TABLE 5.
Subgroup-specific BKV SNPs
| Positiona | BKV Dunlop strain sequenceb | Nucleotides corresponding to BKV Dunlop strain at specified positionc
|
Subgroupd | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Ia | Ib1 | Ib2 | Ic | II | III | IVa | IVb | IVc | |||
| Agnogene | |||||||||||
| 427 (1) | GTT (V) | ... | ... | C.. (L) | ... | A.. (I) | ... | ..N (X) | ... | ... | Ib2 |
| VP2/VP3 | |||||||||||
| 1022 (3) | ATT (I) | ... | ... | ..A | ... | ... | ... | ... | ... | ... | Ib2 |
| 1023 (1) | CTG (L) | ... | T.. | T.. | T.. | T.. | T.. | T.. | T.. | T.. | Ia |
| 1091 (3) | TCT (S) | ... | ..C | ... | ... | ... | ... | ... | ... | ... | Ib1 |
| 1146 (1) | TCT (S) | ... | G.. (A) | G.. (A) | G.. (A) | G.. (A) | G.. (A) | G.. (A) | G.. (A) | G.. (A) | Ia |
| 1166 (3) | TTG (L) | ... | ... | ... | ..A | ... | ... | ... | ... | ... | Ic |
| 1169 (3) | CAG (Q) | ... | ..A | ..A | ..A | ..A | ..A | ..A | ..A | ..A | Ia |
| 1272 (1) | CAA (Q) | ... | G.. (E) | G.. (E) | G.. (E) | G.T (D) | G.T (D) | G.T (D) | G.T (D) | G.T (D) | Ia |
| 1322 (3) | GTA (V) | ... | ..G | ... | ... | ... | ... | ..T | ..T | ..T | Ib1 |
| 1343 (3) | CGT (R) | ... | ... | ... | ... | .A. (H) | .A. (H) | .AG (Q) | .AA (Q) | .AG (Q) | IVb |
| VP1 | |||||||||||
| 1575 (3) | ACC (T) | ... | ... | ..A | ... | ... | ... | ... | ... | ... | Ib2 |
| 1908 (3) | ACT (T) | ... | ... | ..A | ... | ... | ... | ... | ... | ... | Ib2 |
| 1977 (3) | GAG (E) | ... | ... | ... | ... | ... | ... | ... | ..N (X) | ..A | IVc |
| 1989 (3) | GGA (G) | ... | ..T | ..T | ..G | ..C | ..T | ..C | ..C | ..C | Ia, Ic |
| 1992 (3) | AAA (K) | ... | ... | ... | ..G | ... | ... | ... | ... | ... | Ic |
| 2076 (3) | TCA (S) | A.. (T) | A.C (T) | A.. (T) | A.. (T) | A.. (T) | A.. (T) | A.. (T) | A.. (T) | A.. (T) | Ib1 |
| 2127 (3) | CAG (Q) | ... | ... | ..A | ... | ... | ... | ... | ... | ... | Ib2 |
| LTA gene | |||||||||||
| 5103 (3) | TTA (L) | ... | ... | ..G | ... | ... | ... | ... | ... | ... | Ib2 |
| 5076 (3) | AAT (N) | ... | ..C | ..C | ..C | ..C | ..C | ..C | ..C | ..C | Ia |
| 5055 (3) | GCT (A) | ... | ..C | ..C | ..C | ..C | ..C | ..C | ..C | ..C | Ia |
| 4947 (3) | GCT (A) | ... | ... | ... | ..C | ... | ... | ... | ... | ... | Ic |
| 4525 (3) | AGT (S) | ... | ..C | ..N (X) | ... | ..C | ..C | ..C | ..N (X) | ..G (R) | IVc |
| 4435 (3) | TCA (S) | ... | ..C | ... | ... | ... | ... | ..N (X) | ... | ... | Ib1 |
| 4417 (3) | AAA (K) | ... | ..G | ... | ... | ... | ... | ... | ... | ... | Ib1 |
| 4075 (3) | ACT (T) | ... | ..A | ..A | ..A | .TA (I) | .TA (I) | .TA (I) | .TA (I) | .TA (I) | Ia |
| 3919 (3) | TTT (F) | ... | ... | ... | ... | ... | ... | ..C | ... | ... | IVa |
| 3844 (3) | CAC (H) | ... | ..T | ..T | ..T | ..T | ..T | ..T | ..T | ..T | Ia |
| 3749 (2) | ACC (T) | ... | ... | .G. (S) | ... | ... | ... | ... | ... | ... | Ib2 |
| 3709 (3) | TTC (F) | ... | ..T | ..T | ..T | ..T | ..T | ..T | ..T | ..T | Ia |
| 3673 (3) | GGA (G) | ... | ... | ..G | ... | ... | ... | ... | ... | ... | Ib2 |
| 3654 (1) | CTA (L) | ... | ..G | T.. | ... | ... | ... | ... | ... | ... | Ib2 |
| 3652 (3) | CTA (L) | ... | ..G | T.. | ... | ... | ... | ... | ... | ... | Ib1 |
| 3562 (3) | TTC (F) | ... | ..T | ..T | ..T | ..T | ..T | ..T | ..T | ..T | Ia |
| 3535 (3) | TTA (L) | ... | ... | ... | ... | ... | ... | ... | ..G | ... | IVb |
| 3523 (3) | CCC (P) | ... | ... | ... | ..T | ..A | ..A | ..A | ..A | ..A | Ic |
| 3454 (3) | GTA (V) | ... | ... | ... | ... | ..N (X) | ... | ..T | ..N (X) | ..G | IVa |
| 3424 (3) | GAG (E) | ... | ..A | ..A | ..A | ..A | ..A | ..A | ..A | ..A | Ia |
| 3315 (1) | TTG (L) | ... | ... | ... | C.C | ... | ... | ..N (X) | ..A | ..A | Ic |
| 3238 (3) | CCA (P) | ... | ... | ... | ..T | ... | ... | ... | ... | ... | Ic |
| 3190 (3) | CAA (Q) | ... | ..G | ..G | ..G | ..G | ..G | ..G | ..G | ..G | Ia |
| 3172 (3) | CAA (Q) | ... | ..G | ..G | ..G | ..G | ..G | ..G | ..G | ..G | Ia |
| 3100 (3) | ATT (I) | ... | ... | ... | ..C | ..A | ..A | ..A | ..A | ..A | Ic |
| 3079 (3) | TTG (L) | ... | ... | ... | ..A | C.T | C.T | ... | ... | ... | Ic |
| 2908 (3) | GAG (E) | ... | ..A | ..A | ..A | ..A | ..A | ..A | ..A | ..A | Ia |
| 2761 (3) | TTT (F) | ... | ... | ... | ..C | ... | ... | ... | ... | ... | Ic |
a
Nucleotide position using the Seif convention as applied to the BKV Dunlop strain (accession no. V01108). The number in parentheses indicates the position of this nucleotide in the corresponding codon.
b
Nucleotides corresponding to those in the BKV Dunlop strain at the specified position. The coded amino acid is indicated in parentheses.
c
Alphanumeric designations indicate BKV subtypes. Dots indicate nucleotide homology with the Dunlop strain sequence. Any change in coded amino acid is indicated in parentheses.
d
Genotype assignment corresponding to the SNP in question.