• Comparative Analysis of Codon...

Treffer: Comparative Analysis of Codon Usage Patterns and Host Adaptation in Merbecoviruses .

Title:
Comparative Analysis of Codon Usage Patterns and Host Adaptation in Merbecoviruses .
Authors:
Yan G; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China., Li Y; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China., Zhou H; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China., Franzo G; Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy., Zheng M; Department of Mathematics, College of Science, Nanjing Agricultural University, Nanjing 210095, China., Liu H; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China., Chen X; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China., Dai J; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China., He WT; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.
Source:
Viruses [Viruses] 2025 Nov 06; Vol. 17 (11). Date of Electronic Publication: 2025 Nov 06.
Publication Type:
Journal Article; Comparative Study
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel, Switzerland : MDPI
MeSH Terms:
Codon Usage* , Host Adaptation*/genetics, Animals ; Phylogeny ; Genome, Viral ; Selection, Genetic ; Swine ; Humans ; Codon ; Host Specificity ; Evolution, Molecular
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Grant Information:
2023QNRC001 Young Elite Scientists Sponsorship Program by CAST
Contributed Indexing:
Keywords: Merbecovirus; codon usage pattern; cross-species transmission; viral host adaptability
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20251127 Date Completed: 20251127 Latest Revision: 20251130
Update Code:
20251130
PubMed Central ID:
PMC12656749
DOI:
10.3390/v17111479
PMID:
41305501
Database:
MEDLINE

Weitere Informationen

Merbecovirus , 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 Merbecovirus sequences. Phylogenetic analysis confirmed the division of Merbecoviruses 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 Merbecovirus exhibits potential host adaptation to Sus scrofa (pigs), Equus caballus (horses), and Oryctolagus cuniculus (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 Merbecovirus 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 ( Neogale vison ) 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 Merbecovirus 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.