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Updated: Jan 10, 2026
07:06
Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
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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
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.
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.
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