Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses
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Abstract
Several studies have reported the presence of pre-existing humoral or cell-mediated cross-reactivity to SARS-CoV-2 peptides in healthy individuals unexposed to SARS-CoV-2. In particular, the current literature suggests that this pre-existing cross-reactivity could, in part, derive from prior exposure to ‘common cold’ endemic human coronaviruses (HCoVs). In this study, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the entire diversity of the Coronaviridae family. Slightly over half (54.8%) of the tested epitopes did not have noticeable homology to any of the human endemic coronaviruses (HKU1, OC43, NL63 and 229E), suggesting prior exposure to these viruses cannot explain the full cross-reactive profiles observed in healthy unexposed individuals. Further, we find that the proportion of cross-reactive SARS-CoV-2 epitopes with noticeable sequence homology is extremely well predicted by the phylogenetic distance to SARS-CoV-2 ( R 2 = 96.6%). None of the coronaviruses sequenced to date showed a statistically significant excess of T-cell epitope homology relative to the proportion of expected random matches given the sequence similarity of their core genome to SARS-CoV-2. Taken together, our results suggest that the repertoire of cross-reactive epitopes reported in healthy adults cannot be primarily explained by prior exposure to any coronavirus known to date, or any related yet-uncharacterised coronavirus.
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SciScore for 10.1101/2020.12.08.415703: (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
Experimental Models: Organisms/Strains Sentences Resources Non-Coronaviridae protein BLAST: To determine if any proteome outside of the Coronaviridae had detectable homology to any of the 177 epitopes reported in the literature, we performed a protein BLAST using the online blastp suite (https://tinyurl.com/y22o4t9z) against the non-redundant protein sequence database (accessed 7/12/2020), while excluding sequences associated with the Coronaviridae (taxid: 11118). taxid: 11118suggested: NoneSoftware and Algorithms Sentences Resources Next, the Roary pipeline v3.11.12 (50) was used to cluster all Coronaviridae ORFs at a minimum … SciScore for 10.1101/2020.12.08.415703: (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
Experimental Models: Organisms/Strains Sentences Resources Non-Coronaviridae protein BLAST: To determine if any proteome outside of the Coronaviridae had detectable homology to any of the 177 epitopes reported in the literature, we performed a protein BLAST using the online blastp suite (https://tinyurl.com/y22o4t9z) against the non-redundant protein sequence database (accessed 7/12/2020), while excluding sequences associated with the Coronaviridae (taxid: 11118). taxid: 11118suggested: NoneSoftware and Algorithms Sentences Resources Next, the Roary pipeline v3.11.12 (50) was used to cluster all Coronaviridae ORFs at a minimum amino-acid homology threshold of 30%. Roarysuggested: (Roary, RRID:SCR_018172)Sequences for the four genes ORF1ab, S, M and N were each found to cluster in a minimum of 2531 assemblies, which were then extracted, concatenated and aligned using MAFFT v7.453 (51). MAFFTsuggested: (MAFFT, RRID:SCR_011811)The resulting alignment was trimmed of gaps found in 20% or more isolates and used to build a Maximum Likelihood phylogeny using RAxML v8.2.12 (52) with 1000 bootstraps for node support. RAxMLsuggested: (RAxML, RRID:SCR_006086)Each assembly contained a ORF1ab CDS annotated ORF, the only gene shared by all members of the Nidovirales (53), which were decomposed into 11-mer sequences using MASH v2.1.1 (54). MASHsuggested: (Mash, RRID:SCR_019135)Translated protein sequences of all ORFs from each of the 2531 assemblies were retrieved from Prokka (49) and used to construct a protein BLAST database. Prokkasuggested: (Prokka, RRID:SCR_014732)Separately, a protein BLAST database was also constructed from the protein annotations associated with the 2531 assemblies, which were downloaded using NCBI Batch Entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez). https://www.ncbi.nlm.nih.gov/sites/batchentrezsuggested: (Batch Entrez, RRID:SCR_016634)Subsequently, we used blastp from BLAST+ v2.11.0 (55) to determine the sequence similarity of the 15-mer peptides from the SARS-CoV-2 proteome and the 177 published epitopes using the two databases and. BLAST+suggested: (Japan Bioinformatics, RRID:SCR_012250)Proportion of published epitopes and cophenetic distance: Using the merged output of the protein BLAST search querying the 177 published epitopes, we analysed the proportion of epitopes that had detectable homology to each virus in a representative filtered dataset of all combinations of unique host and virus species (n = 155). 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: We detected the following sentences addressing limitations in the study:Deconvolving the relationship between sequence homology and cross-reactivity is evidently non-trivial and remains a limitation of our work. Indeed, we do not rule out the possibility that peptides of lower homology from members of the Coronaviridae can result in cross-reactivity. However, we note that the sequence homology analysis of HCoVs and SARS-CoV-2 epitopes by Mateus et al. (19) suggests a positive association of sequence homology and the frequency of cross-reactivity, providing an empirical basis for our approach. Our results highlight the importance of considering the wider phylogenetic context of circulating antigens contributing to immunological memory to novel pathogens. The widespread and repeated exposure of global human populations to circulating endemic HCoVs is expected to have left an immunological legacy which might modulate COVID-19 pathogenesis. However, our results suggest that the extensive observed T-cell cross-reactivity is unlikely to have been caused by prior exposure to any known coronavirus in global circulation. It is nonetheless clear that the potential cross-reactive repertoire is widespread and present in cohorts of healthy people from multiple countries around the globe (19–28), even if perhaps at low avidity (27). It remains to be established to what extent such cross-reactivity translates into immunity to SARS-CoV-2, both in terms of susceptibility to infection and symptom severity upon infection.
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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SciScore for 10.1101/2020.12.08.415703: (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
Experimental Models: Organisms/Strains Sentences Resources Non-Coronaviridae protein BLAST To determine if any proteome outside of the Coronaviridae had detectable homology to any of the epitopes reported in the literature, we performed a protein BLAST using the online blastp suite (https://tinyurl.com/y22o4t9z) against the non-redundant protein sequence database (accessed 7/12/2020), while excluding sequences associated with the Coronaviridae (taxid: 11118) taxid: 11118suggested: NoneSoftware and Algorithms Sentence… SciScore for 10.1101/2020.12.08.415703: (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
Experimental Models: Organisms/Strains Sentences Resources Non-Coronaviridae protein BLAST To determine if any proteome outside of the Coronaviridae had detectable homology to any of the epitopes reported in the literature, we performed a protein BLAST using the online blastp suite (https://tinyurl.com/y22o4t9z) against the non-redundant protein sequence database (accessed 7/12/2020), while excluding sequences associated with the Coronaviridae (taxid: 11118) taxid: 11118suggested: NoneSoftware and Algorithms Sentences Resources First, open reading frames (ORFs) were identified using the genome annotation tool Prokka v1.14.6 (49). Prokkasuggested: (Prokka, RRID:SCR_014732)Next, the Roary pipeline v3.11.12 (50) was used to cluster all Coronaviridae ORFs at a minimum amino-acid homology threshold of 30%. Roarysuggested: (Roary, RRID:SCR_018172)Sequences for the four genes ORF1ab, S, M and N were each found to cluster in a minimum of assemblies, which were then extracted, concatenated and aligned using MAFFT v7.453 (51). MAFFTsuggested: (MAFFT, RRID:SCR_011811)The resulting alignment was trimmed of gaps found in 20% or more isolates and used to build a Maximum Likelihood phylogeny using RAxML v8.2.12 (52) with 1000 bootstraps for node support. RAxMLsuggested: (RAxML, RRID:SCR_006086)Each assembly contained a ORF1ab CDS annotated ORF, the only gene shared by all members of the Nidovirales (53), which were decomposed into 11-mer sequences using MASH v2.1.1 (54). MASHsuggested: (Mash, RRID:SCR_019135)Separately, a protein BLAST database was also constructed from the protein annotations associated with the 2531 assemblies, which were downloaded using NCBI Batch Entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez). https://www.ncbi.nlm.nih.gov/sites/batchentrezsuggested: (Batch Entrez, RRID:SCR_016634)Subsequently, we used blastp from BLAST+ v2.11.0 (55) to determine the sequence similarity of the 15-mer peptides from the SARS-CoV-2 proteome and the 177 published epitopes using the two databases and. BLAST+suggested: (Japan Bioinformatics, RRID:SCR_012250)In addition, to optimise the protein BLAST search for short sequences, -task was set to blastp-short. 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: We detected the following sentences addressing limitations in the study:
Deconvolving the relationship between sequence homology and cross-reactivity is evidently non-trivial and remains a limitation of our work. Indeed, we do not rule out the possibility that peptides of lower homology from members of the Coronaviridae can result in cross-reactivity. However, we note that the sequence homology analysis of HCoVs and SARS-CoV-2 epitopes by Mateus et al. (19) suggests a positive association of sequence homology and the frequency of cross-reactivity, providing an empirical basis for our approach. Our results highlight the importance of considering the wider phylogenetic context of circulating antigens contributing to immunological memory to novel pathogens. The widespread and repeated exposure of global human populations to circulating endemic HCoVs is expected to have left an immunological legacy which might modulate COVID-19 pathogenesis. However, our results suggest that the extensive observed T-cell cross-reactivity is unlikely to have been caused by prior exposure to any known coronavirus in global circulation. It is nonetheless clear that the potential cross-reactive repertoire is widespread and present in cohorts of healthy people from multiple countries around the globe (19–28), even if perhaps at low avidity (27). It remains to be established to what extent such cross-reactivity translates into immunity to SARS-CoV-2, both in terms of susceptibility to infection and symptom severity upon infection. Methods Data acquisition publicly available...
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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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