Lowry Kym, Bauer Michelle J, Buckley Cameron, Wang Claire, Bordin Amanda, Badman Steven, Harris Patrick N A, Mackay Ian, Whiley David
The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
J Virol Methods. 2023 Dec;322:114827. doi: 10.1016/j.jviromet.2023.114827. Epub 2023 Sep 29.
The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants. In the present study, we evaluated the performance of the Illumina COVIDSeq Assay as a streamlined amplicon-based NGS platform for detection and typing of Omicron variants. Our results demonstrate the high performance of SARS-CoV-2 sequencing using the COVIDSeq approach, with good repeatability, reproducibility and sensitivity for samples approaching C 31. The COVIDSeq approach was 100% concordant with samples previously characterized by sequencing methods. The quick library preparation process and high throughput kit made it ideal for reflex testing, with a total time required for sequencing and analysis of approximately two days. This study demonstrates the effectiveness and versatility of the amplicon-based NGS characterisation method for SARS-CoV-2, providing a foundation for further research and development of custom-designed amplicon panels targeting different microorganisms.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体的持续出现和传播需要持续的基因监测，以支持公共卫生应对措施。可靠的下一代测序（NGS）平台的扩展使得能够使用鼻咽拭子标本快速鉴定新出现的SARS-CoV-2变体。多项研究评估了COVIDSeq对早期SARS-CoV-2毒株（德尔塔毒株之前）进行快速分型的能力，然而，针对奥密克戎变体适用性的数据有限。在本研究中，我们评估了Illumina COVIDSeq检测法作为一种简化的基于扩增子的NGS平台，用于检测和分型奥密克戎变体的性能。我们的结果表明，使用COVIDSeq方法进行SARS-CoV-2测序具有高性能，对于接近C 31的样本具有良好的重复性、再现性和灵敏度。COVIDSeq方法与先前通过测序方法鉴定的样本100%一致。快速的文库制备过程和高通量试剂盒使其非常适合进行补充检测，测序和分析所需的总时间约为两天。本研究证明了基于扩增子的NGS鉴定方法对SARS-CoV-2的有效性和通用性，为进一步研发针对不同微生物的定制扩增子面板奠定了基础。
