The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host.

A highly significant positive correlation of first two principal axes ( f1 and f2 ) with U% ( f1 = 0.411, f2 = 0.187; p < 0.0001), and negative correlation with A%( f1 = -0.149, f2 = -0.168; p < 0.0001) and C% ( f1 = -0.379, f2 = -0.111; p < 0.0001), indicates that compositional constraints (especially U and C nucleotides) affected the codon usage bias of the SARS-CoV-2 genome (Table S3).

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Contrary to nucleotide composition and ENC, the CAI values over time failed to reveal a clear trend.

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