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LitCovid-PAS-Enju

LitCovid-ArguminSci

{"project":"LitCovid-ArguminSci","denotations":[{"id":"T1","span":{"begin":0,"end":106},"obj":"DRI_Background"},{"id":"T2","span":{"begin":107,"end":243},"obj":"DRI_Background"},{"id":"T3","span":{"begin":244,"end":452},"obj":"DRI_Background"},{"id":"T4","span":{"begin":453,"end":571},"obj":"DRI_Background"},{"id":"T5","span":{"begin":572,"end":695},"obj":"DRI_Background"},{"id":"T6","span":{"begin":846,"end":1005},"obj":"DRI_Outcome"},{"id":"T7","span":{"begin":1006,"end":1184},"obj":"DRI_Outcome"},{"id":"T8","span":{"begin":1185,"end":1408},"obj":"DRI_Outcome"},{"id":"T9","span":{"begin":1409,"end":1576},"obj":"DRI_Outcome"},{"id":"T10","span":{"begin":1577,"end":1699},"obj":"DRI_Outcome"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-OGER

{"project":"LitCovid-OGER","denotations":[{"id":"T1","span":{"begin":353,"end":374},"obj":"GO:0001171"},{"id":"T1","span":{"begin":136,"end":149},"obj":"GO:0019015"},{"id":"T2","span":{"begin":253,"end":258},"obj":"GO:0019012"},{"id":"T3","span":{"begin":402,"end":414},"obj":"GO:0019015"},{"id":"T4","span":{"begin":1687,"end":1692},"obj":"GO:0019012"},{"id":"T1","span":{"begin":926,"end":930},"obj":"PR:000014459"},{"id":"T1","span":{"begin":1,"end":8},"obj":"SO:0001026"},{"id":"T2","span":{"begin":142,"end":149},"obj":"SO:0001026"},{"id":"T3","span":{"begin":353,"end":360},"obj":"SO:0001031"},{"id":"T4","span":{"begin":361,"end":374},"obj":"SO:0000673"},{"id":"T5","span":{"begin":408,"end":414},"obj":"SO:0001026"},{"id":"T6","span":{"begin":508,"end":515},"obj":"SO:0001026"},{"id":"T7","span":{"begin":537,"end":544},"obj":"SO:0001026"},{"id":"T8","span":{"begin":580,"end":587},"obj":"SO:0001026"},{"id":"T9","span":{"begin":615,"end":629},"obj":"SO:0001148"},{"id":"T10","span":{"begin":680,"end":694},"obj":"SO:0001148"},{"id":"T11","span":{"begin":724,"end":730},"obj":"SO:0001026"},{"id":"T12","span":{"begin":884,"end":890},"obj":"SO:0001026"},{"id":"T13","span":{"begin":910,"end":916},"obj":"SO:0001026"},{"id":"T14","span":{"begin":1016,"end":1021},"obj":"SO:0000704"},{"id":"T15","span":{"begin":1034,"end":1041},"obj":"SO:0001026"},{"id":"T16","span":{"begin":1045,"end":1050},"obj":"SO:0000704"},{"id":"T17","span":{"begin":1091,"end":1096},"obj":"SO:0000704"},{"id":"T18","span":{"begin":1145,"end":1149},"obj":"SO:0000704"},{"id":"T19","span":{"begin":1189,"end":1195},"obj":"SO:0001026"},{"id":"T20","span":{"begin":1344,"end":1375},"obj":"SO:0000694"},{"id":"T21","span":{"begin":1425,"end":1431},"obj":"SO:0001026"},{"id":"T22","span":{"begin":1483,"end":1490},"obj":"SO:0001026"},{"id":"T23","span":{"begin":1591,"end":1597},"obj":"SO:0001026"},{"id":"T24","span":{"begin":1693,"end":1698},"obj":"SO:0000704"},{"id":"T1","span":{"begin":280,"end":286},"obj":"UBERON:0000341"},{"id":"T2","span":{"begin":296,"end":302},"obj":"UBERON:0007311"}],"namespaces":[{"prefix":"PR","uri":"http://purl.obolibrary.org/obo/PR_"},{"prefix":"UBERON","uri":"http://purl.obolibrary.org/obo/UBERON_"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PubTatorCentral

{"project":"LitCovid-PubTatorCentral","denotations":[{"id":"T1","span":{"begin":62,"end":69},"obj":"Species:9606"},{"id":"T2","span":{"begin":210,"end":217},"obj":"Species:9606"},{"id":"T3","span":{"begin":317,"end":324},"obj":"Species:9606"},{"id":"T4","span":{"begin":922,"end":947},"obj":"Species:1508227"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-sentences-v1

{"project":"LitCovid-sentences-v1","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":106},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":107,"end":117},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":118,"end":243},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":244,"end":252},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":253,"end":452},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":453,"end":571},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":572,"end":695},"obj":"Sentence"},{"id":"TextSentencer_T8","span":{"begin":696,"end":704},"obj":"Sentence"},{"id":"TextSentencer_T9","span":{"begin":705,"end":845},"obj":"Sentence"},{"id":"TextSentencer_T10","span":{"begin":846,"end":1005},"obj":"Sentence"},{"id":"TextSentencer_T11","span":{"begin":1006,"end":1184},"obj":"Sentence"},{"id":"TextSentencer_T12","span":{"begin":1185,"end":1408},"obj":"Sentence"},{"id":"TextSentencer_T13","span":{"begin":1409,"end":1420},"obj":"Sentence"},{"id":"TextSentencer_T14","span":{"begin":1421,"end":1576},"obj":"Sentence"},{"id":"TextSentencer_T15","span":{"begin":1577,"end":1699},"obj":"Sentence"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-MONDO-v1

{"project":"LitCovid-PD-MONDO-v1","denotations":[{"id":"T1","span":{"begin":53,"end":61},"obj":"Disease"},{"id":"T2","span":{"begin":201,"end":209},"obj":"Disease"},{"id":"T3","span":{"begin":926,"end":930},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-FMA-UBERON-v1

LitCovid-TimeML

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":280,"end":286},"obj":"Body_part"},{"id":"T2","span":{"begin":296,"end":302},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T1","span":{"begin":53,"end":61},"obj":"Disease"},{"id":"T2","span":{"begin":201,"end":209},"obj":"Disease"},{"id":"T3","span":{"begin":926,"end":930},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1","span":{"begin":21,"end":22},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T2","span":{"begin":107,"end":116},"obj":"http://purl.obolibrary.org/obo/BFO_0000030"},{"id":"T3","span":{"begin":169,"end":170},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T4","span":{"begin":705,"end":706},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T5","span":{"begin":920,"end":921},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T6","span":{"begin":922,"end":925},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T7","span":{"begin":1016,"end":1021},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T8","span":{"begin":1045,"end":1050},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T9","span":{"begin":1091,"end":1096},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T10","span":{"begin":1145,"end":1149},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T11","span":{"begin":1157,"end":1158},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T12","span":{"begin":1693,"end":1698},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":1351,"end":1361},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":353,"end":374},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T2","span":{"begin":361,"end":374},"obj":"http://purl.obolibrary.org/obo/GO_0006351"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T1","span":{"begin":0,"end":106},"obj":"Sentence"},{"id":"T2","span":{"begin":107,"end":117},"obj":"Sentence"},{"id":"T3","span":{"begin":118,"end":243},"obj":"Sentence"},{"id":"T4","span":{"begin":244,"end":252},"obj":"Sentence"},{"id":"T5","span":{"begin":253,"end":452},"obj":"Sentence"},{"id":"T6","span":{"begin":453,"end":571},"obj":"Sentence"},{"id":"T7","span":{"begin":572,"end":695},"obj":"Sentence"},{"id":"T8","span":{"begin":696,"end":704},"obj":"Sentence"},{"id":"T9","span":{"begin":705,"end":845},"obj":"Sentence"},{"id":"T10","span":{"begin":846,"end":1005},"obj":"Sentence"},{"id":"T11","span":{"begin":1006,"end":1184},"obj":"Sentence"},{"id":"T12","span":{"begin":1185,"end":1408},"obj":"Sentence"},{"id":"T13","span":{"begin":1409,"end":1420},"obj":"Sentence"},{"id":"T14","span":{"begin":1421,"end":1576},"obj":"Sentence"},{"id":"T15","span":{"begin":1577,"end":1699},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"5","span":{"begin":171,"end":180},"obj":"Species"},{"id":"6","span":{"begin":201,"end":209},"obj":"Disease"},{"id":"7","span":{"begin":210,"end":217},"obj":"Species"},{"id":"29","span":{"begin":922,"end":947},"obj":"Species"},{"id":"30","span":{"begin":1444,"end":1453},"obj":"Species"},{"id":"31","span":{"begin":1581,"end":1590},"obj":"Species"}],"attributes":[{"id":"A5","pred":"tao:has_database_id","subj":"5","obj":"Tax:2697049"},{"id":"A6","pred":"tao:has_database_id","subj":"6","obj":"MESH:C000657245"},{"id":"A7","pred":"tao:has_database_id","subj":"7","obj":"Tax:9606"},{"id":"A29","pred":"tao:has_database_id","subj":"29","obj":"Tax:1508227"},{"id":"A30","pred":"tao:has_database_id","subj":"30","obj":"Tax:2697049"},{"id":"A31","pred":"tao:has_database_id","subj":"31","obj":"Tax:2697049"}],"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":"[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].\nObjective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes."}