There are 3 mutations in the Spike region.
| msa_position | p | q | ref_position | ref_seq | type | gene | start | end | protein_id | feature_position | feature_position_mod3 | triplet_start | triplet_end | ref_triplet | mut_triplet | ref_position_inProtein | ref_AA | ref_AAPosition | mut_AA | ref_freq | mut_freq | mut_seq | CHR | |
| 3654 | 36985 | 0.00453724672342917 | 0.0019392834243773 | 23730 | C | CDS | S | 21563 | 25384 | YP_009724390.1 | 2169 | 0 | 23728 | 23730 | ACC | ACT | 7910 | T | T723 | T | 40314 | 1381 | T | 1 |
| 3655 | 37185 | 0 | 0 | 23928 | C | CDS | S | 21563 | 25384 | YP_009724390.1 | 2367 | 0 | 23926 | 23928 | TAC | TAT | 7976 | Y | Y789 | Y | 41149 | 530 | T | 1 |
| 3653 | 36626 | 1.98774342659889E-68 | 4.81792614569765E-68 | 23402 | A | CDS | S | 21563 | 25384 | YP_009724390.1 | 1841 | 2 | 23401 | 23403 | GAT | GGT | 7801 | D | D614 | G | 11231 | 30413 | G | 1 |
| ef_triplet | mut_triplet | ref_position_inProtein | ref_AA | ref_AAPosition | mut_AA | ref_freq | mut_freq |
| GAT | GGT | 7801 | D | D614 | G | 11231 | 30413 | G |
| ACC | ACT | 7910 | T | T723 | T | 40314 | 1381 | T |
| TAC | TAT | 7976 | Y | Y789 | Y | 41149 | 530 |
Are synonymous codon adaptation in play?
In bat, ACT > ACC, in human, ACC > ACT, so T723T from ACC -> ACT change from human major codon to human minor codon.
In human, TAT > TAC, so Y789Y change from human major codon to minor codon.
So, the answer seems to be NO.
Bat virus codon usage versus human codon bias usage
West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=249584
West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)
fields: [triplet] [frequency: per thousand] ([number])
UUU 18.9( 28) UCU 29.8( 44) UAU 22.3( 33) UGU 12.9( 19) UUC 21.0( 31) UCC 18.9( 28) UAC 18.3( 27) UGC 8.8( 13) UUA 10.8( 16) UCA 18.9( 28) UAA 0.7( 1) UGA 1.4( 2) UUG 20.3( 30) UCG 4.1( 6) UAG 0.7( 1) UGG 12.9( 19) CUU 14.2( 21) CCU 18.3( 27) CAU 12.9( 19) CGU 3.4( 5) CUC 12.9( 19) CCC 13.5( 20) CAC 16.2( 24) CGC 1.4( 2) CUA 8.8( 13) CCA 14.2( 21) CAA 16.9( 25) CGA 2.7( 4) CUG 16.2( 24) CCG 2.7( 4) CAG 10.1( 15) CGG 1.4( 2) AUU 16.2( 24) ACU 15.6( 23) AAU 26.4( 39) AGU 16.2( 24) AUC 27.1( 40) ACC 12.2( 18) AAC 17.6( 26) AGC 6.8( 10) AUA 18.3( 27) ACA 22.3( 33) AAA 23.7( 35) AGA 29.8( 44) AUG 23.7( 35) ACG 3.4( 5) AAG 35.2( 52) AGG 17.6( 26) GUU 17.6( 26) GCU 15.6( 23) GAU 37.9( 56) GGU 10.1( 15) GUC 18.9( 28) GCC 13.5( 20) GAC 23.0( 34) GGC 6.1( 9) GUA 9.5( 14) GCA 14.2( 21) GAA 38.6( 57) GGA 21.7( 32) GUG 21.0( 31) GCG 2.0( 3) GAG 32.5( 48) GGG 19.6( 29)
Coding GC 43.96% 1st letter GC 46.75% 2nd letter GC 39.17% 3rd letter GC 45.94%
homo sapiens
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606
Homo sapiens [gbpri]: 93487 CDS's (40662582 codons)
fields: [triplet] [frequency: per thousand] ([number])
UUU 17.6(714298) UCU 15.2(618711) UAU 12.2(495699) UGU 10.6(430311) UUC 20.3(824692) UCC 17.7(718892) UAC 15.3(622407) UGC 12.6(513028) UUA 7.7(311881) UCA 12.2(496448) UAA 1.0( 40285) UGA 1.6( 63237) UUG 12.9(525688) UCG 4.4(179419) UAG 0.8( 32109) UGG 13.2(535595) CUU 13.2(536515) CCU 17.5(713233) CAU 10.9(441711) CGU 4.5(184609) CUC 19.6(796638) CCC 19.8(804620) CAC 15.1(613713) CGC 10.4(423516) CUA 7.2(290751) CCA 16.9(688038) CAA 12.3(501911) CGA 6.2(250760) CUG 39.6(1611801) CCG 6.9(281570) CAG 34.2(1391973) CGG 11.4(464485) AUU 16.0(650473) ACU 13.1(533609) AAU 17.0(689701) AGU 12.1(493429) AUC 20.8(846466) ACC 18.9(768147) AAC 19.1(776603) AGC 19.5(791383) AUA 7.5(304565) ACA 15.1(614523) AAA 24.4(993621) AGA 12.2(494682) AUG 22.0(896005) ACG 6.1(246105) AAG 31.9(1295568) AGG 12.0(486463) GUU 11.0(448607) GCU 18.4(750096) GAU 21.8(885429) GGU 10.8(437126) GUC 14.5(588138) GCC 27.7(1127679) GAC 25.1(1020595) GGC 22.2(903565) GUA 7.1(287712) GCA 15.8(643471) GAA 29.0(1177632) GGA 16.5(669873) GUG 28.1(1143534) GCG 7.4(299495) GAG 39.6(1609975) GGG 16.5(669768)
Coding GC 52.27% 1st letter GC 55.72% 2nd letter GC 42.54% 3rd letter GC 58.55%
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