HIV-1 Env C2-V4 diversification in a slow-progressor infant reveals a flat but rugged fitness landscape

PLoS One. 2013 Apr 29;8(4):e63094. doi: 10.1371/journal.pone.0063094. Print 2013.

Abstract

Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. 'Winners' and 'losers' were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N = 33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a 'survival of the fittest' evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless significantly impact viral fitness suggests fitness is best defined by head-to-head competition.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles
  • CD4-Positive T-Lymphocytes / virology
  • Cloning, Molecular
  • Genetic Variation*
  • Growth and Development*
  • HEK293 Cells
  • HIV-1 / genetics*
  • HIV-1 / physiology*
  • Humans
  • Hybridization, Genetic
  • Infant
  • Mutation
  • Receptors, Virus / metabolism
  • Viral Envelope Proteins / biosynthesis
  • Viral Envelope Proteins / chemistry*
  • Viral Envelope Proteins / genetics*
  • Viral Envelope Proteins / metabolism
  • Virion / genetics
  • Virion / physiology
  • Virus Internalization
  • Virus Replication / genetics

Substances

  • Receptors, Virus
  • Viral Envelope Proteins