Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica

Abstract

Emerging mutations and genotypes of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, have been reported globally. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. To investigate the possible effects of this mutation on the function of the spike, i.e. the biology of the virus, different bioinformatic pipelines based on phylogeny, natural selection and co-evolutionary models, molecular docking and epitopes prediction were implemented. Results of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergency of local lineages. In Costa Rica, the mutation is found in the lineage B.1.1.389 and it is suggested to be a product of positive/adaptive selection. Different changes in the function of the spike protein and more stable interaction with a ligand (nelfinavir drug) were found. Only one epitope out 742 in the spike was affected by the mutation, with some different properties, but suggesting scarce changes in the immune response and no influence on the vaccine effectiveness. Jointly, these results suggest a partial benefit of the mutation for the spread of the virus with this genotype during the year 2020 in Costa Rica, although possibly not strong enough with the introduction of new lineages during early 2021 which became predominant later. In addition, the bioinformatics pipeline offers an integrative and exhaustive in silico strategy to eventually study other mutations of interest for the SARS-CoV-2 virus and other pathogens. HighlightsO_LIIn Costa Rica during the year 2020, a predominant SARS-CoV-2 genotype carrying the mutation T1117I in the spike (S:T1117I) was identified. C_LIO_LIThe S:T1117I was assessed for possible effects of this mutation on the function of the spike with a in silico approach. C_LIO_LIPhylogeny revealed that sequences carrying the S:T1117I worldwide define a polyphyletic group, with the emergency of local lineages, including the lineage B.1.1.389 in Costa Rica. C_LIO_LIA positive/adaptive selection was identified for S:T1117I, with different changes in the function of the spike protein, more stable interaction with ligands and scarce changes in the immune response. C_LIO_LIThe bioinformatics pipeline can be eventually used to study other mutations of the SARS-CoV-2 virus and other pathogens. C_LI