The presence of a vpu gene and the lack of Nef-mediated downmodulation of T cell receptor-CD3 are not always linked in primate lentiviruses

Nef is an accessory protein critical for the ability of human and simian immunodeficiency viruses (HIV and SIV) to replicate efficiently in their respective hosts. Previous analyses of members of 15 different primate lentivirus lineages revealed a link between Nef function and the presence of a vpu gene. In particular, Nef proteins of all vpu-containing viruses had lost their ability to downmodulate the T cell (TCR-CD3) receptor. Here we examined Nef proteins from eight additional SIV lineages, including SIVgor, SIVwrc, SIVolc, SIVgri, SIVdrl, SIVlho, SIVden, and SIVasc, from western lowland gorillas, western red colobus monkeys, olive colobus monkeys, grivet monkeys, drills, L'Hoest's monkeys, Dent's mona monkeys, and red-tailed monkeys, respectively. We found that except for the nef gene of SIVdrl, all of them were efficiently expressed and modulated CD4, major histocompatibility complex class I (MHC-I), CD28, CXCR4, and Ii cell surface expression and/or enhanced viral infectivity and replication. Furthermore, the Nef proteins of SIVgri, SIVlho, SIVwrc, SIVolc, and SIVgor antagonized tetherin. As expected, the Nef protein of SIVgor, which carries vpu, failed to downmodulate CD3, whereas those of SIVwrc, SIVgri, SIVlho, and SIVasc, which lack vpu, were capable of performing this function. Surprisingly, however, the Nef protein of the vpu-containing SIVden strain retained the ability to downmodulate TCR-CD3, whereas that of SIVolc, which does not contain vpu, was unable to perform this function. Although the SIVden Vpu is about 20 amino acids shorter than other Vpu proteins, it degrades CD4 and antagonizes tetherin. Our data show that there are exceptions to the link between the presence of a vpu gene and nef alleles deficient in CD3 modulation, indicating that host properties also affect the selective pressure for Nef-mediated disruption of TCR-CD3 signaling. Our results are also further evidence that tetherin antagonism is a common function of primate lentivirus Nef proteins and that the resistance of human tetherin to Nef represents a relevant barrier to cross-species transmission of SIVs to humans.     

Characterization of a novel simian immunodeficiency virus from guereza colobus monkeys (Colobus guereza) in Cameroon: a new lineage in the nonhuman primate lentivirus family

Exploration of the diversity among primate lentiviruses is necessary to elucidate the origins and evolution of immunodeficiency viruses. During a serological survey in Cameroon, we screened 25 wild-born guereza colobus monkeys (Colobus guereza) and identified 7 with HIV/SIV cross-reactive antibodies. In this study, we describe a novel lentivirus, named SIVcol, prevalent in guereza colobus monkeys. Genetic analysis revealed that SIVcol was very distinct from all other known SIV/HIV isolates, with average amino acid identities of 40% for Gag, 50% for Pol, 28% for Env, and around 25% for proteins encoded by five other genes. Phylogenetic analyses confirmed that SIVcol is genetically distinct from other previously characterized primate lentiviruses and clusters independently, forming a novel lineage, the sixth in the current classification. Cercopithecidae monkeys (Old World monkeys) are subdivided into two subfamilies, the Colobinae and the Cercopithecinae, and, so far, all Cercopithecidae monkeys from which lentiviruses have been isolated belong to the Cercopithecinae subfamily. Therefore, SIVcol from guereza colobus monkeys (C. guereza) is the first primate lentivirus identified in the Colobinae subfamily and the divergence of SIVcol may reflect divergence of the host lineage.     

The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys

Cross-species transmissions of viruses from animals to humans are at the origin of major human pathogenic viruses. While the role of ecological and epidemiological factors in the emergence of new pathogens is well documented, the importance of host factors is often unknown. Chimpanzees are the closest relatives of humans and the animal reservoir at the origin of the human AIDS pandemic. However, despite being regularly exposed to monkey lentiviruses through hunting, chimpanzees are naturally infected by only a single simian immunodeficiency virus, SIVcpz. Here, we asked why chimpanzees appear to be protected against the successful emergence of other SIVs. In particular, we investigated the role of the chimpanzee APOBEC3 genes in providing a barrier to infection by most monkey lentiviruses. We found that most SIV Vifs, including Vif from SIVwrc infecting western-red colobus, the chimpanzee’s main monkey prey in West Africa, could not antagonize chimpanzee APOBEC3G. Moreover, chimpanzee APOBEC3D, as well as APOBEC3F and APOBEC3H, provided additional protection against SIV Vif antagonism. Consequently, lentiviral replication in primary chimpanzee CD4⁺ T cells was dependent on the presence of a lentiviral vif gene that could antagonize chimpanzee APOBEC3s. Finally, by identifying and functionally characterizing several APOBEC3 gene polymorphisms in both common chimpanzees and bonobos, we found that these ape populations encode APOBEC3 proteins that are uniformly resistant to antagonism by monkey lentiviruses.     

Interspecific interactions between wild pygmy chimpanzees (Pan paniscus) and red colobus (Colobus badius)

Interspecific interactions accompanied by physical contacts between wild pygmy chimpanzees (Pan paniscus) and red colobus (Colobus badius) were observed on three occasions at Wamba, Republic of Zaire. In all cases, the red colobus initiated the interactions by approaching the pygmy chimpanzees. Most of the pygmy chimpanzees, which were within 5 m of the red colobus, were juveniles or infants but the adult male pygmy chimpanzees never showed any interest in the red colobus. The red colobus groomed the chimpanzees in two cases, but the latter never groomed the former. No true aggressive interactions were observed between the two species. The lack of any evidence of hunting of red colobus through longitudinal studies of the pygmy chimpanzees of Wamba, together with the present observations, suggests that red colobus are probably not targets of hunting by the pygmy chimpanzees.     

Identification of a new simian immunodeficiency virus lineage with a vpu gene present among different cercopithecus monkeys (C. mona, C. cephus, and C. nictitans) from Cameroon

During a large serosurvey of wild-caught primates from Cameroon, we found 2 mona monkeys (Cercopithecus mona) out of 8 and 47 mustached monkeys (Cercopithecus cephus) out of 302 with human immunodeficiency virus (HIV)-simian immunodeficiency virus (SIV) cross-reactive antibodies. In this report, we describe the full-length genome sequences of two novel SIVs, designated SIVmon-99CMCML1 and SIVmus-01CM1085, isolated from one mona (CML1) and one mustached (1085) monkey, respectively. Interestingly, these viruses displayed the same genetic organization (i.e., presence of a vpu homologue) as members of the SIVcpz-HIV type 1 lineage and SIVgsn isolated from greater spot-nosed monkeys (Cercopithecus nictitans). Phylogenetic analyses of SIVmon and SIVmus revealed that these viruses were genetically distinct from other known primate lentiviruses but were more closely related to SIVgsn all across their genomes, thus forming a monophyletic lineage within the primate lentivirus family, which we designated the SIVgsn lineage. Interestingly, mona, mustached, and greater spot-nosed monkeys are phylogenetically related species belonging to three different groups of the genus Cercopithecus, the C. mona, C. cephus, and Cercopithecus mitis groups, respectively. The presence of new viruses closely related to SIVgsn in two other species reinforces the hypothesis that a recombination event between ancestral SIVs from the family Cercopithecinae is the origin of the present SIVcpz that is widespread among the chimpanzee population.     

Density Estimation of the Endangered Udzungwa Red Colobus (Procolobus gordonorum) and Other Arboreal Primates in the Udzungwa Mountains Using Systematic Distance Sampling

Estimates of population density and abundance are essential for the assessment of nonhuman primate conservation status, especially in view of increasing threats. We undertook the most extensive systematic primate survey yet of the Udzungwa Mountains of Tanzania, an outstanding region for primate endemism and conservation in Africa. We used distance sampling to survey three arboreal monkey species, including the endangered and endemic Udzungwa red colobus (Procolobus gordonorum). Overall, we encountered 306 primate clusters over 287 km walked along 162 line transects. We found the lowest cluster densities for both red colobus and Angolan colobus (Colobus angolensis; 0.8 clusters/km²) in the least protected forest (Uzungwa Scarp Forest Reserve, US), while we found the highest densities (3.2 and 2.6 clusters/km² for red colobus; 3.2 and 2.7 clusters/km²for Angolan colobus) in two large and protected forests in the national park. Unexpectedly, Magombera, a small forest surrounded by plantations, had the highest densities of red colobus (5.0 clusters/km²), most likely a saturation effect due to the rapid shrinking of the forest. In contrast, Sykes’ monkey (Cercopithecus mitis monoides/moloneyi) had more similar densities across forests (3.1–6.6 clusters/km²), including US, suggesting greater resilience to disturbance in this species. For the endemic red colobus monkey, we estimated an abundance of 45–50,000 individuals across all forests, representing ca. 80% of the global population. Though this is a relatively high abundance, the increasing threats in some of the Udzungwa forests are of continued concern for the long-term survival of red colobus and other primates in the area.     

Partial molecular characterization of two simian immunodeficiency viruses (SIV) from African colobids: SIVwrc from Western red colobus (Piliocolobus badius) and SIVolc from olive colobus (Procolobus verus)

In order to study primate lentivirus evolution in the Colobinae subfamily, in which only one simian immunodeficiency virus (SIV) has been described to date, we screened additional species from the three different genera of African colobus monkeys for SIV infection. Blood was obtained from 13 West African colobids, and HIV cross-reactive antibodies were observed in 5 of 10 Piliocolobus badius, 1 of 2 Procolobus verus, and 0 of 1 Colobus polykomos specimens. Phylogenetic analyses of partial pol sequences revealed that the new SIVs were more closely related to each other than to the other SIVs and especially did not cluster with the previously described SIVcol from Colobus guereza. This study presents evidence that the three genera of African colobus monkeys are naturally infected with an SIV and indicates also that there was no coevolution between virus and hosts at the level of the Colobinae subfamily.     

Effects of habitat disturbance on the behavioral ecology and demographics of the Tana river red colobus (Colobus badius rufomitratus)

Annual surveys in 1985–1987 revealed that, since 1975, the total population of the Tana River red colobus (Colobus badius rufomitratus)declined by approximately 80%. An intensive study in 1986–1988 of two groups of colobus in the Tana River Primate National Reserve indicated that habitat disturbance from the changing river course and shifting agricultural practices were primarily responsible for the decline. Clearcutting around Mchelelo forest in the late 1960s compressed colobus populations to levels probably above the carrying capacity. Between 1975 and 1986 primate population density declined dramatically, the number of red colobus groups in Mchelelo forest decreased by half, and the size of the remaining group was greatly reduced. In 1986, there were fewer solitary colobus and small parties in the forest, harem male takeovers did not occur, infant survivorship increased, and demographic parameters generally had improved. The colobus groups in Mchelelo in 1973–1975, living at higher densities, showed different feeding and ranging behaviors than 1986–1988 groups. Range size was smaller in 1975, range overlap occurred, and a greater portion of the forest was used per day and per month. Mature leaves accounted for a much higher proportion of the diet. Time spent feeding and resting was the same in both studies. Social organization in predominantly one- male groups was maintained and adult and subadult females transferred between groups.     

Absence of Frequent Herpesvirus Transmission in a Nonhuman Primate Predator-Prey System in the Wild

Emergence of viruses into the human population by transmission from nonhuman primates (NHPs) represents a serious potential threat to human health that is primarily associated with the increased bushmeat trade. Transmission of RNA viruses across primate species appears to be relatively frequent. In contrast, DNA viruses appear to be largely host specific, suggesting low transmission potential. Herein, we use a primate predator-prey system to study the risk of herpesvirus transmission between different primate species in the wild. The system was comprised of western chimpanzees (Pan troglodytes verus) and their primary (western red colobus, Piliocolobus badius badius) and secondary (black-and-white colobus, Colobus polykomos) prey monkey species. NHP species were frequently observed to be coinfected with multiple beta- and gammaherpesviruses (including new cytomegalo- and rhadinoviruses). However, despite frequent exposure of chimpanzees to blood, organs, and bones of their herpesvirus-infected monkey prey, there was no evidence for cross-species herpesvirus transmission. These findings suggest that interspecies transmission of NHP beta- and gammaherpesviruses is, at most, a rare event in the wild.     

Do Nematode Infections of Red Colobus (Procolobus rufomitratus) and Black-and-White Colobus (Colobus guereza) on Humanized Forest Edges Differ from Those on Nonhumanized Forest Edges?

Forested edges, especially those that border humanized landscapes, provide opportunities for nonhuman primates and people to interact, and such interactions are predicted to alter disease dynamics. Given the rapid expansion of edge habitats globally, understanding changes occurring on edges is important in evaluating primate behavioral ecology and developing conservation plans. Our research investigates predictions concerning how gastrointestinal parasite and stress levels (cortisol) in red colobus and black-and-white colobus (Procolobus rufomitratus; Colobus guereza) in Kibale National Park, Uganda, differ between humanized and nonhumanized forest edges. We found Trichuris sp., an unidentified strongyle, and Strongyloides sp. in the fecal samples. Results did not generally support our expectation that humanized forest edges increase parasite infection and, counter to what we predicted, fecal cortisol did not differ between habitats, suggesting that proximity to edges and/or to humans did not result in increased stress. We conclude that broad habitat classifications, e.g., “humanized,” may be too general to identify consistent differences in parasite infection, as other factors, specific to the parasite (e.g., life cycled), host (e.g., immune systems strength), or environment (e.g., moisture level), likely also play important roles.     

Characterization of a Novel Simian Immunodeficiency Virus (SIV) from L’Hoest Monkeys (Cercopithecus l’hoesti): Implications for the Origins of SIVmnd and Other Primate Lentiviruses

The human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) appear to have originated by cross-species transmission of simian immunodeficiency virus (SIV) from asymptomatically infected African primates. Few of the SIVs characterized to date efficiently infect human primary lymphocytes. Interesting, two of the three identified to infect such cultures (SIVsm and SIVcpz) have appeared in human populations as genetically related HIVs. In the present study, we characterized a novel SIV isolate from an East African monkey of the Cercopithecus genus, the l’hoest monkey (C. l’hoesti), which we designated SIVlhoest. This SIV isolate efficiently infected both human and macaque lymphocytes and resulted in a persistent infection of macaques, characterized by high primary virus load and a progressive decline in circulating CD4 lymphocytes, consistent with progression to AIDS. Phylogenetic analyses showed that SIVlhoest is genetically distinct from other previously characterized primate lentiviruses but clusters in the same major lineage as SIV from mandrills (SIVmnd), a West African primate species. Given the geographic distance between the ranges of l’hoest monkeys and mandrills, this may indicate that SIVmnd arose through cross-species transmission from close relatives of l’hoest monkeys that are sympatric with mandrills. These observations lend support to the hypothesis that the primate lentiviruses originated and coevolved within monkeys of the Cercopithecus genus. Regarded in this light, lentivirus infections of primates not belonging to the Cercopithecus genus may have resulted from cross-species transmission in the not-too-distant past.     

Correlates of Ranging Behavior in a Group of Red Colobus Monkeys (Colobus badius tephrosceles)

Data are presented from 17 months of systematic sampling ofthe food habits, ranging patterns and distribution of food ofa group of red colobus monkeys. No positive or negative correlationswere found between the diversity of ranging patterns and thediversity of diet, distribution of food species, or percentageof young growth in the diet. There was, however, a significantcorrelation between the diversity of ranging pattern and thenumber of days per monthly sample that the group was proximalto or had aggressive encounters with another group of red colobusmonkeys.     

Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface

The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity.     

Nutritional ecology of Preuss's red colobus monkey (Colobus badius preussi Rahm 1970) in Korup National Park, Cameroon

Studies on the nutritive ecology of red colobus monkeys (Colobus badius preussi) in Korup National Park, Cameroon, investigated food plants and the parts eaten as well as nutritive values of the various food items. Food plants were identified through direct observations and collected for laboratory determination of nutrient content. Food plants were analysed for crude protein (CP), crude fibre (CF), ether extract (EE), nitrogen‐free‐extractive (NFE) and total ash (A). A total of seventeen species belonging to nine different families were identified as food plants for red colobus. Food and feeding habits showed that the species were highly folivorous, tending to prefer the young leaves of food plants. Lecomtedoxa klaineana (27.0%) and Xylopia aethiopica (22.2%) of families Sapotaceae and Annonaceae, respectively, constituted about 50% of total food items consumed. Results of nutrient composition indicated individual nutrients varied significantly (P < 0.01) with food species.     

Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny

Primate lentiviruses (PLV) from closely related primate species have been observed to be more closely related to each other than to PLV from more distantly related primate species. The current explanation for this observation is the codivergence hypothesis; that is, the divergence of a virus lineage results from the divergence of the host lineage. We show that, alternatively, frequent cross-species transmission of PLV, coupled with a tendency for more closely related primate species to exchange viruses "successfully," can result in apparent codivergence. This host-switching hypothesis reconciles several puzzling observations related to the evolution of PLV.     

Dyadic associations of red Colobus and diana monkey groups in the Taï National Park, Ivory Coast

Members of the genus Colobus have been observed to associate frequently with Cercopithecus monkeys in several African sites. In the Taï National Park, Ivory Coast, one group of western red colobus was found to be in association with one particular group of diana monkeys more than could be expected by chance (Holenweg et al., 1996). We show that dyadic association is not an idiosyncrasy of these two groups, but rather a pattern that is general for our study site. All five red colobus groups we studied were closely associated with diana monkeys during more than 60% of the time. Four groups had one particular diana partner group, the fifth two different partners. Apart from the red colobus, three more primate species, the olive colobus, Campbell's monkey, and the lesser spot-nosed monkey, were also strongly attracted to diana monkeys.     

New Strain of Simian Immunodeficiency Virus Identified in Wild-Born Chimpanzees from Central Africa

Studies of primate lentiviruses continue to provide information about the evolution of simian immunodeficiency viruses (SIVs) and the origin and emergence of HIV since chimpanzees in west–central Africa (Pan troglodytes troglodytes) were recognized as the reservoir of SIVcpzPtt viruses, which have been related phylogenetically to HIV-1. Using in-house peptide ELISAs to study SIV prevalence, we tested 104 wild-born captive chimpanzees from Gabon and Congo. We identified two new cases of SIVcpz infection in Gabon and characterized a new SIVcpz strain, SIVcpzPtt-Gab4. The complete sequence (9093 bp) was obtained by a PCR-based ‘genome walking’ approach to generate 17 overlapping fragments. Phylogenetic analyses of separated genes (gag, pol-vif and env-nef) showed that SIVcpzPtt-Gab4 is closely related to SIVcpzPtt-Gab1 and SIVcpzPtt-Gab2. No significant variation in viral load was observed during 3 years of follow-up, but a significantly lower CD4+ T cells count was found in infected than in uninfected chimpanzees (p<0.05). No clinical symptoms of SIV infection were observed in the SIV-positive chimpanzees. Further field studies with non-invasive methods are needed to determine the prevalence, geographic distribution, species association, and natural history of SIVcpz strains in the chimpanzee habitat in Gabon.     

A note on the ecology of the red-colobus monkeys (Colobus badius tephrosceles) living in the Mahali Mountains

Red-colobus monkeys of the Mahali Mountains utilize many vegetation types; although their main habitat is composed of forest vegetation (gallery forest and montane forest), they sometimes penetrate into even theMiombo woodland.Red-colobus monkeys mainly live on leaves of trees, but sometimes eat flowers, fruits, and barks. Most of the plant leaves which the chimpanzees eat have proved to be delicacies to colobus monkeys also. Colobus monkeys live in compact bisexual groups, ranging from 30 to 50 in size. No solitary male has so far been observed.A colobus group living in the gallery forest moved 100 to 200 meters daily within its welldocumented home range. The home ranges of groups do not seem to overlap each other extensively.Their natural enemies are leopards, birds of prey and probably chimpanzees. The Tongwe inhabitants avail themselves of the colobus coat as part of their native bellows (mufuba) and some pagan inhabitants kill them for their meat.The research was financed by the Scientific Research Fund of the Ministry of Education and in part by the Wenner-Gren Foundation. This report is a part of the results of the Kyoto University Africa Primatological Expedition.     

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses

To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.