Figure 1.
Location of wild chimpanzee study sites.
Field sites are shown in relation to the ranges of the four proposed chimpanzee subspecies. White circles indicate forest areas where fecal samples were collected for prevalence studies (Table 3). These were located in Cote d'Ivoire (TA), Cameroon (MF, WE, MP, MT, DG, DP, BQ, CP, EK, BB, MB, LB), the Central African Republic (ME), Gabon (LP), Republic of Congo (GT), Democratic Republic of Congo (BD, WL, WK), Uganda (KB), Rwanda (NY), and Tanzania (GM-MT, GM-KK, GM-KL, MH). Black circles indicate forest sites where eight ancillary samples (BA432, BF1167, EP479, EP486, KS310, UB446, WA466, WA543) were collected. International borders and major rivers are shown.
Figure 2.
Detection of SFVcpz antibodies in chimpanzee fecal samples.
Enhanced chemiluminescent (ECL) Western blot analysis of fecal extracts from (A) human volunteers and captive chimpanzees, and (B) SFVcpz infected wild chimpanzees representing four different chimpanzee subspecies. Strips were prepared using an infectious molecular clone (pMod-1) of SFVcpzPts (see Methods). Samples are numbered, with letters indicating the species (panel A) or collection site (panel B) of origin. Molecular weights of SFVcpz specific Gag and Bet proteins are shown. The banding pattern of plasma from an SFVcpz infected chimpanzee (used at a 1∶100,000 dilution) and an uninfected human are shown as positive (Pos) and negative (Neg) controls, respectively.
Table 1.
Validation of Fecal-Based Antibody and Nucleic Acid Detection Assays Using Samples from SFVcpz Infected Captive Chimpanzees and Uninfected Human Volunteers.
Figure 3.
Location of RT-PCR derived amplicons in the SFVcpz genome.
Amplification products are shown in relation to the corresponding regions in the SFVcpz genome, with the length of the amplified fragments indicated. The genomic organization of SFVcpz is shown on the top (structural and accessory genes are drawn to scale) [79].
Table 2.
Sensitivities of Antibody and Viral RNA Detection in Fecal Samples From Captive and Wild Chimpanzees.
Table 3.
Prevalence Rates of SFVcpz Infection in Wild Chimpanzees throughout Equatorial Africa.
Figure 4.
Inverse correlation of fecal antibody and viral RNA detection at different field sites.
Fecal viral RNA (x-axis) and antibody (y-axis) detection sensitivities are plotted for field sites with known numbers of infected chimpanzees (Table 2). The size of the circle is directly proportional to the number of samples tested (results from the three Gombe communities were combined). Color coding and corresponding two letter codes are as in Figure 1. Test sensitivities are significantly inversely correlated (P<0.001).
Table 4.
Number of SFVcpz and SIVcpz Infections in Chimpanzee Communities Harboring Both Viruses.
Figure 5.
Increase of SFVcpz infection rates with age.
Members of the habituated Mitumba and Kasekela communities in Gombe National Park were non-invasively tested for SFVcpz infection and their infection rate (y-axis) plotted by age group (x-axis). Group 1 comprises 4 infants age 2 or younger; group 2 comprises 10 chimpanzees age 2.1 to 9 years; and group 3 comprises 13 adult chimpanzees age 14 to 45.
Table 5.
SFVcpz Infection in Three Mother-Offspring Pairs in Gombe National Park.
Figure 6.
Evolutionary relationships of newly derived SFVcpz strains in the pol-IN region.
Pol-IN (425 bp) sequences were analyzed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in BEAST. Sequence LM183 (from a wild bonobo) was included as an outgroup. The maximum clade credibility (MCC) tree topology inferred using TreeAnnotator v1.4.7 is shown, with branch lengths depicting the mean value for that branch in the upper half of the MCMC sample. Posterior probabilities (expressed as percentages) are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (as shown in Figure 1). Representative strains from the database are shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (a complete list is provided in Table S2). Sample WE464 (boxed) was collected in the P. t. vellerosus range, but has a P. t. troglodytes mtDNA haplotype (Figure S1). Arrows identify distinct SFVcpz strains (termed A or B) that were found in the same sample. The scale bar represents 0.02 substitutions per site.
Figure 7.
Evolutionary relationships of newly derived SFVcpz strains in the gag region.
Gag (616 bp) sequences were analyzed as described in Figure 6. The gag tree was rooted using a relaxed clock. Posterior probabilities are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (Figure 1). Representative strains from the database are shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (Table S2). Sample WE464 (boxed) was collected in the P. t. vellerosus range, but has a P. t. troglodytes mtDNA haplotype (Figure S1). The scale bar represents 0.02 substitutions per site.
Figure 8.
Evolutionary relationships of newly derived SFVcpz strains in the pol-RT region.
Pol-RT (718 bp) sequences were analyzed as described in Figure 6. The tree was rooted using LM183 as an outgroup. Posterior probabilities are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (Figure 1). One representative strain from the database (HFV) is shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (Table S2). Sample WE464 (boxed) was collected in the P. t. vellerosus range, but has a P. t. troglodytes mtDNA haplotype (Figure S1). Arrows identify distinct SFVcpz strains (termed A or B) that were found in the same sample. The scale bar represents 0.02 substitutions per site.
Figure 9.
Coinfection and recombination in SFVcpz.
(A) The maximum clade credibility (MCC) topology of pol-IN sequences is shown, with branch lengths as described in Figure 6. Brackets indicate the number of distinct SFVcpz strains that are present in samples DP157 and MF1279, respectively. Bulk PCR derived sequences are shown in red; SGA derived sequences are shown in blue. Numbers on nodes indicate posterior probabilities expressed as percentages (only values of 90% or higher are shown). The scale bar represents 0.009 substitutions per site. (B) Maximum clade credibility (MCC) topologies of gag sequences in two adjacent fragments are shown. Viruses that exhibit discordant branching patterns are highlighted. Numbers on nodes indicate percentage posterior probabilities. The scale bars represent 0.02 substitutions per site.
Figure 10.
Cross-species transmission of SFV in the wild.
The maximum clade credibility (MCC) topology of pol-IN sequences is shown, with branch lengths as described in Figure 6. The chimpanzee SFV strain LB309 (red box) significantly clusters within a group of SFVs previously derived from captive L'Hoest's (LHO), Hamlyn's (HAM), mustached (MUS), DeBrazza's (DEB), mona (MON), Sykes's (SYK) and blue (BLU) monkeys (GenBank accession numbers are indicated in parentheses), thus strongly suggesting a Cercopithecus monkey origin. Newly derived SFV sequences from a bonobo (LM183), gorilla (LP5), mandrill (LP47) and DeBrazza's monkey (CNE01) are also shown (blue) in relation to reference sequences from Chlorocebus and Mandrillus species (black). Numbers on nodes indicate posterior probabilities expressed as percentages (only 90% or higher are shown). The scale bar represents 0.08 substitutions per site.