Life Science/Next Generation Sequencing/

SARS-CoV-2 genome sequencing and bioinformatic analysis

SARS-CoV-2 Genome Sequencing: Uncover the Virus Variants – Implementation of sequencing  workflow in Just One Week

Together with with the Johannes Gutenberg University Mainz (Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis) and the University Medical Center (Institute for Virology and Research Center for Immunotherapy (FZI), the Institute for Humangenetics, the Department of Hygiene and Infection Prevention – Hospital Hygiene -, the Medical Management Department and the Transfusion Unit & Test Center) StarSEQ founded the SARS-CoV-2 Sequencing Consortium Mainz. The goal of this high-level scientific cooperation is the massive parallel sequencing of SARS-CoV-2 genomes in rhineland-palatinate and the rhine-main area to uncover genetic changes (mutations) of the Covid-19 virus for regional SARS-CoV-2 variant surveillance. We already have started the sequencing and bioinformatic analyis for uploading the data to the RKI (Robert Koch Institut) and the GISAID Initiative. Read the press release here (German)

 

Update: Here you can read the preprint of our newest puplication SARS-CoV-2 genome surveillance in Mainz, Germany, reveals convergent origin of the N501Y spike mutation in a hospital setting

Full sequencing service of SARS-CoV-2 starting from total RNA

 

  • starting from total RNA that was already prepared for qPCR (excess material)
  • additional RNA clean-up if needed
  • cDNA synthesis
  • Amplicon based library preparation using RC-PCR based on ARTIC protocol
  • Quality check of resulting libraries
  • Pooling of libraries
  • Sequencing with Illumina’s MiSeq or NextSeq with a minimum amount of 50.000 reads per sample
  • Demultiplexing

SARS-CoV-2 bioinformatic service

 

  • Adapter Trimming
  • Trimming of primer sequences
  • Quality trimming and length filter
  • Mapping to SARS-CoV-2 reference sequences
  • Variant detection
  • Consensus sequence + variants
  • Assign consensus sequence to clades using nextclade or pangolin
  • Report
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