PDF(Pubmed)
Abstract：
The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.
摘要：
SARS-CoV-2的出现和迅速传播促使全球社会确定了诊断感染和对病毒基因组进行测序的创新方法，因为在大流行阳性病例的几个点，其数量超过了实验室表征足够样本以充分响应新出现的变异的传播的能力。从2020年第10周到2023年第13周，斯洛文尼亚常规全基因组测序（CGS）监测网络产生了41.537个完整基因组，并揭示了典型的分子流行病学，早期谱系逐渐被Alpha取代，Delta,最后是Omicron.我们通过样本合并和选择性SARS-CoV-2尖峰基因扩增与个体病例的CGS相结合，开发了一种基于靶向下一代测序的变异监测策略，称为SpikeScreen，以提高吞吐量和成本效益。SpikeScreen可识别关注变体（VOC）和感兴趣变体（VOI）特征突变，分析它们在样本池中的频率，并计算人口水平的VOCs/VOIs数量。在通过CGS确认之前，该策略已成功应用于检测特定的VOC/VOI突变。SpikeScreen补充了CGS的工作，在两个时间段内进行了额外的22.897个样本测序：2020年第42周和2021年第24周之间，以及2021年第37周和2022年第2周之间。结果表明，SpikeScreen可以通过在人群水平上可靠，快速地检测新的变异，在测序能力有限的环境中，应用于监测大量样品中的VOC/VOI突变，并可以作为公共卫生政策规划的基础。
