PMC:7036342 / 4608-6169 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"109","span":{"begin":50,"end":57},"obj":"Species"},{"id":"110","span":{"begin":760,"end":770},"obj":"Species"},{"id":"111","span":{"begin":1021,"end":1028},"obj":"Species"},{"id":"112","span":{"begin":1077,"end":1084},"obj":"Species"},{"id":"113","span":{"begin":111,"end":119},"obj":"Disease"}],"attributes":[{"id":"A109","pred":"tao:has_database_id","subj":"109","obj":"Tax:694002"},{"id":"A110","pred":"tao:has_database_id","subj":"110","obj":"Tax:2697049"},{"id":"A111","pred":"tao:has_database_id","subj":"111","obj":"Tax:694002"},{"id":"A112","pred":"tao:has_database_id","subj":"112","obj":"Tax:694002"},{"id":"A113","pred":"tao:has_database_id","subj":"113","obj":"MESH:D007239"}],"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_"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T111","span":{"begin":10,"end":16},"obj":"SO:0001026"},{"id":"T110","span":{"begin":35,"end":40},"obj":"NCBITaxon:10239"},{"id":"T109","span":{"begin":100,"end":104},"obj":"CL_6"},{"id":"T108","span":{"begin":183,"end":188},"obj":"NCBITaxon:10239"},{"id":"T107","span":{"begin":539,"end":544},"obj":"SO:0000150"},{"id":"T106","span":{"begin":550,"end":552},"obj":"SO:0000028"},{"id":"T105","span":{"begin":709,"end":714},"obj":"SO:0000150"},{"id":"T104","span":{"begin":726,"end":731},"obj":"SO:0000150"},{"id":"T103","span":{"begin":760,"end":770},"obj":"SP_7"},{"id":"T102","span":{"begin":771,"end":777},"obj":"SO:0001026"},{"id":"T101","span":{"begin":930,"end":936},"obj":"SO:0001026"},{"id":"T100","span":{"begin":968,"end":974},"obj":"SO:0001026"},{"id":"T99","span":{"begin":1242,"end":1249},"obj":"SO:0001026"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T26","span":{"begin":10,"end":16},"obj":"Body_part"},{"id":"T27","span":{"begin":105,"end":110},"obj":"Body_part"},{"id":"T28","span":{"begin":133,"end":136},"obj":"Body_part"},{"id":"T29","span":{"begin":149,"end":152},"obj":"Body_part"},{"id":"T30","span":{"begin":189,"end":192},"obj":"Body_part"},{"id":"T31","span":{"begin":277,"end":280},"obj":"Body_part"},{"id":"T32","span":{"begin":333,"end":336},"obj":"Body_part"},{"id":"T33","span":{"begin":771,"end":777},"obj":"Body_part"},{"id":"T34","span":{"begin":930,"end":936},"obj":"Body_part"},{"id":"T35","span":{"begin":968,"end":974},"obj":"Body_part"},{"id":"T36","span":{"begin":1242,"end":1249},"obj":"Body_part"},{"id":"T37","span":{"begin":1529,"end":1539},"obj":"Body_part"}],"attributes":[{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma82740"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T37","span":{"begin":760,"end":768},"obj":"Disease"},{"id":"T38","span":{"begin":760,"end":764},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T51","span":{"begin":35,"end":40},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T52","span":{"begin":100,"end":104},"obj":"http://purl.obolibrary.org/obo/CLO_0009524"},{"id":"T53","span":{"begin":100,"end":104},"obj":"http://purl.obolibrary.org/obo/CLO_0050515"},{"id":"T54","span":{"begin":105,"end":110},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T55","span":{"begin":516,"end":517},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T56","span":{"begin":758,"end":759},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T57","span":{"begin":839,"end":840},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T58","span":{"begin":863,"end":865},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T59","span":{"begin":1303,"end":1304},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T60","span":{"begin":1485,"end":1486},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T28","span":{"begin":699,"end":704},"obj":"Chemical"},{"id":"T29","span":{"begin":975,"end":979},"obj":"Chemical"},{"id":"T30","span":{"begin":1529,"end":1539},"obj":"Chemical"}],"attributes":[{"id":"A28","pred":"chebi_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}

{"project":"LitCovid-sentences","denotations":[{"id":"T25","span":{"begin":0,"end":148},"obj":"Sentence"},{"id":"T26","span":{"begin":149,"end":276},"obj":"Sentence"},{"id":"T27","span":{"begin":277,"end":353},"obj":"Sentence"},{"id":"T28","span":{"begin":354,"end":433},"obj":"Sentence"},{"id":"T29","span":{"begin":434,"end":715},"obj":"Sentence"},{"id":"T30","span":{"begin":716,"end":1102},"obj":"Sentence"},{"id":"T31","span":{"begin":1103,"end":1227},"obj":"Sentence"},{"id":"T32","span":{"begin":1228,"end":1561},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"For whole genome sequencing of the virus isolate (BetaCoV/Korea/SNU01/2020), culture supernatant of Vero cells infected was used for RNA extraction. RNA was extracted by using QIAamp viral RNA mini kit (QIAGEN, Valencia, CA, USA), according to the manufacturer's instructions. RNA libraries were prepared using TruSeq Stranded Total RNA Kit (catalog No. 20020596; Illumina, San Diego, CA, USA) according to the manufacturer protocol. Sequencing was performed on an Illumina Nextseq 500 platform, produced on average a total of 150 million reads, 150 bp per sample, as per the manufacturer's instructions in Macrogen Inc. (Seoul, Korea).8910 FASTQ was used to trim the adapter and remove low quality bases and reads. Qualified reads were mapped to NC_045512, a SARS-CoV-2 genome reference using Burrows-Wheeler Aligner (v0.7.12-r1039), and a bam file was produced.11 In this bam file, the variation was confirmed by comparing with genome using SAMtools (v1.3.1).12 For genome-base phylogeny analysis, 37 strains including BetaCoV/Korea/KCDC03/2020 were used in combination with BetaCoV/Korea/SNU01/2020. The sequences used for analysis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) and GISAID (http://www.gisaid.org). The 37 strain genomes were multiple-sequence aligned using MAFFT (v7.450), a sequence alignment tool, and were used to generate phylogenetic tree.13 Phylogenetic analysis of the aligned sequence was performed with 1,000 bootstrap replicates using MEGAX and a general time-reversible model used as the nucleotide substitution model.14"}