Table 1.
Nucleotide and amino acid changes in S. mystax animals with acute resolving (SM911, SM920 and SM918) and persistent (SM912) GBV-B infection
The consensus sequence corresponding to nt 36–9107 of pGBB, including the entire ORF of recovered GBV-B viruses, was determined for each sample, using a long nested RT-PCR procedure. Positions with differences from pGBB are shown for each animal (mutations in p13 originally introduced into these viruses are not shown). Only dominant changes observed at one or more time point in an individual animal are included. Dominant sequences are shown in capital letters and minor sequences are shown in lower-case letters.
| Genome region [nt (aa)]* | pGBB | SM912 | SM911 | SM920 | SM918 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| wk 2 | wk 5 | wk 12 | wk 20 | wk 26 | wk 52 | wk 104 | wk 5 | wk 12 | wk 2 | wk 9 | wk 20 | wk 2 | wk 19 | wk 25 | ||
| 5′ UTR (1–445) | ||||||||||||||||
| 237 | A | A | A | A | A | A | G | G | ||||||||
| C (446–913) | ||||||||||||||||
| 710 (89) | A (I) | A (I) | A (I) | A (I) | A (I) | G/a (V/i) | A (I) | A (I) | A (I) | G (V) | A (I) | |||||
| 846 (134) | C (A) | C (A) | C (A) | T (V) | ||||||||||||
| E1 (914–1489) | ||||||||||||||||
| 982 | C | A | A | |||||||||||||
| E2 (1490–2284) | ||||||||||||||||
| 1528 | T | T | T | T | T/C | T | C | C | ||||||||
| 1550 (369) | A (I) | A (I) | A (I) | A (I) | A (I) | A (I) | G (V) | G (V) | ||||||||
| 1842 (466) | A (H) | A (H) | A (H) | A (H) | A/g (H/r) | A/G (H/R) | A (H) | A (H) | ||||||||
| 1895 (484) | A (M) | A (M) | A (M) | A (M) | A (M) | A (M) | T (L) | T (L) | ||||||||
| 1976 (511) | G (V) | G (V) | G (V) | G (V) | G/A (V/M) | G (V) | A (M) | A (M) | ||||||||
| 2053 | A | A | A | A | A | A | G | G | ||||||||
| 2267 (608) | T (F) | T (F) | T (F) | T (F) | T (F) | T (F) | G (V) | G (V) | ||||||||
| 2276 (611) | G (A) | G (A) | G (A) | G (A) | G (A) | G (A) | G (A) | A (T) | ||||||||
| p13 (2285–2641) | ||||||||||||||||
| 2304 (620) | T (L) | T (L) | T (L) | T (L) | T (L) | C/t (P/l) | T (L) | T (L) | ||||||||
| 2552 (703) | A (N) | A (N) | A/G (N/D) | G (D) | G (D) | G (D) | G (D) | G (D) | A (N) | G (D) | A (N) | G (D) | G (D) | |||
| NS2 (2642–3265) | ||||||||||||||||
| 3136 | A | A | A | G | ||||||||||||
| 3212 (923) | G (G) | G (G) | G (G) | A (S) | A (S) | A (S) | A (S) | A (S) | G (G) | A/g (S/g) | G (G) | A (S) | A (S) | |||
| NS3 (3266–5125) | ||||||||||||||||
| 3367 | C | C | C | C | C | C | T | T | ||||||||
| 3463 | T | T | C | T | ||||||||||||
| 4198 | A | A | A | G | G | G | G | G | ||||||||
| 4246 | C | C | T | C | ||||||||||||
| 4285 | C | C | C | C | C | C | C | T | ||||||||
| 4915 | T | G | G | |||||||||||||
| NS4A (5126–5290) | ||||||||||||||||
| 5200 | T | T | T | A | ||||||||||||
| 5272 | A | A | A | A | A | A/G | A | A | ||||||||
| NS4B (5291–6034) | ||||||||||||||||
| 5353 | C | C | C | C | C | C | C | T | ||||||||
| 5386 | T | T | T | T | T | T | T | C | ||||||||
| 5674 | C | C | C | T | ||||||||||||
| 5794 | C | C | C | T | ||||||||||||
| 5910 (1822) | A (N) | A (N) | G (S) | A (N) | ||||||||||||
| 5914 (1823) | G (E) | G (E) | G (E) | G (E) | G (E) | C/g (D/e) | G (E) | G (E) | G (E) | G (E) | T (D) | |||||
| NS5A (6035–7267) | ||||||||||||||||
| 6131 (1896) | A (N) | A (N) | G (D) | A (N) | ||||||||||||
| 6472 | G | G | G | G | G | G | G | A | ||||||||
| 6690 (2082) | C (T) | C (T) | T (I) | C (T) | ||||||||||||
| 6849 (2135) | T (F) | T (F) | T (F) | T (F) | T (F) | T (F) | C (S) | C (S) | ||||||||
| 6956 (2171) | A (N) | A (N) | A (N) | A (N) | A (N) | A (N) | A (N) | G (D) | ||||||||
| 7031 (2196) | T (F) | T (F) | T (F) | T (F) | C/t (L/f) | T (F) | C (L) | C (L) | ||||||||
| 7072 | C | C | C | C | T/c | C | T | T/c | ||||||||
| 7105 | G | G | G | A | ||||||||||||
| 7248 (2268) | G (G) | G (G) | G (G) | G (G) | A/g (E/g) | G/a (G/e) | A (E) | A (E) | ||||||||
| NS5B (7268–9037) | ||||||||||||||||
| 7440 (2332) | T (L) | T (L) | T (L) | T (L) | T (L) | T (L) | A (Q) | A (Q) | ||||||||
| 7994 (2517) | A (S) | A (S) | G (G) | |||||||||||||
| 8001 (2519) | A (Q) | A (Q) | A (Q) | G/a (R/q) | ||||||||||||
| 8122 | A | A | A | A | A | A | G | G | ||||||||
| 8314 | T | T | T | C | ||||||||||||
| 8336 | T | T | T | C | T | T | T | T | ||||||||
| 8472 (2676) | G (S) | G (S) | G (S) | A (N) | G (S) | G (S) | G (S) | G (S) | ||||||||
| 8653 | T | T | C/t | |||||||||||||
| 8663 (2740) | A (I) | A (I) | A (I) | G (V) | ||||||||||||
| 8727 (2761) | C (T) | C (T) | C (T) | C (T) | C (T) | C (T) | C (T) | T (I) | ||||||||
| 8766 (2774) | A (K) | A (K) | A (K) | G (R) | ||||||||||||
| 8860 | A | A | A | A | A | A | A | G | ||||||||
| 8938 | G | G | A/g | |||||||||||||
| 8942 (2833) | A (I) | A (I) | G (V) | A (I) | ||||||||||||
| 8971 | C | C | C | C | C | C | C | T | ||||||||
| 3′ UTR (9038–9399) | ||||||||||||||||
| 9046 | C | C | T/c | |||||||||||||
*Nucleotide and amino acid positions corresponding to pGBB (GenBank accession no. AF179612).