Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution
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Author(s)
Jungreis, Irwin
Nelson, Chase W.
Ardern, Zachary
Finkel, Yaara
Krogan, Nevan J.
Sato, Kei
Ziebuhr, John
Stern-Ginossar, Noam
Pavesi, Angelo
Firth, Andrew E.
Date Issued
March 2021
Journal
Virology
Publisher
Elsevier BV
Citation
Jungreis, Irwin et al. "Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution." Virology 558 (June 2021): 145-151 © 2021 The Author(s)
Version
Final published version
Abstract
At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
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Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1016/j.virol.2021.02.013
