PMC:7565482 / 25487-26972 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7565482","sourcedb":"PMC","sourceid":"7565482","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7565482","text":"We here present the first SARS-CoV-2 Consensus sequence for all described SARS-CoV-2 ORF, including those in alternative frames covering the SARS-CoV-2 sequence variability represented by 1700 available sequences. The description of this sequence and of the matching OLP sets will aid the further immune analyses in SARS-CoV-2 infection and ensure reproducibility between laboratories. In light of recent studies, the T cell response to SARS-CoV-2 can be crucial to control SARS-CoV-2 infection. To date, published studies are generally limited to a few viral proteins, using recall antigens that do not reflect sequence diversity nor alternative ORFs. To overcome these limitations, the description of the global landscape of T cell responses to SARS-CoV-2 urgently needs unbiased, comparable, full-proteome screens for virus-specific T cell responses. The CoV-2-cons and matched OLP sets described here will allow to integrate data globally, generating crucial information for vaccine development. We also include measures of sequence entropy to identify the most variable segments and design additional OLP sequences that cover these sites. Of note, these entropy analyses, together with sequence alignments across a wide range of coronaviruses, also allowed the identification of highly conserved regions among different coronaviruses. These regions may be targeted by T cells, which could target a wide range of coronaviruses and may be relevant targets for T cell vaccine design.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T114","span":{"begin":420,"end":424},"obj":"Body_part"},{"id":"T115","span":{"begin":560,"end":568},"obj":"Body_part"},{"id":"T116","span":{"begin":729,"end":733},"obj":"Body_part"},{"id":"T117","span":{"begin":838,"end":842},"obj":"Body_part"},{"id":"T118","span":{"begin":1375,"end":1380},"obj":"Body_part"},{"id":"T119","span":{"begin":1465,"end":1469},"obj":"Body_part"}],"attributes":[{"id":"A114","pred":"fma_id","subj":"T114","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A116","pred":"fma_id","subj":"T116","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma68646"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T116","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T117","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T118","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T69","span":{"begin":141,"end":149},"obj":"Disease"},{"id":"T67","span":{"begin":26,"end":34},"obj":"Disease"},{"id":"T68","span":{"begin":74,"end":82},"obj":"Disease"},{"id":"T70","span":{"begin":316,"end":324},"obj":"Disease"},{"id":"T71","span":{"begin":327,"end":336},"obj":"Disease"},{"id":"T72","span":{"begin":437,"end":445},"obj":"Disease"},{"id":"T73","span":{"begin":474,"end":482},"obj":"Disease"},{"id":"T74","span":{"begin":485,"end":494},"obj":"Disease"},{"id":"T75","span":{"begin":747,"end":755},"obj":"Disease"}],"attributes":[{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A73","pred":"mondo_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A74","pred":"mondo_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A75","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T69","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T67","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T68","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T70","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T75","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T235","span":{"begin":418,"end":424},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T236","span":{"begin":548,"end":549},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T237","span":{"begin":727,"end":733},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T238","span":{"begin":821,"end":826},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T239","span":{"begin":836,"end":842},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T240","span":{"begin":1218,"end":1219},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T241","span":{"begin":1373,"end":1380},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T242","span":{"begin":1401,"end":1402},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T243","span":{"begin":1463,"end":1469},"obj":"http://purl.obolibrary.org/obo/CL_0000084"}],"attributes":[{"subj":"T235","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T236","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T237","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T238","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T239","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T240","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T241","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T242","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T243","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"325","span":{"begin":26,"end":36},"obj":"Species"},{"id":"326","span":{"begin":74,"end":84},"obj":"Species"},{"id":"327","span":{"begin":141,"end":151},"obj":"Species"},{"id":"328","span":{"begin":437,"end":447},"obj":"Species"},{"id":"329","span":{"begin":747,"end":757},"obj":"Species"},{"id":"330","span":{"begin":858,"end":863},"obj":"Species"},{"id":"331","span":{"begin":1234,"end":1247},"obj":"Species"},{"id":"332","span":{"begin":1325,"end":1338},"obj":"Species"},{"id":"333","span":{"begin":1417,"end":1430},"obj":"Species"},{"id":"334","span":{"begin":316,"end":336},"obj":"Disease"},{"id":"335","span":{"begin":474,"end":494},"obj":"Disease"}],"attributes":[{"id":"A325","pred":"tao:has_database_id","subj":"325","obj":"Tax:2697049"},{"id":"A326","pred":"tao:has_database_id","subj":"326","obj":"Tax:2697049"},{"id":"A327","pred":"tao:has_database_id","subj":"327","obj":"Tax:2697049"},{"id":"A328","pred":"tao:has_database_id","subj":"328","obj":"Tax:2697049"},{"id":"A329","pred":"tao:has_database_id","subj":"329","obj":"Tax:2697049"},{"id":"A330","pred":"tao:has_database_id","subj":"330","obj":"Tax:2697049"},{"id":"A331","pred":"tao:has_database_id","subj":"331","obj":"Tax:11118"},{"id":"A332","pred":"tao:has_database_id","subj":"332","obj":"Tax:11118"},{"id":"A333","pred":"tao:has_database_id","subj":"333","obj":"Tax:11118"},{"id":"A334","pred":"tao:has_database_id","subj":"334","obj":"MESH:C000657245"},{"id":"A335","pred":"tao:has_database_id","subj":"335","obj":"MESH:C000657245"},{"subj":"325","pred":"source","obj":"LitCovid-PubTator"},{"subj":"326","pred":"source","obj":"LitCovid-PubTator"},{"subj":"327","pred":"source","obj":"LitCovid-PubTator"},{"subj":"328","pred":"source","obj":"LitCovid-PubTator"},{"subj":"329","pred":"source","obj":"LitCovid-PubTator"},{"subj":"330","pred":"source","obj":"LitCovid-PubTator"},{"subj":"331","pred":"source","obj":"LitCovid-PubTator"},{"subj":"332","pred":"source","obj":"LitCovid-PubTator"},{"subj":"333","pred":"source","obj":"LitCovid-PubTator"},{"subj":"334","pred":"source","obj":"LitCovid-PubTator"},{"subj":"335","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T173","span":{"begin":0,"end":213},"obj":"Sentence"},{"id":"T174","span":{"begin":214,"end":385},"obj":"Sentence"},{"id":"T175","span":{"begin":386,"end":495},"obj":"Sentence"},{"id":"T176","span":{"begin":496,"end":652},"obj":"Sentence"},{"id":"T177","span":{"begin":653,"end":853},"obj":"Sentence"},{"id":"T178","span":{"begin":854,"end":999},"obj":"Sentence"},{"id":"T179","span":{"begin":1000,"end":1143},"obj":"Sentence"},{"id":"T180","span":{"begin":1144,"end":1339},"obj":"Sentence"},{"id":"T181","span":{"begin":1340,"end":1485},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T173","pred":"source","obj":"LitCovid-sentences"},{"subj":"T174","pred":"source","obj":"LitCovid-sentences"},{"subj":"T175","pred":"source","obj":"LitCovid-sentences"},{"subj":"T176","pred":"source","obj":"LitCovid-sentences"},{"subj":"T177","pred":"source","obj":"LitCovid-sentences"},{"subj":"T178","pred":"source","obj":"LitCovid-sentences"},{"subj":"T179","pred":"source","obj":"LitCovid-sentences"},{"subj":"T180","pred":"source","obj":"LitCovid-sentences"},{"subj":"T181","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#9e93ec","default":true},{"id":"LitCovid-PD-MONDO","color":"#a1ec93"},{"id":"LitCovid-PD-CLO","color":"#ec93bb"},{"id":"LitCovid-PubTator","color":"#93d5ec"},{"id":"LitCovid-sentences","color":"#ece893"}]}]}}