在没有NGS的发展中国家检测SARS-CoV-2变体的多重RT-qPCR策略:玻利维亚的经验。

IF 2.2 4区 医学 Q3 INFECTIOUS DISEASES
Rudy Parrado, Carolina X Cuba-Grandy, Eugenia Fuentes-Luppichini, Nattaly Grecia Torrico Villarroel, Yercin Mamani-Ortiz, Jaqueline Mendez, Betty Melgarejo, Irenice Coronado-Arrázola, Nair A Montaño, Leonardo I Almonacid, Rafael A Medina, Lineth Garcia, Catalina Pardo-Roa
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引用次数: 0

摘要

SARS-CoV-2的快速进化导致了关注变异(VOCs)的出现,其特征是传播性、致病性和对中和抗体的抗性增强。识别这些变异对于指导控制COVID-19的公共卫生工作至关重要。尽管全基因组测序(WGS)是变异鉴定的金标准,但由于资源限制,其在发展中国家的实施往往受到限制。在玻利维亚,由于技术基础设施和资源有限,基因组监测是一项挑战。设计了一种基于rt - qpcr的策略来解决这些局限性,并检测与VOCs和感兴趣变异(voi)相关的突变。多重RT-qPCR商用试剂盒AllplexTM Master和variant I (Seegene®)和ValuPanelTM (Biosearch®)用于靶向HV69/70del、E484K、N501Y、P681H和K417N/T等突变。它们是Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621)和Zeta (P.2)变体的特征。对2021年1 - 11月在科科班巴采集的157份样本进行评估,鉴定出44份Gamma、2份Zeta、20份Mu和10份Omicron。利用Oxford NanoporeTM技术生成的WGS数据验证了该策略的有效性,一致性率为0.96。这突出了RT-qPCR策略在指导WGS样本选择方面的价值,能够更广泛地检测到仅通过RT-qPCR无法识别的新变异。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience.

Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience.

The rapid evolution of SARS-CoV-2 has led to the emergence of variants of concern (VOCs) characterized by increased transmissibility, pathogenicity, and resistance to neutralizing antibodies. Identifying these variants is essential for guiding public health efforts to control COVID-19. Although whole genome sequencing (WGS) is the gold standard for variant identification, its implementation is often limited in developing countries due to resource constraints. In Bolivia, genomic surveillance is a challenge due to its limited technological infrastructure and resources. An RT-qPCR-based strategy was designed to address these limitations and detect the mutations associated with VOCs and variants of interest (VOIs). The multiplex RT-qPCR commercial kits AllplexTM Master and Variants I (Seegene®) and the ValuPanelTM (Biosearch®) were used to target mutations such as HV69/70del, E484K, N501Y, P681H, and K417N/T. They are characteristic of the Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621), and Zeta (P.2) variants. A total of 157 samples collected in Cochabamba from January to November 2021 were evaluated, identifying 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron were identified. The strategy's effectiveness was validated against WGS data generated with Oxford NanoporeTM technology, showing a concordance rate of 0.96. This highlights the value of the RT-qPCR strategy in guiding the selection of samples for WGS, enabling broader detection of new variants that cannot be identified by RT-qPCR alone.

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来源期刊
Epidemiology and Infection
Epidemiology and Infection 医学-传染病学
CiteScore
4.10
自引率
2.40%
发文量
366
审稿时长
3-6 weeks
期刊介绍: Epidemiology & Infection publishes original reports and reviews on all aspects of infection in humans and animals. Particular emphasis is given to the epidemiology, prevention and control of infectious diseases. The scope covers the zoonoses, outbreaks, food hygiene, vaccine studies, statistics and the clinical, social and public-health aspects of infectious disease, as well as some tropical infections. It has become the key international periodical in which to find the latest reports on recently discovered infections and new technology. For those concerned with policy and planning for the control of infections, the papers on mathematical modelling of epidemics caused by historical, current and emergent infections are of particular value.
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