ArticleVirology2021
Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.
Article in Virology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 50 citations in OpenAlex.
- Targeting SARS-CoV-2 Structural and Accessory Proteins: Emerging Opportunities for Small-Molecule Coronavirus Antivirals.Pharmaceutics · 2026Review
- Synthetic Integration of an FCS into Coronaviruses-Hype or an Unresolved Biorisk? An Integrative Analysis of DNA Repair, Cancer Research, Drug Development, and Escape Mutant Traits.Life (Basel, Switzerland) · 2026Article
- Targeting SARS-CoV-2 main protease (3CLIn silico pharmacology · 2026Article
- SARS-CoV-2-host and interactions: the dual roles of E3 ubiquitin ligases and ubiquitin-like modification mechanisms in viral infection.Frontiers in immunology · 2026Review
- Antigenic remodeling of the SARS-CoV-2 Spike N-terminal domain links sequence variability to structural reorganization of a neutralizing antibody supersite.Frontiers in cellular and infection microbiology · 2026Article
- Transcriptomic profiles of monocyte-derived macrophages exposed to SARS-CoV-2 VOCs reveal immune-evasion escape driven by delta.Journal of translational medicine · 2025Article
- Examining the feasibility of replacing ORF3a with fluorescent genes to construct SARS-CoV-2 reporter viruses.The Journal of general virology · 2025Article
- Hidden players of COVID-19: the evolving roles of SARS-CoV-2 accessory proteins.Frontiers in immunology · 2025Review
- Is Autophagy a Friend or Foe in SARS-CoV-2 Infection?Viruses · 2024Review
- Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- SARS-CoV-2 biology and host interactions.Nature reviews. Microbiology · 2024Review
- Article
- ORF3c is expressed in SARS-CoV-2-infected cells and inhibits innate sensing by targeting MAVS.EMBO reports · 2023Article
- Article
- Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty.Journal of molecular evolution · 2023Review
- Fitness effects of mutations to SARS-CoV-2 proteins.bioRxiv : the preprint server for biology · 2023Article
- Interferon antagonists encoded by SARS-CoV-2 at a glance.Medical microbiology and immunology · 2023Review
- GENCODE: reference annotation for the human and mouse genomes in 2023.Nucleic acids research · 2023Article
- Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh.Frontiers in genetics · 2023Article
- Fitness effects of mutations to SARS-CoV-2 proteins.Virus evolution · 2023Article
Corrections and comments
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Authors and funding
12 authors at 10 institutions in 9 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.