LitCovid-sentences  

PMC:7140597 / 4255-12836 JSONTXT 14 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T27 0-21 Sentence denotes Phylogenetic analysis
T28 22-428 Sentence denotes To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material).
T29 429-564 Sentence denotes Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6].
T30 565-861 Sentence denotes Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7].
T31 862-938 Sentence denotes Support for the tree topology was estimated with 1,000 bootstrap replicates.
T32 939-1041 Sentence denotes The maximum likelihood phylogenetic tree in the Figure shows a main clade containing several clusters.
T33 1042-1285 Sentence denotes The viral genome sequence of the Chinese tourist (GISAID accession ID: EPI_ISL_412974) was identical to that retrieved from one sample of another Chinese tourist, hospitalised at the same hospital in Rome (GISAID accession ID: EPI_ISL_410546).
T34 1286-1409 Sentence denotes The latter was closely related to that of another sample taken from the same patient (GISAID accession ID: EPI_ISL_410545).
T35 1410-1593 Sentence denotes These three genome sequences were located in a cluster with genomes mainly from Europe (England, France, Italy, Sweden), but also one from Australia (Figure, highlighted in dark red).
T36 1594-1778 Sentence denotes Figure Phylogenetic analysis of two SARS-CoV-2 complete genome sequences retrieved in this study, with available complete sequences from different countriesa (n = 40 genome sequences)
T37 1779-1786 Sentence denotes GISAID:
T38 1787-1840 Sentence denotes Global Initiative on Sharing All Influenza Data; HKY:
T39 1841-1877 Sentence denotes Hasegawa, Kishino, and Yano; MEGA X:
T40 1878-2005 Sentence denotes Molecular Evolutionary Genetics Analysis across Computing Platforms; SARS-CoV-2: severe acute respiratory syndrome coronavirus.
T41 2006-2057 Sentence denotes Main clusters are highlighted in different colours.
T42 2058-2143 Sentence denotes The Wuhan reference genome is in larger font (GenBank accession number: NC_045512.2).
T43 2144-2268 Sentence denotes The filled circles represent the main supported clusters (bootstrap support values are indicated at the level of the nodes).
T44 2269-2355 Sentence denotes The scale bar at the bottom of the tree represents 0.000050 nt substitutions per site.
T45 2356-2502 Sentence denotes The cluster containing the viral sequence of the Chinese tourist who had visited Rome, Italy (GISAID accession ID: EPI_ISL_412974) is in dark red.
T46 2503-2699 Sentence denotes This cluster includes viral sequences derived from two samples (sputum and nasopharyngeal swabs) of another Chinese tourist visiting Rome (GISAID accession IDs: EPI_ISL_410545 and EPI_ISL_410546).
T47 2700-2918 Sentence denotes The viral genome sequence (GISAID accession ID: EPI_ISL_412973) derived from a patient from Lombardy, Italy, is in a cluster highlighted in green, which is different from that containing the Chinese tourist’s sequence.
T48 2919-3014 Sentence denotes a The tree wasbuilt by using the best fitting substitution model (HKY) through MEGA X software.
T49 3015-3349 Sentence denotes The genome sequence from the Italian patient in Lombardy (EPI_ISL_412973) appeared in contrast to be located in a different cluster including two genome sequences from Germany (EPI_ISL_406862 Bavaria/Munich and EPI_ISL_412912 Baden-Wuerttemberg-1) and one genome sequence from Mexico (EPI_ISL_ 412972), (Figure, highlighted in green).
T50 3350-3546 Sentence denotes In the tree, some sequences from other SARS-CoV-2 collected in Europe segregated in separate clusters from the two clusters containing the respective patient sequences characterised in this study.
T51 3547-3668 Sentence denotes There was for example a cluster formed by two sequences from England and a cluster formed by three sequences from France.
T52 3669-4104 Sentence denotes Using an alignment, the single nt polymorphisms (SNPs) composition and the potentially resulting variable amino-acids in derived protein sequences compared with the Wuhan reference sequences (MN908947 and NC_045512), were investigated for the genome sequences retrieved in this study, as well as three other genome sequences (EPI_ISL_412972, EPI_ISL_ 412912, EPI_ISL_406862) that clustered with the sequence of the patient in Lombardy.
T53 4105-4242 Sentence denotes The genome-wide SNPs are reported in Table 1 (positions referred respect to the reference sequence; GenBank accession number: NC_045512).
T54 4243-4338 Sentence denotes The corresponding amino-acid positions and variations inside the proteins are shown in Table 2.
T55 4339-4536 Sentence denotes Table 1 Single nt polymorphisms (SNPs)a deduced by comparison of two whole genome sequences of SARS-CoV-2 characterised in this studyb with selected SARS-CoV-2 sequences (n = 7 compared sequences)
T56 4537-4685 Sentence denotes SARS-CoV-2 sequence ID (country from which the sequence originated) 241 3037 10265 11083 13206 14408 15806 23403 26144 28881 28882 28883
T57 4686-4815 Sentence denotes 5' UTR ORF1ab gene ORF1ab gene ORF 1ab gene ORF1ab gene ORF1ab gene ORF1ab gene Gene S ORF3a gene Gene N Gene N Gene N
T58 4816-4869 Sentence denotes NC_045512 (China) C C G G C C A A G G G G
T59 4870-4922 Sentence denotes MN908947 (China) C C G G C C A A G G G G
T60 4923-4982 Sentence denotes EPI_ISL:412972 (Mexico) T T G G G T - G G A A C
T61 4983-4991 Sentence denotes EPI_ISL:
T62 4992-5044 Sentence denotes 412912 (Germany) T T A G C T A G G A A C
T63 5045-5053 Sentence denotes EPI_ISL:
T64 5054-5106 Sentence denotes 406862 (Germany) T T G G C C A G G G G G
T65 5107-5165 Sentence denotes EPI_ISL_412973 (Italy) T T G G C T A G G G G G
T66 5166-5224 Sentence denotes EPI_ISL_412974 (Italy) C C G T C C A A T G G G
T67 5225-5447 Sentence denotes N: nucleocapsid protein; ORF: open reading frame; ORF1ab: ORF encoding polyprotein; S: surface glycoprotein; SARS-CoV-2: severe acute respiratory syndrome coronavirus; SNP: single nt polymorphism; UTR: untranslated region.
T68 5448-5532 Sentence denotes a SNPs are shown according to nt positions in the genome sequence and gene location.
T69 5533-5641 Sentence denotes b The two sequences characterised in this study are the ones from Italy (EPI_ISL_412973 and EPI_ISL_412974).
T70 5642-5851 Sentence denotes Table 2 Amino acid variationsa deduced by comparing translations of two whole genome sequences of SARS-CoV-2 characterised in this studyb with those of selected SARS-CoV-2 sequences (n = 7 compared sequences)
T71 5852-5925 Sentence denotes SARS-CoV-2 strains 924 3334 3606 4314 4704 5170 614 251 203 204
T72 5926-6059 Sentence denotes ORF1ab ORF1ab ORF1ab ORF1ab ORF1ab ORF1ab Surface glycoprotein ORF3a Nucleocapsid phosphoprotein Nucleocapsid phosphoprotein
T73 6060-6107 Sentence denotes NC_045512 (China) F G L A P Q D G R G
T74 6108-6154 Sentence denotes MN908947 (China) F G L A P Q D G R G
T75 6155-6209 Sentence denotes EPI_ISL:412972 (Mexico) F G L G L -c G G K R
T76 6210-6218 Sentence denotes EPI_ISL:
T77 6219-6265 Sentence denotes 412912 (Germany) F S L A L Q G G K R
T78 6266-6274 Sentence denotes EPI_ISL:
T79 6275-6321 Sentence denotes 406862 (Germany) F G L A P Q G G R G
T80 6322-6374 Sentence denotes EPI_ISL_412973 (Italy) F G L A L Q G G R G
T81 6375-6427 Sentence denotes EPI_ISL_412974 (Italy) F G F A P Q D V R G
T82 6428-6545 Sentence denotes ORF: open reading frame; ORF1ab: ORF encoding polyprotein; SARS-CoV-2: severe acute respiratory syndrome coronavirus.
T83 6546-6720 Sentence denotes a The amino acid positions refer to those in each respective protein sequence of the Wuhan reference (GenBank accession number: MN908947), starting from the first methionine.
T84 6721-6829 Sentence denotes b The two sequences characterised in this study are the ones from Italy (EPI_ISL_412973 and EPI_ISL_412974).
T85 6830-6861 Sentence denotes c -: possible sequencing error.
T86 6862-7109 Sentence denotes The genome sequence from the Chinese tourist hospitalised in Rome differed in two nt positions from that of the COVID-19 patient in Wuhan (NC_045512), while the genome sequence isolated from the Italian patient showed four nt variations (Table 1).
T87 7110-7237 Sentence denotes For the sequence of the Chinese tourist, the first SNP inside ORF1ab (bps 3037, AA 924) did not result in an amino acid change.
T88 7238-7771 Sentence denotes In the Table 2 that depicts five sequences characterised outside of China, overall eight missense mutations can be observed compared to the two reference Wuhan sequences: four locate to the ORF1ab polyprotein, whereby only the mutation L3606F has previously been reported by Phan, 2020 [8]; one, D614G, locates to the surface glycoprotein and has been prior observed [8], but is not in the receptor binding domain (RDB), responsible for virus entry into host cell; one is in the ORF3a protein and two are in the nucleocapsid protein.
T89 7772-7944 Sentence denotes The sequence of the Chinese tourist hospitalised in Rome on 29 January (EPI_ISL_412974) presented a mutation 3606F in ORF1ab with respect to the reference Wuhan genome (L).
T90 7945-8052 Sentence denotes In ORF3a, this sequence had a V at amino acid position 251, as opposed to a G in the references from Wuhan.
T91 8053-8223 Sentence denotes Meanwhile, the sequence of the Italian patient from Lombardy (EPI_ISL 412973) presented an L at amino acidic position 4704 with respect to the reference Wuhan genome (P).
T92 8224-8409 Sentence denotes It also had a mutation in the surface glycoprotein, at amino acidic position 614, where it showed a G compared to the reference sequences from Wuhan that presented a D at that position.
T93 8410-8581 Sentence denotes With regard to the nucleocapsid protein, both of the sequences from the Italian patient and Chinese tourist presented the same amino acids of the references Wuhan genomes.