Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

I. Jungreis; C. Nelson; Z. Ardern; Y. Finkel; N. Krogan; K. Sato; J. Ziebuhr; N. Stern-Ginossar; A. Pavesi; A. Firth; A. Gorbalenya; M. Kellis

Статья

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

I. Jungreis, C. Nelson, Z. Ardern, Y. Finkel, N. Krogan, K. Sato, J. Ziebuhr, N. Stern-Ginossar, A. Pavesi, A. Firth, A. Gorbalenya, M. Kellis,

2021

https://doi.org/10.1016/j.virol.2021.02.013

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.

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1. Version of Record от 2021-06-01

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Об авторах

I. Jungreis
MIT Computer Science & Artificial Intelligence Laboratory, Broad Institute
C. Nelson
Academia Sinica, Biodiversity Research Center, American Museum of Natural History
Z. Ardern
Technical University of Munich
Y. Finkel
Weizmann Institute of Science Israel
N. Krogan
California Institute for Quantitative Biosciences, University of California, San Francisco, The J. David Gladstone Institutes
K. Sato
The University of Tokyo
J. Ziebuhr
Justus-Liebig-Universität Gießen
N. Stern-Ginossar
Weizmann Institute of Science Israel
A. Pavesi
University of Parma
A. Firth
University of Cambridge
A. Gorbalenya
Leiden University Medical Center - LUMC, Lomonosov Moscow State University
M. Kellis
MIT Computer Science & Artificial Intelligence Laboratory, Broad Institute

Название журнала

Virology

Том

Страницы

145-151

Финансирующая организация

National Institutes of Health

Номер гранта

R01 HG004037

Тип документа

journal article

Тип лицензии Creative Commons

CC BY

Правовой статус документа

Свободная лицензия

Источник

scopus

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Статья

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

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