Table 2.
Ten most frequently mutated genome positions among Latvian SARS-CoV-2 isolates (n = 133).
| Position in genome | Reference | Variant | Variant | Variant class | Region affected | Amino acid change | Function of the mature peptide | Variant | Occurrence among | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| frequency | Latvian isolates | ||||||||||
| 241 | C | 5′UTR:241 | T | Extragenic | 5′UTR | 241 | N/A | 129 | 96.99% | ||
| 3,037 | C | NSP3:F106F | T | Silent | NSP3 | F106F | Predicted phosphoesterase, papain-like proteinase | 128 | 96.24% | ||
| 14,408 | C | NSP12b:P314L | T | SNP | NSP12b | P314L | RNA-dependent RNA polymerase, post-ribosomal frameshift | 128 | 96.24% | ||
| 23,403 | A | S:D614G | G | SNP | S | D614G | Spike | 128 | 96.24% | ||
| GGG | N:RG203KR | AAC | RG203KR | 59 | 44.36% | ||||||
| 28,881 | G | N:R203K | A | SNP* | N | R203K | Nucleocapsid protein | 32 | 96 | 24.06% | 72.18% |
| GGGG | N:RG203KL | AACT | RG203KL | 5 | 3.76% | ||||||
| 25,563 | G | ORF3a:Q57H | T | SNP | ORF3a | Q57H | ORF3a protein | 41 | 30.83% | ||
| 18,877 | C | NSP14:C279C | T | Silent | NSP14 | C279C | 3′-to-5′ exonuclease | 36 | 27.07% | ||
| 1,202 | A | NSP2:N133D | G | SNP | NSP2 | N133D | Non-Structural protein 2 | 34 | 25.56% | ||
| 12,513 | C | NSP8:T141M | T | SNP | NSP8 | T141M | Non-Structural Protein 8 | 34 | 25.56% | ||
| 25,710 | C | ORF3a:L106L | T | Silent | ORF3a | L106L | ORF3a protein | 33 | 24.81% | ||
Color coding is based on the variant class, as follows: red represents extragenic variants; green, silent variants; and blue, single nucleotide polymorphisms. Asterisk
(*)
in “Variant class” column represents that there are multiple variants present at a given genome position (28,881); some of them are neighboring loci polynucleotide variants rather than SNP.