ArticleScientific reports2020
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- Clinical applications of detecting IgG, IgM or IgA antibody for the diagnosis of COVID-19: A meta-analysis and systematic review.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2021Pooled it
- Strengthening microbial genomics capacity in Africa for epidemic preparedness: key lessons from the AFROSCREEN programme.Journal of global health · 2026Article
- Toward Setting Minimum and Optimal Data to Report for Malaria Molecular Surveillance with Targeted Sequencing: The "What" and "Why".The American journal of tropical medicine and hygiene · 2025Article
- Review
- Colliding Challenges: An Analysis of SARS-CoV-2 Infection in Patients with Pulmonary Tuberculosis versus SARS-CoV-2 Infection Alone.Medicina (Kaunas, Lithuania) · 2024Article
- Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.Briefings in functional genomics · 2024Review
- COVID Variants, Villain and Victory: A Bioinformatics Perspective.Microorganisms · 2023Article
- Evolution of the newest diagnostic methods for COVID-19: a Chinese perspective.Journal of Zhejiang University. Science. B · 2023Review
- Next-Generation Sequencing: A Promising Tool for Vaccines and Other Biological Products.Vaccines · 2023Article
- Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform.International journal of molecular sciences · 2023Article
- Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.JMIR bioinformatics and biotechnology · 2022Article
- Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era.Viruses · 2022Review
- MULTI-OMICS as Invaluable Tools for the Elucidation of Host-Microbe-Microbiota Interactions.International journal of molecular sciences · 2022Article
- Review
- SARS-CoV-2 variants and vulnerability at the global level.Journal of medical virology · 2022Review
- Performance of COVIDSeq and Swift Normalase Amplicon SARS-CoV-2 Panels for SARS-CoV-2 Genome Sequencing: Practical Guide and Combining FASTQ Strategy.Journal of clinical microbiology · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- Article
- Fast-track development of vaccines for SARS-CoV-2: The shots that saved the world.Frontiers in immunology · 2022Review
- COVID-19 Diagnosis: Current and Future Techniques.International journal of biological macromolecules · 2021Review
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses, for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses.
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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.