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Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

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Fast Phylogeny of SARS-CoV-2 by Compression.

Rudi L Cilibrasi¹, Paul M B Vitányi²

¹Centre for Nathematics & Computer Science CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands.

Entropy (Basel, Switzerland)

|April 23, 2022

Summary

This summary is machine-generated.

A novel compression method efficiently analyzes viral genome similarity, identifying SARS-CoV-2

Keywords:

COVID-19 virus compression phylogeny

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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.