| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T196 |
0-4 |
Sentence |
denotes |
Orf8 |
| T197 |
5-87 |
Sentence |
denotes |
orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. |
| T198 |
88-223 |
Sentence |
denotes |
Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23]. |
| T199 |
224-422 |
Sentence |
denotes |
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]. |
| T200 |
423-633 |
Sentence |
denotes |
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]. |
| T201 |
634-813 |
Sentence |
denotes |
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. |
| T202 |
814-1293 |
Sentence |
denotes |
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)). |
| T203 |
1294-1438 |
Sentence |
denotes |
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. |
| T204 |
1439-1649 |
Sentence |
denotes |
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). |
| T205 |
1650-1727 |
Sentence |
denotes |
This new orf8 of 2019-nCoV does not contain known functional domain or motif. |
| T206 |
1728-1969 |
Sentence |
denotes |
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. |
| T207 |
1970-2159 |
Sentence |
denotes |
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)). |
| T208 |
2160-2169 |
Sentence |
denotes |
Figure 5. |
| T209 |
2170-2582 |
Sentence |
denotes |
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. |
| T210 |
2583-2762 |
Sentence |
denotes |
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. |
| T211 |
2763-2998 |
Sentence |
denotes |
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). |
| T212 |
2999-3088 |
Sentence |
denotes |
Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively. |
