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The coding capacity of SARS-CoV-2.
Finkel, Yaara; Mizrahi, Orel; Nachshon, Aharon; Weingarten-Gabbay, Shira; Morgenstern, David; Yahalom-Ronen, Yfat; Tamir, Hadas; Achdout, Hagit; Stein, Dana; Israeli, Ofir; Beth-Din, Adi; Melamed, Sharon; Weiss, Shay; Israely, Tomer; Paran, Nir; Schwartz, Michal; Stern-Ginossar, Noam.
  • Finkel Y; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
  • Mizrahi O; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
  • Nachshon A; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
  • Weingarten-Gabbay S; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Morgenstern D; Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Yahalom-Ronen Y; de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel.
  • Tamir H; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Achdout H; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Stein D; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Israeli O; Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Beth-Din A; Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Melamed S; Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Weiss S; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Israely T; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Paran N; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Schwartz M; Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  • Stern-Ginossar N; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Nature ; 589(7840): 125-130, 2021 01.
Article in English | MEDLINE | ID: covidwho-752477
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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Semantic information from SemMedBD (by NLM)
1. 2019 novel coronavirus LOCATION_OF Open Reading Frames
Subject
2019 novel coronavirus
Predicate
LOCATION_OF
Object
Open Reading Frames
2. Open Reading Frames PART_OF Reading Frames (Nucleotide Sequence)
Subject
Open Reading Frames
Predicate
PART_OF
Object
Reading Frames (Nucleotide Sequence)
3. Open Reading Frames PRODUCES Polypeptides
Subject
Open Reading Frames
Predicate
PRODUCES
Object
Polypeptides
4. 2019 novel coronavirus LOCATION_OF Open Reading Frames
Subject
2019 novel coronavirus
Predicate
LOCATION_OF
Object
Open Reading Frames
5. Open Reading Frames PART_OF Reading Frames (Nucleotide Sequence)
Subject
Open Reading Frames
Predicate
PART_OF
Object
Reading Frames (Nucleotide Sequence)
6. Open Reading Frames PRODUCES Polypeptides
Subject
Open Reading Frames
Predicate
PRODUCES
Object
Polypeptides
ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic1. To understand the pathogenicity and antigenic potential of SARS-CoV-2 and to develop therapeutic tools, it is essential to profile the full repertoire of its expressed proteins. The current map of SARS-CoV-2 coding capacity is based on computational predictions and relies on homology with other coronaviruses. As the protein complement varies among coronaviruses, especially in regard to the variety of accessory proteins, it is crucial to characterize the specific range of SARS-CoV-2 proteins in an unbiased and open-ended manner. Here, using a suite of ribosome-profiling techniques2-4, we present a high-resolution map of coding regions in the SARS-CoV-2 genome, which enables us to accurately quantify the expression of canonical viral open reading frames (ORFs) and to identify 23 unannotated viral ORFs. These ORFs include upstream ORFs that are likely to have a regulatory role, several in-frame internal ORFs within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. We further show that viral mRNAs are not translated more efficiently than host mRNAs; instead, virus translation dominates host translation because of the high levels of viral transcripts. Our work provides a resource that will form the basis of future functional studies.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Protein Biosynthesis / Viral Proteins / Open Reading Frames / Genome, Viral / Gene Expression Profiling / SARS-CoV-2 Type of study: Prognostic study Limits: Animals / Humans Language: English Journal: Nature Year: 2021 Document Type: Article Affiliation country: S41586-020-2739-1

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Protein Biosynthesis / Viral Proteins / Open Reading Frames / Genome, Viral / Gene Expression Profiling / SARS-CoV-2 Type of study: Prognostic study Limits: Animals / Humans Language: English Journal: Nature Year: 2021 Document Type: Article Affiliation country: S41586-020-2739-1