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

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

Population^a	Genomic residues^b	Number of clones	Total nt. sequenced	Drug treatment^c	Mutations^d	Transitions^e	Transversions^e	Minimum mutation frequency (×10^-3)^f	Maximum mutation frequency (×10^-3)^g	Min/max ratio	H^h	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

^aThe origin of the FMDV populations is detailed in Methods and depicted schematically in Figure 1.
^bThe genomic residues analyzed correspond to the 3D-coding region of the FMDV genome; residue numbering is according to [47].
^cDrug treatment (AZC, azacytidine; FU, 5-fluorouracil; R, ribavirin), and concentrations are as described in Figure 1.
^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.
^eExpressed per 1 in each population.
^fMinimum mutation frequency is the number of different mutations divided by the total number of nucleotides sequenced.
^gMaximum mutation frequency is the total number of mutations (including repeated mutations) divided by the total number of nucleotides sequenced.
^hH is the normalized Shannon entropy [65].
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.

ISSN: 2730-7182