COMPUTATIONAL IDENTIFICATION OF VIRAL/BACTERIAL EPITOPES FOR TYPE AND STRAIN CHARACTERIZATION, LEADING TO THE DEVELOPMENT OF VACCINES AGAINST HUMAN ADENOVIRUS, HIV, AND STAPHYLOCOCCUS AUREUS
Date
2021
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Abstract
Identifying newly isolated adenovirus is important to the understanding of pathogens and molecular evolution. With the advancement of sequencing technology, virus sequences are accumulated. New genotypes emerge due to recombination in capsid proteins, penton base, hexon, and fiber. A rapid identification of newly emerging genotypes became necessary for current HAdV scientists, and a software tool was developed to accurately identify and characterize the genotypes based on recombination. The genotyping tool characterizes newly emergent adenoviruses by identifying the type-specific epitopes and complementing them with the referencing database. The genotyping outcomes are based on BLAST results, phylogenetic trees, and sequence identity with the pre-existing epitopes. The performance of the genotyping was tested on 52 human adenovirus genotype sequences, resulting in 100% sensitivity and specificity. Genotyping enables quick and accurate detection of novel strains. Staphylococcus aureus is the leading cause of skin and soft tissue infections worldwide. Strain identification is critical for understanding the epidemiology of this pathogen. The highly variable spa gene provides a sensitive method for distinguishing S. aureus isolates. The spa gene product is a surface antigen with Ig-binding activity that is involved in immune evasion. Spa includes a variable Xr region that has multiple repeats, usually 8 amino acids in length. Repeats within an Xr region may have different amino acid sequences. Over 19,817 variants of the spa gene are known to date. Combined with other methods such as multilocus sequence typing, spa typing can provide high resolution strain identification. This is an open-source spa typing program that: requires no helper applications; it can be integrated into bioinformatics pipelines and can analyze complete draft genome sequences.