Table 1.
SARS-CoV-2 hot-spot positions (GISAID frequency > 0.04)
| RefP | RefN | AltN | FreqGis | Feature | Gene product | AltAA | Mutation* | IR | CpG |
|---|---|---|---|---|---|---|---|---|---|
| 241 | C | T | 0.69 | 5′ UTR | – | – | – | N | Y |
| 1059 | C | T | 0.21 | ORF1ab | nsp2 | T85I | NS | Y | N |
| 1605 | A | C | 0.04 | ORF1ab | non-structural polyprotein 1AB | N267T | NS | Y | N |
| 2891 | G | R | 0.06 | ORF1ab | nsp3 | A58T | NS | Y | N |
| 3037 | C | T | 0.65 | ORF1ab | nsp3 | F106F | S | N | N |
| 8782 | C | T | 0.14 | ORF1ab | nsp4 | S76S | S | N | N |
| 11 083 | G | T | 0.15 | ORF1ab | nsp6 | L37F | NS | Y | N |
| 14 408 | C | T | 0.64 | ORF1ab | RNA-dependent rna polymerase (nsp12) | P314L | NS | N | N |
| 14 805 | C | T | 0.11 | ORF1ab | RNA-dependent rna polymerase (nsp12) | Y446Y | S | Y | N |
| 17 247 | T | C | 0.04 | ORF1ab | helicase (nsp13) | R337R | S | Y | Y |
| 17 747 | C | T | 0.09 | ORF1ab | helicase (nsp13) | P504L | NS | Y | N |
| 17 858 | A | G | 0.08 | ORF1ab | helicase (nsp13) | Y541C | NS | Y | N |
| 18 060 | C | T | 0.1 | ORF1ab | 3′-5′ exonuclease activity | L7L | S | Y | N |
| 23 403 | A | G | 0.64 | S | spike glycoprotein | D614G | NS | Y | N |
| 25 563 | G | T | 0.24 | ORF3a | ORF3a protein | Q57H | NS | N | N |
| 26 144 | G | T | 0.11 | OR3a | ORF3a protein | G251V | NS | N | Y |
| 28 144 | T | C | 0.13 | ORF8 | ORF8 protein | L84S | NS | Y | N |
| 28 881 | G | A | 0.2 | ORF9/N | nucleocapsid phosphoprotein | R203K | NS | Y | N |
Notes: RefP—reference position in NC_045512.2 genome, RefN—reference nucleotide, AltN—mutation according to GISAID, standard IUPAC code used, FreqGis—mutation frequency according to GISAID, Feature—annotated features according to NCBI, AltAA—mutation of amino acids, Mutation—type of mutations, IR—presence of IR, CpG—presence of CpG island
*S—synonymous mutation, NS—non-synonymous mutation