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Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers

Komi Nambou1, Manawa Anakpa2

  • 1Shenzhen Nambou1 Biotech, 506, Block B, West Silicon Valley, 5010 Baoan Avenue, Baoan District, Shenzhen, China.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
|July 25, 2020
PubMed

Insights

Researchers analyzed SARS-CoV-2 codon usage and identified human genes affected by the virus. This study predicts potential drugs for COVID-19 treatment and aids vaccine development.

Area of Science:

  • Genomics
  • Virology
  • Computational Biology

Background:

  • Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is a global health crisis.
  • Understanding SARS-CoV-2's interaction with the human host is crucial for developing effective treatments.

Purpose of the Study:

  • To analyze codon usage co-adaptation profiles of SARS-CoV-2 and other respiratory coronaviruses (CoVs) with their human host.
  • To identify CoV-responsive human genes and their functional roles.
  • To predict potential drugs for COVID-19 treatment based on identified genes.

Main Methods:

  • Analysis of publicly available genomic data.
  • Relative Synonymous Codon Usage (RSCU)-based correlation between viral and human genes.
  • Differential gene expression analysis.
  • Functional enrichment analysis.
  • Drug-gene interaction database screening.

Main Results:

  • High Codon Adaptation Index (CAI) values (>0.70) indicate efficient CoV gene expression in humans.
  • SARS-CoV-2 genome shows strict selection pressure; SARS-CoV and MERS-CoV exhibit selection and mutational pressures.
  • Identified human genes potentially affected by SARS-CoV-2 infection through RSCU correlation and differential expression.
  • Affected human genes are enriched in host response to viral infection and immune response pathways.

Conclusions:

  • The study contributes to vaccine development strategies.
  • Identified genes and predicted drugs offer guidance for COVID-19 monitoring and treatment.
  • Further screening of predicted drugs is recommended for COVID-19 therapeutic validation.
Keywords:
COVID-19Codon usageCoronavirusTranscriptomeTreatment drugsVirus-host co-adaptation

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