TABLE 5.
SNVs unique to the primary or recurrent infection in subject A or B
| Gene | Nucleotide/amino acid position | Nucleotide variant |
Amino acid variant |
Function | ||
|---|---|---|---|---|---|---|
| Primary infection (sample 8) ≫ recurrent infection (sample 14) | Primary (sample 16) ≫ recurrent (sample 19) | Primary infection | Recurrent infection | |||
| Subject A | ||||||
| UL13a,b | 569/190 | C (86)c, T (14) ≫ C (98), T (1), A (1) | A (86), V (14) | A (98) | Protein kinase | |
| UL13b | 685/229 | G (100) ≫ G (90), T (10) | D (100) | D (90), Y (10) | Protein kinase | |
| UL14 | 321/107 | T (10), C (90) ≫ T (74), C (26) | Tegument protein | |||
| UL14 | 334/112 | C (70), T (30) ≫ C (99), A (1) | R (70), C(30) | R (100) | Tegument protein | |
| UL27 | 206/69 | C (100) ≫ T (52), C (48) | P (100) | L (52), P (48) | Glycoprotein B | |
| UL30 | 3398/1133 | C (98), T (1), A (1) ≫ T (60), C (40) | P (98) | L (60), P (40) | DNA polymerase | |
| UL36 | 7942/2648 | G (100) ≫ G (65), A (35) | A (100) | A (65), T (35) | Tegument protein | |
| UL37b | 1478/493 | A (7), C (93) ≫ A (99), G (1) | P (93) | H (99) | Tegument protein | |
| UL44 | 321/107 | G (82), C (15), A (1), T (2) ≫ G (91), C (8), T (1) | Tegument protein | |||
| Intergenic space | 145807d | G (89), A (11) ≫ G (99), A (1) | ||||
| Subject B | ||||||
| UL12 | 1305/435 | C (100) ≫ T (24), C (76) | DNase | |||
| UL13b | 862/288 | C (86), T (14) ≫ C (98), T (2) | R (86), STOP (14) | R (98) | Protein kinase | |
| UL13b | 1133/378 | G (100) ≫ G (86), T (14) | G (100) | G (86), V (14) | Protein kinase | |
| UL14 | 241/81 | G (99), T (1) ≫ G (79), A (21) | V (99) | V (79), M (21) | Tegument protein | |
| UL14 | 321/107 | T (81), C (19) ≫ T (45), C (55) | Tegument protein | |||
| UL14 | 396/132 | C (100) ≫ C (90), T (10) | Tegument protein | |||
| UL21b | 1039/347 | G (67), A (33) ≫ G (100) | A (67), T (33) | A (100) | Tegument protein | |
| UL24 | 165/55 | G (89), A (11) ≫ G (100) | Nuclear protein | |||
| UL30b | 2852/951 | G (80), A (20) ≫ G (100) | C (80), Y (20) | C (100) | DNA polymerase | |
a
Boldface indicates nonsynonymous substitutions.
b
The secondary and tertiary structures of the protein that contained the polymorphisms were analyzed using the Phyre2 Web portal (Table 6).
c
The numbers in parentheses are the percentages of Novoalign mapped reads supporting each polymorphism. The reported polymorphisms appeared in ≥10% of mapped reads. Underlining indicates the polymorphic variant allele.
d
Polymorphism position observed in an intergenic space derived from the Novoalign alignments (BAM files).