Abstract
BackgroundFitness recovery of HIV-1 “in vitro” was studied using viral clones that had their fitness decreased as a result of plaque-to-plaque passages.Principal FindingsAfter ten large population passages, the viral populations showed an average increase of fitness, although with wide variations among clones. While 5 clones showed significant fitness increases, 3 clones showed increases that were only marginally significant (p<0.1), and 4 clones did not show any change. Fitness recovery was not accompanied by an increase in p24 production, but was associated with an increase in viral titer. Few mutations (an average of 2 mutations per genome) were detected in the consensus nucleotide sequence of the entire genome in all viral populations. Five of the populations did not fix any mutation, and three of them displayed marginally significant fitness increases, illustrating that fitness recovery can occur without detectable alterations of the consensus genomic sequence. The investigation of other possible viral factors associated with the initial steps of fitness recovery, showed that viral quasispecies heterogeneity increased between the initial clones and the passaged populations. A direct statistical correlation between viral heterogeneity and viral fitness was obtained.ConclusionsThus, the initial fitness recovery of debilitated HIV-1 clones was mediated by an increase in quasispecies heterogeneity. This observation, together with the invariance of the consensus sequence despite fitness increases demonstrates the relevance of quasispecies heterogeneity in the evolution of HIV-1 in cell culture.
Highlights
Experiments of virus evolution in cell culture have been employed to study the relevance of genetic concepts for RNA viruses
Conclusions: the initial fitness recovery of debilitated human immunodeficiency virus type 1 (HIV-1) clones was mediated by an increase in quasispecies heterogeneity
This observation, together with the invariance of the consensus sequence despite fitness increases demonstrates the relevance of quasispecies heterogeneity in the evolution of HIV-1 in cell culture
Summary
Experiments of virus evolution in cell culture have been employed to study the relevance of genetic concepts for RNA viruses (including Muller’s ratchet, the Red Queen hypothesis, genetic drift in bottleneck transfers, among others; as review see [1]) Such studies have been extremely useful in the understanding of the generation and quantification of genetic variation of human immunodeficiency virus type 1 (HIV-1) [2,3,4].These investigations showed that HIV-1 populations are composed of swarms of related variants, often centered around a high frequency variant or master sequence, forming what is known as viral quasispecies [5,6]. Fitness recovery of HIV-1 ‘‘in vitro’’ was studied using viral clones that had their fitness decreased as a result of plaque-to-plaque passages
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