Article Figures & Data
Figures
- FIG 1
Species-level phylogenetic relationships of all known pegiviruses (A) and arteriviruses (B). Viruses are shown adjacent to the silhouette of their respective host, with host common names in italics. Primate hosts are shown in black, and nonprimate hosts are shown in gray. Viruses discovered in this study are depicted by host silhouettes with solid coloring: green for AGM pegiviruses and blue for AGM arteriviruses. Host silhouettes with a colored outline draw attention to viruses of importance. Sabaeus SPgV (SPgVsab) has a green outline because this virus does not group with the AGM pegiviruses presented here. SHEV has a blue outline because of its close relationship to the AGM arteriviruses presented here. White host silhouettes symbolize arteriviruses that have caused outbreaks of viral hemorrhagic fever in captive macaques. Question marks emphasize that the natural host(s) of these viruses remains unknown. Shown is a maximum likelihood tree with 1,000 bootstrap replicates. Black dots indicate splits that are supported by 100% of bootstrap replicates. Bootstrap values below 70 are not shown. The bar shows the calculated genetic distance. SPgVkrc, Kibale red colobus; SPgVkrtg, Kibale red-tailed guenon; SPgVob, SPgV from olive baboon; SPgVmyb, Mikumi yellow baboon; BPgV, bat pegivirus; SPgVtri, owl monkey; SPgVcal-mx, marmoset-mystax; SPgVlab, tamarin; EqPgV, equine pegivirus; TDAV, Theiler's disease-associated virus; RPgV, rat PgV; KRTGV-1, Kibale red-tailed guenon virus; DeMBV-1, Debrazza's monkey virus; PBJV, Peter B. Jahrling virus; KKCBV-1, Kafue kinda-chacma baboon virus; MYBV-1, Mikumi yellow baboon virus; SWBV-1, Southwest baboon virus; KRCV-1, Kibale red colobus virus; LaDV-1, lactate dehydrogenase elevating virus; PRRSV-1, porcine reproductive and respiratory syndrome virus; APRAV-1, African pouched rat virus; EAV, equine arteritis virus; WPDV, wobbly possum disease virus.
- FIG 2
Geographic distribution and prevalence of AGM plasma viruses. Shown are prevalences of SIV, SPgV, and simian arteriviruses in wild AGMs sampled from Zambia (malbrouck monkey [Chlorocebus cynosuros]) and South Africa (vervet monkey [Chlorocebus pygerythrus]). Venn diagrams of each monkey population show the percentages of uninfected, monoinfected, coinfected, and triple-infected monkeys for each of these three viruses. Gray circles represent the total numbers of monkeys sampled and are proportional to the sample size from each location. Numbers within the gray circles but outside the colored circles are the percentages of each population that are triple negative for virus (white). Colored circles within gray circles show the percentages of each population infected with SIV, SPgV, or DMVV-1/ZMbV-1 that are monoinfected, coinfected, or triple infected. Adjacent colored numbers outside the circles show the percentages of each population infected with the respective virus. Sites I and J are from the Riverside Rehabilitation Center, which houses vervet monkeys from across the region. The prevalence of each virus was determined by using a combination of deep sequencing, qRT-PCR, and RT-PCR.
- FIG 3
Phylogenetic relationships of all SPgV variants discovered in this study. A PCR amplicon spanning the putative NS3 coding region of the SPgVver genome was sequenced from samples that tested positive for SPgV RNA by qRT-PCR that were not subjected to unbiased deep sequencing. Shown is a maximum likelihood tree, not rooted, with 1,000 bootstrap replicates. Black dots indicate splits that are supported by 100% of bootstrap replicates. Bootstrap values below 70 are not shown. The bar shows the calculated genetic distance.
- FIG 4
Phylogenetic relationships of all AGM simian arteriviruses discovered in this study. A PCR amplicon spanning ORF1b of the DMVV-1 genome was sequenced from samples that tested positive for DMVV-1 RNA by qRT-PCR that were not subjected to unbiased deep sequencing. Shown is a maximum likelihood tree, not rooted, with 1,000 bootstrap replicates. Black dots indicate splits that are supported by 100% of bootstrap replicates. Bootstrap values below 70 are not shown. The bar shows the calculated genetic distance.
- FIG 5
Viremia of the AGM plasma viruses. (A) SPgVver and DMVV-1 RNA concentrations were quantified from plasma samples of 161 South African vervet monkeys by using highly sensitive virus-specific qRT-PCR assays designed from deep-sequencing data. Only positive results are shown. SIVver loads were determined previously (23) by the same method. Significance was assessed by using a two-tailed unpaired t test on log-transformed values, with error bars showing the standard errors of the means. (B) South African vervets were stratified by coinfection status, and plasma viral load values for the virus in question were plotted. Significance was assessed by using a two-tailed unpaired t test on log-transformed values, with error bars showing the standard errors of the means. (C) Linear regression correlating the viral load of each virus in coinfected individuals. Data points with a colored halo indicate triple-infected individuals.
- FIG 6
Genetic diversity of AGM plasma viruses. (A) Complete consensus sequences spanning the entire coding region of each virus were aligned, and a pairwise comparison between each aligned sequence was performed. Percent identity values from each comparison were plotted and compared by using a two-tailed unpaired t test. Boxes show the middle two quartiles, and whiskers show the minimum and maximum percent identities observed. (B) Synonymous (πS) and nonsynonymous (πN) viral nucleotide diversities within each infected monkey, determined by calculating πS and πN values across the entire viral genome. Only samples that yielded virus sequences with >100× coverage for >99% of the protein-coding region of the genome were used for this analysis. Significance was assessed by using a two-tailed unpaired t test, with error bars showing the standard errors of the means. (C) Linear regression correlating within-host nucleotide diversity and plasma viral load for each virus.
- FIG 7
Known geographic and host ranges of African monkey plasma viruses. (A) Map of Africa showing the sampling locations of monkeys in which simian pegivirus or simian arterivirus infection was identified. In the table, a colored dot indicates that SIV (red), SPgV (green), or a simian arterivirus (blue) infection was detected in that particular primate from that particular location (61–64). NYP, not yet published. (B) Genus-level phylogenetic tree of African OWMs and great apes. Colored dots indicate that SIV (red), GBV-C (green), or SHFV (blue) infection was detected in a primate from that genus. Names in boldface type indicate genera from which we have sampled more than 10 wild primates by unbiased deep sequencing (for a comprehensive list of species naturally infected with SIV, see reference 65). (Adapted from PLoS Genetics [66].)
Tables
- TABLE 1
Nonsynonymous and synonymous nucleotide diversities for all open reading frames of SPgVver, SIVver, and DMVV-1 in African green monkeysa
Virus ORF Mean πN ± SE Mean πS ± SE P valueb SIVver gag*** 0.002387 ± 0.00029 0.02153 ± 0.00185 1.24 × 10−35 pol*** 0.001595 ± 0.00014 0.01808 ± 0.00101 8.59 × 10−70 vif*** 0.002705 ± 0.00038 0.00939 ± 0.00216 5.05 × 10−6 vpx*** 0.001078 ± 0.00033 0.01158 ± 0.00319 1.62 × 10−6 tat 0.006165 ± 0.00118 0.00351 ± 0.00137 0.189 rev*** 0.005369 ± 0.00117 0.02000 ± 0.00324 9.87 × 10−6 env*** 0.006657 ± 0.00057 0.02102 ± 0.00138 1.20 × 10−30 nef*** 0.004809 ± 0.00069 0.01738 ± 0.00218 1.19 × 10−10 SPgVver SPgV*** 0.000214 ± 0.00003 0.00208 ± 0.00019 7.00 × 10−33 DMVV-1 1a*** 0.000954 ± 0.00008 0.01208 ± 0.00078 9.02 × 10−65 TF 0.001643 ± 0.00035 0.00287 ± 0.00088 0.0251 1b*** 0.000385 ± 0.00006 0.01289 ± 0.00071 1.70 × 10−82 2a′*** 0.001221 ± 0.00027 0.01175 ± 0.00158 5.73 × 10−13 3′*** 0.002715 ± 0.00052 0.01108 ± 0.00203 1.96 × 10−6 4′*** 0.001358 ± 0.00036 0.01023 ± 0.00195 1.96 × 10−8 2a*** 0.001255 ± 0.00044 0.01212 ± 0.00262 5.41 × 10−5 2b** 0.001889 ± 0.00032 0.00551 ± 0.00109 0.000391 3*** 0.003706 ± 0.00064 0.01117 ± 0.00179 3.34 × 10−5 4 0.005481 ± 0.00082 0.00730 ± 0.00124 0.0433 5a* 0.007072 ± 0.00153 0.02214 ± 0.00511 0.000655 5 0.009080 ± 0.00181 0.01100 ± 0.00195 0.156 6*** 0.000371 ± 0.00014 0.00705 ± 0.00180 4.45 × 10−6 7*** 0.001382 ± 0.00033 0.00887 ± 0.00197 2.68 × 10−5 ↵a Bonferroni significance levels were used to account for the use of 23 tests, one for each open reading frame, as follows: *, α value of <0.05 if the P value was <0.00217; **, α value of <0.01 if the P value was <0.000435; ***, α value of <0.001 if the P value was <4.35 × 10−5. Significance levels refer to a paired t test where πN equals πS.
↵b Determined by a paired t test.
- TABLE 2
Peaks of nonsynonymous nucleotide diversity for all open reading frames of SPgVver, SIVver, and DMVV-1 in South African vervet monkeysa
Virus ORF Start position Stop position Length (no. of codons) % of variants with nonsynonymous polymorphism SIVver (n = 13) gag — — — — pol — — — — vif — — — — vpx — — — — tat 5685 5735 17 31 7980 8120 47 85 rev — — — — env 6107 6226 40 92 6335 6376 14 85 7013 7078 22 62 nef — — — — SPgVver (n = 17) 1053 1082 10 24 1326 1376 17 29 2244 2282 13 24 2403 2438 12 12 2604 2630 9 29 6696 6746 17 12 8922 8966 15 47 DMVV-1 (n = 14) 1a 733 768 12 21 TF 2924 3064 47 71 3152 3232 27 50 3512 3541 10 21 1b — — — — 2a′ — — — — 3′ 11389 11442 18 64 11527 11565 13 57 4′ — — — — 2a — — — — 2b 12470 12526 19 79 3 13201 13230 10 64 4 13227 13307 27 86 13512 13571 20 71 5a — — — — 5 13748 13849 34 79 13922 13987 22 100 6 — — — — 7 — — — — ↵a Peaks were identified conservatively as 9-codon sliding windows in which πN exceeded both the respective window's πS and the mean value of πS for the ORF. Start and stop sites refer to approximate nucleotide coordinates in the genome sequence. Dashes indicate the absence of a nonsynonymous peak in that ORF.
- TABLE 3
Relationship between viral infection status and demographic features of South African vervet monkeys
Response variable Predictor variablea df t P SIVver Age* 112 6.208 <0.001 Male sex* −2.287 0.02 SPgV infection* 4.402 <0.001 DMVV-1 infection 0.585 0.559 SPgVver Age 112 −0.938 0.350 Male sex 1.241 0.217 SIV infection* 4.402 <0.001 DMVV-1 infection 1.420 0.158 DMVV-1 Age 112 −0.361 0.719 Male sex −0.675 0.501 SIV infection 0.585 0.560 SPgV infection 1.420 0.158 ↵a Asterisks signify predictor variables with a statistically significant relationship.
- TABLE 4
Relationship between viral infection status and plasma cytokine concentrations in South African vervet monkeysa
Virus Cytokine t value for cytokine P value (uncorrected) for cytokine P (corrected) for cytokine Model covariate t value for model covariate P value (uncorrected) for model covariate P (corrected) for model covariate DMVV-1 EGF 2.27 0.040 >1.0 Age −2.07 0.040 >1.0 GM-CSF 3.19 0.002 0.05 Age −0.27 0.788 >1.0 Sex (male) 2.22 0.029 0.81 IL-1β 2.29 0.024 0.67 Age −2.42 0.017 0.48 Sex (male) 3.19 0.002 0.05 IL-10 2.36 0.020 0.56 Sex (male) 1.71 0.089 >1.0 MCP-1 1.95 0.049 >1.0 Age −2.05 0.043 >1.0 Sex (male) 3.83 <0.01 <0.01 MIP-1β 3.09 0.003 0.07 Age −2.53 0.012 0.36 TNF-α 2.10 0.038 >1.0 Sex (male) 2.10 0.038 >1.0 SPgVver MIG −2.24 0.027 0.76 Sex (male) 4.06 <0.01 <0.01 SIV −0.84 0.404 >1.0 SIV*SPgV 2.46 0.016 0.43 SIVver IFN-γ −2.79 0.006 0.18 IL-6 1.79 0.043 >1.0 SPgV −1.19 0.236 >1.0 SIV*SPgV 1.52 0.131 >1.0 I-TAC 2.20 0.030 0.84 MIF 2.15 0.034 0.95 Age −2.14 0.034 0.95 ↵a A multivariate linear model was developed, and model covariates were identified by using stepwise backward elimination. Uncorrected P values are those inferred by the model. Corrected P values represent Bonferroni-corrected P values for a total of 28 hypotheses tested (one for each cytokine). For a full list of cytokines tested, see Table S1 in the supplemental material.
Supplemental material
- Supplemental file 1 -
Table S1 (Viral loads, sequence accession numbers, animal identifiers and demographic information, and cytokine levels for each animal or virus in this study.)
XLSX, 145K
- Supplemental file 1 -
