ArticleFrontiers in microbiology2021
Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 77 citations in OpenAlex.
- Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication.Antimicrobial agents and chemotherapy · 2026Article
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Coronaviruses reprogram the tRNA epitranscriptome to favor viral protein expression.Nature communications · 2026Article
- Article
- Analysis of Preferred Codon Usage in the ZIKA Virus Genome and Their Implications for Genome Evolution and Vaccine Design.Indian journal of microbiology · 2025Review
- Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan.Scientific reports · 2025Article
- SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.Virus evolution · 2025Article
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
- Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype.Microbial genomics · 2024Article
- Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak.International journal of molecular sciences · 2023Article
- Codon usage bias of Venezuelan equine encephalitis virus and its host adaption.Virus research · 2023Article
- Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies.Virology journal · 2023Article
- Variation in synonymous evolutionary rates in the SARS-CoV-2 genome.Frontiers in microbiology · 2023Article
- Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias.Transboundary and emerging diseases · 2023Article
- Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA.Briefings in bioinformatics · 2022Article
- Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants.Briefings in bioinformatics · 2022Article
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.Virology · 2022Article
- Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen.bioRxiv : the preprint server for biology · 2022Article
- SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation.Journal of applied genetics · 2022Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading rapidly all over the world and has raised grave concern globally. The present research aims to conduct a robust base compositional analysis of SARS-CoV-2 to reveal adaptive intricacies to the human host. Multivariate statistical analysis revealed a complex interplay of various factors including compositional constraint, natural selection, length of viral coding sequences, hydropathicity, and aromaticity of the viral gene products that are operational to codon usage patterns, with compositional bias being the most crucial determinant. UpG and CpA dinucleotides were found to be highly preferred whereas, CpG dinucleotide was mostly avoided in SARS-CoV-2, a pattern consistent with the human host. Strict avoidance of the CpG dinucleotide might be attributed to a strategy for evading a human immune response. A lower degree of adaptation of SARS-CoV-2 to the human host, compared to Middle East respiratory syndrome (MERS) coronavirus and SARS-CoV, might be indicative of its milder clinical severity and progression contrasted to SARS and MERS. Similar patterns of enhanced adaptation between viral isolates from intermediate and human hosts, contrasted with those isolated from the natural bat reservoir, signifies an indispensable role of the intermediate host in transmission dynamics and spillover events of the virus to human populations. The information regarding avoided codon pairs in SARS-CoV-2, as conferred by the present analysis, promises to be useful for the design of vaccines employing codon pair deoptimization based synthetic attenuated virus engineering.
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