PDF(Pubmed)
Abstract：
SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread.
摘要：
SARS-CoV-2关注（VOC）和关注（VOI）变体相对于原始病毒存在突变，更容易传播。我们实施了使用实时RT-PCR筛选SARS-CoV-2VOC/VOIs的快速策略，并对我们地区的变体进行了监测和监视。连续实时RT-PCR，用于检测VOC/VOIs中尖峰蛋白中存在的相关突变/缺失（TaqMan™SARS-CoV-2突变面板，应用生物系统）实施。使用不同的算法分析了2021年来自阿根廷中部受感染个体的6,640个SARS-CoV-2RNA样本（Cts<30），这些算法逐渐适应了局部变异循环的变化情况。制定的策略允许及早发现和识别全年传播的VOC/VOIs，与WGS100%一致。样本分析显示，分别于2021年2月和3月引入了VOCsAlpha和Gamma。伽马呈指数增长,检测高峰在7月份(72%)，负责阿根廷第二波COVID19。自从VOC三角洲进入该地区以来，它逐渐增加，与VOILambda一起，替换VOCGamma,直到11月成为主要变体（84.9%）。到12月,这些变体在2周内被新兴的VOCOmicron取代，产生第三波。我们报告了一种用于VOC/VOI检测的有用工具，能够在资源有限的环境中快速且经济高效地监控当前公认的变体，它允许追踪最近Omicron在我们地区的扩张，并有助于实施控制疾病传播的公共卫生措施。
