Bundschuh Christian, Weidner Niklas, Klein Julian, Rausch Tobias, Azevedo Nayara, Telzerow Anja, Jost Katharina Laurence, Schnitzler Paul, Kräusslich Hans-Georg, Benes Vladimir
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany.
Medical Faculty Heidelberg, Department of Infectious Diseases, Microbiology and Hygiene, Heidelberg University, Heidelberg, Germany.
Data Brief. 2024 Jun 12;55:110607. doi: 10.1016/j.dib.2024.110607. eCollection 2024 Aug.
In January 2021, Germany commenced surveillance of SARS-CoV-2 variants under the Corona Surveillance Act, which ceased in July 2023. The objective was to bolster pandemic control, as specific alterations in amino acids, particularly within the spike protein, were linked to heightened transmission and decreased vaccine effectiveness. Consequently, our team conducted whole genome sequencing using the commercially accessible ARTIC protocol on Illumina's NextSeq500 platform and MiSeq for SARS-CoV-2 positive samples obtained from patients at Heidelberg University Hospital, affiliated hospitals, and the public health office in the Rhine-Neckar/Heidelberg region. Throughout the pandemic, we refined the existing ARTIC V4 protocol as well as our bioinformatics pipeline, the details of which are outlined in this report. This report reflects the protocol for the MiSeq analysis, the protocol for the NextSeq500 can be found in our previous publication.
2021年1月，德国根据《新冠监测法》开始对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体进行监测，该监测于2023年7月结束。目的是加强疫情防控，因为氨基酸的特定改变，尤其是刺突蛋白内的改变，与传播增强和疫苗效力降低有关。因此，我们的团队使用商业上可获取的ARTIC方案，在Illumina的NextSeq500平台和MiSeq上，对从海德堡大学医院、附属医院以及莱茵-内卡/海德堡地区公共卫生办公室的患者中获得的SARS-CoV-2阳性样本进行全基因组测序。在整个疫情期间，我们完善了现有的ARTIC V4方案以及我们的生物信息学流程，本报告概述了其详细信息。本报告反映了MiSeq分析的方案，NextSeq500的方案可在我们之前的出版物中找到。
