Description

These tracks show curated SARS-CoV-2 protein-coding genes conserved within the Sarbecovirus subgenus as determined using PhyloCSF [1], FRESCo [2], and other comparative genomics methods, consistent with experimental evidence in SARS-CoV-2. Ambiguous gene names were resolved according to the recommendations in [3]. For a complete description of the evidence, see [4].

• The PhyloCSF Genes track shows the conserved protein-coding genes, namely ORF1a, ORF1ab, S, ORF3a, ORF3c, E, M, ORF6, ORF7a, ORF7b, ORF8, N, and ORF9b.

  Notes:

  • ORF3c is a 41 codon ORF overlapping ORF3a in a different frame with coordinates 25457-25582; it has also been referred to as ORF3h, ORF3a*, and 3a.iORF1.
  • ORF9b is a 97 codon ORF overlapping N in a different frame with coordinates 28284-28577; it has also been referred to as ORF9a.


• The PhyloCSF Rejected Genes track shows other gene candidates that have been proposed that do not show the signature of conserved protein-coding genes or persuasive experimental evidence of function [4], and are thus unlikely to be actual protein-coding genes, namely ORF2b, ORF3d, ORF3d-2, ORF3b, ORF9c, and ORF10.

  Notes:

  • ORF2b is a 39 codon ORF with coordinates 21744-21860 overlapping the spike protein in a different frame; it has also been referred to as S.iORF1.
  • ORF3d is a 57 codon ORF with coordinates 25524-25697 overlapping ORF3a in a different frame; it has also been referred to as ORF3b.
  • ORF3d-2 is a 33 codon ORF with coordinates 25596-25697 that is a subset of ORF3d starting at a downstream in-frame AUG codon; it has also been referred to as 3a.iORF2.
  • ORF3b is the 22 codon ortholog of the 5' end of SARS-CoV ORF3b with coordinates 25814-25882, ending at an in-frame stop codon that is not present in SARS-CoV.
  • ORF9c is a 73 codon ORF overlapping N in a different frame with coordinates 28734-28955; it has also been referred to as ORF9b and ORF14.

Data Access

For automated analysis, the genome annotations are stored in bed and bigBed files that can be downloaded from the SARS-CoV-2 PhyloCSF Genes track hub.

Credits

Questions should be directed to Irwin Jungreis.

If you use the SARS-CoV-2 PhyloCSF Genes Track Hub, please cite Jungreis et al. 2021 [4].

References

[1] Lin MF, Jungreis I, and Kellis M (2011). PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Bioinformatics 27(13), i275-i282. doi.org/10.1093/bioinformatics/btr209

[2] Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC (2015). FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biol. 16(1), 1-14. doi: 10.1186/s13059-015-0603-7

[3] Jungreis, I., Nelson, C. W., Ardern, Z., Finkel, Y., Krogan, N. J., Sato, K., ... & Kellis, M. (2021). Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Virology 558, 145-151. doi.org/10.1016/j.virol.2021.02.013

[4] Jungreis I, Sealfon R, Kellis M (2021). SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nature Communications 12(1), 1-20. doi:10.1038/s41467-021-22905-7