Table 1.
Schematic representation of four unique patterns of variations (A to D) discovered in the Epstein-Barr virus latent membrane protein 1 (LMP-1) gene hypervariable region by Lei et al. [18]
| Characteristic | LMP-2B Exon1 | LMP-1 Promoter | LMP-1 Exon1 | LMP-1 Exon3 | |||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nt position | 1. −426 | 2. −412 | 3. −410 | 4. −367 | −372 | −356 | 5. −354 | −329 | −328 | −315 | −286 | −284 | −240 | −238 | −234 | −233 | 6. −227 | −207 | −199 | 7. −184 | 8. −172 | −163 | −136 | −70 | 9. −50 | −44 | −43 | −37 | −34 | 10. −39 | −17 | 11. −12 | −6 | −4 | −3 | +11 | +12 | 12. +18 | +26 | +32 | +41 | 13. E2D | 14.15. H3L | R17L | 16. V43I | 17. S57A | 18.19. I63V | 20. I124V | 21. I152L | 22. H213N | 23. E214Q |
| nt change | G>A | T>G | C>A | G>A | G>A | C>A | A>G | C>T | G>A | C>T | A>G | G>T | G>A | A>G | G>T | G>A | G>A | C>T | C>T | A>T | T>C | C>T | A>T | A>C | T>A | G>T | A>T | C>G | C>G | A>C | A>T | G>A | C>T | C>A | C>G | A>G | C>T | T>G | A>C | G>A | G>C | GAA>GAC | CAC>CTG | CGA>CTA | GTT>ATT | TCC>GCC | ATA>GTG | ATC>GTC | ATC>CTC | CAT>AAT | GAA>CAA |
|
Pattern A
(23 variants) |
A | G | A | A | G | C | G | C | G | C | A | G | G | A | G | C | A | C | C | T | C | C | A | A | A | C | A | C | C | C | A | A | C | C | C | A | C | G | A | G | C | C | TG | G | A | G | GG | G | C | A | C |
|
Pattern B
(29 variants) |
G | T | C | G | A | A | A | T | A | T | G | T | A | G | T | A | G | T | T | A | T | T | T | C | T | C | T | G | G | A | T | G | T | A | G | G | T | T | C | A | G | A | AC | T | G | T | AA | A | A | C | G |
|
Pattern C
(3 variants) |
G | T | C | G | G | C | A | C | G | C | A | G | G | A | G | G | G | C | C | A | T | C | A | A | T | T | A | C | C | A | A | G | C | C | C | A | C | T | A | G | C | C | AC | G | G | T | AA | A | A | C | G |
|
Pattern D
(wild-type) |
G | T | C | G | G | C | A | C | G | C | A | G | G | A | G | G | G | C | C | A | T | C | A | A | T | G | A | C | C | A | A | G | C | C | C | A | C | T | A | G | G | A | AC | G | G | T | AA | A | A | C | G |
Abbreviations: nt nucleotide; Pattern A: 23 single nucleotide variants, including 11 variants in the promoter and 9 amino acid changes in the coding sequence of LMP-1. The single nucleotide variations used to define Pattern A are numbered for ease of reference to guide the definition of Pattern A in other datasets. Pattern B: 29 single nucleotide variants, including 28 variants in the promoter and 1 amino acid change in the coding sequence of LMP-1. Pattern C: 3 single nucleotide variants, including 2 variants in promoter and sharing amino acid change E2D with Pattern A. Pattern D: The LMP-1 wild type sequence of the EBV reference genome NC_007605. The colors indicate the specific nucleotides that vary (dark green for Pattern A, lime green for Pattern B, and blue for Pattern C); only nt changes in Pattern A are numbered.