Evolutionary gamut of in vivo Gag substitutions during early HIV-1 subtype C infection

Abstract

Two analyses of HIV-1 subtype C Gag quasispecies were performed in a prospective cohort of 42 acutely and recently infected individuals by SGA on viral RNA/proviral DNA templates. First, in vivo Gag substitutions were assessed in relation to the HIV-1C consensus sequence, which revealed that 29.3% of detected amino acid substitutions can be classified as reversions to subtype consensus, 61.3% as forward substitutions from subtype consensus, and 9.3% as polymorphisms not associated with the subtype consensus sequence. Second, the proportion, dynamics, and relationships within individual pools of viral quasispecies were analyzed. Among reverse substitutions, 16.1% were minor, 11.0% transient, 13.6% dominant, and 59.2% fixed. In contrast, 31.6% of forward substitutions were minor, 59.3% transient, 3.8% dominant, and 5.3% fixed. The distinct patterns in the spectrum and dynamics of reverse and forward Gag substitutions suggest that these differences should be considered in HIV-1 evolutionary studies and analyses of viral mutational pathways.

Figure 1

Profile and location of total amino acid substitutions across Gag in a cohort of 42 HIV-1 subtype C-infected individuals. The cumulative non-synonymous substitutions identified by SGA during the time period from seroconversion to up to 500 days p/s are presented. The study subjects' code is shown at the left. Eight acutely infected subjects are highlighted. Three types of Gag substitutions are outlined as follows: green up triangle shows amino acid substitutions toward the HIV-1 subtype C consensus sequence – reverse substitutions, red down triangle denotes amino acid substitutions from the subtype C consensus – forward substitutions, and gray circle delineates viral amino acid polymorphisms not associated with the subtype C consensus sequence. Gray bars on the background denote HIV-1 Gag p17, p24, p2/p7p1/p6 for each subject.

Figure 2

Profile and location of dominant and fixed amino acid substitutions across HIV-1C Gag. See legend to Figure 1. The dashed line highlights 12 amino acid substitutions observed at Gag codon position 242.

Figure 3

Relationships between reverse and forward substitutions in HIV-1C Gag over time. The number of identified amino acid substitutions is shown in the left bottom corner of each graph. Analyzed time intervals in days from estimated seroconversion, the number of subjects, and the number of analyzed sequences per time interval including total, RNA, and DNA are shown at the bottom. A: Minor Gag substitutions (did not reach dominance or fixation, and did not disappear over the follow up time). B: Transient Gag substitutions. C: Dominant Gag substitutions (did not reach fixation over the follow up time). D: Fixed substitutions.

Figure 4

Relationships between different types of reverse and forward Gag substitutions over time. The number of identified substitutions is shown in the left bottom corner of each graph. Analyzed time intervals in days from estimated seroconversion are shown at the bottom. A: Reverse substitutions. B: Forward substitutions.

Figure 5

Proportion of individuals with detectable amino acid substitutions in Gag over time. Individuals with detectable reverse substitutions are shown by dark bars. Individuals with detectable forward substitutions are shown by light bars. Analyzed time intervals in days from estimated seroconversion are shown at the bottom.

Figure 6

Relationships between different types of Gag amino acid substitutions. A: Overall relationships between reverse substitutions, forward substitutions, and viral polymorphisms not directly associate with the subtype consensus sequence. B: Relationships within reverse substitutions, forward substitutions, and viral polymorphisms not directly associate with the subtype C consensus sequence. C: Breakdown of viral substitutions in Gag that either reached or did not reach dominance and/or fixation.