VIRAL ENTRY PROTEINS BEYOND SPIKE: DIVERSITY, EVOLUTION, AND FUNCTIONAL CONVERGENCE ACROSS VIRUS FAMILIES

Viruses, the most abundant biological entities on Earth, have a significant impact on life across all domains. Infecting millions of hosts, they are crucial targets for scientific research. Entry proteins, which enable pathogens to invade host cells, are essential for infection. The recent COVID-19 pandemic, caused by SARS-CoV-2 from the Coronaviridae family, highlighted the role of the Spike protein, a key fusion protein that mediates  host cell entry. Notably, several viruses outside Coronaviridae family also possess proteins with analogous functions to Spike. This study aims to explore the diversity and evolutionary relationships of these spike-like viral entry proteins. A systematic literature search was conducted using PubMed (https://pubmed.ncbi.nlm.nih.gov/) with the terms ("virus" AND "spike protein") NOT "SARS" NOT "MERS" NOT "CORONAVIRUS" NOT "COVID-19" to identify viruses reported to carry spike-like proteins. Protein sequences in FASTA format were retrieved from UniProt (https://www.uniprot.org/). Alignments were performed using UGENE and ClustalOmega. Phylogenetic analysis was carried out with IQ-TREE v1.6.12 (http://iqtree.cibiv.univie.ac.at/), applying the Maximum Likelihood method. The best-fit substitution model, JTTDCMut+F+G4, was selected via ModelFinder using the Bayesian Information Criterion (BIC). The alignment showed no structural errors according to the log file. The final dataset comprised 329 protein sequences from 67 viral species across 19 families, as well as three unclassified bacteriophage species. Sequence alignments revealed both conserved and divergent regions, grouping proteins by evolutionary proximity. The resulting phylogenetic tree, built with 1,000 bootstrap replicates, reflects a Maximum Likelihood topology. Unexpectedly, proteins from the same species appeared on different branches of the tree, suggesting potential functional divergence, annotation errors, or evolutionary events yet to be clarified. Further analysis is ongoing to interpret this result. The next step involves using the AAindex database to cluster proteins based on key physicochemical and biochemical properties, including secondary structure propensity, hydrophobicity, solubility, molecular volume, electrostatic charge, solvent interaction, and amino acid composition patterns. This work seeks to deepen our understanding of the evolutionary dynamics and functional convergence of viral entry proteins beyond the Coronaviridae family.