Can the protection be among us? Previous viral contacts and prevalent HLA alleles avoiding an even more disseminated COVID-19 pandemic
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Abstract
COVID-19 is bringing scenes of sci-fi movies into real life, and it seems to be far from over. Infected individuals exhibit variable severity, suggesting the involvement of the genetic constitution of populations and previous cross-reactive immune contacts in the individuals’ disease outcome. To investigate the participation of MHC alleles in COVID-19 severity, the combined use of HLA-B*07, HLA-B*44, HLA-DRB1*03, and HLA-DRB1*04 grouped affected countries presenting similar death rates, based only on their allele frequencies. To prospect T cell targets in SARS-CoV-2, we modeled 3D structures of HLA-A*02:01 complexed with immunogenic epitopes from SAR-CoV-1 and compared them with models containing the corresponding SARS-CoV-2 peptides. It reveals molecular conservation between SARS-CoV peptides, evidencing that the corresponding current sequences are putative T cell epitopes. These structures were also compared with other HCoVs sequences, and with a panel of epitopes from unrelated viruses, looking for the triggers of cross-protection in asymptomatic and uninfected individuals. 229E, OC43, and impressively, viruses involved in endemic human infections share fingerprints of immunogenicity with SARS-CoV peptides. Wide-scale HLA genotyping in COVID-19 patients shall improve prognosis prediction. Structural identification of previous triggers paves the way for herd immunity examination and wide spectrum vaccine development.
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SciScore for 10.1101/2020.06.15.20131987: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To verify if those epitopes have a counterpart in the SARS-CoV-2 proteome, we used a Needleman-Wunsch Global Align Nucleotide Sequences (BLAST) using the protein sequences of the 2002/2003 SARS virus and the SARS-CoV-2 from Wuhan. BLASTsuggested: (BLASTX, RRID:SCR_001653)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to …SciScore for 10.1101/2020.06.15.20131987: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To verify if those epitopes have a counterpart in the SARS-CoV-2 proteome, we used a Needleman-Wunsch Global Align Nucleotide Sequences (BLAST) using the protein sequences of the 2002/2003 SARS virus and the SARS-CoV-2 from Wuhan. BLASTsuggested: (BLASTX, RRID:SCR_001653)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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