ArticleJournal of medical virology2020
From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.
Article in Journal of medical virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
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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
106 citing papers in PubMed, 1 synthesis or guideline pooled it, 195 citations in OpenAlex.
- What you need to know about children's COVID-19: a systematic review.Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2021Pooled it
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- Differentiation and validation of mild and severe strains of citrus tristeza virus through codon usage bias, host adaptation, and biochemical profiling.Frontiers in microbiology · 2025Article
- Non-spike protein inhibition of SARS-CoV-2 by natural products through the key mediator protein ORF8.Molecular biology research communications · 2025Article
- Could Ocular Glands Be Infected by SARS-CoV-2?Diseases (Basel, Switzerland) · 2024Article
- Individualized Prediction of SARS-CoV-2 Infection in Mexico City Municipality during the First Six Waves of the Pandemic.Healthcare (Basel, Switzerland) · 2024Article
- Harnessing CRISPR technology for viral therapeutics and vaccines: from preclinical studies to clinical applications.Virus research · 2024Review
- Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia.Microorganisms · 2024Article
- Macrophage Activation Syndrome in Coinciding Pandemics of Obesity and COVID-19: Worse than Bad.Advances in experimental medicine and biology · 2024Review
- Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures.PloS one · 2024Article
- Probable human origin of the SARS-CoV-2 polybasic furin cleavage motif.BMC genomic data · 2023Article
- Exploring the Immunomodulatory Properties of Stem Cells in Combating COVID-19: Can We Expect More?Bioengineering (Basel, Switzerland) · 2023Article
- Drugs for COVID-19 Treatment: A New Challenge.Applied biochemistry and biotechnology · 2023Review
- Stability and expression of SARS-CoV-2 spike-protein mutations.Molecular and cellular biochemistry · 2023Article
- Article
- Oligomer formation of SARS-CoV-2 ORF8 through 73YIDI76 motifs regulates immune response and non-infusion antiviral interactions.Frontiers in molecular biosciences · 2023Article
- Statins: Beneficial Effects in Treatment of COVID-19.Advances in experimental medicine and biology · 2023Article
- Pulsed-Xenon Ultraviolet Light Highly Inactivates Human Coronaviruses on Solid Surfaces, Particularly SARS-CoV-2.International journal of environmental research and public health · 2022Article
- A Review: Highlighting the Links between Epigenetics, COVID-19 Infection, and Vitamin D.International journal of molecular sciences · 2022Review
46 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 4 institutions in 3 countries.
Funding
Abstract
backgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.
methodsThe genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.
resultsSARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.
conclusionExtreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.
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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.