Initial Fitness Recovery of HIV-1 Is Associated with Quasispecies Heterogeneity and Can Occur without Modifications in the Consensus Sequence

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.

Dynamics of In Vitro Fitness Recovery of HIV-1

“…The results of the recovery of the same clones after the initial 10 passages have been presented previously (1). This work summarizes and compares the results after 10 additional passages, until passage 21.…”

“…Subsequent large-population passages of these debilitated clones showed a rapid fitness increase in only 10 passages (1,40). We disclosed that this recovery was found to be associated with an increase in viral quasispecies heterogeneity and occasionally with an invariable consensus sequence (1).…”

“…In the present work, we have extended, until passage 21, the large-population recovery passages in 10 HIV-1 clones, two of which were passaged in duplicate (1). At passage 21, there was an increase in the global fitness and in the genetic heterogeneity of the clones.…”

“…Several RNA viruses, mainly vesicular stomatitis virus (VSV), foot-andmouth disease virus (FMDV), or ⌽6, have been used in in vitro works to study viral evolution after serial passages (26,27), plaque to plaque (Muller's ratchet) (3,4,25), in large or alternating population sizes (11). Moreover, quasispecies heterogeneity has been found to be implicated in viral pathogenesis in poliovirus (37), mumps (31), West Nile virus (19), and HIV (1).…”

“…In these experiments, biological clones obtained from a patient's viral isolate (30) were subjected to serial bottleneck passages which produced drastic fitness losses (42) with an unusual distribution of associated mutations (41). Subsequent large-population passages of these debilitated clones showed a rapid fitness increase in only 10 passages (1,40). We disclosed that this recovery was found to be associated with an increase in viral quasispecies heterogeneity and occasionally with an invariable consensus sequence (1).…”