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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":4757,"end":4761},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"}],"text":"4. Discussion\nWe here report the design of a CoV-2-cons sequence and the matched OLP sets for the comprehensive analysis of the adaptive T cell immune response against SARS-CoV-2. Three sets of OLP reported here provide enough flexibility to balance exhaustive screening for T cell responses and available resources. Ideally, the wide use of such a CoV-2-cons sequence and a specific OLP set (ideally 15 mer with 11 overlap) would ensure the comparability and reproducibility of immunological data across laboratories worldwide to accelerate SARS-CoV-2 immunological studies.\nFifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].\nCanonical and alternative frame ORF were considered in the present CoV-2-consensus sequence design to ensure an as broad as possible screening for all potentially expressed protein sequences. Whether all these putative ORF are indeed expressed remains to be confirmed. If shown that not all these sequences are indeed expressed, the OLP set could be reduced by some 65 peptides, focusing exclusively on the canonical ORF. Consensus sequence design is highly dependent on the sequences included in the alignments used to construct them. We used publicly available sequences in the growing SARS-CoV-2 NCBI repository as a representative set of worldwide sequences. As noted, coverage of sequence diversity for in-vitro antigen test sets is critical as responses to autologous viral variants may be missed if these variant sequences are not matched [27]. This may be most critical for highly variable pathogens, such as HCV and HIV, where it has been shown that sequence entropy was directly related to the frequency of OLP reactivity in vitro and essential to identify the potential emergence of immune escape variants [59,60]. However, even genetically more stable pathogens such DNA viruses (for instance Epstein Barr Virus, EBV) have been reported to exist as a swarm of quasi-species and to lose specific T cell epitopes over time [61,62]. This is also supported by recent data showing some degree of adaptation to host immunity and sequence variability for SARS-CoV-2 as it moves through the global human population [63]. To cover these variant sites, variant OLP can be synthesized. An alternative approach to the synthesis of individual variant peptide sequences is the use of “toggled peptides”, where the sequence variation is directly incorporated into the peptide synthesis. To achieve this, peptide synthesis uses mixes of amino acids at variable positions, so that the resulting OLP resembles a mini-peptide library that can achieve an a-priori set coverage of circulating viral variants [64]. This would readily allow to cover more sequence diversity beyond the 25% frequency cut-off that was applied in the present study.\nThe existence of protein fragments conserved among different coronavirus species has several implications. For the interpretation of T cell responses, it has to be taken into account that some degree of cross-reactivity can exist among human coronavirus [5,65]. This implies that responses to these regions could be associated with previous infections by other human coronaviruses, some of them triggering much milder infections that can pass unnoticed, like those by coronaviruses causing a common cold. This observation will need to be taken into consideration when interpreting immune data on SARS-CoV-2. On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible. Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans. However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them. These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated. At the same time, the existence of SARS-CoV-2 homologous regions in the human genome, together with the existence of described epitopes in these regions raise some concern that coronaviruses could be involved in a molecular mimicry process triggering autoimmune diseases like the Guillain-Barré syndrome [66,67,68,69].\nThe present study is currently limited to the design of the CoV-2 consensus sequence, without functional immune analyses of the OLP sets in samples from infected individuals. However, the principal aim here was to provide a SARS-CoV-2 T cell test reagent, including all described ORF and covering as much viral variability as possible, for its implementation in future screening efforts. In addition, the OLP sets will certainly elicit T cell responses in vitro as partial evaluation has been performed by others in studies using peptides spanning some of the regions covered by the present consensus sequence [5,9,11] and since the current peptide designs (length, overlap) has been shown to be effective in the past [55,70]. Thus, the present peptide designs will afford a high-resolution analysis of the T cell response to SARS-CoV-2, the nature of the targeted epitopes and the functionality and T cell receptor use of the T cells targeting these epitopes, thereby increasing our knowledge of factors that drive COVID-19 disease progression and which could be implemented in vaccine development."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PubTator

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":null,"span":{"begin":5712,"end":5731},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":null,"obj":"http://purl.obolibrary.org/obo/HP_0002721"},{"id":"A2","pred":"hp_id","subj":null,"obj":"http://purl.obolibrary.org/obo/HP_0002960"}],"text":"4. Discussion\nWe here report the design of a CoV-2-cons sequence and the matched OLP sets for the comprehensive analysis of the adaptive T cell immune response against SARS-CoV-2. Three sets of OLP reported here provide enough flexibility to balance exhaustive screening for T cell responses and available resources. Ideally, the wide use of such a CoV-2-cons sequence and a specific OLP set (ideally 15 mer with 11 overlap) would ensure the comparability and reproducibility of immunological data across laboratories worldwide to accelerate SARS-CoV-2 immunological studies.\nFifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].\nCanonical and alternative frame ORF were considered in the present CoV-2-consensus sequence design to ensure an as broad as possible screening for all potentially expressed protein sequences. Whether all these putative ORF are indeed expressed remains to be confirmed. If shown that not all these sequences are indeed expressed, the OLP set could be reduced by some 65 peptides, focusing exclusively on the canonical ORF. Consensus sequence design is highly dependent on the sequences included in the alignments used to construct them. We used publicly available sequences in the growing SARS-CoV-2 NCBI repository as a representative set of worldwide sequences. As noted, coverage of sequence diversity for in-vitro antigen test sets is critical as responses to autologous viral variants may be missed if these variant sequences are not matched [27]. This may be most critical for highly variable pathogens, such as HCV and HIV, where it has been shown that sequence entropy was directly related to the frequency of OLP reactivity in vitro and essential to identify the potential emergence of immune escape variants [59,60]. However, even genetically more stable pathogens such DNA viruses (for instance Epstein Barr Virus, EBV) have been reported to exist as a swarm of quasi-species and to lose specific T cell epitopes over time [61,62]. This is also supported by recent data showing some degree of adaptation to host immunity and sequence variability for SARS-CoV-2 as it moves through the global human population [63]. To cover these variant sites, variant OLP can be synthesized. An alternative approach to the synthesis of individual variant peptide sequences is the use of “toggled peptides”, where the sequence variation is directly incorporated into the peptide synthesis. To achieve this, peptide synthesis uses mixes of amino acids at variable positions, so that the resulting OLP resembles a mini-peptide library that can achieve an a-priori set coverage of circulating viral variants [64]. This would readily allow to cover more sequence diversity beyond the 25% frequency cut-off that was applied in the present study.\nThe existence of protein fragments conserved among different coronavirus species has several implications. For the interpretation of T cell responses, it has to be taken into account that some degree of cross-reactivity can exist among human coronavirus [5,65]. This implies that responses to these regions could be associated with previous infections by other human coronaviruses, some of them triggering much milder infections that can pass unnoticed, like those by coronaviruses causing a common cold. This observation will need to be taken into consideration when interpreting immune data on SARS-CoV-2. On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible. Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans. However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them. These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated. At the same time, the existence of SARS-CoV-2 homologous regions in the human genome, together with the existence of described epitopes in these regions raise some concern that coronaviruses could be involved in a molecular mimicry process triggering autoimmune diseases like the Guillain-Barré syndrome [66,67,68,69].\nThe present study is currently limited to the design of the CoV-2 consensus sequence, without functional immune analyses of the OLP sets in samples from infected individuals. However, the principal aim here was to provide a SARS-CoV-2 T cell test reagent, including all described ORF and covering as much viral variability as possible, for its implementation in future screening efforts. In addition, the OLP sets will certainly elicit T cell responses in vitro as partial evaluation has been performed by others in studies using peptides spanning some of the regions covered by the present consensus sequence [5,9,11] and since the current peptide designs (length, overlap) has been shown to be effective in the past [55,70]. Thus, the present peptide designs will afford a high-resolution analysis of the T cell response to SARS-CoV-2, the nature of the targeted epitopes and the functionality and T cell receptor use of the T cells targeting these epitopes, thereby increasing our knowledge of factors that drive COVID-19 disease progression and which could be implemented in vaccine development."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T17","span":{"begin":144,"end":159},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T18","span":{"begin":692,"end":709},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T19","span":{"begin":700,"end":709},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T20","span":{"begin":963,"end":980},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T21","span":{"begin":971,"end":980},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T22","span":{"begin":3619,"end":3628},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T23","span":{"begin":3766,"end":3783},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T24","span":{"begin":3774,"end":3783},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T25","span":{"begin":3802,"end":3819},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T26","span":{"begin":3810,"end":3819},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"4. Discussion\nWe here report the design of a CoV-2-cons sequence and the matched OLP sets for the comprehensive analysis of the adaptive T cell immune response against SARS-CoV-2. Three sets of OLP reported here provide enough flexibility to balance exhaustive screening for T cell responses and available resources. Ideally, the wide use of such a CoV-2-cons sequence and a specific OLP set (ideally 15 mer with 11 overlap) would ensure the comparability and reproducibility of immunological data across laboratories worldwide to accelerate SARS-CoV-2 immunological studies.\nFifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].\nCanonical and alternative frame ORF were considered in the present CoV-2-consensus sequence design to ensure an as broad as possible screening for all potentially expressed protein sequences. Whether all these putative ORF are indeed expressed remains to be confirmed. If shown that not all these sequences are indeed expressed, the OLP set could be reduced by some 65 peptides, focusing exclusively on the canonical ORF. Consensus sequence design is highly dependent on the sequences included in the alignments used to construct them. We used publicly available sequences in the growing SARS-CoV-2 NCBI repository as a representative set of worldwide sequences. As noted, coverage of sequence diversity for in-vitro antigen test sets is critical as responses to autologous viral variants may be missed if these variant sequences are not matched [27]. This may be most critical for highly variable pathogens, such as HCV and HIV, where it has been shown that sequence entropy was directly related to the frequency of OLP reactivity in vitro and essential to identify the potential emergence of immune escape variants [59,60]. However, even genetically more stable pathogens such DNA viruses (for instance Epstein Barr Virus, EBV) have been reported to exist as a swarm of quasi-species and to lose specific T cell epitopes over time [61,62]. This is also supported by recent data showing some degree of adaptation to host immunity and sequence variability for SARS-CoV-2 as it moves through the global human population [63]. To cover these variant sites, variant OLP can be synthesized. An alternative approach to the synthesis of individual variant peptide sequences is the use of “toggled peptides”, where the sequence variation is directly incorporated into the peptide synthesis. To achieve this, peptide synthesis uses mixes of amino acids at variable positions, so that the resulting OLP resembles a mini-peptide library that can achieve an a-priori set coverage of circulating viral variants [64]. This would readily allow to cover more sequence diversity beyond the 25% frequency cut-off that was applied in the present study.\nThe existence of protein fragments conserved among different coronavirus species has several implications. For the interpretation of T cell responses, it has to be taken into account that some degree of cross-reactivity can exist among human coronavirus [5,65]. This implies that responses to these regions could be associated with previous infections by other human coronaviruses, some of them triggering much milder infections that can pass unnoticed, like those by coronaviruses causing a common cold. This observation will need to be taken into consideration when interpreting immune data on SARS-CoV-2. On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible. Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans. However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them. These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated. At the same time, the existence of SARS-CoV-2 homologous regions in the human genome, together with the existence of described epitopes in these regions raise some concern that coronaviruses could be involved in a molecular mimicry process triggering autoimmune diseases like the Guillain-Barré syndrome [66,67,68,69].\nThe present study is currently limited to the design of the CoV-2 consensus sequence, without functional immune analyses of the OLP sets in samples from infected individuals. However, the principal aim here was to provide a SARS-CoV-2 T cell test reagent, including all described ORF and covering as much viral variability as possible, for its implementation in future screening efforts. In addition, the OLP sets will certainly elicit T cell responses in vitro as partial evaluation has been performed by others in studies using peptides spanning some of the regions covered by the present consensus sequence [5,9,11] and since the current peptide designs (length, overlap) has been shown to be effective in the past [55,70]. Thus, the present peptide designs will afford a high-resolution analysis of the T cell response to SARS-CoV-2, the nature of the targeted epitopes and the functionality and T cell receptor use of the T cells targeting these epitopes, thereby increasing our knowledge of factors that drive COVID-19 disease progression and which could be implemented in vaccine development."}

LitCovid-sentences

PMC:7565482 / 18591-25470 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7565482 / 18591-25470 JSON TXT