Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis.

Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis.

Publication date: Dec 24, 2024

An unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the receptor binding motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in variants of concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 were detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible at https://ai-ve. org to provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.

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Concepts Keywords
Apess ACE2 protein, human
Biochemical Amino Acid Substitution
D467 Angiotensin-Converting Enzyme 2
Mutational Angiotensin-Converting Enzyme 2
Viral COVID-19
genetics
genomics
Humans
infectivity
Machine Learning
Mutation
Protein Binding
protein prediction
SARS-CoV-2
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
Virus Internalization
viruses

Semantics

Type Source Name
disease IDO infectivity
disease MESH infectious diseases
disease IDO process
drug DRUGBANK Amino acids
drug DRUGBANK L-Lysine
drug DRUGBANK L-Arginine
disease MESH COVID-19

Original Article

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