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Table 1 PepMV strains used in the study and changes in the genomes

From: Strain-dependent mutational effects for Pepino mosaic virus in a natural host

Strain Isolate Gene Location in particular genea Codon substitution Amino acid change Effectb t-test P
CH2 P22 RdRp 926 (309) GTC-GAC V-D Beneficial <0.0001
CH2 P22 RdRp 1647 (549) GAC-CAC D-H Neutral 0.0686
CH2 P22 RdRp 4192 (1398) CAA-AAA Q-K Neutral 0.1904
CH2 P22 TGB1 118 (40) AGG-TGG R-W Neutral 0.3804
CH2 P22 TGB1 235 (79) GAC – CAC D-H Neutral 0.0920
CH2 P22 TGB1 272 (91) CCU-CAU P-H Neutral 0.8217
CH2 P22 TGB1 431 (144) GCA-GAA A-E Lethal <0.0001
CH2 P22 TGB1 467 (156) GCA-GAA A-E Lethal <0.0001
CH2 P22 TGB2 130 (44) AGA – GGA R-G Neutral 0.0203
CH2 P22 TGB2 193 (65) CAA-AAA Q-K Beneficial <0.0001
CH2 P22 TGB2 310 (104) CAT-TAT H-Y Beneficial 0.0106
CH2 P22 TGB2 313 (105) CAT-TAT H-Y Beneficial 0.0004
CH2 P22 TGB3 50 (17) ATA-AGA I-R Neutral 0.0858
CH2 P22 TGB3 68 (23) TTA-TCA L-S Neutral 0.2530
CH2 P22 TGB3 175 (59) TGT - CGT C-R Neutral 0.0237
CH2 P22 TGB3 199 (67) AAA- GAA K-E Neutral 0.9274
CH2 P22 TGB3 397 (133) CAG-AAG Q-K Beneficial 0.0006
CH2 P22 CP 5 (2) GAA-GCA E-A Deleterious 0.0026
CH2 P22 CP 22 (8) TCT-GCT S-A Neutral 0.0113
CH2 P22 CP 26 (9) AAC-AGC N-S Lethal <0.0001
CH2 P22 CP 127 (43) GTC-ATC V-I Neutral 0.0420
CH2 P22 CP 233 (78) GCC-GAC A-D Lethal <0.0001
CH2 P22 CP 418 (140) GAC-CAC D-H Neutral 0.0827
CH2 P22 CP 463 (155) GAA-AAA E-K Neutral 0.0183
CH2 P22 CP 497 (166) GAT-GGT D-G Beneficial 0.0029
EU P11 RdRp 4192 (1398) GAG-AAG E-K Neutral 0.0607
EU P11 TGB2 130 (44) CGT-GGT R-G Neutral 0.0292
EU P11 TGB3 68 (23) TTA-TCA L-S Neutral 0.1023
EU P11 CP 463 (155) GAA-AAA E-K Deleterious 0.0171
EU P11 CP 497 (166) GAT-GGT D-G Neutral 0.6633
EU P11 CP (155/166) GAA-AAA
GAT-GGT
E-K
D-G
Beneficial 0.0030
  1. aFirst number indicates the genomic nucleotide position; number in parenthesis indicates the amino acid in the corresponding protein
  2. bEffects were classified as beneficial, neutral or deleterious according to the result of the 2-samples t-tests comparing the fitness values obtained for each mutant to the values measured for the non-mutated parental virus. P-values are reported in the last column