Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis

被引：0
作者：
Bundschuh, Christian [1 ]
Weidner, Niklas [1 ,2 ]
Klein, Julian [1 ]
Rausch, Tobias [3 ]
Azevedo, Nayara [3 ]
Telzerow, Anja [1 ,3 ]
Jost, Katharina Laurence [1 ]
Schnitzler, Paul [1 ]
Kraeusslich, Hans-Georg [1 ,4 ]
Benes, Vladimir [3 ]
机构：
[1] Heidelberg Univ, Med Fac Heidelberg, Dept Infect Dis Virol, Heidelberg, Germany
[2] Heidelberg Univ, Med Fac Heidelberg, Dept Infect Dis Microbiol & Hyg, Heidelberg, Germany
[3] European Mol Biol Lab EMBL, Genom Core Facil, Heidelberg, Germany
[4] Deutsch Zentrum Infekt Forsch, Partner Site Heidelberg, Heidelberg, Germany
来源：
DATA IN BRIEF | 2024年 / 55卷
关键词：
Virology; Epidemiology; Whole genome sequencing; Bioinformatics; SARS-CoV-2;
D O I：
10.1016/j.dib.2024.110607
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
In January 2021, Germany commenced surveillance of SARSCoV-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 NextSeq50 0 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 NextSeq50 0 can be found in our previous publication.
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页数：13
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