Table 5.
SS4 clusters and additional mutations. On the bottom left column, the absolute harbored SS4 genomes number by countries are shown. On the top, additional mutations, their genomic positions, the effect on protein translation and the affected codons are reported.
| SS4 signature C241T, C3037T, A23403G | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Additional mutations bp position | 14408 | 28881 | 28882 | 28883 | 25563 | 1059 | 27046 | 20268 | 15324 | 26530 | 10323 | 29734 | 24862 | 2416 | 12832 | 23731 | 187 | 24077 | 10097 | 25688 | 6446 | 12790 | 13568 | |
| ancestral/mutate | C/T | G/A | G/A | G/C | G/T | C/T | C/T | A/G | C/T | A/G | A/G | G/C | A/G | C/T | G/A | C/T | A/G | G/T | G/A | C/T | G/A | A/G | C/T | |
| AA change | P > L | RG > KR | Q > H | T > I | T > M | / | / | D > G | K > R | / | / | / | / | / | / | D > Y | G > S | A > V | V > I | / | A > V | |||
| gene | ORF1ab | N | ORF3a | ORF1ab | M | ORF1ab | ORF1ab | M | ORF1ab | 3’utr | S | ORF1ab | ORF1ab | S | 5’utr | S | ORF1ab | ORF3a | ORF1ab | ORF1ab | ORF1ab | |||
| product | nsp12 | nucleocaps. | orf3a | nsp2 | memb | / | / | memb | nsp5a | / | / | / | / | / | / | spike | nsp5 | orf3a | nsp3 | nsp9 | nsp12 | |||
| Codon number | 4715 | 203–204 | 57 | 265 | 175 | / | / | 3 | 3353 | / | / | / | / | / | / | 839 | 3278 | 99 | 2061 | / | 4435 | |||
| Country | SS4 | |||||||||||||||||||||||
| AT | 150 | 150 | 70 | 70 | 70 | 50 | 49 | 19 | 14 | 1 | 0 | 0 | 5 | 3 | 0 | 41 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| BE | 151 | 151 | 62 | 62 | 62 | 19 | 12 | 17 | 1 | 28 | 16 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 |
| BA | 10 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| HR | 3 | 3 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 0 |
| CZ | 2 | 2 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| DK | 241 | 240 | 21 | 21 | 21 | 190 | 188 | 8 | 7 | 0 | 0 | 0 | 3 | 4 | 0 | 0 | 3 | 1 | 0 | 3 | 0 | 0 | 0 | 0 |
| FI | 17 | 17 | 3 | 3 | 3 | 8 | 2 | 3 | 2 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| FR | 180 | 180 | 11 | 11 | 11 | 101 | 65 | 2 | 1 | 61 | 0 | 1 | 0 | 0 | 28 | 0 | 0 | 2 | 0 | 0 | 7 | 0 | 0 | 0 |
| DE | 78 | 63 | 29 | 29 | 29 | 25 | 25 | 11 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 10 | 0 | 0 |
| GR | 54 | 53 | 44 | 44 | 44 | 6 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| HU | 12 | 12 | 6 | 6 | 6 | 2 | 2 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| IS | 256 | 256 | 76 | 76 | 76 | 53 | 52 | 42 | 68 | 5 | 15 | 58 | 3 | 8 | 1 | 0 | 6 | 5 | 4 | 6 | 3 | 0 | 0 | 0 |
| IE | 7 | 7 | 5 | 5 | 5 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| IT | 100 | 100 | 40 | 40 | 40 | 1 | 0 | 3 | 5 | 0 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 1 | 0 | 0 | 0 | 0 | 0 |
| LV | 3 | 3 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| LT | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| LU | 64 | 64 | 2 | 2 | 2 | 25 | 25 | 0 | 2 | 17 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 9 | 0 | 0 | 12 | 0 | 0 | 0 |
| NL | 217 | 217 | 79 | 79 | 79 | 35 | 33 | 62 | 15 | 1 | 5 | 0 | 13 | 28 | 0 | 0 | 2 | 5 | 5 | 2 | 8 | 0 | 0 | 0 |
| NO | 13 | 13 | 2 | 2 | 2 | 5 | 5 | 0 | 1 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| PL | 6 | 6 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| PT | 143 | 143 | 77 | 77 | 77 | 7 | 3 | 3 | 11 | 1 | 3 | 1 | 3 | 0 | 2 | 0 | 4 | 0 | 25 | 4 | 1 | 0 | 0 | 0 |
| RU | 35 | 35 | 17 | 17 | 17 | 7 | 6 | 6 | 1 | 1 | 4 | 0 | 0 | 0 | 1 | 0 | 3 | 1 | 0 | 3 | 0 | 0 | 0 | 0 |
| SK | 3 | 3 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| SI | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ES | 121 | 118 | 15 | 15 | 15 | 5 | 5 | 0 | 84 | 0 | 0 | 0 | 25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| SE | 223 | 223 | 106 | 106 | 106 | 37 | 33 | 42 | 1 | 0 | 10 | 0 | 0 | 0 | 4 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 18 | 18 |
| CH | 75 | 75 | 31 | 31 | 31 | 5 | 5 | 0 | 5 | 25 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| TR | 3 | 3 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| UK | 256 | 256 | 100 | 100 | 100 | 21 | 19 | 20 | 15 | 2 | 4 | 0 | 4 | 0 | 5 | 0 | 18 | 5 | 4 | 16 | 0 | 0 | 0 | 0 |
| Tot | 2425 | 2405 | 801 | 801 | 801 | 608 | 531 | 241 | 239 | 146 | 81 | 60 | 58 | 47 | 45 | 41 | 40 | 39 | 39 | 38 | 35 | 10 | 18 | 18 |