SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
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DOI：
10.1093/clinchem/hvaa187
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发表时间：
2020-11-01
影响因子：
9.3
通讯作者：
Abou Tayoun, Ahmad
中科院分区：
文献类型：
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作者：
Harilal, Divinlal;Ramaswamy, Sathishkumar;Abou Tayoun, Ahmad
背景：随着经济的逐步重新开放和社会生活的恢复，应实施强有力的监测机制，以控制正在进行的COVID-19大流行。与RT-qPCR不同，SARS-CoV-2全基因组测序（cWGS）具有额外的优势，可以确定病毒的神秘起源，以及社区传播与新病毒引入的程度，这反过来可以影响公共卫生政策决策。然而，在广泛实施cWGS之前，应先考虑其实用性和成本问题。方法：我们使用从COVID-19患者鼻咽拭子中提取的RNA进行鸟枪转录组测序，并将其与靶向SARS-CoV-2基因组扩增和测序在病毒检测、可扩展性和成本效益方面进行比较。为了追踪病毒起源，我们使用开源的多序列比对和系统发育工具将组装的SARS-CoV-2基因组与公开可用的序列进行比较。结果：我们发现利用基于扩增子的SARS-CoV-2靶向富集技术，在全基因组测序数据质量和病毒检测方面有了相当大的改善。富集后，超过99%的测序读数映射到病毒基因组，而未富集时平均为0.63%。因此，使用更少的测序数据获得了基因组覆盖率的增加，从而实现了更高的可扩展性和相当大的成本降低。我们还演示了如何通过系统发育分析（包括其他病毒株）使用SARS-CoV-2基因组序列来确定其可能的起源。结论：SARS-CoV-2全基因组测序是下一阶段基于人群的病毒传播监测和控制的一种实用、经济、有效的方法。
BACKGROUND: With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented.METHODS: We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences.RESULTS: We found considerable improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome, compared to an average of 0.63% without enrichment. Consequently, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.CONCLUSIONS: SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.