Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression

  1. Rudi L. Cilibrasi
  2. Paul M.B. Vitányi

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Abstract

We analyze the whole genome phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new fast alignment-free method called the “normalized compression distance” (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole genome method, which makes it the ideal tool to explore phylogeny.

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    SciScore for 10.1101/2020.07.22.216242: (What is this?)

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  2. Version published to 10.1101/2020.07.22.216242 on bioRxiv