Table 2.
Characterization of the mutant spectra represented in the DNA amplified from FMDV populations passaged in the presence of ribavirin
| Parameter | Result at passage no. and Tda shownb |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| p0 (89.7°C) | p1 |
p2 |
p3 |
p4 |
p5 |
||||||
| 88.4°C | 89.1°C | 88.4°C | 89.1°C | 88.4°C | 89.1°C | 88.4°C | 89.1°C | 88.4°C | 89.1°C | ||
| No. of clonesc | 56 | 52 | 81 | 58 | 57 | 60 | 69 | ||||
| No. of ntd | 10,584 | 9,828 | 15,309 | 10,962 | 10,773 | 11,340 | 13,041 | ||||
| No. of mutationse | 49 | 92 | 50 | 52 | 83 | 36 | 64 | ||||
| Mutation frequencyf | 4.6 × 10−3 | 8.8 × 10−3 | 3.2 × 10−3 | 4.7 × 10−3 | 7.7 × 10−3 | 3.1 × 10−3 | 4.8 × 10−3 | ||||
| Shanon entropy valueg | 0.71 | 1.00 | 0.61 | 0.79 | 1.00 | 0.63 | 0.92 | ||||
| No. (%) of substitutions vs. C-S88c1h | |||||||||||
| G→A | 13 (26) | 32 (34) | 11 (22) | 17 (32) | 23 (27) | 9 (25) | 16 (25) | ||||
| C→U | 21 (42) | 35 (38) | 12 (24) | 22 (42) | 31 (37) | 10 (27) | 23 (35) | ||||
| Others | 15 (30) | 25 (27) | 27 (54) | 13 (25) | 29 (34) | 17 (47) | 25 (39) | ||||
| No. (%) of substitutionsi | |||||||||||
| Synonymous | 19 (38) | 34 (36) | 18 (36) | 20 (38) | 26 (31) | 10 (27) | 21 (32) | ||||
| Nonsynonymous | 30 (61) | 58 (63) | 32 (64) | 32 (61) | 57 (68) | 26 (72) | 43 (67) | ||||
| No. of synynomous/nonsynonymous substitutions | |||||||||||
| Synonymousj | |||||||||||
| G→A | 7 | 8 | 5 | 6 | 7 | 3 | 2 | ||||
| C→U | 10 | 14 | 6 | 10 | 14 | 4 | 12 | ||||
| Others | 2 | 12 | 7 | 4 | 5 | 3 | 7 | ||||
| Nonsynonymousk | |||||||||||
| G→A | 6 | 24 | 6 | 11 | 16 | 6 | 14 | ||||
| C→U | 11 | 21 | 6 | 12 | 17 | 6 | 11 | ||||
| Others | 13 | 13 | 20 | 9 | 24 | 14 | 18 | ||||
Denaturation temperature at which the mutant spectra were obtained.
The FMDV populations and amplified DNAs are those described in Fig. 2 to 4 in the presence of ribavirin.
Number of molecular clones analyzed (as detailed in Materials and Methods).
Number of nucleotides sequenced.
Number of different mutations found comparing the sequence of each individual clone with the corresponding sequence of FMDV C-S8c1 (28, 72).
Mutation frequency (number of different mutations found divided by the number of nucleotides sequenced), expressed as substitutions per nucleotide. Results are based on the sequencing of 52 to 81 clones per population.
The normalized Shannon entropy is calculated as −Σi[(pi × ln pi)/ln N], in which pi is the frequency of each sequence in the mutant spectrum and N is the total number of sequences compared.
Number of different G→A, C→U, or other substitutions found comparing the sequence of each clone with the corresponding sequence of FMDV C-S8c1.
Total number of different synonymous and nonsynonymous substitutions.
Number of different synonymous G→A, C→U, or other substitutions, comparing the sequence of each clone with the corresponding sequence of FMDV C-S8c1.
Number of different nonsynonymous G→A, C→U, or other substitutions, comparing the sequence of each clone with the corresponding sequence of FMDV C-S8c1.