Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology

Abstract

Infection of CD8-depleted rhesus macaques with the genetically heterogeneous simian immunodeficiency virus (SIV)mac251 viral swarm provides a rapid-disease model for simian acquired immune deficiency syndrome and SIV-encephalitis (SIVE). The objective was to evaluate how the diversity of the swarm influences the initial seeding of the infection that may potentially affect disease progression. Plasma, lymphoid and non-lymphoid (brain and lung) tissues were collected from two infected macaques euthanized at 21 days post-infection (p.i.), as well as longitudinal specimens and post-mortem tissues from four macaques followed throughout the infection. About 1300 gp120 viral sequences were obtained from the infecting SIVmac251 swarm and the macaques longitudinal and post-mortem samples. Phylogenetic and amino acid signature pattern analyses were carried out to assess frequency, transmission dynamics and persistence of specific viral clusters. Although no significant reduction in viral heterogeneity was found early in infection (21 days p.i.), transmission and replication of SIV variants was not entirely random. In particular, two distinct motifs under-represented (<4 %) in the infecting swarm were found at high frequencies (up to 14 %) in all six macaques as early as 21 days p.i. Moreover, a macrophage tropic variant not detected in the viral swarm (<0.3 %) was present at high frequency (29-100 %) in sequences derived from the brain of two macaques with meningitis or severe SIVE. This study demonstrates the highly efficient transmission and persistence in vivo of multiple low frequency SIVmac251 founder variants, characterized by specific gp120 motifs that may be linked to pathogenesis in the rapid-disease model of neuroAIDS.

Fig. 1.

SIV copy number and the CD8 absolute count over time in infected macaques. (a) SIV copy number (y-axis) is given in eq ml⁻¹; time (x-axis) is in days p.i. Inoculated macaques were treated with an anti-CD8 antibody at 6 days p.i. Macaques D01 and D02 were euthanized at 21 days p.i. Macaques D03, D04, D05 and D06 followed throughout the duration of the infection until death. (b) CD8 absolute counts (y-axis); time (x-axis) is given in days p.i. for macaques D03, D04, D05 and D06.

Fig. 2.

Early transmission of SIVmac251 gp120 clusters in intravenous CD8-depleted macaques. The black bar denotes the frequency of the cluster within the viral swarm. The white bar represents the frequency of the weighted cluster in all the primates combined. The asterisk shows P-values ≤0.05 based on the Fisher’s exact test.

Fig. 3.

Representative sequences with distinctive gp120 amino acid signature from infected macaques. Sequences were aligned to the 1A11 (AC: M76764) and the SIVmac239 (AC: M33262) clone. Identical amino acids are indicated by a dot. Motifs detected by signature pattern analysis are highlighted with a box. Sequences labelled as SIVmac251 are from viral swarm used to infect the macaques. Sequences labelled as D01–D06 are from different infected macaques; sampling time is given in days p.i. (a) Representative SIVmac251 and plasma sequences belonging to clusters 9 and 14. UC, Unclassified sequences. (b) Representative sequences of the macrophage-tropic viral variant I_E_D detected in plasma and different post-mortem tissues from infected macaques.

Fig. 4.

ML genealogies of gp120 sequences from infected macaques. Each tree includes all plasma and tissue sequences sampled from macaque D01 (a), D02 (b), D03 (c), D04 (d), D05 (e) or D06 (f), respectively. Branches are scaled in substitutions per site according to the scale bar (0.005) at the bottom left corner and coloured to represent the tissue of origin as follows: plasma and lymphoid 21 days p.i. (blue), plasma and lymphoid 61 days p.i. (green), plasma and lymphoid post-mortem (red), brain (cyan), BAL 61 days p.i. (dark brown), BAL post-mortem (light brown). Sequences containing the R_ AQN_S_V, L_V and I_E_D motifs are indicated by an oval, triangle and square, respectively. Branches with bootstrap support >75 % are denoted with an asterisk. Bootstrap values >50 % for the divergent branch in D05 and D06 are provided.