PMC:7258756 / 8767-9640 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7258756","sourcedb":"PMC","sourceid":"7258756","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7258756","text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1).","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"155","span":{"begin":867,"end":871},"obj":"Gene"},{"id":"156","span":{"begin":32,"end":42},"obj":"Species"},{"id":"157","span":{"begin":748,"end":758},"obj":"Species"},{"id":"158","span":{"begin":835,"end":845},"obj":"Species"},{"id":"159","span":{"begin":515,"end":517},"obj":"Chemical"}],"attributes":[{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Gene:6195"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"Tax:2697049"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"Tax:2697049"},{"id":"A158","pred":"tao:has_database_id","subj":"158","obj":"Tax:2697049"},{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"MESH:D009711"},{"subj":"155","pred":"source","obj":"LitCovid-PubTator"},{"subj":"156","pred":"source","obj":"LitCovid-PubTator"},{"subj":"157","pred":"source","obj":"LitCovid-PubTator"},{"subj":"158","pred":"source","obj":"LitCovid-PubTator"},{"subj":"159","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T38","span":{"begin":12,"end":18},"obj":"Body_part"},{"id":"T39","span":{"begin":503,"end":513},"obj":"Body_part"},{"id":"T40","span":{"begin":515,"end":517},"obj":"Body_part"},{"id":"T41","span":{"begin":615,"end":625},"obj":"Body_part"},{"id":"T42","span":{"begin":641,"end":651},"obj":"Body_part"},{"id":"T43","span":{"begin":653,"end":655},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma82739"},{"subj":"T38","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T39","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T40","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T42","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T43","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T83","span":{"begin":32,"end":40},"obj":"Disease"},{"id":"T84","span":{"begin":32,"end":36},"obj":"Disease"},{"id":"T85","span":{"begin":748,"end":756},"obj":"Disease"},{"id":"T86","span":{"begin":748,"end":752},"obj":"Disease"},{"id":"T87","span":{"begin":835,"end":843},"obj":"Disease"},{"id":"T88","span":{"begin":835,"end":839},"obj":"Disease"}],"attributes":[{"id":"A83","pred":"mondo_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A84","pred":"mondo_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A85","pred":"mondo_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A86","pred":"mondo_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A87","pred":"mondo_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A88","pred":"mondo_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T83","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T84","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T85","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T86","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T87","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T88","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T71","span":{"begin":400,"end":401},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T72","span":{"begin":606,"end":609},"obj":"http://purl.obolibrary.org/obo/CLO_0008190"},{"id":"T73","span":{"begin":653,"end":655},"obj":"http://purl.obolibrary.org/obo/CLO_0001627"},{"id":"T74","span":{"begin":759,"end":766},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"attributes":[{"subj":"T71","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T18","span":{"begin":274,"end":278},"obj":"Chemical"},{"id":"T19","span":{"begin":503,"end":513},"obj":"Chemical"},{"id":"T20","span":{"begin":515,"end":517},"obj":"Chemical"},{"id":"T21","span":{"begin":589,"end":593},"obj":"Chemical"},{"id":"T22","span":{"begin":615,"end":625},"obj":"Chemical"},{"id":"T23","span":{"begin":641,"end":651},"obj":"Chemical"},{"id":"T24","span":{"begin":641,"end":646},"obj":"Chemical"},{"id":"T25","span":{"begin":647,"end":651},"obj":"Chemical"},{"id":"T26","span":{"begin":653,"end":655},"obj":"Chemical"}],"attributes":[{"id":"A18","pred":"chebi_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A22","pred":"chebi_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"subj":"T18","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T19","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T20","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T22","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T23","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T24","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T25","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T26","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T70","span":{"begin":0,"end":221},"obj":"Sentence"},{"id":"T71","span":{"begin":222,"end":399},"obj":"Sentence"},{"id":"T72","span":{"begin":400,"end":605},"obj":"Sentence"},{"id":"T73","span":{"begin":606,"end":714},"obj":"Sentence"},{"id":"T74","span":{"begin":715,"end":873},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T70","pred":"source","obj":"LitCovid-sentences"},{"subj":"T71","pred":"source","obj":"LitCovid-sentences"},{"subj":"T72","pred":"source","obj":"LitCovid-sentences"},{"subj":"T73","pred":"source","obj":"LitCovid-sentences"},{"subj":"T74","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32242873-31565258-47036565","span":{"begin":83,"end":85},"obj":"31565258"},{"id":"32242873-27004904-47036566","span":{"begin":298,"end":301},"obj":"27004904"},{"id":"32242873-27004904-47036567","span":{"begin":602,"end":604},"obj":"27004904"},{"id":"32242873-27004904-47036568","span":{"begin":711,"end":713},"obj":"27004904"},{"id":"T62421","span":{"begin":83,"end":85},"obj":"31565258"},{"id":"T79581","span":{"begin":298,"end":301},"obj":"27004904"},{"id":"T13164","span":{"begin":602,"end":604},"obj":"27004904"},{"id":"T93390","span":{"begin":711,"end":713},"obj":"27004904"}],"attributes":[{"subj":"32242873-31565258-47036565","pred":"source","obj":"2_test"},{"subj":"32242873-27004904-47036566","pred":"source","obj":"2_test"},{"subj":"32242873-27004904-47036567","pred":"source","obj":"2_test"},{"subj":"32242873-27004904-47036568","pred":"source","obj":"2_test"},{"subj":"T62421","pred":"source","obj":"2_test"},{"subj":"T79581","pred":"source","obj":"2_test"},{"subj":"T13164","pred":"source","obj":"2_test"},{"subj":"T93390","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#93ecae","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#ec9493"},{"id":"LitCovid-PD-MONDO","color":"#93acec"},{"id":"LitCovid-PD-CLO","color":"#c6ec93"},{"id":"LitCovid-PD-CHEBI","color":"#ec93e0"},{"id":"LitCovid-sentences","color":"#93ecde"},{"id":"2_test","color":"#ecc493"}]}]}}