INTRODUCTION
CD4 is expressed on the surface of a subset of human T cells, where it stimulates interaction between the T cell receptor and major histocompatibility complex class II (MHC-II) molecules expressed on antigen-presenting cells (
Fig. 1A). While the T cell receptor interacts with the presented peptide antigen, the D1 domain of CD4 interacts with an invariant portion of the MHC class II molecule itself (
1), an interaction that is expected to be preserved over evolutionary time. Despite this, we and others previously demonstrated that
CD4 is evolving under diversifying selection in primates, with natural selection working in favor of new allelic forms (
2–4). This is presumably because the CD4 D1 domain also interacts with the envelope (Env) surface protein of the lentiviruses human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) (
Fig. 1B) (
5). This interaction is required for virus entry into cells, and over evolutionary time, primate genomes may have experienced selection for new allelic forms of
CD4 that limit lentiviral entry. In turn, lentiviruses would have been selected for new allelic forms of
env that permit entry using new forms of CD4. Tit-for-tat evolution such as this is referred to as an evolutionary arms race and results in accelerated evolution at the binding interface of the two interacting proteins (
6). Indeed, codons in both primate
CD4 and HIV-1
env that correspond to residues in this interaction interface have been previously characterized by us and others to evolve under positive natural selection (
2–4,
7–9). While these evolutionary findings show that primate
CD4 is genetically diverse, the functional significance of this genetic diversity has not been well characterized.
Humans, chimpanzees, and white-handed gibbons are the only mammals that are known to support HIV type 1 (HIV-1) replication, but the latter two primates are endangered and only rarely develop immunodeficiencies upon infection (
10). Cells from all other nonhuman primate species are resistant to HIV-1 infection even in cell culture, in most cases due to restriction factors that they encode (
11,
12). However, entry into the cell is also a major barrier to HIV-1 infection of nonhuman primate cells (
13). For example, HIV-1 variants isolated directly from individuals at early stages of infection, which are most relevant to the HIV-1 pandemic, have been shown to be compatible only with human CD4 (
14), whereas lab-adapted or chronic-stage isolates of HIV-1 can use the CD4 receptor encoded by multiple nonhuman primate species (
15,
16). Species-specific differences at three sites in the CD4 D1 domain, N39, P48, and R59, have been shown to alter interactions with HIV-1 (
14,
17). For instance, a single amino acid difference at position 39 of CD4 between human (asparagine) and pig-tailed macaque (
Macaca nemestrina; isoleucine) accounts for the species-specific differences in the ability of these CD4s to function as receptors for early-stage isolates of HIV-1 (
14). Studies of viral pathogenesis as well as vaccine and prevention studies typically employ viruses that are chimeras between SIV and HIV-1, called SHIVs, that infect macaques. SHIVs encode antagonists of key macaque restriction factors, and to make these viruses relevant to vaccine studies, they encode an Env derived from HIV-1. Because most Envs from circulating HIV-1 variants do not use macaque CD4 efficiently, SHIVs typically only replicate well in macaques after serial passage and adaptation in this species.
Because Env is a major antigen targeted by human antibodies, the constraints placed on Env by macaque CD4 may fundamentally compromise the SHIV/macaque model for vaccine studies. First, the process of adapting SHIVs to replicate in macaques leads to changes in Env (
18), and these have antigenic consequences, changing the ability of HIV-1-specific antibodies to recognize Env (
19). More recent studies have identified HIV-1 variants that can replicate in macaques without passage (
20), suggesting that there are rare variants that can use the macaque CD4 receptor. Whether these represent the key antigenic features of the majority of transmitted variants remains to be determined. Second, the specific viral variants that are actually transmitted between humans best represent the molecular properties that successful vaccines and prevention approaches will need to target to limit new infections. However, most SHIVs bear Env from lab-adapted HIV-1 strains, which were typically originally isolated from chronic rather than early stages of infection. Finally, the majority of SHIVs represent subtype B Env sequences, and few are representative of subtypes A, C, and D, which are the most prevalent types in sub-Saharan Africa and account for the highest percentage of new infections and HIV-1-related mortality.
Many nonhuman primate species have previously been explored as possible animal models for HIV-1. However, like in humans, significant genetic polymorphism exists within nonhuman primate populations, and this remains largely unexplored. In this study, we analyzed small populations representing different nonhuman primate species and evaluated these individual animals for CD4 polymorphisms. Three CD4 alleles were identified in one New World monkey species, Spix's owl monkey (Aotus vociferans), that support entry mediated by Envs isolated from unpassaged or minimally passaged early isolates of HIV-1. Further, CD4 encoded by these alleles, but not another allele found in the same Spix's owl monkey population, supports entry by all of the major clades of HIV-1 group M. Interestingly, we find that only some Envs isolated from subtype C can use the CD4 receptor encoded by these permissive alleles, suggesting distinct architectures within group C Envs. In summary, some Spix's owl monkeys encode a CD4 that is broadly permissive to diverse, early isolates of HIV-1. We find that these permissive alleles are common in a captive Spix's owl monkey colony that we have surveyed. We also find that two other species of owl monkeys, Azara's (Aotus azarae) and Nancy Ma's (Aotus nancymaae) owl monkeys, also encode CD4 receptors that are functional for HIV-1 variants isolated from early-stage human infections.
MATERIALS AND METHODS
Primate samples.
Nonhuman primate samples were acquired from the Michale E. Keeling Center for Comparative Medicine and Research (KCCMR) in Bastrop, TX, or from the New England Primate Research Center (NEPRC) in Southborough, MA. For each individual sampled at KCCMR, 2.5 ml of blood was collected in PaxGene blood RNA tubes (BD; 762165). All tissue collections performed for this study were reviewed and approved through The University of Texas MD Anderson Cancer Center Institutional Animal Care and Use Committee (IACUC). For each individual housed at NEPRC, B cell lines were received and expanded in suspension culture in RPMI medium, 20% fetal bovine serum (FBS), penicillin-streptomycin (Pen-Strep), l-glutamine, HEPES, and zidovudine (AZT). Genomic DNA and RNA from blood and cell lines were isolated using the PaxGene microRNA (miRNA) kit (Qiagen; 763134) and/or the Qiagen All Prep DNA/RNA minikit (Qiagen; 80204). cDNA libraries were generated using oligo(dT) primers with isolated primate RNA and the Superscript III First-Strand Synthesis System (Invitrogen; 18080-051).
CD4 genotyping.
The CD4 coding region from rhesus macaques and owl monkeys was amplified using cDNA templates and primers that recognize the untranslated regions (NRM238 [5′-AAGCAGCGGGCAAGAAAGACG-3′] and NRM242 [5′-CAAGTTCCTGCCCTCTGTGG-3′]). PCR with cDNA templates was performed using PCR SuperMix High Fidelity (Invitrogen; 10790-020) with an annealing temperature of 58°C. Rhesus macaque CD4 amplicons were sequenced using NRM240 (5′-AGAAAGACGCAAGCCCAGAGG-3′), and owl monkey amplicons were sequenced using NRM799 (5′-GCCTGCTGGAAAGCTAGTACC-3′). The CD4 coding region from cynomolgus macaques and squirrel monkeys was amplified from genomic DNA. Two amplicons that span the D1 domain of CD4 were generated using primers that sit in introns and amplify exons 1 and 2 (NRM457 [5′-TCTTGCTTCTGCTCCTACTCATTCC-3′] and NRM459 [5′-TGGGCCACCAGCAGTTGG-3′]) or exons 3 to 6 (NRM465 [5′-GGAGTTGGTGCTCTCCAAATAAGG-3′] and NRM471 [5′-TCTCTGCCAACCACAGGAAGG-3′]). PCR with genomic DNA (gDNA) templates was performed using Phusion High Fidelity PCR master mix (NEB; F-531S) with annealing temperatures of 58°C for exons 1 and 2 and 67°C for exons 3 to 6. CD4 exons 1 and 2 were sequenced using NRM457 (5′-TCTTGCTTCTGCTCCTACTCATTCC-3′), and exon 3 was sequenced using NRM484 (5′-AGCTCAGGCTGGATTTGGTGC-3′). All newly identified single nucleotide polymorphisms (SNPs) were verified with independent PCR and sequencing reactions.
Expression constructs.
Human
CD4 was amplified from RNA isolated from Jurkat T cells. Owl monkey
CD4 was amplified from RNA isolated from blood samples as described above. Each
CD4 was subcloned into the pCR8 Gateway entry vector using TA cloning (Invitrogen; K2500-20). An LR Clonase II reaction (Invitrogen; 11791-100) was used to move these constructs into a Gateway-converted pLPCX retroviral packaging vector (Clontech; 631511). The expression plasmid encoding rhesus macaque CD4 was described previously (
22).
Envelope clones.
The following envelope clones from early HIV-1 infections were used: Q461e2 (
23); QH343.21M.A10 (
24); Q23ENV.17 (
25); BG505.W6M.B1 (
26); WITO4160.33 and TRO.11 (
27); CAP210.2.00.E8, ZM53M.PB12, ZM109F.PB4, ZM197M.PB7, ZM214M.PL15, Du156.12, Du172.17, and Du422.1 (
28); QC406.70M.F3 (
24); and QA013.70I.H1 and QB857.110I.B3 (
24). As a control, 2 subtype B HIV-1
env clones (BaL.01 and SF162) representing variants known to infect macaque cells (
14) were also used. GFP reporter pseudoviruses were generated in HEK293T cells by cotransfecting 667 ng of Q23ΔEnvGFP (
21) and 333 ng of the HIV-1
env clone of interest using Fugene 6 (Roche) transfection reagent at a ratio of 3 μl of Fugene 6 to 1 μg of DNA according to the manufacturer's protocol.
Generation of stable cell lines.
HEK293T and Cf2Th/syn CCR5 (
29) cells were cultured in Dulbecco's modified Eagle medium (Invitrogen) with 10% FBS (Gibco), 2 mM
l-glutamine (Gibco), and 1% antibiotic (Gibco) (complete medium) at 37°C and 5% CO
2. Cf2Th/syn CCR5 cells, which are canine thymocytes engineered to express human CCR5 (
29), were further supplemented with 400 μg/ml of Geneticin (Gibco) to maintain CCR5 expression. For generation of CD4-expressing cell lines, retroviral virus-like particles (VLPs) were generated in HEK293T cells by cotransfecting pLPCX (retroviral vector encoding the CD4 of interest), pJK3 (MLV-based packaging plasmid), and pMD.G (vesicular stomatitis virus glycoprotein [VSV-G] envelope plasmid) at a ratio of 1:1:0.5 using Fugene 6 (Roche) transfection reagent according to the manufacturer's protocol. Forty-eight hours posttransfection, the supernatants containing VLPs were collected, filtered through 0.22-micrometer filters, and concentrated using Amicon Ultracel 100K filters (Millipore). The concentrated VLPs (∼200 μl) were used immediately to transduce Cf2Th/syn CCR5 cells that had been plated 24 h prior at a density of 10
5 cells/well in a 6-well plate in 2 ml of drug-free complete medium. The cells were transduced in the presence of 10 μg/ml of DEAE-dextran by spinoculation at 1,200 ×
g for 90 min. The following day, cells were split and transferred in new T75 flasks in 10 ml of drug-free complete medium and cultured for 48 h. The cells were then passaged and maintained in complete medium supplemented with 400 μg/ml of Geneticin (to maintain CCR5 expression) and 2 μg/ml of puromycin (to select for CD4 expression). The transduced cells with high levels of CD4 expression were obtained by sorting the cells on a FACSAria II cell sorter using an allophycocyanin (APC)-conjugated CD4 monoclonal antibody (BD Biosciences; 551980) as described previously (
14). Cf2Th/syn CCR5 cells stably expressing rhesus CD4 have been described previously (
14).
CD4 infectivity assay.
Cf2Th/syn CCR5 cells stably expressing CD4 (2.5 × 104 cells/well in a 12-well plate in 1 ml of drug-free complete medium) were seeded 24 h prior to infection. The cells were infected with HIV-1 pseudoviruses in duplicate wells at a multiplicity of infection (MOI) of 0.5 in the presence of 10 μg/ml of DEAE-dextran by spinoculation at 1,200 × g for 90 min. After 72 h, the cells were washed once with 200 μl of 1× phosphate-buffered saline (PBS), harvested using 200 μl of 0.05% trypsin-EDTA (Gibco), and fixed in 200 μl of 2% paraformaldehyde. The fixed cells were washed twice with 500 μl of fluorescence-activated cell sorter (FACS) buffer (1× PBS buffer containing 1% FBS and 1 mM EDTA). The cells were resuspended in 400 μl of FACS buffer, filtered through a 35-μm-pore-size nylon mesh cap (BD Falcon), and analyzed for GFP expression on BD FACSCanto II flow cytometer. The data from ∼104 cells were analyzed using FlowJo version 9.7.5.
Infectivity assay for cells transiently expressing CD4 and CCR5.
HEK293T cells (2.5 × 10
5 cells/well in a 6-well plate in 2 ml of complete medium) were seeded 24 h prior to transfection. Cells were cotransfected with plasmids encoding the desired CD4 (0.5 μg) and human CCR5 (1 μg) using Fugene 6 (Roche) transfection reagent by following the manufacturer's protocol. Forty-eight hours posttransfection, cells were trypsinized, counted, and reseeded at a density of 8 × 10
4/well in a 12-well plate in 1 ml of complete medium. Six hours later, when the cells had adhered to the plate, cells were infected with HIV-1 pseudoviruses in duplicate wells at an MOI of 15 in the presence of 10 μg/ml of DEAE-dextran by spinoculation at 1,200 ×
g for 90 min. The percentage of green fluorescent protein (GFP)-positive cells was measured by flow cytometry as described above. Forty-eight hours posttransfection, CD4 and CCR5 expression levels were determined using flow cytometry on aliquots of transfected cells using APC-conjugated CD4 antibody (BD Biosciences; 551980) and fluorescein isothiocyanate (FITC)-conjugated CCR5 antibody (BD Biosciences; 561747) as described previously (
21).
Evolutionary analysis.
An alignment of primate
CD4 was analyzed using the codeml program contained in PAML 4 (
30). The free-ratio model was used to estimate the ratio of nonsynonymous to synonymous evolutionary changes (
dN/
dS ratio) that occurred along each branch. Accession numbers for the primate
CD4 sequences (all from GenBank unless otherwise indicated) are as follows: human, BC025782.1; chimpanzee, M31135.1; gorilla, KJ531711.1; Bornean orangutan, KJ531712.1; Sumatran orangutan, not applicable (assembled from the UCSC genome database [
31]); siamang, KJ531713.1; agile gibbon, KJ531714.1; white-cheeked gibbon, KJ531715.1; rhesus macaque, D63347.1; Japanese macaque, D63348.1; cynomolgus macaque, D63349.1; pig-tailed macaque, D63346.1; black mangabey, KJ531719.1; olive baboon, KJ531718.1; sooty mangabey, X73327.1; grivet, AF001226; tantalus monkey, AF001221.1; sabaeus monkey, AF001225; patas monkey, X73324.1; talapoin, KJ531716.1; wolf's guenon, KJ531717.1; colobus, KJ531721.1; leaf monkey, KJ531722.1; Nancy Ma's owl monkey, KR902343; Azara's owl monkey, KR902342; Spix's owl monkey, KR902344; marmoset, AF452616.1; squirrel monkey, AF452617.1; Bolivian/Peruvian squirrel monkey, not applicable (assembled from the UCSC genome database [
31]); howler monkey, KJ531724.1; and titi monkey, KJ531723.1.
Nucleotide sequence accession numbers.
Newly generated full-length owl monkey CD4 gene sequences have been deposited in GenBank (accession numbers KR902342 to KR902344).
DISCUSSION
A host-virus arms race appears to exist between CD4 and lentiviral env, and this has driven the positive selection of CD4 over evolutionary time, leaving behind substantial sequence and functional variation even in the CD4 alleles carried by different individuals of the same species. In this study, we have identified three nonhuman primate species, all in the Aotus genus of owl monkeys, in which some individuals encode a CD4 receptor that is functional for circulating variants of HIV-1 associated with the worldwide pandemic. We have characterized the CD4 alleles circulating in one of these species, Spix's owl monkey, in depth. Unlike macaque CD4, Spix's owl monkey CD4 functions as a receptor for most early-stage HIV-1 variants, including representatives from the main circulating subtypes, not just lab-adapted and rare HIV-1 Env variants. Although further work will be needed, Spix's owl monkeys possibly represent a novel model organism for a new class of SHIVs bearing HIV-1 Envs that better represent successful vaccine targets.
The next hurdle will be to determine whether a SHIV bearing Env from early-stage human infections can be engineered to replicate in peripheral blood mononuclear cells (PBMCs) from owl monkeys. New World monkeys became a subject of interest as potential models for HIV-1 when it was observed that their cellular blocks to infection are minimal. For instance, cells from various species of squirrel monkeys, marmosets, and tamarins are infected at high levels by VSV-G-pseudotyped HIV-1 vectors, suggesting that no restriction factor blocks exist after virus entry up to the stage of genome integration (
39). Further, primary cells from common marmosets (
Callithrix jacchus) and squirrel monkeys (
Saimiri sciureus) were found to support each of the post entry steps of HIV-1 replication, including reverse transcription, integration, transcription, translation, assembly, and budding (
17). Owl monkeys, on the other hand, have been found to harbor three restriction factors active against HIV-1. First, all species of owl monkeys, including Spix's owl monkey (data not shown), encode the TRIM5-CypA restriction factor (
33–35). It is possible to bypass this restriction with a single amino acid mutation in the HIV-1 capsid protein (G89V) (
33,
34). It has also been shown that the SIVmac capsid, which is used in most SHIV strains, is not susceptible to owl monkey TRIM5-CypA (
40). Second, some species of owl monkeys, including Spix's owl monkey, have functional versions of the BST-2/tetherin restriction factor (
16). Third, some species of owl monkeys express levels of APOBEC3G high enough to interfere with HIV-1 replication, but HIV-1 Vif can partially overcome this block (
16). The use of owl monkeys, including Spix's owl monkey, as a model organism for vaccine studies is not precluded by any of these, as it is possible to bypass these restrictions through modifications of HIV or SIV that are independent of Env. Alternately, by surveying populations of individuals, it may be possible to identify functional
CD4 alleles in other New World monkey species that do not have as many restriction factor blocks against HIV-1.
New World primates, including owl monkeys, are well-established models of human disease in biomedical research (
41). This is in part due to the fact that most New World species are relatively small in body size and have rapid reproduction rates which facilitate the maintenance of productive breeding colonies. Owl monkeys are particularly good models for research in that they are easily acclimated to handling and do not generally require pharmaceutical sedation for routine blood collections, in contrast to most larger primate species. This helps minimize any confounding effects on research that may be associated with repeated sedations. The use of owl monkeys in research is further promoted by the fact that these species harbor no known zoonotic pathogens. One potential drawback in the use of owl monkeys in research is their reduced size, and therefore smaller attainable blood volume, compared to other primate species. However, it is noteworthy that owl monkeys are a lymphocyte-predominant species. That is, unlike macaques and most other Old World monkeys in which lymphocytes usually represent only 20 to 35% of the total blood leukocytes, in owl monkey species the lymphocytes routinely constitute between 65 and 75% of the differential leukocyte count (
42).
The major circulating subtypes of HIV-1 in sub-Saharan Africa include subtypes A, C, and D. In the United States, subtype B is the most common variant. Here we show that strains from each of these subtypes can use the owl monkey CD4 protein as an entry receptor. However, variation on the side of the virus also has specific effects on the interaction with owl monkey CD4 (
Fig. 5). We show that some strains of subtype C can utilize owl monkey CD4, whereas others do not. It is unclear whether this variation is specific to subtype C or is a characteristic of other subtypes as well. Further testing with a larger panel of Envs will be necessary to delineate these scenarios and provide enough information to carry out genetic mapping studies.
In summary, some Spix's owl monkey individuals encode CD4 receptors that are broadly permissive to circulating strains of HIV-1. These permissive alleles were discovered by bioprospecting within populations of monkeys, and similar future studies may continue to reveal alleles that will be useful in HIV research. The literature suggests that there is rich genetic variation to be unearthed. Primate SNPs at restriction factor loci have been shown to dramatically affect the outcome of infection experiments (
43–48). Less is known about polymorphism at host loci that encode the HIV-1 receptors, but this can be elucidated through population studies such as the one described here.