SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants

Abstract

Motivation The SARS-CoV-2 virus has shown a remarkable ability to evolve and spread across the globe through successive waves of variants since the original Wuhan lineage. Despite all the efforts of the last two years, the early and accurate prediction of variant severity is still a challenging issue which needs to be addressed to help, for example, the decision of activating COVID-19 plans long before the peak of new waves. Upstream preparation would indeed make it possible to avoid the overflow of health systems and limit the most severe cases. Results We recently developed SpikePro, a structure-based computational model capable of quickly and accurately predicting the viral fitness of a variant from its spike protein sequence. It is based on the impact of mutations on the stability of the spike protein as well as on its binding affinity for the angiotensin-converting enzyme 2 (ACE2) and for a set of neutralizing antibodies. It yields a precise indication of the virus transmissibility, infectivity, immune escape and basic reproduction rate. We present here an updated version of the model that is now available on an easy-to-use webserver, and illustrate its power in a retrospective study of fitness evolution and reproduction rate of the main viral lineages. SpikePro is thus expected to be great help to assess the fitness of newly emerging SARS-CoV-2 variants in genomic surveillance and viral evolution programs. Availability SpikePro webserver http://babylone.ulb.ac.be/SpikePro/ Supplementary information Supplementary data are available at Bioinformatics online.

Impact of mAb-induced A475V substitution on viral fitness and antibody neutralization of SARS-CoV-2 omicron variants in the presence of monoclonal antibodies and human convalescent sera

“…To investigate the impact of A475V on the overall fitness of BA.5, we utilized SpikePro, a recently developed structure-based computational tool designed to predict the viral fitness of a variant based on its spike protein sequence ( 21 , 22 ). Our analysis of the prediction data revealed that the presence of a single A475V substitution in the spike protein resulted in improved immune escape from convalescent plasma ( Figure 7 ).…”

Critical review of conformational B-cell epitope prediction methods

“…In order to evaluate the ability of the benchmarked methods to predict the known epitopes in the spike protein, we gathered 83 spike protein-antibody complexes resolved by X-ray crystallography or cryo-electron microscopy and deposited in the PDB [5] (see [57,58] for the list of PDB ids). We extracted 83 epitopes from these complexes; 75 of them are localized on the RBD of the spike protein, while the remaining eight target its N-terminal domain (NTD).…”

Applying the digital data and the bioinformatics tools in SARS-CoV-2 research

“…For the interaction between the RBD in the spike protein and the host receptor (ACE2) is critical in the invasion of virus, both the Peptide Inhibition Covid 19 Repository [105] and the SARS-CoV-2 Interactome 3D [106] visualize the interaction between RDB and ACE2, facilitating further exploration of this mechanism. Mutations present on the spike protein are likely relevant to viral adaptation and immune escape, SpikePro enables a rapid prediction of the adaptation of some mutant based on the structural models [107] . VirHostNet contains a relatively complete virus-host protein interaction resources that facilitates target determination and drug design [108] .…”