Table 2.

Amino acid variants with significantly positive fitness effects in the post-2020-09 data.

Variant	MLE	95% CI	Frequency
nsp3 K384N	1.057	1.05–1.07	0.016
nsp3 T1189I	1.057	1.03–1.06	0.012
nsp3 G1300D	1.052	1.05–1.07	0.023
nsp4 T429I	1.093	1.04–1.13	0.019
nsp13 Q88H	1.077	1.04–1.14	0.012
nsp14 V381L	1.06	1.05–1.07	0.014
S E484K	1.117	1.10–1.15	0.016
S N501T	1.091	1.07–1.13	0.011
S N501Y	1.090	1.05–1.11	0.026
S Q677H	1.026	1.02–1.04	0.054
S P681H	1.069	1.04–1.09	0.095
ORF3a T151I	1.074	1.07–1.11	0.015
ORF3a D155Y	1.053	1.04–1.06	0.018
ORF3a T223I	1.053	1.04–1.06	0.033
ORF3a E226G	1.124	1.12–1.15	0.014
ORF9 D3L	1.068	1.03–1.08	0.015
ORF9 P207S	1.063	1.05–1.07	0.015
ORF9 M234I	1.063	1.03–1.086	0.054
ORF9 E378Q	1.055	1.05–1.08	0.012