Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis
Christian Bundschuh,
Niklas Weidner,
Julian Klein,
Tobias Rausch,
Nayara Azevedo,
Anja Telzerow,
Katharina Laurence Jost,
Paul Schnitzler,
Hans-Georg Kräusslich,
Vladimir Benes
Affiliations
Christian Bundschuh
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany; Corresponding author.
Niklas Weidner
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
Julian Klein
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
Tobias Rausch
Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
Nayara Azevedo
Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
Anja Telzerow
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany; Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
Katharina Laurence Jost
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
Paul Schnitzler
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
Hans-Georg Kräusslich
Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany; Deutsches Zentrum für Infektionsforschung, partner site Heidelberg, Germany
Vladimir Benes
Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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.
