Table 2.
Sites with non-synonymous substitution frequency over 20 or synonymous substitution frequency over 200.
| Gene | Substitutions | AA change | Changes in properties of aa | Frequency/Proportion | Sampling date |
|---|---|---|---|---|---|
| ORF1ab | T225A | D75E | No | 29/0.89 % | 2020-01-21 to 2020-03-25 |
| C794T* | T265I | (polar, none-charge) to (non-polar) | 464/14.32 % | 2020-02-21 to 2020-03-31 | |
| G1132A | V378I | No | 73/2.25 % | 2020-01-18 to 2020-03-30 | |
| G1175A | G392D | (polar, none-charge) to (polar, negative-charge) | 68/2.10 % | 2020-02-25 to 2020-03-31 | |
| A2215G | I739V | No | 77/2.38 % | 2020-02-09 to 2020-03-29 | |
| C2293T | P765S | (non-polar) to (polar, none-charge) | 91/2.81 % | 2020-02-09 to 2020-03-29 | |
| G2626A | A876T | (non-polar) to (polar, none-charge) | 65/2.00 % | 2020-02-25 to 2020-03-31 | |
| C2772T* | No | No | 1719/53.06 % | 2020-01-28 to 2020-04-01 | |
| C2912T | P971L | No | 30/0.93 % | 2020-01-28 to 2020-03-25 | |
| C8517T* | No | No | 660/20.37 % | 2020-01-05 to 2020-03-26 | |
| T9212A | F3071Y | (non-polar) to (polar, none-charge) | 49/1,51 % | 2020-02-01 to 2020-03-23 | |
| G9832A | G3278S | No | 26/0.80 % | 2020-03-02 to 2020-03-29 | |
| A10058G | K3353R | No | 44/1.36 % | 2020-01-30 to 2020-03-21 | |
| G10818T* | L3606F | No | 439/13.55 % | 2020-01-17 to 2020-03-31 | |
| C11651T | S3884L | (polar, none-charge) to (non-polar) | 30/0.93 % | 2020-03-12 to 2020-03-23 | |
| C14144T* | P4715L | No | 1700/52.47 % | 2020-02 to 2020-04-01 | |
| C14541T* | No | No | 284/8.77 % | 2020-02-09 to 2020-03-29 | |
| C17483T* | P5828L | No | 390/12.04 % | 2020-02-20 to 2020-03-25 | |
| A17594G* | Y5865C | No | 405/12.50 % | 2020-02-20 to 2020-03-25 | |
| C17796T* | No | No | 410/12.65 % | 2020-01-19 to 2020-03-25 | |
| T18472C | F6158L | No | 28 | 2020-03-03 to 2020-03-25 | |
| C18734T | A6245V | No | 27 | 2020-03-12 to 2020-03-23 | |
| G19420T | V6474L | No | 24 | 2020-03-05 to 2020-03-20 | |
| Gene | Substitutions | AA change | Changed in properties of aa | Frequency/Proportion | Sampling date |
| S | A1841G* | D614G | (polar, negative-charge) to (polar, none-charge) | 1720/53.09 % | 2020-01-28 to 2020-04-01 |
| G2025C& | Q675H | (polar, none-charge) to (polar, positive-charge) | 7/0.22 % | 2020-03-03 to 2020-03-27 | |
| A2024G& | Q675R | (polar, none-charge) to (polar, positive-charge) | 1/0.03 % | 2020-03-04 | |
| AG2827CC | S943P | (polar, none-charge) to (non-polar) | 22/0.68 % | 2020-02-29 to 2020-03-20 | |
| ORF3a | G171T* | Q57H | (polar, none-charge) to (polar, positive-charge) | 578/17.84 % | 2020-02-21 to 2020-03-31 |
| C296T | A99V | No | 23/0.71 % | 2020-02-29 to 2020-03-31 | |
| G587T | G196V | (polar, none-charge) to (non-polar) | 48/1.48 % | 2020-02-25 to 2020-03-23 | |
| G752T* | G251V | (polar, none-charge) to (non-polar) | 299/9.23 % | 2020-01 to 2020-03-29 | |
| M | A8G | D3G | (polar, negative-charge) to (polar, none-charge) | 41/1.27 % | 2020-02 to 2020-03-30 |
| C524T | T175M | (polar, none-charge) to (non-polar) | 117/3.61 % | 2020-03-01 to 2020-03-29 | |
| ORF7a | C242T | S81L | (polar, none-charge) to (non-polar) | 25/0.77 % | 2020-03-07 to 2020-03-25 |
| ORF8 | G184C | V62L | No | 41/1.27 % | 2020-01-15 to 2020-03-25 |
| G184T | V62L | No | 3/0.09 % | 2020-03-18 to 2020-03-24 | |
| T251C* | L84S | (non-polar) to (polar, none-charge) | 646/19.94 % | 2020-01-05 to 2020-03-26 | |
| N | C38T | P13L | No | 29/0.89 % | 2020-02-27 to 2020-03-23 |
| G578T | S193I | (polar, none-charge) to (non-polar) | 27/0.83 % | 2020-01-21 to 2020-03-23 | |
| C581T | S194L | (polar, none-charge) to (non-polar) | 21/0.65 % | 2020-01-16 to 2020-03-21 | |
| C590T | S197L | (polar, none-charge) to (non-polar) | 49/1.51 % | 2020-02-25 to 2020-03-23 | |
| G605A | S202N | No | 34/1.05 % | 2020-01-25 to 2020-03-26 | |
| GGG608-609-610AAC* | R203K | No | 499/15.40 % | 2020-02-25 to 2020-04-01 | |
| G204R | (polar, none-charge) to (polar, positive-charge) |
*
Represents the substitution hotspots.
&
These sites were near furin cleavage region of S protein though the substitution frequency was below 20.