Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Conflicting and Ambiguous Names of Overlapping ORFs in SARS-CoV-2: A Homology-Based Resolution

Irwin Jungreis
* ,
Chase W. Nelson
,
Zachary Ardern
,
Yaara Finkel
,
Nevan J. Krogan
,
Kei Sato
,
John Ziebuhr
ORCID logo ,
Noam Stern-Ginossar
,
Angelo Pavesi
,
Andrew E. Firth
ORCID logo ,
Alexander E. Gorbalenya
,
Manolis Kellis
Version 1 : Received: 30 November 2020 / Approved: 2 December 2020 / Online: 2 December 2020 (08:04:06 CET)

A peer-reviewed article of this Preprint also exists.

Jungreis, I.; Nelson, C. W.; Ardern, Z.; Finkel, Y.; Krogan, N. J.; Sato, K.; Ziebuhr, J.; Stern-Ginossar, N.; Pavesi, A.; Firth, A. E.; et al. Conflicting and Ambiguous Names of Overlapping ORFs in the SARS-CoV-2 Genome: A Homology-Based Resolution. Virology, 2021, 558, 145–151. https://doi.org/10.1016/j.virol.2021.02.013. Jungreis, I.; Nelson, C. W.; Ardern, Z.; Finkel, Y.; Krogan, N. J.; Sato, K.; Ziebuhr, J.; Stern-Ginossar, N.; Pavesi, A.; Firth, A. E.; et al. Conflicting and Ambiguous Names of Overlapping ORFs in the SARS-CoV-2 Genome: A Homology-Based Resolution. Virology, 2021, 558, 145–151. https://doi.org/10.1016/j.virol.2021.02.013.

Abstract

At least six small alternate-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 ICTV. 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 due to prior usage of alternative names.

Keywords

accessory protein; alternate reading frame; nomenclature; open reading frame; ORF3b; ORF3d; ORF9a; ORF9b; overlapping ORF; SARS-CoV-2

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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