Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2

Mulpuru, Viswajit; Mishra, Nidhi

doi:10.21203/rs.3.rs-24566/v1

Cited by 4 publications

(3 citation statements)

References 8 publications

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“…Numerous search efforts for epitopes for peptide vaccines based on bioinformatics have been performed [44][45][46][47] . Potential CTL epitopes have been identi ed in silico and in mice [48][49][50][51] . However, the concept of self-nonself discrimination has not been incorporated.…”

Section: Discussionmentioning

confidence: 99%

Self and Nonself Short Constituent Sequences of Amino Acids in the SARS-CoV-2 Proteome for Vaccine Development

Otaki

Nakasone

Nakamura

2021

COVID

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Current SARS-CoV-2 vaccines take advantage of the viral spike protein required for infection in humans. Considering that spike proteins may contain both “self” and “nonself” sequences (sequences that exist in the human proteome and those that do not, respectively), nonself sequences are likely to be better candidate epitopes than self sequences for vaccines to efficiently eliminate pathogenic proteins and to reduce the potential long-term risks of autoimmune diseases. This viewpoint is likely important when one considers that various autoantibodies are produced in COVID-19 patients. Here, we comprehensively identified self and nonself short constituent sequences (SCSs) of 5 amino acid residues in the proteome of SARS-CoV-2. Self and nonself SCSs comprised 91.2% and 8.8% of the SARS-CoV-2 proteome, respectively. We identified potentially important nonself SCS clusters in the receptor-binding domain of the spike protein that overlap with previously identified epitopes of neutralizing antibodies. These nonself SCS clusters may serve as functional epitopes for effective, safe, and long-term vaccines against SARS-CoV-2 infection. Additionally, analyses of self/nonself status changes in mutants revealed that the SARS-CoV-2 proteome may be evolving to mimic the human proteome. Further SCS-based proteome analyses may provide useful information to predict epidemiological dynamics of the current COVID-19 pandemic.

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Section: Discussionmentioning

confidence: 99%

Self and Nonself Short Constituent Sequences of Amino Acids in the SARS-CoV-2 Proteome for Vaccine Development

Otaki

Nakasone

Nakamura

2021

COVID

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“…AREGA et al [ 17 ] applied bioinformatics and immunoinformatics methods to computer docking and molecular dynamics simulation of tuberculosis receptors to screen out candidate subunit vaccines that can cause tuberculosis-specific cellular and humoral immune responses. MULPURU et al [ 18 ] identified CTL epitopes of COVID-19 based on immunoinformatics and used sequence conservation studies and molecular dynamics models to identify the epitopes further. SADAT et al [ 19 ] compared and analyzed the protein sequence's structural characteristics and immunogenicity in COVID-19, established a model, and evaluated the MHC-I and MHC-II epitopes with higher antigenicity.…”

Section: Discussionmentioning

confidence: 99%

Development of an indirect ELISA to specifically detect antibodies against African swine fever virus: bioinformatics approaches

Gao¹,

Shao

Zhang

et al. 2021

Virol J

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Background African swine fever (ASF), characterized by acute, severe, and fast-spreading, is a highly lethal swine infectious disease caused by the African swine fever virus (ASFV), which has caused substantial economic losses to the pig industry worldwide in the past 100 years. Methods This study started with bioinformatics methods and verified the epitope fusion protein method's reliability that does not rely on traditional epitope identification. Meanwhile, it will also express and purify the constructed genes through prokaryotic expression and establish antibody detection methods. Results The results indicated that the protein had good reactivity and did not cross-react with other swine diseases. The receiver-operating characteristic analysis was performed to verify the determination. The area under the receiver-operating characteristic curve was 0.9991 (95% confidence interval 0.9973 to 1.001). Conclusions It was proved that the recombinant protein is feasible as a diagnostic antigen to distinguish ASFV and provides a new idea for ASFV antibody detection.

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“…The peptides encoded by both RNA motifs are, V-A-E-W-F-L-A and A-V-L-Q-S-G-F-R, respectively. The peptide V-A-E-W-F-L-A appear related with the identification of potential cytotoxic T lymphocyte epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate 45 ; the peptide A-V-L-Q-S-G-F-R, could serve as a starting point for determining effective drug candidates for the treatment of SARS-CoV; the octapeptide naturally becomes an ideal good inhibitor for the SARS proteinase 46,47 . The second repeated motif (double underlined), is inserted on selected RNA-motifs 8 and 10, namely, (GC ATT GAT TTA GAT GAG TGG AGT ATG GC) and (AT GAG TAT GGTA), respectively (Table 5).…”

Section: Discussionmentioning

confidence: 99%

New Short RNA Motifs Potentially Relevant in the Severe Acute Respiratory Syndrome Coronavirus 2 Genome

Fuertes

Alonso

2021

Preprint

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As time passes, identifying new pharmacological targets is becoming more difficult. Shortly, it will be necessary to devise new strategies to tackle the problem. The coronavirus disease outbreak caused by the severe acute respiratory syndrome coronavirus 2 , represents a threat to human health serving as example from what we just said. The present study was aimed to collect a set of short RNA motifs with potential biological impact, most of which have not been observed heretofore. Categorizing RNA triplets by their gross-composition, the study collected 88 short RNA motifs, shared by most coronavirus genera independent on the percent identity between genomes. Selected motifs contain all nearest-neighbours of the triplets A, T, G and A, C, G. The high percent identity between severe acute respiratory syndrome coronavirus genomes makes it difficult these peptides to be found by current methods. The results provide 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf and 6 in the nucleocapsid-encoding orf. They also provide insights about the validity of the procedure, confirming some motifs interspersed or attached to known relevant functional fragments of the genome, although most of them have not yet been associated to any known function. The high level of preservation of these motifs in most coronavirus genera suggest they might have potential to be used for diagnostic, in vaccines, or as substrate for protease inhibitors.

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Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2

Cited by 4 publications

References 8 publications

Self and Nonself Short Constituent Sequences of Amino Acids in the SARS-CoV-2 Proteome for Vaccine Development

Self and Nonself Short Constituent Sequences of Amino Acids in the SARS-CoV-2 Proteome for Vaccine Development

Development of an indirect ELISA to specifically detect antibodies against African swine fever virus: bioinformatics approaches

New Short RNA Motifs Potentially Relevant in the Severe Acute Respiratory Syndrome Coronavirus 2 Genome

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