.24%; Gamma, 0.03%; Delta, 45.26%; and Omicron, 14.19%. Three principal phases of VOCs per ISO-week were shown: Alpha 3/2021–25/2021; Delta 26/2021–2/2022; and Omicron 3/2022–6/2022. Levels of compliance were identified; from a total of 12 requirements, 7 were considered as “not met”, 4 as “partially met”, and 1 as “fully met” but including not totally achieved objectives. In conclusion, the internal audit of the national SARS-CoV-2 sequencing strategy revealed an overall “not met” level of compliance. The results offered a trigger to collaborate with all stakeholders to develop a surveillance strategy for early detection and response to outbreaks caused by VOCs.

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Epidemiologia

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