PMC:7405836 / 66297-67322 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T205","span":{"begin":259,"end":265},"obj":"Body_part"},{"id":"T206","span":{"begin":352,"end":362},"obj":"Body_part"},{"id":"T207","span":{"begin":404,"end":414},"obj":"Body_part"},{"id":"T208","span":{"begin":619,"end":621},"obj":"Body_part"},{"id":"T209","span":{"begin":639,"end":641},"obj":"Body_part"}],"attributes":[{"id":"A205","pred":"fma_id","subj":"T205","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A206","pred":"fma_id","subj":"T206","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A207","pred":"fma_id","subj":"T207","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A208","pred":"fma_id","subj":"T208","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A209","pred":"fma_id","subj":"T209","obj":"http://purl.org/sig/ont/fma/fma82740"}],"text":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T618","span":{"begin":741,"end":749},"obj":"Disease"},{"id":"T619","span":{"begin":741,"end":745},"obj":"Disease"},{"id":"T620","span":{"begin":815,"end":823},"obj":"Disease"},{"id":"T621","span":{"begin":815,"end":819},"obj":"Disease"},{"id":"T622","span":{"begin":1008,"end":1016},"obj":"Disease"},{"id":"T623","span":{"begin":1008,"end":1012},"obj":"Disease"}],"attributes":[{"id":"A618","pred":"mondo_id","subj":"T618","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A619","pred":"mondo_id","subj":"T619","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A620","pred":"mondo_id","subj":"T620","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A621","pred":"mondo_id","subj":"T621","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A622","pred":"mondo_id","subj":"T622","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A623","pred":"mondo_id","subj":"T623","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T673","span":{"begin":529,"end":533},"obj":"http://purl.obolibrary.org/obo/CLO_0007486"},{"id":"T674","span":{"begin":715,"end":716},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T97092","span":{"begin":352,"end":362},"obj":"Chemical"},{"id":"T55801","span":{"begin":404,"end":414},"obj":"Chemical"},{"id":"T94039","span":{"begin":404,"end":409},"obj":"Chemical"},{"id":"T11522","span":{"begin":410,"end":414},"obj":"Chemical"}],"attributes":[{"id":"A81191","pred":"chebi_id","subj":"T97092","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A11693","pred":"chebi_id","subj":"T55801","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A244","pred":"chebi_id","subj":"T94039","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A10684","pred":"chebi_id","subj":"T11522","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"}],"text":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T475","span":{"begin":0,"end":272},"obj":"Sentence"},{"id":"T476","span":{"begin":273,"end":421},"obj":"Sentence"},{"id":"T477","span":{"begin":422,"end":549},"obj":"Sentence"},{"id":"T478","span":{"begin":550,"end":679},"obj":"Sentence"},{"id":"T479","span":{"begin":680,"end":810},"obj":"Sentence"},{"id":"T480","span":{"begin":811,"end":1025},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2030","span":{"begin":539,"end":540},"obj":"Gene"},{"id":"2031","span":{"begin":522,"end":523},"obj":"Gene"},{"id":"2032","span":{"begin":529,"end":530},"obj":"Gene"},{"id":"2033","span":{"begin":629,"end":633},"obj":"Gene"},{"id":"2034","span":{"begin":52,"end":57},"obj":"Species"},{"id":"2035","span":{"begin":741,"end":751},"obj":"Species"},{"id":"2036","span":{"begin":815,"end":825},"obj":"Species"},{"id":"2037","span":{"begin":1008,"end":1018},"obj":"Species"}],"attributes":[{"id":"A2030","pred":"tao:has_database_id","subj":"2030","obj":"Gene:43740575"},{"id":"A2031","pred":"tao:has_database_id","subj":"2031","obj":"Gene:43740568"},{"id":"A2032","pred":"tao:has_database_id","subj":"2032","obj":"Gene:43740571"},{"id":"A2033","pred":"tao:has_database_id","subj":"2033","obj":"Gene:43740577"},{"id":"A2034","pred":"tao:has_database_id","subj":"2034","obj":"Tax:2697049"},{"id":"A2035","pred":"tao:has_database_id","subj":"2035","obj":"Tax:2697049"},{"id":"A2036","pred":"tao:has_database_id","subj":"2036","obj":"Tax:2697049"},{"id":"A2037","pred":"tao:has_database_id","subj":"2037","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":"Recently, 95 full-length genomic sequences of SARAS-CoV-2 strains available in the National Center for Biotechnology Information and GISAID databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome (260). All the viral strains revealed high homology of 99.99% (99.91% to 100%) at the nucleotide level and 99.99% (99.79% to 100%) at the amino acid level. Overall variation was found to be low in ORF regions, with 13 variation sites recognized in 1a, 1b, S, 3a, M, 8, and N regions. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at nt 28144 (ORF8) and nt 8782 (ORF1a) positions, respectively. Owing to such selective mutations, a few specific regions of SARS-CoV-2 should not be considered for designing primers and probes. The SARS-CoV-2 reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering SARS-CoV-2 (260)."}