| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T1 |
0-121 |
DRI_Outcome |
denotes |
From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. |
| T2 |
122-238 |
DRI_Challenge |
denotes |
BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. |
| T3 |
239-537 |
DRI_Challenge |
denotes |
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. |
| T4 |
538-980 |
DRI_Approach |
denotes |
METHODS: 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. |
| T5 |
981-1043 |
DRI_Background |
denotes |
RESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. |
| T6 |
1044-1269 |
DRI_Outcome |
denotes |
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. |
| T7 |
1270-1373 |
DRI_Background |
denotes |
This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. |
| T8 |
1374-1456 |
DRI_Outcome |
denotes |
SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. |
| T9 |
1457-1572 |
DRI_Outcome |
denotes |
Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV. |
| T10 |
1573-1779 |
DRI_Challenge |
denotes |
CONCLUSION: 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. |
