LitCovid-sentences  

PMC:7055038 / 5779-8641 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T54 0-24 Sentence denotes Genome sequence analysis
T55 25-440 Sentence denotes Comparing the two genome sequences with a non-redundant selection of representatives from all known CoV families by alignment [10] and phylogenetic tree (Figure 1A) [11] shows that they belong to the SARS family of betacoronaviruses and while related to SARS-CoV (80% genome identity), they were most closely related to SARS-like bat CoV from China (88% identity) as closest known sequence at the time of emergence.
T56 441-673 Sentence denotes Figure 1 Phylogenetic trees of Thai sequences in context of all coronavirus families (A) and structural mapping of mutations in the spike glycoprotein between SARS CoV (PDB:6CG [12]) and the current SARS-CoV-2 using YASARA [20] (B)
T57 674-697 Sentence denotes CoV: coronavirus; MERS:
T58 698-784 Sentence denotes Middle East respiratory syndrome coronavirus; SARS: severe acute respiratory syndrome.
T59 785-856 Sentence denotes Panel A: blue: SARS-CoV-2; red: SARS; purple: MERS; green: common cold.
T60 857-903 Sentence denotes Panel B: cyan: ACE2 human host receptor; grey:
T61 904-992 Sentence denotes CoV spike glycoprotein trimer (PDB:6ACG); red: mutations between SARS-CoV vs SARS-CoV-2.
T62 993-1204 Sentence denotes The phylogenetic tree was created from whole genome alignment with MAFFT using the neighbour-joining method with maximum composite likelihood (MCL) model, uniform site rates and 500 bootstrap tests using MEGA X.
T63 1205-1387 Sentence denotes Structural mapping of mutations in the spike glycoprotein between SARS CoV and the two cases of the SARS-CoV-2 reported here shows only 76% identity at the protein level (Figure 1B).
T64 1388-1508 Sentence denotes This surface protein is critical for ACE2 host receptor interaction and is also a target of the immune response [12,13].
T65 1509-1710 Sentence denotes Given several mutations in the binding interface, it may differ in host cell binding efficiency compared with SARS-CoV which could result in differences in virulence and transmission potential [14,15].
T66 1711-2097 Sentence denotes The genomes of the two separate cases of coronavirus disease 2019 (COVID-19) are identical over the full length of close to 30 kb and are furthermore identical to five other sequences (four from Wuhan and one from Zhejiang); together these sequences form the largest cluster of identical cases within the early outbreak, comprising a core of at least indirectly linked cases (Figure 2).
T67 2098-2344 Sentence denotes Within-outbreak sequence divergence is generally low with 0–9 nt differences over the whole genome and mutations unique to individual strains are possibly related to quality differences of the samples and noise of the methods used for sequencing.
T68 2345-2448 Sentence denotes Figure 2 Within-outbreak SARS-CoV-2 sequence divergence and clusters, China and Thailand, January 2020
T69 2449-2550 Sentence denotes Number of pair-wise nt differences across whole genomes colour-coded from zero (green) to nine (red).
T70 2551-2556 Sentence denotes Blue:
T71 2557-2575 Sentence denotes Thai sample names.
T72 2576-2654 Sentence denotes Orange: samples with sequences identical to each other and the Thai sequences.
T73 2655-2862 Sentence denotes We gratefully acknowledge the authors, the originating and submitting laboratories for their sequence and metadata shared through GISAID, on which this research is based (as listed in Supplementary Table 1).