Schema for Pot. pathogenic indels - Potential pathogenic insertions and deletions from Gussow et al, PNAS 2020
  Database: wuhCor1    Primary Table: potPathoIndel Data last updated: 2020-08-28
Big Bed File: /gbdb/wuhCor1/bbi/potPathoIndel.bb
Item Count: 12
Format description: Browser Extensible Data
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart3604Start position in chromosome
chromEnd3604End position in chromosome
nameDeletionName of item.

Sample Rows
 
chromchromStartchromEndname
NC_045512v236043604Deletion
NC_045512v264376442Insertion
NC_045512v297509750Deletion
NC_045512v22014120141Deletion
NC_045512v22235822358Deletion
NC_045512v22297923021Potential Zoonotic Insert
NC_045512v22422824239Insertion
NC_045512v22500125001Deletion
NC_045512v22700127001Deletion
NC_045512v22911429126Insertion

Pot. pathogenic indels (potPathoIndel) Track Description
 

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.