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Table 1 Number and type of mutations scored, and resulting mutation frequencies, calculated for the mutant spectra of the FMDV populations analyzed in the present study

From: Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

Populationa Genomic residuesb Number of clones Total nt. sequenced Drug treatmentc Mutationsd Transitionse Transversionse Minimum mutation frequency (×10-3)f Maximum mutation frequency (×10-3)g Min/max ratio Hh ADi
No Drug p1 6609–8013 5 7025 None 2/2 0.50 0.50 0.28 0.28 1 0.58 0.50
AZCp1 6609–8013 5 7025 [10 μg/ml] AZC 1/1 0 1 0.14 0.14 1 0.31 0.25
FUp1 6609–8013 5 7025 [200 μg/ml] FU 2/2 1 0 0.28 0.28 1 0.58 0.50
No drug p25 6609–8013 5 7025 None 1/3 1 0 0.14 0.42 0.33 0.61 0.75
AZCp25 6609–8013 18 25290 [10 μg/ml]AZC 13/19 0.21 0.79 0.51 0.75 0.68 0.73 2.31
FUp25 6609–8013 5 7025 [200 μg/ml] FU 14/19 1 0 1.99 2.7 0.74 1 6.75
CAp35 6667–7997 21 27951 None 17/17 0.88 0.12 0.61 0.61 1 0.69 0.85
RA0p35 7150–8020 21 18291 [800 μM] R, No drug 17/68 0.75 0.25 0.93 3.71 0.25 1 3.62
RAp35 6667–7997 14 18634 [500–800 μM] R 55/139 0.91 0.09 2.95 7.46 0.39 1 13.15 (7.85)
RAp45 6667–7997 12 15972 [800 μM] R 31/49 0.76 0.24 1.96 3.07 0.64 1 6.91
RAp60 6667–7997 14 18634 [800–5000 μM] R 55/80 0.97 0.02 2.95 4.29 0.69 1 7.62
  1. aThe origin of the FMDV populations is detailed in Methods and depicted schematically in Figure 1.
  2. bThe genomic residues analyzed correspond to the 3D-coding region of the FMDV genome; residue numbering is according to [47].
  3. cDrug treatment (AZC, azacytidine; FU, 5-fluorouracil; R, ribavirin), and concentrations are as described in Figure 1.
  4. dThe first number indicates the total amount of different mutations found in all the clones analyzed; when repeated mutations were found the second number refers to the total number of mutations.
  5. eExpressed per 1 in each population.
  6. fMinimum mutation frequency is the number of different mutations divided by the total number of nucleotides sequenced.
  7. gMaximum mutation frequency is the total number of mutations (including repeated mutations) divided by the total number of nucleotides sequenced.
  8. hH is the normalized Shannon entropy [65].
  9. iAD is the average genetic distance, calculated as detailed in Methods. The value in brackets was calculated with residues 7150–8020 (to compare with population RA0p35) of the FMDV genome.