Natural Selection Determines Synonymous Codon Usage Patterns of Neuraminidase (NA) Gene of the Different Subtypes of Influenza A Virus in Canada

Table 1

Codon usage comparison between the four major subtypes found in Canada using RSCU values. Only the codons with some RSCU values >1.2 across the four subtypes are considered for comparison of codon usage preference. The largest RSCU value for each of these codons is marked in boldface to see the most preferred subtype.

Codons	H1N1	H3N2	H3N8	H4N6	Mixed
GCA	1.141	1.483	2.487	2.142	2.116
GCC	0.777	0.857	0.719	0.512	0.665
GCG	0.233	0.394	0.22	0.552	0.328
GCU	1.848	1.266	0.574	0.793	0.891
UGC	0.979	0.998	1.053	1.175	1.114
UGU	1.021	1.002	0.947	0.825	0.886
GAC	0.96	0.895	0.785	0.897	0.861
GAU	1.04	1.105	1.215	1.103	1.139
GAA	1.27	1.017	1.246	1.306	1.203
GAG	0.73	0.983	0.754	0.694	0.797
UUC	1.003	0.952	0.941	1.203	1.048
UUU	0.997	1.048	1.059	0.797	0.952
GGA	1.563	1.317	2.016	2.118	1.986
GGC	0.605	0.763	0.537	0.422	0.459
GGG	0.981	0.937	0.811	1.082	0.954
GGU	0.85	0.983	0.636	0.378	0.601
CAC	0.731	0.255	0.522	0.378	0.516
CAU	1.269	1.745	1.478	1.622	1.484
AUA	1.365	1.215	1.088	1.423	1.311
AUC	0.643	0.764	0.501	0.896	0.668
AUU	0.992	1.021	1.411	0.681	1.021
AAA	1.029	1.313	1.259	1.256	1.179
AAG	0.971	0.687	0.741	0.744	0.821
CUA	1.406	0.962	1.269	1.283	1.309
CUC	0.349	0.882	0.88	0.64	0.705
CUG	0.794	0.833	0.633	0.635	0.779
CUU	0.444	1.089	0.828	0.675	0.642
UUA	1.419	0.616	0.968	0.938	0.943
UUG	1.587	1.617	1.422	1.83	1.621
AUG	1	1	1	1	1
AAC	0.844	0.748	0.534	0.867	0.683
AAU	1.156	1.252	1.466	1.133	1.317
CCA	1.91	0.932	1.815	1.951	1.829
CCC	0.602	0.703	1.165	0.441	0.791
CCG	0.402	0.267	0.301	0.672	0.42
CCU	1.086	2.097	0.719	0.935	0.959
CAA	1.101	1.19	1.07	0.897	1.027
CAG	0.899	0.81	0.93	1.103	0.973
AGA	3.389	2.763	3.071	2.95	3.023
AGG	1.238	2.084	2.616	2.108	2.222
CGA	0.924	0.37	0.032	0.472	0.285
CGC	0.299	0.257	0.003	0.009	0.068
CGG	0.056	0.502	0.277	0.461	0.379
CGU	0.095	0.023	0.002	0	0.023
AGC	1.133	1.209	0.806	1.164	1.034
AGU	1.342	0.887	1.319	1.07	1.244
UCA	1.414	1.703	1.853	1.923	1.798
UCC	0.758	1.103	0.956	1.066	0.944
UCG	0.334	0.234	0.304	0.44	0.339
UCU	1.019	0.863	0.761	0.337	0.642
ACA	1.579	1.477	1.553	1.973	1.709
ACC	1.044	1.128	0.671	1.176	0.931
ACG	0.063	0.246	0.538	0.321	0.416
ACU	1.314	1.149	1.238	0.53	0.943
GUA	1.067	1.042	1.281	1.829	1.481
GUC	0.805	0.739	0.562	0.62	0.613
GUG	1.123	1.168	1.091	1.248	1.116
GUU	1.005	1.051	1.066	0.303	0.79
UGG	1	1	1	1	1
UAC	0.916	0.351	1.125	1.039	1.103
UAU	1.084	1.649	0.875	0.961	0.897