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In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

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SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-ArguminSci","denotations":[{"id":"T1","span":{"begin":0,"end":121},"obj":"DRI_Outcome"},{"id":"T2","span":{"begin":122,"end":238},"obj":"DRI_Challenge"},{"id":"T3","span":{"begin":239,"end":537},"obj":"DRI_Challenge"},{"id":"T4","span":{"begin":538,"end":980},"obj":"DRI_Approach"},{"id":"T5","span":{"begin":981,"end":1043},"obj":"DRI_Background"},{"id":"T6","span":{"begin":1044,"end":1269},"obj":"DRI_Outcome"},{"id":"T7","span":{"begin":1270,"end":1373},"obj":"DRI_Background"},{"id":"T8","span":{"begin":1374,"end":1456},"obj":"DRI_Outcome"},{"id":"T9","span":{"begin":1457,"end":1572},"obj":"DRI_Outcome"},{"id":"T10","span":{"begin":1573,"end":1779},"obj":"DRI_Challenge"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-OGER","denotations":[{"id":"T1","span":{"begin":1312,"end":1327},"obj":"GO:0010467"},{"id":"T2","span":{"begin":1707,"end":1722},"obj":"GO:0010467"},{"id":"T1","span":{"begin":80,"end":85},"obj":"GO:0019012"},{"id":"T2","span":{"begin":739,"end":747},"obj":"GO:0031975"},{"id":"T3","span":{"begin":753,"end":761},"obj":"GO:0016020"},{"id":"T4","span":{"begin":771,"end":783},"obj":"GO:0019013"},{"id":"T5","span":{"begin":1655,"end":1663},"obj":"GO:0031975"},{"id":"T1","span":{"begin":5,"end":9},"obj":"PR:000014459"},{"id":"T2","span":{"begin":27,"end":31},"obj":"PR:000014459"},{"id":"T3","span":{"begin":183,"end":187},"obj":"PR:000014459"},{"id":"T4","span":{"begin":278,"end":281},"obj":"PR:P34288;PR:P09124"},{"id":"T5","span":{"begin":379,"end":383},"obj":"PR:000014459"},{"id":"T6","span":{"begin":409,"end":413},"obj":"PR:000014459"},{"id":"T7","span":{"begin":474,"end":478},"obj":"PR:000014459"},{"id":"T8","span":{"begin":913,"end":917},"obj":"PR:000014459"},{"id":"T9","span":{"begin":954,"end":958},"obj":"PR:000014459"},{"id":"T10","span":{"begin":970,"end":974},"obj":"PR:000014459"},{"id":"T11","span":{"begin":990,"end":994},"obj":"PR:000014459"},{"id":"T12","span":{"begin":1161,"end":1165},"obj":"PR:000014459"},{"id":"T13","span":{"begin":1239,"end":1243},"obj":"PR:000014459"},{"id":"T14","span":{"begin":1249,"end":1253},"obj":"PR:000014459"},{"id":"T15","span":{"begin":1342,"end":1346},"obj":"PR:000014459"},{"id":"T16","span":{"begin":1374,"end":1378},"obj":"PR:000014459"},{"id":"T17","span":{"begin":1506,"end":1510},"obj":"PR:000014459"},{"id":"T18","span":{"begin":1543,"end":1547},"obj":"PR:000014459"},{"id":"T19","span":{"begin":1553,"end":1557},"obj":"PR:000014459"},{"id":"T20","span":{"begin":1622,"end":1626},"obj":"PR:000014459"},{"id":"T21","span":{"begin":1749,"end":1753},"obj":"PR:000014459"},{"id":"T22","span":{"begin":1759,"end":1763},"obj":"PR:000014459"},{"id":"T1","span":{"begin":65,"end":70},"obj":"SO:0000360"},{"id":"T2","span":{"begin":115,"end":120},"obj":"SO:0000704"},{"id":"T3","span":{"begin":278,"end":281},"obj":"SO:0000730"},{"id":"T4","span":{"begin":297,"end":299},"obj":"SO:0000999"},{"id":"T5","span":{"begin":551,"end":557},"obj":"SO:0001026"},{"id":"T6","span":{"begin":592,"end":597},"obj":"SO:0000360"},{"id":"T7","span":{"begin":622,"end":639},"obj":"SO:0001819"},{"id":"T8","span":{"begin":671,"end":677},"obj":"SO:0000360"},{"id":"T9","span":{"begin":721,"end":726},"obj":"SO:0000704"},{"id":"T10","span":{"begin":788,"end":793},"obj":"SO:0000704"},{"id":"T11","span":{"begin":839,"end":844},"obj":"SO:0000704"},{"id":"T12","span":{"begin":1025,"end":1031},"obj":"SO:0000360"},{"id":"T13","span":{"begin":1064,"end":1070},"obj":"SO:0000360"},{"id":"T14","span":{"begin":1124,"end":1128},"obj":"SO:0001653"},{"id":"T15","span":{"begin":1129,"end":1135},"obj":"SO:0000360"},{"id":"T16","span":{"begin":1290,"end":1295},"obj":"SO:0000360"},{"id":"T17","span":{"begin":1312,"end":1316},"obj":"SO:0000704"},{"id":"T18","span":{"begin":1449,"end":1455},"obj":"SO:0000360"},{"id":"T19","span":{"begin":1674,"end":1679},"obj":"SO:0000704"},{"id":"T20","span":{"begin":1681,"end":1684},"obj":"SO:0001853"},{"id":"T21","span":{"begin":1707,"end":1711},"obj":"SO:0000704"}],"namespaces":[{"prefix":"PR","uri":"http://purl.obolibrary.org/obo/PR_"},{"prefix":"UBERON","uri":"http://purl.obolibrary.org/obo/UBERON_"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-PubTatorCentral","denotations":[{"id":"T1","span":{"begin":14,"end":18},"obj":"Species:1335626"},{"id":"T2","span":{"begin":483,"end":521},"obj":"Species:1335626"},{"id":"T3","span":{"begin":960,"end":964},"obj":"Species:1335626"},{"id":"T4","span":{"begin":1259,"end":1263},"obj":"Species:1335626"},{"id":"T5","span":{"begin":1563,"end":1571},"obj":"Species:1335626"},{"id":"T6","span":{"begin":1769,"end":1773},"obj":"Species:1335626"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-sentences-v1","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":38},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":39,"end":121},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":122,"end":133},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":134,"end":238},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":239,"end":537},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":538,"end":546},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":547,"end":980},"obj":"Sentence"},{"id":"TextSentencer_T8","span":{"begin":981,"end":1043},"obj":"Sentence"},{"id":"TextSentencer_T9","span":{"begin":1044,"end":1160},"obj":"Sentence"},{"id":"TextSentencer_T10","span":{"begin":1161,"end":1269},"obj":"Sentence"},{"id":"TextSentencer_T11","span":{"begin":1270,"end":1373},"obj":"Sentence"},{"id":"TextSentencer_T12","span":{"begin":1374,"end":1456},"obj":"Sentence"},{"id":"TextSentencer_T13","span":{"begin":1457,"end":1572},"obj":"Sentence"},{"id":"TextSentencer_T14","span":{"begin":1573,"end":1584},"obj":"Sentence"},{"id":"TextSentencer_T15","span":{"begin":1585,"end":1779},"obj":"Sentence"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-PD-MONDO-v1","denotations":[{"id":"T1","span":{"begin":5,"end":9},"obj":"Disease"},{"id":"T2","span":{"begin":27,"end":35},"obj":"Disease"},{"id":"T3","span":{"begin":134,"end":181},"obj":"Disease"},{"id":"T4","span":{"begin":183,"end":191},"obj":"Disease"},{"id":"T5","span":{"begin":379,"end":387},"obj":"Disease"},{"id":"T6","span":{"begin":409,"end":417},"obj":"Disease"},{"id":"T7","span":{"begin":474,"end":478},"obj":"Disease"},{"id":"T8","span":{"begin":913,"end":921},"obj":"Disease"},{"id":"T9","span":{"begin":954,"end":958},"obj":"Disease"},{"id":"T10","span":{"begin":970,"end":974},"obj":"Disease"},{"id":"T11","span":{"begin":990,"end":998},"obj":"Disease"},{"id":"T12","span":{"begin":1161,"end":1169},"obj":"Disease"},{"id":"T13","span":{"begin":1239,"end":1243},"obj":"Disease"},{"id":"T14","span":{"begin":1249,"end":1253},"obj":"Disease"},{"id":"T15","span":{"begin":1342,"end":1350},"obj":"Disease"},{"id":"T16","span":{"begin":1374,"end":1382},"obj":"Disease"},{"id":"T17","span":{"begin":1506,"end":1514},"obj":"Disease"},{"id":"T18","span":{"begin":1543,"end":1547},"obj":"Disease"},{"id":"T19","span":{"begin":1553,"end":1557},"obj":"Disease"},{"id":"T20","span":{"begin":1622,"end":1630},"obj":"Disease"},{"id":"T21","span":{"begin":1749,"end":1753},"obj":"Disease"},{"id":"T22","span":{"begin":1759,"end":1763},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

{"project":"LitCovid-PD-FMA-UBERON-v1","denotations":[{"id":"T1","span":{"begin":551,"end":557},"obj":"Body_part"},{"id":"T2","span":{"begin":571,"end":581},"obj":"Body_part"},{"id":"T3","span":{"begin":710,"end":726},"obj":"Body_part"},{"id":"T4","span":{"begin":856,"end":859},"obj":"Body_part"},{"id":"T5","span":{"begin":870,"end":873},"obj":"Body_part"},{"id":"T6","span":{"begin":1009,"end":1019},"obj":"Body_part"},{"id":"T7","span":{"begin":1035,"end":1042},"obj":"Body_part"},{"id":"T8","span":{"begin":1183,"end":1191},"obj":"Body_part"},{"id":"T9","span":{"begin":1312,"end":1316},"obj":"Body_part"},{"id":"T10","span":{"begin":1364,"end":1372},"obj":"Body_part"},{"id":"T11","span":{"begin":1707,"end":1711},"obj":"Body_part"}],"attributes":[{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma82772"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma82773"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.\nBACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses.\nMETHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs.\nRESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV.\nCONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs."}

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