Table 1.
SARS-CoV-2 genome single nucleotide variants (SNVs) in postmortem tissues and plasma of case 13.
| Genea | Nt change | AA change | Frequency of detection per anatomical compartment (%)b | |||||
|---|---|---|---|---|---|---|---|---|
| Lungs | Plasma | Heart | Kidney | Liver | Spleen | |||
| ORF1a | T322A | / | 40,81 | 0 | 6,57 | 0 | 0 | 0 |
| ORF1a | G1068A | NSP2:G268E | 0 | 0 | 0 | 0 | 0 | 28,5 |
| ORF1a | C1862T | NSP2:L533F | 33,28 | 5,9 | 8,78 | 0 | 0 | 3,11 |
| ORF1a | C2094T | NSP2:S610L | 99,56 | 99,55 | 99,62 | 100 | 100 | 99,62 |
| ORF1a | T2149C | / | 20,58 | 1,35 | <1 | <1 | <1 | <1 |
| ORF1a | T5395A | NSP3:F2328V | 39,67 | 5,95 | 4,12 | <1 | 11,9 | 4,03 |
| ORF1a | A5405G | NSP3:I1714V | 17,73 | 10,45 | 30,22 | 5,76 | 10,89 | 4,1 |
| ORF1a | T5406C | NSP3:I1714T | 10,63 | 12,5 | 28,95 | 89,21 | 32,82 | 6,63 |
| ORF1a | C7239T | NSP3:A2325V | 46,19 | 8,06 | 20,07 | <1 | 16,67 | 5,56 |
| ORF1a | T7247G | NSP3:F2328V | 29,24 | 14,66 | 6,78 | 87,36 | 37,5 | 6,77 |
| ORF1a | C7279T | / | 1,17 | 1,84 | <1 | 83,3 | <1 | <1 |
| ORF1a | C8175T | NSP3:A2637V | 14,31 | 45,94 | 42,28 | 1,85 | 38,91 | 11,11 |
| ORF1a | A8387G | NSP3:N2708D | 1,92 | 2,89 | <1 | 88,86 | 2,5 | 1,32 |
| ORF1a | C9438T | NSP4:T3058I | 14,4 | 44,24 | 24,27 | 1,11 | 35,56 | 11,64 |
| ORF1a | C9491T | NSP4:H3076Y | 2,84 | 1,28 | 33,29 | <1 | 5,65 | 4,05 |
| ORF1a | A9737G | NSP4:S3158G | 39,58 | 9,44 | 7,07 | 44,79 | 13,87 | 5,96 |
| ORF1a | C10369T | / | 1,54 | <1 | <1 | <1 | 6,04 | 27,3 |
| ORF1a | C11008T | / | 20,69 | 2,92 | 5,3 | <1 | 3,69 | 2,17 |
| ORF1a | C12439T | NSP8:P4058L | 8,71 | 5,35 | 5,76 | 48,05 | 21,86 | 4,07 |
| ORF1a | C12513T | NSP8:T4083M | <1 | <1 | <1 | 7,04 | <1 | 62,73 |
| ORF1a | T13417C | / | 99,25 | 98,09 | 97,72 | 99,15 | 94,8 | 98,89 |
| ORF1a | A13433G | NSP10:M4390G | 1,13 | 1,59 | <1 | 30,19 | 1,84 | <1 |
| ORF1b | A13947T | / | 99,5 | 99,17 | 99,46 | 99,26 | 99,64 | 98,96 |
| ORF1b | C14786T | RdRp:A440V | 46,74 | 4,66 | 8,13 | <1 | 8,85 | 3,66 |
| ORF1b | C14937T | / | <1 | <1 | <1 | <1 | <1 | 64,31 |
| ORF1b | C15222T | / | 1,84 | 24,59 | 7,67 | 1,24 | 7,97 | 2,96 |
| ORF1b | C16092T | / | <1 | <1 | <1 | 30,42 | <1 | <1 |
| ORF1b | C17004T | / | 39 | 6,46 | 13,84 | 0 | 7,85 | 4,12 |
| ORF1b | T18024C | / | <1 | <1 | <1 | 27,86 | <1 | <1 |
| ORF1b | A18179G | NSP14:K1571R | <1 | 27,26 | 4,86 | <1 | 6,34 | 3,35 |
| ORF1b | T18678C | / | <1 | 30,76 | 6,55 | <1 | 7,03 | 3,55 |
| ORF1b | T18750C | / | <1 | <1 | <1 | 27,13 | <1 | <1 |
| ORF1b | C18979T | NSP14:H1838Y | <1 | <1 | <1 | 40,81 | <1 | <1 |
| S | C21789T | S:T76I | 41,05 | 7,19 | <1 | <1 | 11,52 | 4,13 |
| S | G22363T | / | 4,65 | 2,14 | <1 | 43,97 | 3,4 | 1,06 |
| S | G22661T | S:V367F | 5,62 | <1 | 10,34 | 3,07 | 1,9 | 68,08 |
| S | A22920T | S:Y453F | 52,52 | <1 | <1 | <1 | 11,13 | 5,06 |
| S | A23063T | S:N501Y | 18,46 | 14,29 | 20,69 | 39,63 | 31,27 | 5,04 |
| S | G23782A | S:M740I | 20,87 | 8,26 | <1 | <1 | 4,55 | 1,72 |
| S | G24316T | S:E918D | <1 | 3 | 45,65 | <1 | 11,33 | 1,94 |
| S | T24450C | S:V963A | 36,09 | 6,21 | 16,15 | <1 | 11,27 | 3,15 |
| S | C24642T | S:T1027I | 44,18 | 27,94 | 27,48 | 49,78 | 23,26 | 7,74 |
| E | C26333T | E:T30I | 83,41 | 49,57 | 81,39 | 2,25 | 60,29 | 41,17 |
| E | C26351T | E:A36V | <1 | <1 | <1 | <1 | <1 | 33,61 |
| ORF7a | A27574T | ORF7a:T61S | 2 | 2,1 | <1 | 88,65 | 3,16 | <1 |
| N | A28336T | / | <1 | <1 | <1 | <1 | <1 | 62,93 |
| N | C29200T | / | <1 | <1 | 54,51 | <1 | <1 | <1 |
| N | A29424G | N:Q384R | < 1 | <1 | <1 | 27,03 | <1 | <1 |
| ORF10 | C29592T | ORF10:T34M | 1,78 | 1,45 | 1,98 | 49,64 | 2,76 | <1 |
| 3’ UTR | G29744A | / | <1 | <1 | <1 | <1 | <1 | 61,12 |
Variants were mapped to clade 20B genome and called if case frequencies were higher than 20% in at least one anatomical compartment. SNV frequency is noted per organ.
aGene names are italicized in the table.
bBold numbers indicate that the latter variant was also identified in SARS-CoV-2 progeny on Vero E6 cells of respective tissue samples (frequencies >1%).