CoVigator-A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

Viruses. 2023 Jun 17;15(6):1391. doi: 10.3390/v15061391.

Abstract

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern.

Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de.

Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts.

Keywords: SARS-CoV-2; dashboard; genomic variants; intrahost; knowledge base; pipeline; software; virus genome assemblies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 Vaccines
  • COVID-19* / epidemiology
  • Genomics
  • Humans
  • Knowledge Bases
  • Mutation
  • Pandemics
  • SARS-CoV-2* / genetics
  • Spike Glycoprotein, Coronavirus

Substances

  • COVID-19 Vaccines
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

BioNTech SE: Mainz, Germany, supports the study. The funder provided support in the form of a salary for author U.S., but did not have any additional role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. The specific roles of this author are articulated in the ‘Author Contributions’ section. In addition, the other authors are employees of the non-profit company TRON gGmbH and are supported in the form of salaries. TRON gGmbH did not have any additional role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. Intel is committed to accelerating access to technology that can combat the current pandemic and enabling scientific discovery that better prepares our world for future crises. Funding for this solution was funded in part by Intel’s Pandemic Response Technology Initiative. For more information about healthcare solutions from Intel, visit intel.com/healthcare. For more information about Intel’s COVID-19 response, visit https://www.intel.com/content/www/us/en/corporate-responsibility/covid-19-response.html, accessed on 16 June 2023.