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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T17","span":{"begin":2079,"end":2084},"obj":"Body_part"},{"id":"T18","span":{"begin":3004,"end":3009},"obj":"Body_part"}],"attributes":[{"id":"A17","pred":"uberon_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"},{"id":"A18","pred":"uberon_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"}],"text":"orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).\nFigure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively."}

LitCovid_AGAC

{"project":"LitCovid_AGAC","denotations":[{"id":"p12770s30","span":{"begin":1835,"end":1842},"obj":"PosReg"},{"id":"p12770s31","span":{"begin":1843,"end":1856},"obj":"CPA"},{"id":"p12770s35","span":{"begin":1877,"end":1886},"obj":"PosReg"},{"id":"p12770s37","span":{"begin":1893,"end":1906},"obj":"MPA"}],"text":"orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).\nFigure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T197","span":{"begin":0,"end":82},"obj":"Sentence"},{"id":"T198","span":{"begin":83,"end":218},"obj":"Sentence"},{"id":"T199","span":{"begin":219,"end":417},"obj":"Sentence"},{"id":"T200","span":{"begin":418,"end":628},"obj":"Sentence"},{"id":"T201","span":{"begin":629,"end":808},"obj":"Sentence"},{"id":"T202","span":{"begin":809,"end":1288},"obj":"Sentence"},{"id":"T203","span":{"begin":1289,"end":1433},"obj":"Sentence"},{"id":"T204","span":{"begin":1434,"end":1644},"obj":"Sentence"},{"id":"T205","span":{"begin":1645,"end":1722},"obj":"Sentence"},{"id":"T206","span":{"begin":1723,"end":1964},"obj":"Sentence"},{"id":"T207","span":{"begin":1965,"end":2154},"obj":"Sentence"},{"id":"T208","span":{"begin":2155,"end":2164},"obj":"Sentence"},{"id":"T209","span":{"begin":2165,"end":2577},"obj":"Sentence"},{"id":"T210","span":{"begin":2578,"end":2757},"obj":"Sentence"},{"id":"T211","span":{"begin":2758,"end":2993},"obj":"Sentence"},{"id":"T212","span":{"begin":2994,"end":3083},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).\nFigure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively."}

2_test

{"project":"2_test","denotations":[{"id":"31987001-15695582-27754491","span":{"begin":214,"end":216},"obj":"15695582"},{"id":"31987001-17928347-27754492","span":{"begin":413,"end":415},"obj":"17928347"},{"id":"31987001-26269185-27754493","span":{"begin":624,"end":626},"obj":"26269185"},{"id":"31987001-31231549-27754494","span":{"begin":1908,"end":1910},"obj":"31231549"}],"text":"orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).\nFigure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively."}

MyTest

{"project":"MyTest","denotations":[{"id":"31987001-15695582-27754491","span":{"begin":214,"end":216},"obj":"15695582"},{"id":"31987001-17928347-27754492","span":{"begin":413,"end":415},"obj":"17928347"},{"id":"31987001-26269185-27754493","span":{"begin":624,"end":626},"obj":"26269185"},{"id":"31987001-31231549-27754494","span":{"begin":1908,"end":1910},"obj":"31231549"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24]. In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25]. Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C). This new orf8 of 2019-nCoV does not contain known functional domain or motif. An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).\nFigure 5. Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000. The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively. The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED). Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively."}

PMC:7067204 / 18520-21603 JSONTXT

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PMC:7067204 / 18520-21603 JSON TXT