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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Updated: Jan 10, 2026

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
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Comparative Analysis of Codon Usage Patterns and Host Adaptation in Merbecoviruses.

Ge Yan1, Yue Li1, Huimin Zhou1

  • 1School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.

Viruses
|November 27, 2025
PubMed
Summary

Merbecoviruses, including MERSr-CoV, show host adaptation to pigs, horses, and rabbits. Genomic analysis reveals potential for cross-species transmission, highlighting surveillance needs for zoonotic threats.

Keywords:
Merbecoviruscodon usage patterncross-species transmissionviral host adaptability

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Area of Science:

  • Virology
  • Genomics
  • Evolutionary Biology

Background:

  • Merbecovirus, a coronavirus subgenus, includes MERSr-CoV and presents zoonotic risks.
  • Understanding Merbecovirus host adaptation is crucial for predicting cross-species transmission.
  • Phylogenetic analysis reveals seven distinct Merbecovirus clusters.

Purpose of the Study:

  • To analyze codon usage patterns in Merbecovirus to understand host adaptation.
  • To investigate the evolutionary mechanisms driving Merbecovirus host tropism.
  • To identify potential animal reservoirs and mitigate zoonotic spillover risks.

Main Methods:

  • Comprehensive analysis of 1967 Merbecovirus sequences.
  • Phylogenetic analysis to determine viral clustering.
  • Codon Usage Bias (CUB) analysis using Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI).

Main Results:

  • Low codon usage bias shaped by natural selection with A/U-rich composition.
  • Genomic adaptation predicted for pigs, horses, and rabbits.
  • Functional evidence supports genomic predictions, with diverse cell entry receptors (DPP4/ACE2) utilized by different lineages.

Conclusions:

  • Merbecovirus exhibits genomic adaptation to specific hosts, indicating cross-species transmission potential.
  • Viral entry receptor usage (DPP4/ACE2) aligns with genomic adaptation trends.
  • This study provides a framework for Merbecovirus surveillance and risk assessment.