Pot. pathogenic indels Track Settings
 
Potential pathogenic insertions and deletions from Gussow et al, PNAS 2020   (All Variation and Repeats tracks)

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Assembly: SARS-CoV-2 Jan. 2020 (NC_045512.2)
Data last updated at UCSC: 2020-08-28 02:38:49

Description

This track shows genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), from less pathogenic coronaviruses. These features include:

  • Enhancement of the nuclear localization signals in the nucleocapsid protein
  • Inserts in the spike glycoprotein that appear to be associated with the high case fatality rate of these coronaviruses
  • Inserts in the spike glycoprotein that appear to be associated with the host switch from animals to humans

Methods

We searched for specific regions, within an alignment of 944 human coronaviruses, that contributed the most to the separation between coronaviruses with a high case fatality rate and those with a low case fatality rate, using a combination of comparative genomics and machine learning techniques. For the zoonotic insertions, we scanned an alignment of human and nonhuman coronaviruses to find regions in which over 50% of the strains in the alignment differed from the human strain, and for which the differing strains were explicitly the most distant from human. We identified only one such location, across all three high case fatality rate virus groups.

References

Ayal B. Gussow*, Noam Auslander*, Guilhem Faure, Yuri I. Wolf, Feng Zhang, Eugene V. Koonin. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proceedings of the National Academy of Sciences Jun 2020, 117 (26) 15193-15199; DOI: 10.1073/pnas.2008176117.