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

In silico codon optimization of VP1 and VP2 from 12 human Sapovirus strains for Escherichia coli raised CAI to 1.000 for every optimized sequence without changing amino acids.

• Why it matters: With no approved vaccine or therapies and low yields of recombinant capsid protein, improving capsid gene expression is a key need for Sapovirus research.
• What they did: VP1 and VP2 sequences were aligned and phylogenetic trees were built by maximum likelihood (Tamura-Nei, 1,000 bootstrap replicates), then both genes were optimized in silico for Escherichia coli using OPTIMIZER.
• The result: Mean CAI and GC% increased significantly (p < 0.001) for VP1 by 3.07 and 1.11 fold, and for VP2 by 3.11 and 1.14 fold, with AT% decreasing and encoded amino acid sequences unchanged.

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