Computational analysis and identification of amino acid motifs in the SARS-CoV-2 spike protein relevant to vaccine and antiviral therapeutic development
Open AccessThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the recognized etiologic agent of Coronavirus Disease 19 (COVID-19). Infection by SARS-CoV-2 follows interaction between the viral glycoprotein spike (S) and the angiotensin-converting enzyme 2 (ACE2) expressed on the surface of host cells leading to respiratory symptoms ranging from mild to severe and sometimes fatal. With greater than 20 million cases worldwide and over a half million COVID-19-associated deaths in the United States, rates of infection and mortality continue to rise, making the need for effective vaccines and antiviral therapeutics increasingly critical in the struggle to control the global pandemic. Using publicly available sequences data derived from infected patients, we employ innovative bioinformatics analyses to predict immunogenic amino acid (aa) residues and motifs under negative/purifying selective pressure located within S protein which may be important in the SARS-CoV-2 viral lifecycle. Initially, 49 S protein amino acid motifs were discovered that contained at least three predicted negatively selected residues. Subsequent ranking based on a scheme designed to identify conserved, immunogenic motifs best suited for further experimentation, revealed 10 epitopes located in varying regions of spike, including the receptor binding domain (RBD). These top ranked motifs can now be evaluated in vitro and in vivo for immunogenicity, relevance to viral fitness, and potential as diagnostic indicators and targets for inhibition of viral attachment, entry and infection by vaccines and other antiviral therapeutics.
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