Comparative Analysis of Codon Usage Patterns and Host Adaptation in Merbecoviruses

<i>Merbecovirus</i>, a subgenus of coronaviruses that includes the highly pathogenic Middle East respiratory syndrome coronavirus (MERSr-CoV), poses a significant zoonotic threat. To better understand its host adaptation and potential for cross-species transmission, we conducted a comprehensive analysis of codon usage patterns in 1967 <i>Merbecovirus</i> sequences. Phylogenetic analysis confirmed the division of <i>Merbecoviruses</i> into seven distinct clusters. Codon usage bias was found to be low and predominantly shaped by natural selection, with a consistent A/U-rich composition across the genome. Codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses indicate that <i>Merbecovirus</i> exhibits potential host adaptation to <i>Sus scrofa</i> (pigs), <i>Equus caballus</i> (horses), and <i>Oryctolagus cuniculus</i> (rabbits), suggesting a risk of cross-species transmission. Strikingly, this genomic-level adaptation prediction is supported by emerging functional evidence: recent studies have demonstrated that key <i>Merbecovirus</i> lineages utilize diverse cell entry receptors (DPP4 or ACE2), a fundamental determinant of host tropism. For instance, the ability of the HKU5 lineage to utilize ACE2 receptors from mustelids like minks (<i>Neogale vison</i>) provides mechanistic support for the host adaptability trends inferred from our genomic analyses. By integrating existing receptor specificity data, this study provides the first systematic, large-scale analysis of codon usage across the <i>Merbecovirus</i> subgenus, elucidating key mechanisms of genomic adaptation and viral evolution. Our analytical framework provides a novel comparative perspective on host diversity and pinpoints specific surveillance priorities for mitigating future spillover risks.