Your browser doesn't support javascript.
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time.
Cilibrasi, Luca; Pinoli, Pietro; Bernasconi, Anna; Canakoglu, Arif; Chiara, Matteo; Ceri, Stefano.
  • Cilibrasi L; Dept. of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy.
  • Pinoli P; Dept. of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy.
  • Bernasconi A; Dept. of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy.
  • Canakoglu A; Dept. of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy.
  • Chiara M; Dept. of BioSciences, University of Milano, 20133 Milano, Italy.
  • Ceri S; Dept. of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy.
Bioinformatics ; 2022 Jan 18.
Article in English | MEDLINE | ID: covidwho-1631198
ABSTRACT
MOTIVATION The ongoing evolution of SARS-CoV-2 and the rapid emergence of variants of concern (VOCs) at distinct geographic locations have relevant implications for the implementation of strategies for controlling the COVID-19 pandemic. Combining the growing body of data and the evidence on potential functional implications of SARS-CoV-2 mutations can suggest highly effective methods for the prioritization of novel variants of potential concern, e.g., increasing in frequency locally and/or globally. However, these analyses may be complex, requiring the integration of different data and resources. We claim the need for a streamlined access to up-to-date and high-quality genome sequencing data from different geographic regions/countries, and the current lack of a robust and consistent framework for the evaluation/comparison of the results.

RESULTS:

To overcome these limitations, we developed ViruClust, a novel tool for the comparison of SARS-CoV-2 genomic sequences and lineages in space and time. ViruClust is made available through a powerful and intuitive web-based user interface. Sophisticated large scale analyses can be executed with a few clicks, even by users without any computational background. To demonstrate potential applications of our method, we applied ViruClust to conduct a thorough study of the evolution of the most prevalent lineage of the Delta SARS-CoV-2 variant, and derived relevant observations. Conclusions By allowing the seamless integration of different types of functional annotations and the direct comparison of viral genomes and genetic variants in space and time, ViruClust represents a highly valuable resource for monitoring the evolution of SARS-CoV-2, facilitating the identification of variants and/or mutations of potential concern.

AVAILABILITY:

ViruClust is openly available at http//gmql.eu/viruclust/.

Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal subject: Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bioinformatics

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal subject: Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bioinformatics