In silico codon optimization and phylogenetic analysis of various strains of Sapovirus
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…
Sapovirus (SaV) is a rising concern in public health, causing gastroenteritis in individuals of all ages, particularly children under five. The virus's genome is a single-stranded RNA, around 7.1-7.7 kb long, with two main open reading frames. Processing the ORF1 product generates seven non-structural proteins and the major capsid protein VP1, while ORF2 produces the minor structural protein VP2.
Due to the lack of treatments and vaccines and low yields of recombinant capsid protein, optimizing gene expression is crucial. Researchers aligned VP1 and VP2 sequences of twelve human SaV strains, reconstructed phylogenetic trees using maximum likelihood under the Tamura-Nei model with 1,000 bootstrap replicates, and in silico optimized both genes for Escherichia coli using the OPTIMIZER.
The trees categorized the strains into three genogroups, GI, GII, and GV, placing each strain similarly based on both genes. Both optimized sequences achieved a codon adaptation index (CAI) of 1.000, with a 3.07 (207.0%) and 3.11 (210.9%) fold increase in mean CAI and GC% for VP1 and VP2, respectively, while decreasing AT%. These changes were statistically significant (p).
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