Maintenance and reappearance of extremely divergent intra-host HIV-1 variants

Abstract

Understanding genetic variation in human immunodeficiency virus (HIV) is clinically and immunologically important for patient treatment and vaccine development. We investigated the longitudinal intra-host genetic variation of HIV in over 3,000 individuals in the US National HIV Surveillance System with at least four reported HIV-1 polymerase (pol) sequences. In this population, we identified 149 putative instances of superinfection (i.e. an individual sequentially infected with genetically divergent, polyphyletic viruses). Unexpectedly, we discovered a group of 240 individuals with consecutively sampled viral strains that were >0.015 substitutions/site divergent, despite remaining monophyletic in the phylogeny. Viruses in some of these individuals had a maximum genetic divergence approaching that found between two random, unrelated HIV-1 subtype-B pol sequences within the US population. Individuals with these highly divergent viruses tended to be diagnosed nearly a decade earlier in the epidemic than people with superinfection or virus with less intra-host genetic variation, and they had distinct transmission risk factor profiles. To better understand this genetic variation in cases with extremely divergent, monophyletic viruses, we performed molecular clock phylogenetic analysis. Our findings suggest that, like Hepatitis C virus, extremely divergent HIV lineages can be maintained within an individual and reemerge over a period of years.

Keywords: HIV; genetic variation; molecular evolution; superinfection.

Figure 1.

Maximum intra-host genetic distance. Color denotes group: gray are the 2,914 individuals with monophyletic virus in which no consecutive virus is >0.015 substitutions/site divergent; red are the 240 individuals with monophyletic virus in which ≥1 consecutive virus is >0.015 substitutions/site; blue are the 149 individuals with monophyletic virus in which ≥1 consecutive virus is >0.015 substitutions/site divergent.

Figure 2.

Comparison of individuals with monophyletic (mono) and polyphyletic (poly) viruses. (A) Density plots of year of diagnosis. Mean diagnosis year is shown with dashed lines. (B) Percentage composition of each group by transmission risk factor. (C) Frequency of different DRAMs in each group. Color denotes group: gray are the 2, 914 individuals with monophyletic virus in which no consecutive virus is >0.015 substitutions/site divergent; red are the 240 individuals with monophyletic virus in which ≥1 consecutive virus is >0.015 substitutions/site divergent; blue are the 149 individuals with monophyletic virus in which ≥1 consecutive virus is >0.015 substitutions/site divergent.

Figure 3.

Maximum clade credibility trees from BEAST analysis. These eleven cases (A–K) were monophyletic in the phylogeny, have maximum genetic distance >0.025 substitutions/site, and at least ten reported viral genotypes. The earliest sampled (i.e. baseline) genotype is highlighted in bold. The height of the tips in these trees corresponds with date of sampling, and tips are labeled with year and month of sampling. Circles denote virus that is >0.015 substitutions/site from previously sampled genotype. All trees are shown on same time-scale. Branch color denotes drug resistance profile at M184V; clades are colored only when entire clade shares same profile. Asterisks indicate posterior support ≥0.90.

Figure 4.

Longitudinal genetic distance from the earliest sampled (i.e. baseline) sequence. These eleven cases (A–K) were monophyletic in the phylogeny, have maximum genetic distance >0.025 substitutions/site, and at least ten reported viral genotypes. Node shape denotes the genetic relationship to the previous sequence. Note that the resolution of ambiguous bases can result in violations of the triangle inequality for genetic distance among viruses. Color denotes drug resistance profile at M184V. Dashed horizontal lines indicate 0.015 substitutions/site from baseline sequence.