SpikePro

SpikePro predicts SARS-CoV-2 fitness from spike protein amino acid sequence and structure to estimate transmissibility, infectivity, and immune escape.

Key Features:

• Fitness Prediction: Aligns input spike protein sequences in FASTA format to a reference, identifies mutations, and calculates their individual and cumulative effects on viral fitness.
• Transmissibility Assessment: Estimates effects on transmissibility by evaluating spike protein stability and structural changes that influence viral transmission.
• Infectivity Analysis: Computes infectivity from predicted ACE2 receptor binding affinity of spike variants.
• Immune Escape Prediction: Predicts potential immune escape by assessing spike binding affinity to a set of neutralizing antibodies.

Scientific Applications:

• Genomic Surveillance: Predicts emergence and potential dominance of SARS-CoV-2 strains based on fitness advantages derived from spike mutations.
• Epidemiological Studies: Provides fitness estimates that can be correlated with experimental, epidemiological, and clinical data to study variant impacts.
• Public Health Decision-Making: Informs assessment of emerging strain risk and vaccine relevance by forecasting transmissibility, infectivity, and immune escape potential.

Methodology:

Uses a computational model that integrates structural biology and virology, employing biophysical characteristics of the spike protein—stability, receptor binding affinity, and antibody interaction—to simulate and predict the fitness landscape of SARS-CoV-2 variants.