PMC:7519301 / 7257-8661 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T26","span":{"begin":513,"end":519},"obj":"Body_part"},{"id":"T27","span":{"begin":796,"end":803},"obj":"Body_part"},{"id":"T28","span":{"begin":986,"end":994},"obj":"Body_part"},{"id":"T29","span":{"begin":1081,"end":1089},"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/fma67257"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T66","span":{"begin":647,"end":656},"obj":"Disease"},{"id":"T67","span":{"begin":679,"end":684},"obj":"Disease"},{"id":"T68","span":{"begin":820,"end":828},"obj":"Disease"},{"id":"T69","span":{"begin":820,"end":824},"obj":"Disease"},{"id":"T70","span":{"begin":1166,"end":1174},"obj":"Disease"},{"id":"T71","span":{"begin":1166,"end":1170},"obj":"Disease"},{"id":"T72","span":{"begin":1220,"end":1228},"obj":"Disease"},{"id":"T73","span":{"begin":1220,"end":1224},"obj":"Disease"}],"attributes":[{"id":"A66","pred":"mondo_id","subj":"T66","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005737"},{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A73","pred":"mondo_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T73","span":{"begin":38,"end":43},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T74","span":{"begin":55,"end":61},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T75","span":{"begin":228,"end":229},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T76","span":{"begin":291,"end":296},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T77","span":{"begin":387,"end":388},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T78","span":{"begin":439,"end":440},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T79","span":{"begin":690,"end":697},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T80","span":{"begin":727,"end":728},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T81","span":{"begin":729,"end":734},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T82","span":{"begin":888,"end":893},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T83","span":{"begin":910,"end":916},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T84","span":{"begin":1195,"end":1201},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"}],"text":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T24","span":{"begin":796,"end":803},"obj":"Chemical"},{"id":"T25","span":{"begin":986,"end":994},"obj":"Chemical"},{"id":"T26","span":{"begin":1081,"end":1089},"obj":"Chemical"}],"attributes":[{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}

{"project":"LitCovid-PubTator","denotations":[{"id":"165","span":{"begin":845,"end":846},"obj":"Gene"},{"id":"166","span":{"begin":55,"end":61},"obj":"Species"},{"id":"167","span":{"begin":679,"end":684},"obj":"Species"},{"id":"168","span":{"begin":820,"end":830},"obj":"Species"},{"id":"169","span":{"begin":910,"end":916},"obj":"Species"},{"id":"170","span":{"begin":1166,"end":1176},"obj":"Species"},{"id":"171","span":{"begin":1195,"end":1201},"obj":"Species"},{"id":"172","span":{"begin":1220,"end":1230},"obj":"Species"},{"id":"173","span":{"begin":647,"end":656},"obj":"Species"},{"id":"174","span":{"begin":181,"end":189},"obj":"Disease"},{"id":"175","span":{"begin":240,"end":253},"obj":"Disease"},{"id":"176","span":{"begin":270,"end":283},"obj":"Disease"},{"id":"177","span":{"begin":873,"end":880},"obj":"Disease"}],"attributes":[{"id":"A165","pred":"tao:has_database_id","subj":"165","obj":"Gene:43740568"},{"id":"A166","pred":"tao:has_database_id","subj":"166","obj":"Tax:9606"},{"id":"A167","pred":"tao:has_database_id","subj":"167","obj":"Tax:1570291"},{"id":"A168","pred":"tao:has_database_id","subj":"168","obj":"Tax:2697049"},{"id":"A169","pred":"tao:has_database_id","subj":"169","obj":"Tax:9606"},{"id":"A170","pred":"tao:has_database_id","subj":"170","obj":"Tax:2697049"},{"id":"A171","pred":"tao:has_database_id","subj":"171","obj":"Tax:9606"},{"id":"A172","pred":"tao:has_database_id","subj":"172","obj":"Tax:2697049"},{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Tax:11309"},{"id":"A174","pred":"tao:has_database_id","subj":"174","obj":"MESH:D007239"},{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"MESH:D012640"}],"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":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}

{"project":"LitCovid-sentences","denotations":[{"id":"T46","span":{"begin":0,"end":62},"obj":"Sentence"},{"id":"T47","span":{"begin":63,"end":190},"obj":"Sentence"},{"id":"T48","span":{"begin":191,"end":254},"obj":"Sentence"},{"id":"T49","span":{"begin":255,"end":520},"obj":"Sentence"},{"id":"T50","span":{"begin":521,"end":698},"obj":"Sentence"},{"id":"T51","span":{"begin":699,"end":804},"obj":"Sentence"},{"id":"T52","span":{"begin":805,"end":917},"obj":"Sentence"},{"id":"T53","span":{"begin":918,"end":1202},"obj":"Sentence"},{"id":"T54","span":{"begin":1203,"end":1404},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"New mutations will be observed as the virus spreads in humans. The viral evolutionary dynamics can be characterized by analyzing viral sequences sampled from individuals who became infected. The accumulation of mutations can be a marker of viral fitness: An increase in viral fitness as the virus adapts to its host will be associated with pervasive mutations at specific sites, whereas a neutral evolution context will be associated with a minimal number of fixed mutations distributed stochastically across the genome. Indicators of viral evolution have been shown to be robust predictors of transmission dynamics for several pathogens, such as influenza (19), Lassa (20), and Ebola (21) viruses. Typically, the evolution of a virus is driven by genotypic and phenotypic changes in its surface protein. In the case of SARS-CoV-2, mutations in S are most likely to confer fitness to the virus as it adapts to humans. However, adaptive changes can occur in structural and nonstructural proteins, and these changes, as well as different patterns across structural and nonstructural proteins, may provide insights into the near- and long-term evolutionary dynamics of SARS-CoV-2, as it spreads in humans. Here we analyzed SARS-CoV-2 sequences sampled since the beginning of the pandemic and found that mutations were rare, indicating that potential vaccine candidates should cover all circulating variants."}