Fast Phylogeny of SARS-CoV-2 by Compression

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The SARS-CoV-2 virus, responsible for COVID-19, necessitates rapid and accurate phylogenetic analysis.
• Traditional whole-genome comparison methods can be computationally intensive.

Purpose of the Study:

• To evaluate the utility of an alignment-free compression method for whole-genome phylogenetic and taxonomic analysis of SARS-CoV-2.
• To compare SARS-CoV-2 with a large database of viral genomes.

Main Methods:

• Utilized a normalized compression distance (NCD) approach based on algorithmic information theory to assess genomic similarity.
• Applied this method to the SARS-CoV-2 whole genome and a database of over 6500 viruses.
• Compared NCD results with those from mitochondrial DNA of familiar species and alignment-based methods.

Main Results:

• The compression method identified SARS-CoV-2 as most closely related to the RaTG13 virus and bat coronaviruses (bat-SL-CoVZXC21, bat-SL-CoVZC45).
• Phylogenetic and taxonomic results closely mirrored those obtained from alignment-based and machine-learning methods.
• The method provided insights into potential pangolin involvement in SARS-CoV-2 origins.

Conclusions:

• The alignment-free compression method is a simple, fast, and effective tool for whole-genome phylogenetic analysis.
• This approach offers a viable alternative to complex alignment-based methods for viral taxonomy and similarity assessment.
• The findings support the compression method's potential for rapid exploration of viral evolution and relationships.