Research ArticleVirology

Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection

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Science Translational Medicine  16 Sep 2015:
Vol. 7, Issue 305, pp. 305ra144
DOI: 10.1126/scitranslmed.aab3467
  • Fig. 1. Phylogenetic relationships between pegiviruses and their primate hosts.

    (A) Sampling locations of olive and yellow baboons that naturally harbor SPgVs used in this study. The prevalence of SPgVkob in the Kibale olive baboon and SPgVmyb in the Mikumi yellow baboon is also shown. (B) Phylogenetic tree of known pegiviruses including those that infect humans (HPgV), simians (SPgV), bats (BPgV), rodents (RPgV), and horses (EqPgV). Specific isolates used to infect macaques (Fig. 2) are shown in color (SPgVmyb, yellow; SPgVkob, green). Black circles denote branches supported by a bootstrap value of 100; bootstrap values <70 are not shown. (C) Phylogenetic tree of primates known to harbor PgVs, highlighting the evolutionary relationships of these primates to macaques [adapted from (51)].

  • Fig. 2. Infection of macaques with baboon SPgVs.

    (A) Plasma SPgVmyb viral loads in the Mikumi yellow baboons (yellow) and the longitudinal viral loads from cy0571 infected with SPgVmyb. (B to E) Plasma SPgVkob viral load in the single Kibale olive baboon (green) and the longitudinal viral loads of macaques infected with SPgVkob from olive baboon plasma (green), cy0500 plasma collected at 8 dpi (D, black), or cy0575 plasma collected at 25 dpi (E, blue, male) or 36 dpi (C, pink, female). Y axis, log10 SPgV gc per milliliter of plasma; x axis, days post-infection unless otherwise stated. Specific colors and symbols refer to the same animal throughout the manuscript. Animal IDs surrounded by a box indicate SIVmac239 infection before SPgV inoculation, with dashed boxes signifying SIVmac239Δnef infection/vaccination. Additional information about each animal can be found in table S2. S, whole genome sequencing; X, splenectomy.

  • Fig. 3. Inoculating dose affects acute-phase, but not chronic-phase, SPgV viremia.

    (A) First 40 days of infection for all animals in this study. Graph highlights the predictable course of SPgVkob viremia in macaques inoculated with a high dose of SPgV and the highly variable course of SPgV viremia in macaques inoculated with a low dose of SPgVkob. (B and C) Quantification of peak viremia and time-to-peak viremia in high-dose versus low-dose groups (two-tailed unpaired t test; error bars represent SEM). (D) Comparison of set-point viremia, as defined by the average of at least three viral load measurements, taken over a period of at least 25 days, which did not differ by more than 1 log10 among groups receiving different doses of SPgVkob. One-way analysis of variance (ANOVA); error bars represent SEM.

  • Fig. 4. SPgV shows little nucleotide variation over the course of infection.

    Deep sequencing reads from the latest available time point from each SPgVkob-infected animal were mapped to the SPgVkob_K23 reference genome (see tables S3 to S5 for sequencing statistics and details). (A to C) Consensus-level variants are shown for (A) each animal, (B) in summary, and (C) graphically. Univariate linear regression analysis with trend lines for synonymous (blue), nonsynonymous (red), and total variants (black). (D) Intrahost frequency of the most common mutation (T746M) over time in five macaques.

  • Fig. 5. SPgV maintains low intrahost diversity over the course of infection.

    Deep sequencing reads from time points throughout the infection of cy0572 were mapped to the SPgVkob_K23 reference genome, and variants >1% were identified (see table S4 for sequencing statistics and coverage details). A schematic of the SPgVkob genome with putative protein products is shown at the top. Blue bars represent synonymous variants present in the viral population, and red bars represent nonsynonymous variants.

  • Fig. 6. SPgV is primarily a bone marrow–tropic virus.

    (A) Tissue viral load (gc/mg) normalized to plasma viral load (gc/μl), one-way ANOVA. Note that bone marrow was not recoverable from cy0493 due to atrophy. (B and C) Plasma viral loads before and after splenectomy, two-tailed paired t test. (D) Cell-associated viral loads (gc/1 × 106 cells) performed in duplicate on RNA extracted from 3 × 106 leukocytes purified from each tissue. One-way ANOVA; error bars represent SEM.

Supplementary Materials

  • www.sciencetranslationalmedicine.org/cgi/content/full/7/305/305ra144/DC1

    Fig. S1. Parameters of SIV-induced disease in study animals.

    Fig. S2. Lack of SPgV-induced disease in study animals.

    Fig. S3. SPgVs exhibit little sequence variability in natural hosts.

    Fig. S4. The tissue tropism of SPgV may vary depending on the duration of infection.

    Table S1. Sequencing of SPgVs from wild baboons.

    Table S2. Demographic information for macaques used in this study.

    Table S3. Sequencing of SPgVmyb in cy0571.

    Table S4. Sequencing of macaques infected with SPgVkob.

    Table S5. SPgVmyb consensus-level variants in cy0571 at 219 dpi not found in inocula.

  • Supplementary Material for:

    Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection

    Adam L. Bailey, Michael Lauck, Mariel Mohns, Eric J. Peterson, Kerry Beheler, Kevin G. Brunner, Kristin Crosno, Andres Mejia, James Mutschler, Matthew Gehrke, Justin Greene, Adam J. Ericsen, Andrea Weiler, Gabrielle Lehrer-Brey, Thomas C. Friedrich, Samuel D. Sibley, Esper G. Kallas, Saverio Capuano III, Jeffrey Rogers, Tony L. Goldberg, Heather A. Simmons, David H. O'Connor*

    *Corresponding author. E-mail: doconnor{at}primate.wisc.edu

    Published 16 September 2015, Sci. Transl. Med. 7, 305ra144 (2015)
    DOI: 10.1126/scitranslmed.aab3467

    This PDF file includes:

    • Fig. S1. Parameters of SIV-induced disease in study animals.
    • Fig. S2. Lack of SPgV-induced disease in study animals.
    • Fig. S3. SPgVs exhibit little sequence variability in natural hosts.
    • Fig. S4. The tissue tropism of SPgV may vary depending on the duration of infection.
    • Table S1. Sequencing of SPgVs from wild baboons.
    • Table S2. Demographic information for macaques used in this study.
    • Table S3. Sequencing of SPgVmyb in cy0571.
    • Table S4. Sequencing of macaques infected with SPgVkob.
    • Table S5. SPgVmyb consensus-level variants in cy0571 at 219 dpi not found in inocula.

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