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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Nat Rev Immunol. Author manuscript; available in PMC 2013 October 1.
Published in final edited form as:
PMCID: PMC3690816
NIHMSID: NIHMS473642

Evolutionary conflicts between viruses and restriction factors shape immunity

Abstract

Preface

Host restriction factors are potent, widely expressed, intracellular blocks to viral replication that are an important component of the innate immune response to viral infection. However, viruses have evolved mechanisms of antagonizing restriction factors. Through evolutionary pressure for both host survival and virus replication, an evolutionary “arms race” has developed that drives continuous rounds of selection for beneficial mutations in restriction factor genes and their viral antagonists. Because viruses can evolve faster than their hosts, the modern-day vertebrate innate immune system is optimized to defend against ancient viruses, rather than current viral threats. Thus, the evolutionary history of restriction factors might, in part, explain why humans are susceptible or resistant to the viruses present in the modern world.

Introduction

Restriction factors are proteins of the innate immune system encoded in the germline genome that inhibit the replication of viruses during their lifecycle in host cells. These host proteins are dedicated antiviral factors that are often induced by interferon (IFN) signaling as part of the innate immune response, are antagonized by viral factors, and are rapidly evolving. The term “restriction factor” was historically adopted by labs studying retroviruses as a result of the characterization of the Fv1 locus in mice that conferred resistance to murine retroviruses 1. However, this term can also be applied more broadly to host-encoded gene products that inhibit the intracellular replication of any animal virus. Recent work has shown that host susceptibility to viral infection and disease is determined, in part, by the components of the innate immune system (such as restriction factors) and the viral proteins that have evolved to evade or destroy these host defenses. In this Review, we describe the general characteristics of restriction factors and show how the evolutionary conflict between viruses and restriction factors has shaped our modern immune systems. We use examples of host restriction factors that block primate lentiviruses, although many of the principles are generally applicable to other viruses and other hosts. These topics are of particular relevance today as a result of many recent discoveries of restriction factors and determinants of viral susceptibility.

Characteristics of restriction factors

Classical innate immunity against viruses is mediated by specialized cells such as natural killer (NK) cells, dendritic cells, and macrophages. By contrast, restriction factors are germline-encoded factors that mediate a “cell-intrinsic" immune response. They are part of the broader innate immune repertoire of cellular molecules that detect and respond to viral infections in the absence of previous exposure. Typically, viral infections are detected by cytoplasmic or membrane-bound pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs), which trigger an IFN response that induces a program of interferon-stimulated genes (ISGs) with broad-ranging effects on cell growth and metabolism (reviewed in 2, 3). Many of these ISGs are restriction factors that specifically inhibit viral growth within the infected cell. Table I lists the general features of the restriction factors that target retroviruses and other viruses that are described in this Review. Table 1 is not a comprehensive list of restriction factors but contains some of the best-studied examples.

Table 1
Characteristics of restriction factors

There are several distinguishing characteristics of restriction factors that allow one to make inferences about their role in the evolution of both the host and the virus. Typically, we define a host gene as a restriction factor if it encodes a protein that: has antiviral activity as its major biological function; is induced by IFN or by virus infection; is antagonized by a viral protein; and shows evolutionary signatures of genetic conflict (positive selection). The majority of true restriction factors share these features, as described in detail below. However, the exceptions to these definitions are also highlighted in Table 1, as they can be enlightening with regard to understanding the additional cellular roles that restriction factors might have.

Activity and expression of viral restriction factors

Many restriction factors are IFN-stimulated genes (Table I), which is consistent with their fundamental role in an antiviral response. The IFN-mediated induction of many restriction factors is also an indication that their major activity is to combat pathogens, rather than some central metabolic or developmental role in the organism. Moreover, as many restriction factors cause destructive events such as protein modifications or nucleotide mutations, their expression needs to be tightly controlled to avoid deleterious effects on cell growth in the absence of viral challenge. However, IFN induction is not a universal property of restriction factors, as some are also expressed constitutively. In cases where protein expression is constitutive, it is probable that the restriction factor has a role in restricting endogenous events as well. For example, in the APOBEC3 family of cytidine deaminases, APOBEC3G is constitutively expressed by many cell types including T cells and germ cells 4, 5. Although it has a well-characterized role in T cells of inhibiting retroviruses through hypermutation of viral genomes during reverse transcription, we suggest that APOBEC3G might have an even more ancient role in protecting the host genome in germ cells from endogenous retrotransposons, which do not lead to IFN responses6.

During an acute viral infection, each productively infected cell generates many infectious particles, leading to exponential viral growth. Therefore, restriction factors must have extremely potent antiviral activity to have any significant effect on viral loads (restriction factors included in Table I, for example, decrease viral infectivity by ten-fold or more in single-round viral infectivity assays, though the level of restriction will vary depending on the system). This antiviral activity can be demonstrated experimentally by over-expression of a restriction factor, which causes a decrease in virus growth, or knockdown of a restriction factor, which causes an increase in virus growth. For example, SAMHD1 was recently defined as a novel restriction factor that is present in monocytes; decreasing its endogenous expression in monocytes using RNAi enhanced the replication of HIV-1, and exogenously expressing SAMHD1 in terminally differentiated myeloid cells restricted HIV-1 replication 7, 8. In addition, the antiviral activity of restriction factors is sometimes specific to families of viruses. For example, TRIM5α seems to be active only against retroviruses because it inhibits viral replication by means of a specific interaction with retroviral capsid proteins 9. By contrast, tetherin can restrict enveloped viruses across several virus families because it non-specifically incorporates into the cell and virus membranes and prevents efficient viral release by tethering enveloped viruses to the cell (Table I) 10.

Further, we propose that the major biological activity of restriction factors is to inhibit viral replication. In many cases where restriction factor function can be examined by gene knockout in mice, ablation of the restriction factor has no untoward effect on mouse development. For example, knockout mice of the single murine Apobec3 gene are viable, and the only reported phenotype is that they are more susceptible to murine retroviruses than are their wild-type counterparts11. In fact, natural mutations in Apobec3 and the Mx locus that abolish function exist in some inbred mouse strains12, 13. Similarly, mice with natural or engineered mutations in mouse Tetherin, Viperin or Ifitm3 genes are also viable but are more sensitive to some viral infections14-18. However, it is possible that some restriction factors have additional cellular roles other than viral restriction. For example, TRIM5α has a more general role in antiviral signaling in addition to its specific role in retroviral restriction19, 20, and mutations in human SAMHD1 are associated with autoimmune disease21 (Box 1). However, perhaps as a result of the duplication of many restriction factors within a host (described further below), restriction factors can undergo sub-functionalization, in which one gene retains an essential cellular function whereas its paralogue becomes a dedicated antiviral factor.

Box 1

Coordination with other arms of the immune system

The relationship between restriction factors and the rest of the innate immune system is a growing area of research. In many ways, restriction factors are similar to pattern recognition receptors (PRRs) because they recognize structural patterns on pathogens. In fact, TRIM5, which binds to a viral capsid lattice structure84 and accelerates capsid uncoating to cause viral restriction, has recently been shown to also function as a PRR for retroviruses20. Upon binding to retroviral capsids, Trim5 leads to the activation of nuclear factor-κB (NFκB) signaling and a distinct innate immune response. Moreover, even in the absence of retroviral capsids, Trim5 has been shown to have a role in innate immune responses, as it functions as a constitutive signaling intermediate in the NFκB cascade 19. Similarly, tetherin has also been shown to activate NFκB in addition to its viral restriction function 85.

SAMHD1 also functions as both a restriction factor and a mediator of the innate immune response to non-viral events. SAMHD1 protects dendritic cells and monocytes from HIV-1 infection by decreasing the level of cellular dNTPs below the level required for synthesis of viral DNA 7, 8, 86. In addition, SAMHD1 has a role in the innate immune response even in the absence of retroviral infection, as genetic mutations in SAMHD1 and TREX1 are associated with autoimmunity in humans21. Similarly to TREX1, SAMHD1 might have a protective role against autoimmune responses by preventing inappropriate retrotransposon by-products such as single-stranded DNA 86, 87. Studying retroviral restriction factors will undoubtedly contribute to our understanding of many aspects of the innate immune system.

Viral antagonists of restriction factors

Viruses have evolved antagonists to restriction factors. These viral proteins are often encoded by ‘accessory genes’ that are not needed for virus replication except in the presence of restriction factors22. Restriction factors, such as Tetherin, that inhibit the replication of multiple virus families can be antagonized by diverse viral proteins from different viral families (Table 1). In cases where there is no known viral antagonist to a particular restriction factor, it is possible that the virus can escape restriction by mutation of the viral protein targeted by a restriction factor, as is the case for lentiviral evasion of TRIM5α-mediated restriction by viral capsid mutations 23, 24. It is also formally possible that a newly evolved restriction factor might not yet have selected for a viral antagonist. However, in most cases, we believe that the inability to identify a viral antagonist is more likely attributed to the fact that the relevant sets of viruses and host species have yet to be examined.

Viral antagonists can overcome restriction factors using several different mechanisms. For example, viral antagonists can couple the restriction factor to protein degradation pathways, cause the mislocalization of the restriction factor and hence downregulate functional expression, or function as mimics of the restriction factor substrate (Figure 1). To antagonize the restriction factor SAMHD1, the Vpx protein encoded by HIV-2 and related primate lentiviruses targets SAMHD1 for ubiquitylation followed by proteasomal degradation (Fig. 1a) by simultaneously binding SAMHD1 and an adapter protein in the Cul4 ubiquitin ligase complex 7, 8. The lentiviral Vif protein antagonizes APOBEC3G by a similar mechanism 25, 26. By contrast, the lentiviral Vpu protein antagonizes the restriction factor Tetherin by altering its normal cellular localization (Fig. 1b). By a direct protein-protein interaction, Vpu sequesters Tetherin in the trans-Golgi network and re-directs it from the cell membrane to the endosome, where it is unable to restrict viral budding from the cell membrane 27. A third mechanism of antagonism is illustrated by K3L, a poxvirus-encoded antagonist of the host antiviral protein kinase R (PKR) pathway. Upon recognition of double-stranded RNA, PKR inhibits protein translation by phosphorylating eukaryotic initiation factor subunit 2-α (eIF2α). K3L is structurally homologous to eIF2α and competes for binding to PKR (Fig. 1c). By acting as a mimic of eIF2α, K3L prevents the activation of eIF2α and the translational shutoff that the PKR pathway would otherwise induce (reviewed in 28). Viruses might also use other strategies that have not yet been characterized to allow viral replication in the face of restriction factors. A key feature common to all these modes of antagonism is the direct interaction between the viral antagonist and the host restriction factor, which has set the stage for the evolutionary arms race that is characteristic of many restriction factors, described below.

Fig. 1
Mechanisms of viral antagonism of host restriction factors

Positive selection as a fundamental principle of virus-host interactions

Many non-coding regions of the genome evolve under neutral selection; for example, non-synonymous (amino acid altering) and synonymous mutations are predicted to occur at the same rate in pseudogenes. Most host protein-coding genes evolve under negative (purifying) selection, which removes non-synonymous mutations from the population in order to maintain the function of the protein. By contrast, the interactions between restriction factors and viral antagonists evolve under “positive selection,” a selective regime that results in an excess of non-synonymous mutations compared with synonymous mutations (Box 2). Positive selection is often a result of two genetic entities evolving in conflict with one another, as illustrated by the “Red Queen” hypothesis proposed by Leigh Van Valen to describe an evolutionary system where continuous adaptation is required to maintain the status quo 29. Virus-host interactions are examples of the “Red Queen” competition, as host restriction factors exert a selective pressure on virus replication and pathogenic viruses exert fitness costs on their hosts. Mutations that allow a restriction factor to evade a viral antagonist provide a means for the host to escape the fitness costs conferred by the virus. This imposes a selective pressure on the viral antagonist to evolve specificity for a new restriction factor encoded by the host species. As a result, a prey-predator-like ‘arms race’ dynamic is established, leading to the rapid evolution of both the host and virus (Fig. 2a). Thus, nearly all of the restriction factors described in Table 1 contain signatures of positive selection.

Fig. 2
Genetic conflict between virus and host

Box 2

Selective sweeps are the mechanism of adaptation

An important aspect of positive selection of restriction factors is that the selection (and therefore evolution) of an advantageous mutation acts on a population level. The cost of a viral infection must affect the population’s ability to reproduce before it will exert a selective pressure on the population to evolve. During a population-wide infection, some individuals may carry a previously neutral genetic mutation that now confers those individuals with a reproductive advantage in the face of infection, and this advantageous genotype will rapidly rise in frequency until the mutation reaches a frequency of 100% (known as fixation). In a classic selective sweep, surrounding regions of the genome are inherited together (known as hitchhiking) with the genomic sequence that confers the fitness advantage, thus decreasing genetic diversity near the region of the genome under positive selection (reviewed in 88-90). Therefore, genomic loci that are under positive selection in a population are predicted to have skewed allele frequencies across long genetic distances surrounding the selected locus. Eventually, if a mutation reaches fixation within a species, between-species comparisons will reveal an excess rate of non-synonymous mutations in this region relative to that expected under neutral selection88.

Because viruses have existed throughout vertebrate evolution, the arms race between host and virus is ancient 30. In fact, many host restriction factors have evolved under positive selection for many millions of years. Under a long-term or recurrent viral selection pressure, a single amino acid in a restriction factor that directly interacts with a viral antagonist may repeatedly mutate many times during evolution, or a restriction factor may accumulate mutations at many different residues in order to escape many different viruses. This will lead to an unusually high ratio of the non-synonymous mutation rate (dN) to synonymous mutation rate (dS) —dN/dS— at single residues or across entire proteins (Fig. 2b). To estimate the dN/dS ratio of a gene, ancestral gene sequences can be reconstructed from orthologous gene sequences from modern-day species that diverged millions of years ago, and statistical methods are used to calculate the rate of evolution across a phylogeny 31. Using this method, many human restriction factors have been found to be evolving under episodic positive selection throughout primate evolution (Table 1).

How do hosts keep up in the arms race?

If single nucleotide changes were the only effector mechanism in the co-evolution of host and virus, the host would be at a seemingly enormous disadvantage because RNA viruses and some small ssDNA viruses have nucleotide substitution rates that are 1000 times faster than those of their hosts32-35. How then does a host restriction factor ever win an arms race with a virus, especially when considering that a host might be simultaneously challenged by many different types of viruses? The answer lies in the types of genetic landscape that viruses and hosts can explore.

Limitations on viral evolution

RNA viruses maintain a densely packed genome that includes overlapping reading frames and RNA hairpin structures involved in genome packaging and replication. The limitations on genome size of RNA viruses necessitate that many viral proteins carry out multiple functions 36. This constrains their evolutionary potential, as mutations to optimize one function (for example, adaptation to a polymorphism in a host restriction factor) might compromise another function of that protein (for example, capsid assembly). In addition, the small viral genome size generally prevents the use of gene duplication-driven strategies for adaptive evolution, which can be used by host, but not viral, genomes. One possible exception to the lack of gene duplication in viruses is the pair of homologous genes vpr and vpx in some lentiviruses 37.

Host heterozygosity

Genetic polymorphisms in genes encoding host restriction factors can be maintained as a result of population-level adaptation against viruses. Balancing selection in restriction factors may result when multiple viruses co-infect a population, such that different host haplotypes are both advantageous against different viruses, essentially maintaining polymorphism within the population (‘frequency-dependent selection’). Several of the best-known examples of genes under balancing selection include genes involved in immunity, such as: genes in the major histocompatibility complex (MHC) 38, which maintain multiple alleles that present a variety of antigens and therefore protect against a variety of pathogens; the glucose-6-phosphate dehydrogenase (G6PD) gene 39, a housekeeping gene that maintains polymorphisms that are associated with clinical disorders and also with malaria resistance; and TRIM5, which has been suggested to be under balancing selection in old world monkey populations40.

Heterozygosity in a restriction factor may be advantageous to a population on a short time scale, as host polymorphisms would force a virus to evolve the ability to target multiple alleles of a given host factor. This was recently suggested for the restriction factor APOBEC3G in African green monkeys 41, a primate species naturally infected with simian immunodeficiency virus (SIV). APOBEC3G is polymorphic in African green monkeys, with some individuals carrying a single amino acid change that renders APOBEC3G resistant to its viral antagonist, Vif. In an experimental infection of African green monkeys with SIV, the virus from a monkey that was heterozygous for the Vif-resistant allele was unable to evolve the ability to antagonize APOBEC3G, while the virus from a monkey that was homozygous for the Vif-resistant allele was quickly able to evolve the ability to antagonize APOBEC3G. This suggests that maintaining polymorphism in a restriction factor can be functionally beneficial.

Gene duplication and innovation

Gene duplication of restriction factors is another evolutionary strategy for accelerating host adaptation to a virus. By duplicating a restriction factor, the host can simultaneously explore multiple evolutionary trajectories. For example, in primate, artiodactyl (cloven-hooved mammal), canine, and feline species, the APOBEC3 repertoires include many more paralogues than in rodents. In these lineages, the ancestral mammalian state, which was a single APOBEC3 gene, has been expanded to a family of APOBEC3 genes 42-46. Most primate genomes now encode 7 paralogs of Apobec3 genes, which vary in terms of their antiviral activity and retroelement targets, suggesting that they are adapted to different viruses. Several APOBEC3 genes show evidence of positive selection in primates, including APOBEC3DE, APOBEC3G and APOBEC3H 43, 47, 48, but the specific residues under positive selection vary between the APOBEC3 genes, further supporting the idea that each paralogue is evolving against different viral targets. In this way, increasing the copy number of a given restriction factor probably gives the host flexibility to rapidly evolve against several different viruses, leading to large families of related restriction factors. Other restriction factor families that are the result of gene duplications include the Mx1 gene family with 2 paralogues in some mice 49, the IFITM gene family with at least 4 paralogues in humans and 5 paralogues in mice 50, and the Trim5 gene family with 8 paralogues in mice and cows and 3 paralogues in rats51, 52.

By contrast, multiple members of a restriction factor family could also evolve to target the same virus in different ways, thereby constraining viral evolution such that the virus must maintain multiple defence strategies. An example of this is the pair of human paralogues APOBEC3F and APOBEC3G. APOBEC3F and APOBEC3G deaminate cytidine residues in the viral genome within different preferential sequence contexts 53. Thus, primate lentiviruses such as HIV-1 have had to evolve multiple mechanisms of antagonizing APOBEC3 proteins by binding to APOBEC3F and APOBEC3G using distinct domains of Vif 54-56. In this way, the host limits the ability of the virus to evolve while increasing antiviral activity.

Although TRIM5 is not duplicated in primates, it has undergone gene innovation in macaques and owl monkeys, who have independently gained additional exons through the insertion of a Cyclophilin A (CYPA) gene into noncoding segments of the TRIM5 gene 57-62. In both species, a TRIM-CYP fusion protein with potent antiviral activity is produced, although the viral targets are not identical. Moreover, TRIM-CYP and TRIM5α can both be expressed in the same individual, allowing the restriction of multiple lentiviruses, and, by restricting viral replication, the host also slows down the evolution of the virus.

Just as restriction factor families expand when more antiviral activity is advantageous in the presence of viruses, restriction factor families can also contract in the absence of a selective pressure. For example, the restriction factor APOBEC3H from macaques and chimpanzees has potent antiviral activity against lentiviruses63. However, two independent loss-of-function mutations in APOBEC3H have risen to high frequency in humans, despite the conservation of antiviral activity in other primates63. This suggests that restriction factors such as APOBEC3H, which are highly active DNA mutators, may impose a cost on the host genome, and they may be selected against in the absence of a viral pressure.

Lessons from the co-evolution of restriction factors and viruses

Studying the evolution of restriction factors can help us to understand why humans are susceptible to modern-day viruses that exist today, as our immune responses to contemporary viruses have been shaped by our evolutionary responses to previous infections. The modern innate immune system is not yet optimized against modern viruses, but rather was selected for by previous rounds of co-evolution with ancient viruses. By determining what type of viral infections occurred in the past and how they were eliminated, we can form new ideas about how to manipulate the immune system to our advantage in the ongoing battle against viruses.

Identifying previous viral infections

Paleovirology is the study of ancient, extinct viruses (paleoviruses) and their effects on modern day host-virus interactions 64. We know that ancient retroviruses infected primates because of remnants of viral sequences found in primate genomes 65. However, many retroviruses did not become endogenous in the host genome, and so we have no direct evidence of their existence. In fact, there have been no endogenous lentiviral sequences found in primate genomes other than in a single genus of prosimians 66-68. However, by identifying signatures of positive selection in host restriction factors, we can infer the existence of many additional paleoviruses, as well as the historical timeframe and species in which the infection took place. By combining evolutionary analyses with functional tests, we can determine the type of virus that likely drove selection in the host (Figure 3).

Fig. 3
Identifying paleoviruses using positive selection

One of the clearest examples of identifying a paleovirus using positive selection comes from the analysis of APOBEC3DE, a member of the APOBEC3 family in primates that restricts retrotransposons. APOBEC3DE has rapidly evolved in primates, particularly in the chimpanzee and bonobo lineages 48. Since its divergence with humans, APOBEC3DE in the chimpanzee lineage has accumulated 24 mutations, of which 23 are non-synonymous changes. These changes have broadened the antiviral activity of chimpanzee APOBEC3DE to include the ability to restrict lentiviruses. Human APOBEC3DE, by contrast, did not evolve the ability to restrict lentiviruses. Therefore, by identifying the adaptive consequences of rapid evolution in chimpanzee APOBEC3DE, we suggest that a lentivirus probably infected the chimpanzee-bonobo common ancestor in the past and, moreover, the infection occurred approximately 2-5 million years ago, after the chimpanzee-bonobo ancestor diverged from humans. Similarly, the acquisition of a TRIM-CYP anti-lentiviral gene fusion in owl monkeys 2-6 million years strongly argues for such a challenge occurring in this lineage of primates, which is both phylogenetically and geographically distinct from the primates that are known to be infected with lentiviruses currently. By studying the evolution of restriction factors, we can form a more accurate picture of the ancient history of retroviral infections in primates.

Predicting viral pathogenicity

In the virus-host arms race, positive selection results when the reproductive fitness of either party is challenged. If a virus is not pathogenic to the host, it is not likely to exert a selective pressure on the host. Therefore, adaptive changes in host restriction factors would not be expected to occur during a non-pathogenic infection. Mildly pathogenic viruses would be expected to impart weak selective pressures that might increase the allele frequency of a selected mutation but would not drive polymorphisms to fixation 69. For example, simian foamy viruses (SFVs) are considered nonpathogenic in their natural hosts 70, 71. Interestingly, SFVs have co-evolved with their hosts for over 30 million years 72, demonstrating that there might not be a selective pressure to stop SFV replication. Furthermore, the rate of evolution of SFVs is many times slower than for other RNA viruses 72, which suggests that the arms race between virus and host has slowed down considerably in this case.

Natural infection of African green monkeys by SIV is also thought to be non-pathogenic, as infection does not cause immunodeficiency despite high viral replication levels 70. Surprisingly, polymorphisms in the African green monkey APOBEC3G gene that allow evasion from antagonism by host-specific SIV Vifs were found in Grivet and Sabeus subspecies41, suggesting a recent selective pressure on APOBEC3G. Furthermore, the SIVs that circulate in these subspecies have re-gained the ability to antagonize APOBEC3G. This suggests that there is an arms race between SIV and African green monkeys and might have implications for SIV pathogenesis in African green monkeys. For example, SIV might have been formerly pathogenic to African green monkeys, or its pathogenesis might be present even now in unmeasured or mild ways. In this way, the evolution of a host restriction factor and the reciprocal viral evolution can inform our views of viral pathogenesis.

Explaining why humans are susceptible to modern-day viruses

HIV-1 and HIV-2 are the result of multiple cross-species transmission events of SIV from chimpanzees and sooty mangabeys, respectively, into humans73. Primate restriction factors have been shown to have an important in vivo role in preventing lentiviral cross-species viral transmission events. For example, experimental infection of rhesus macaques – which are not infected with SIV in the wild – with HIV or SIV can mimic a cross-species transmission event. During experimental HIV-1 infection, rhesus macaque TRIM5α and APOBEC3G completely restrict viral replication23, 24. Furthermore, naturally occurring polymorphisms in rhesus macaque TRIM5 attenuate viral replication by 100- to 1,000-fold during experimental infection with SIV from sooty mangabeys (SIVsm)74. These host genes involved in susceptibility or resistance to SIV infection may help to explain the dynamics of lentiviral zoonoses.

The four groups of HIV-1, which are each the result of an independent cross-species transmission event to humans from chimpanzees infected with SIV (SIVcpz), differ in their global spread, with group M representing the pandemic strain. It has recently been shown that the adaptation of HIV-1 to human-specific mutations in the restriction factor Tetherin was only achieved by group M and N viruses but not the non-pandemic groups O and P 75, 76. Clearly Tetherin did not prevent any of the four cross-species transmission events, but it has been suggested that overcoming Tetherin restriction by HIV-1 group M was necessary for efficient replication within humans and pandemic spread (reviewed in 77).

In studies of humans, the effects of restriction factor expression levels and polymorphisms on HIV-1 susceptibility and disease progression have not yielded a consensus viewpoint (reviewed in 78). However, our immune system may be better at preventing cross-species viral transmissions than intra-species viral transmissions because viruses that have crossed the species barrier have already partially adapted to the host. Perhaps for this reason, the evidence for the effect of restriction factors on within-species viral acquisition is less clear.

Identifying host-virus interaction domains and implications for treatment

The interactions between a virus and host restriction factor can be mapped down to distinct protein-protein interfaces and, in some cases, down to single amino acid residues. Because these interaction domains are directly engaged in genetic conflict, they are often the residues that are most rapidly evolving. By looking at genetic signatures of positive selection, the sites involved in protein-protein interactions can be predicted and then tested functionally, as was recently done with remarkable accuracy for SAMHD179, 80. Without knowing anything about the domains of SAMHD1 required for antagonism by the lentiviral protein Vpx, two groups carried out positive selection analyses of SAMHD1 using the dN/dS test and identified two different regions of SAMHD1 that have evolved very rapidly in primates. When functionally tested, these two regions of SAMHD1 were both shown to confer virus-specific degradation by Vpx from different lentiviruses. This information has helped to explain why lentiviruses and SAMHD1 have evolved on a molecular level. By mapping host-virus interactions, the constraints of the evolutionary arms race can be more fully understood.

Moreover, these protein-protein interactions between host restriction factors and viral antagonists provide tempting targets for small molecule inhibitors. An ideal inhibitor of a viral antagonist would specifically disrupt the ability of the virus to bind the host restriction factor or other host machinery required for antagonism. This would enable a host restriction factor to specifically inhibit viral replication, without any effect on the rest of the immune system of an individual. Inhibitors of viral antagonists could be used as therapeutic treatment in combination with other anti-retroviral drugs. Several inhibitors of HIV-1 Vif have been identified 81, 82, and attempts at disrupting Vpu function have been made 83. Achieving an inhibitor of a viral antagonist without disrupting host functions might be difficult because many viral antagonists use or mimic host machinery for their activity. Also, the virus might be able to quickly evolve resistance mutations, as genes encoding viral antagonists often do not have as many functional constraints as more conserved viral genes.

Conclusion

Restriction factors are early, potent, and specific cellular blocks against retroviral replication. They have clearly had an important role in innate immunity throughout primate evolution, and more work defining how and when they are important in viral zoonoses, global epidemics, and the progression to disease needs to be done. In this way, characterizing the evolution of restriction factor antiviral activity will help us to understand why we are winning or losing current battles against viruses.

Acknowledgments

We thank A. Compton, M. Daugherty, L. Etienne, H. Malik, and P. Mitchell for comments on the review. Related work in the Emerman lab is supported by R01 AI30937.

Glossary terms

Fv1 (Friend virus susceptibility 1) locus
Genomic region in mice encoding the Fv1 gene. Different Fv1 alleles encode versions of a restriction factor that protect mice from murine leukemia viruses.
Positive selection
Selection to increase the frequency of mutations that confer a fitness advantage.
Paralogues
Homologous genes within a species that diverge after gene duplication.
Endogenous retrotransposons
Mobile elements present in the genome that move locations using a mechanism involving reverse transcription.
Neutral evolution
Changes in allele frequency due to genetic drift, rather than a fitness outcome.
Pseudogene
Nonfunctional remnant of a gene.
‘Red Queen’ hypothesis
Evolutionary hypothesis proposed by Leigh Van Valen that states “For an evolutionary system, continuing development is needed just in order to maintain its fitness relative to the systems it is co-evolving with.”
dN/dS
Ratio of the rate of nonsynonymous mutations to the rate of synonymous mutations. Values greater than 1 are indicative of positive selection values less than 1 are indicative of negative selection and values near 1 are indicative of neutral selection. Other methods besides dN/dS can also be used to identify positive selection in different time scales103. and additional background on the relevance and use of positive selection in human evolution can be found in other reviews 104.
Orthologues
Homologous genes across species that diverge after speciation.
Balancing selection
Selection to maintain polymorphism due to frequency-dependent selection or heterozygote advantage.
Frequency-dependent selection
Selection to maintain mutations at an intermediate frequency to confer a fitness advantage.
Pattern recognition receptor (PRR)
A host receptor (such as Toll-like receptors or NOD-like receptors) that can sense pathogen-associated molecular patterns and initiate signalling cascades that lead to an innate immune response. These can be membrane bound (such as TLRs) or soluble cytoplasmic receptors (such as RIG-I, MDA5 and NLRs).
Selective sweep
Decrease in diversity in the genomic region surrounding an allele under positive selection.
Hitchhiking
Genetic linkage between loci under positive selection and nearby loci not under positive selection.

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