Table 3.

Codon-based Neutrality for each SARS-CoV-2 gene against study groups.

SARS-CoV-2 proteins	Molnupiravir	Paxlovid	Drug naive
nsp1	v = −1.4 p = 0.17	v = −0.2 p = 0.83	v = −0.7 p = 0.51
nsp2	v = −1.4 p = 0.18	v = −1.0 p = 0.30	v = −1.4 p = 0.17
nsp3	v = −1.4 p = 0.17	v = 0.2 p = 0.85	v = 1.8 p = 0.08
nsp4	v = −1.2 p = 0.22	v = −0.1 p = 0.94	v = 0.9 p = 0.14
Mpro (nsp5)	v = −0.6 p = 0.56	v = −1.4 p = 0.18	v = −0.7 p = 0.51
nsp6	v = −1.3 p = 0.21	v = −1.5 p = 0.13	v = 1.9 p = 0.07
nsp7	v = 1.1 p = 0.28	v = 0.0 p = 1.00	v = −0.7 p = 0.50
nsp8	v = −0.7 p = 0.50	v = −1.6 p = 0.12	v = 1.1 p = 0.29
nsp9	v = −2.2 p = 0.03	v = 0.0 p = 1.00	v = 1.1 p = 0.29
nsp10	v = −1.4 p = 0.18	v = −1.0 p = 0.30	v = 1.0 p = 0.30
nsp11	v = 0.0 p = 1.00	v = 0.0 p = 1.00	v = 0.0 p = 1.00
RdRp (nsp12)	v = −1.2 p = 0.24	v = −1.7 p = 0.09	v = 1.1 p = 0.29
nsp13	v = −1.6 p = 0.12	v = 0.9 p = 0.33	v = −0.7 p = 0.47
nsp14	v = −1.2 p = 0.23	v = −1.7 p = 0.10	v = −1.2 p = 0.24
nsp15	v = −2.0 p = 0.05	v = 1.5 p = 0.15	v = −1.1 p = 0.27
nsp16	v = −0.9 p = 0.39	v = −0.8 p = 0.41	v = −1.1 p = 0.29
S	V = −1.0 p = 0.33	v = −0.5 p = 0.66	v = 0.1 p = 0.96
orf2b	v = 0.5 p = 0.62	v = 1.1 p = 0.30	v = 0.0 p = 1.00
orf3a	v = 0.2 p = 0.81	v = −1.1 p = 0.30	v = −0.2 p = 0.84
orf3b	v = 0.0 p = 1.00	v = 1.0 p = 0.31	v = 1.0 p = 0.31
orf3c	v = −0.8 p = 0.41	v = −1.0 p = 0.34	v = −1.0 p = 0.34
orf3d	v = −1.0 p = 0.34	v = −1.0 p = 0.33	v = −0.9 p = 0.36
orf3d-2	v = −0.9 p = 0.36	v = −1.0 p = 0.33	v = −0.9 p = 0.36
E	v = −0.6 p = 0.56	v = 1.5 p = 0.14	v = 1.0 p = 0.33
M	v = −0.6 p = 0.58	v = 0.4 p = 0.71	v = 1.1 p = 0.29
orf6	v = 0.7 p = 0.49	v = −0.8 p = 0.41	v = 0.0 p = 1.00
orf7a	v = 1.1 p = 0.29	v = 1.0 p = 0.30	v = −1.1 p = 0.27
orf7b	v = 1.4 p = 0.16	v = −1.0 p = 0.33	v = 0.0 p = 1.00
orf8	v = 3.2 p = 0.001	v = −0.7 p = 0.51	v = 0.0 p = 1.00
orf9b	v = −1.4 p = 0.18	v = −0.5 p = 0.65	v = −0.4 p = 0.69
orf9c	v = −1.6 p = 0.12	v = 0.0 p = 1.00	v = −1.0 p = 0.32
N	v = −2.0 p = 0.05	v = −1.0 p = 0.32	v = 1.0 p = 0.34
orf10	v = 1.8 p = 0.07	v = −0.9 p = 0.35	v = 1.0 p = 0.32

Codon-based Test of Neutrality for each SARS-CoV-2 protein against study group. The test statistic (dN–dS) is reported as V, where dS and dN are the numbers of synonymous and non-synonymous substitutions per site, respectively. The variance of the difference was computed using the bootstrap method (500 replicates). The probability of rejecting the null hypothesis of strict-neutrality (dN = dS) is shown as P-values (P). P-values less than 0.05 are considered significant at the 5% level and are highlighted. Analyses were conducted using the Nei-Gojobori method. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Evolutionary analyses were conducted in MEGA11.