Table 1. Codon usage bias between human ORFeome and polyprotein ORFs from HCoV-OC43 and SARS-CoV-2: a representative analysis of eight codons a b c .
| Aa | Codon | Homo sapiens |
HCoV-OC43
d
Isolate: 1987 |
HCoV-OC43
e
Isolate: 1990 |
HCoV-OC43
f
Isolate: 2011 |
SARS-CoV-2
g
Isolate: 2019 |
SARS-CoV-2
h
Isolate:2020 |
|---|---|---|---|---|---|---|---|
| Asp | GAT | 21.8 | 54.5 | 54.5 | 54.8 | 35.4 | 35.5 |
| Phe | TTT | 17.6 | 50.2 | 49.8 | 50.6 | 35.8 | 35.9 |
| Ile | ATT | 16.0 | 30.7 | 30.6 | 31.1 | 23.8 | 23.9 |
| Leu | TTG | 12.9 | 32.4 | 32.4 | 32.4 | 16.3 | 16.5 |
| Asn | AAT | 17.0 | 41.7 | 41.7 | 41.9 | 37.8 | 37.9 |
| Arg | CGT | 4.5 | 12.0 | 11.8 | 11.7 | 8.3 | 8.2 |
| Ser | AGT | 12.1 | 25.2 | 25.7 | 25.8 | 16.8 | 16.7 |
| Tyr | TAT | 12.2 | 45.5 | 45.5 | 45.9 | 29.3 | 29.2 |
Abbreviations: HCoV-OC43, human coronavirus OC43; ORF, open reading frame; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
a
Codon frequency expressed per thousand.
b
Codon usage of Homo sapiens obtained at www.kazusa.or.jp/codon. 10
c
Codon usage of polyprotein ORFs obtained at www.geneinfinity.org .
d
HCoV-OC43/human/USA/1987; GenBank: KF530083.1; ID = AGT51637.1; taxon:31631.
e
HCoV-OC43/human/USA/1990; GenBank: KF530088.1; ID = AGT51687.1; taxon:31631.
f
HCoV-OC43/UK/London/2011; GenBank: KU131570.1; ID = AMK59674.1; taxon:31631.
g
SARS-CoV-2/Wuhan-Hu-1/2019; GenBank:MN908947.3; ID = QHD43415.1; taxon:2697049.
h
SARS-CoV-2/UW239/2020/USA; GenBank: MT251975.1; ID = QIQ68493.1; taxon:2697049.