A. Aria et al., Molecular intermediates of fitness gain of an RNA virus: characterization of a mutant spectrum by biological and molecular cloning, J GEN VIROL, 82, 2001, pp. 1049-1060
The mutant spectrum of a virus quasispecies in the process of fitness gain
of a debilitated foot-and-mouth disease virus (FMDV) clone has been analyse
d. The mutant spectrum was characterized by nucleotide sequencing of three
virus genomic regions (internal ribosome entry site; region between the two
AUG initiation codons; VP1-coding region) from 70 biological clones (virus
from individual plaques formed on BHK-21 cell monolayers) and 70 molecular
clones (RT-PCR products cloned in E, coli). The biological and molecular c
lones provided statistically indistinguishable definitions of the mutant sp
ectrum with regard to the distribution of mutations among the three genomic
regions analysed and with regard to the types of mutations, mutational hot
-spots and mutation frequencies. Therefore, the molecular cloning procedure
employed provides a simple protocol for the characterization of mutant spe
ctra of viruses that do not grow in cell culture. The number of mutations f
ound repeated among the clones analysed was higher than expected from the m
ean mutation frequencies. Some components of the mutant spectrum reflected
genomes that were dominant in the prior evolutionary history of the virus (
previous passages), confirming the presence of memory genomes in virus quas
ispecies, Other components of the mutant spectrum were genomes that became
dominant at a later stage of evolution, suggesting a predictive value of mu
tant spectrum analysis with regard to the outcome of virus evolution. The r
esults underline the observation that greater insight into evolutionary pro
cesses of viruses may be gained from detailed clonal analyses of the mutant
swarms at the sequence level.