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ANALYSIS OF EPITOPES CONSERVANCY IN NSP1 OF SARS COV-2 AND HUMAN COMMON COLD CORONAVIRUS. A BIOINFORMATIC APPROACHS
Abstract
Background
One explanation to why children are infected less frequently and severely than adults is that cross-reactive human common cold coronavirus (HCoV) immunity, could confer some protection. In addition, it has been reported that children have lower levels of spike protein antibodies than adults, and their accumulative humoral response is more expanded to “accessory proteins” like nsp1. Nsp1 plays a critical role in coronaviruses replication and virulence.
Aims
The aims were to predict B and T cell epitopes that could be recognized in human and to assess the epitope conservancy across different coronavirus species.
Methods
Nsp1 protein sequences of SARS CoV-2, HCoV.229E, HCoV NL63, HCoV OC43 and HCoV HKU1 were obtained from GenBank. MAFFT tool was used for multiple sequence alignment. BepiPred-2.0 and NetMHCpan EL 4.1 prediction methods were used to identify sequential B cells and MHC-I restricted T cell epitopes, respectively, and epitope conservancy was determined.
Results
B epitopes GQEWH67-71, and LHSLGGF109-115 in nsp1 of HCoV HKU1; EAASNGFR33-40 and KFSDRPF77-83 in nsp1 of HCoV 229E, and PLGMSLEAC108-116, and PVQSR135-143 in nsp1 of HCoV OC43 showed levels of epitope conservancy in nsp1 of SARS CoV-2 higher than 30%. PVQSR and its counterpart in nsp1 of SARS CoV-2 (GEIPVAY112-118) contain or are flanked by amino acids conserved in alpha and beta-coronavirus. MHC class I restricted T cell epitopes with levels of conservancy higher than 30% were found. Their counterparts in SARS CoV-2 protein also showed high prediction scores for some HLA molecules.
Conclusions
Cross-reactive immunity could explain aspects of differential clinical outcome in children and adults