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bioRxiv · 10.64898/2026.10.30.762994

In silico codon optimization and phylogenetic analysis of various strains of Sapovirus

Adhikari, S.·Mani, I.
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Abstract

Introduction: Sapovirus (SaV) is an emerging enteric pathogen of rising public health importance, responsible for acute gastroenteritis in people of all ages and most often in children under five. Its genome is approximately 7.1-7.7 kb long, positive-sense, single-stranded RNA, comprising two principal open reading frames; processing of the ORF1 product yields seven non-structural proteins and the major capsid protein VP1, while ORF2 encodes the minor structural protein VP2. Given the absence of therapies or an approved vaccine and the low yields of recombinant capsid protein, improving expression remains a priority. Methods: VP1 and VP2 sequences from twelve selected human SaV strains were aligned, phylogenetic trees were reconstructed by maximum likelihood method under the Tamura-Nei model with 1,000 bootstrap replicates, and both genes were optimized in silico for Escherichia coli using the OPTIMIZER. Results: The trees resolved three genogroups, GI, GII and GV, each strain placed alike by both genes. Every optimized sequence reached the ceiling value of 1.000 for the codon adaptation index (CAI). Mean CAI and GC% increased by 3.07 (207.0%) and 1.11 (11.1%) fold for VP1, and 3.11 (210.9%) and 1.14 (14.1%) fold for VP2, while AT% decreased. All changes were statistically significant (p < 0.001) and the encoded amino acid sequences were unaltered. Conclusion: Our findings indicate that Optmization raised host-matched codon usage in both capsid genes with no truncated proteins produced. The redesigned VP1 and VP2 sequences warrant further investigation as potential candidates for biotherapeutic and vaccine development. KEYWORDS: Sapovirus,CAI, codon optimization, VP1 capsid protein, GC content, DNA, phylogenetic analysis, vaccines

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Adhikari, S., Mani, I.. 2026-10-31. In silico codon optimization and phylogenetic analysis of various strains of Sapovirus. https://doi.org/10.64898/2026.10.30.762994

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