Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates.
College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
Clin Chem. 2020 Nov 1;66(11):1450-1458. doi: 10.1093/clinchem/hvaa187.
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.
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.
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.
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.
随着经济的逐步复苏和社会生活的恢复，应该实施强有力的监测机制来控制当前的 COVID-19 大流行。与 RT-qPCR 不同，SARS-CoV-2 全基因组测序（cWGS）具有识别病毒隐匿起源的额外优势，以及社区传播与新病毒传入的程度，这反过来又会影响公共卫生政策决策。然而，在广泛实施之前，应该解决 cWGS 的实际和成本考虑。
我们使用从 COVID-19 患者的鼻咽拭子中提取的 RNA 进行了鸟枪法转录组测序，并将其与靶向 SARS-CoV-2 基因组扩增和测序进行了比较，以评估病毒检测、可扩展性和成本效益。为了跟踪病毒起源，我们使用开源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。
我们发现，通过基于扩增子的 SARS-CoV-2 靶向富集，全基因组测序数据质量和病毒检测得到了显著改善。使用富集后，测序reads 中超过 99%映射到病毒基因组，而没有富集时平均只有 0.63%。因此，使用大大减少的测序数据获得了更高的基因组覆盖率，从而实现了更高的可扩展性和可观的成本降低。我们还展示了如何通过包括其他病毒株在内的系统发育分析来确定 SARS-CoV-2 基因组序列的可能起源。
SARS-CoV-2 全基因组测序是一种实用、具有成本效益且强大的方法，可用于下一阶段 COVID-19 大流行期间的基于人群的监测和控制病毒传播。
