ArticleVirology journal2020
Characterization of accessory genes in coronavirus genomes.
Article in Virology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 1 of them a synthesis that pooled it.
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Who cites it
116 citing papers in PubMed, 1 synthesis or guideline pooled it, 177 citations in OpenAlex.
- Pooled it
- Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses.Molecular systems biology · 2026Article
- Dysregulated host miRNAs with antiviral potential against SARS-CoV-2 identified from COVID-19 patients.Journal of translational medicine · 2026Article
- Aggregation potency and proinflammatory effects of SARS-CoV-2 proteins.Scientific reports · 2025Article
- Activity and cellular distribution of ORF3a mutants of SARS-CoV-2 variants of concern.The Journal of general virology · 2025Article
- Anti-interferon armamentarium of human coronaviruses.Cellular and molecular life sciences : CMLS · 2025Review
- Swine Acute Diarrhea Syndrome Coronavirus: An Overview of Virus Structure and Virus-Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Analysis of phosphomotifs coupled to phosphoproteome and interactome unveils potential human kinase substrate proteins in SARS-CoV-2.Frontiers in cellular and infection microbiology · 2025Article
- SARS-CoV-2 membrane protein induces neurodegeneration via affecting Golgi-mitochondria interaction.Translational neurodegeneration · 2024Article
- Analysis of the structure and interactions of the SARS-CoV-2 ORF7b accessory protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Detection of SARS-CoV-2 in wastewater as an earlier predictor of COVID-19 epidemic peaks in Venezuela.Scientific reports · 2024Article
- COVID-19 Vaccine mRNA Biodistribution: Maternal and Fetal Exposure Risks.American journal of reproductive immunology (New York, N.Y. : 1989) · 2024Review
- Review
- SARS-CoV-2 ORF10 hijacking ubiquitination machinery reveals potential unique drug targeting sites.Acta pharmaceutica Sinica. B · 2024Article
- Article
- SARS-CoV-2 Protein Nsp9 Is Involved in Viral Evasion through Interactions with Innate Immune Pathways.ACS omega · 2024Article
- An RNA-Seq analysis of coronavirus in the skin of the Pangolin.Scientific reports · 2024Article
- New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic.Frontiers in immunology · 2024Review
- Procoagulant Status and Fibrinolytic Activity in COVID-19 Patients during Illness and Convalescence.Biomedicines · 2023Article
- Article
56 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods.
methodsWe propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes.
resultsWe applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV.
conclusionsOur findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.
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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.