Immunoinformatics prediction of potential immunodominant epitopes from human coronaviruses and association with autoimmunity

Abstract

Cross-reactivity between different human coronaviruses (HCoVs) might contribute to COVID-19 outcomes. Here, we aimed to predict conserved peptides among different HCoVs that could elicit cross-reacting B cell and T cell responses. Three hundred fifty-one full-genome sequences of HCoVs, including SARS-CoV-2 (51), SARS-CoV-1 (50), MERS-CoV (50), and common cold species OC43 (50), NL63 (50), 229E (50), and HKU1 (50) were downloaded aligned using Geneious Prime 20.20. Identification of epitopes in the conserved regions of HCoVs was carried out using the Immune Epitope Database (IEDB) to predict B- and T-cell epitopes. Further, we identified sequences that bind multiple common MHC and modeled the three-dimensional structures of the protein regions. The search yielded 73 linear and 35 discontinuous epitopes. A total of 16 B-cell and 19 T-cell epitopes were predicted through a comprehensive bioinformatic screening of conserved regions derived from HCoVs. The 16 potentially cross-reactive B-cell epitopes included 12 human proteins and four viral proteins among the linear epitopes. Likewise, we identified 19 potentially cross-reactive T-cell epitopes covering viral proteins. Interestingly, two conserved regions: LSFVSLAICFVIEQF (NSP2) and VVHSVNSLVSSMEVQSL (spike), contained several matches that were described epitopes for SARS-CoV. Most of the predicted B cells were buried within the SARS-CoV-2 protein regions’ functional domains, whereas T-cell stretched close to the functional domains. Additionally, most SARS-CoV-2 predicted peptides (80%) bound to different HLA types associated with autoimmune diseases. We identified a set of potential B cell and T cell epitopes derived from the HCoVs that could contribute to different diseases manifestation, including autoimmune disorders. Supplementary Information The online version contains supplementary material available at 10.1007/s00251-021-01250-5.

Design of multi‐epitope chimeric vaccine against Monkeypox virus and SARS‐CoV‐2: A vaccinomics perspective

“… 12 As took place with its counterparts, SARS (severe acute respiratory syndrome) and MERS (Middle‐East respiratory syndrome), SARS‐CoV‐2 may goes through a state of gradual weakness owing to the conserved antigenicity and virulence. 13 To date, no active licensed vaccine against SARS‐CoV‐2 is available despite the accelerating race between biotech industries and medical institutions. This is due to the highly‐demanding nature of vaccine approval that necessitates long years of experimentation and costly clinical trials.…”

“…SARS CoV‐2 belongs to positive‐sense, enveloped viruses thereby speeding replication, transcription, translation as well as assembly of new virions and, at the same time, facilitating its fusion process to host cell membranes 12 . As took place with its counterparts, SARS (severe acute respiratory syndrome) and MERS (Middle‐East respiratory syndrome), SARS‐CoV‐2 may goes through a state of gradual weakness owing to the conserved antigenicity and virulence 13 . To date, no active licensed vaccine against SARS‐CoV‐2 is available despite the accelerating race between biotech industries and medical institutions.…”

Human Coronavirus Spike Protein Based Multi-Epitope Vaccine against COVID-19 and Potential Future Zoonotic Coronaviruses by Using Immunoinformatic Approaches

“…Although there have been numerous attempts to develop vaccines against HCoV infections in recent decades, their considerable sequence diversity is a limiting factor. Given the high homology between SARS-CoV-2 and other coronaviruses, there is a high possibility of conserved antigenic epitopes [ 5 ]. Therefore, previous exposure to MERS, SARS, or seasonal human coronaviruses (i.e., 229E, NL63, OC43, and HKU1) may contribute to modulating immunity against SARS-CoV-2 infection.…”