Chapter 3Benefits of Antigenic Variation

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In this chapter, I describe the benefits that antigenic variation provides to parasites. These benefits help to explain why parasites vary in certain ways.

The first section examines how antigenic variants can extend the time a parasite maintains an infection within a host. The initial parasite type stimulates an immune response against its dominant antigens. If the parasite changes those antigens to new variants, it escapes immunity and continues a vigorous infection until the host generates a new response against the variants. Some parasites generate novel antigens by random mutations during replication. Other parasites store in their genomes alternative genes encoding variants of dominant antigens. Such parasites occasionally switch expression between the archived variants, allowing escape from specific immunity.

The second section presents how antigenic variants can reinfect hosts with immune memory. Host immune memory recognizes and mounts a rapid response against previously encountered antigens. Antigenic variants that differ from a host's previous infections escape that host's memory response. The distribution of immune memory profiles between hosts determines the success of each parasite variant.

The third section suggests that particular antigenic variants can attack some host genotypes but not others. For example, hosts vary in their MHC genotype, which determines the T cell epitopes each host can recognize. An epitope often can be recognized by one rare MHC allele but not by others. Each antigenic variant has its own distribution of host genotypes on which it does best at avoiding MHC recognition. Hosts also vary in the cellular receptors used for attachment by parasite surface antigens. Variation in surface antigens may allow parasites to attach with variable success to cellular receptors of different host genotypes.

The fourth section proposes that variable surface antigens sometimes enhance parasite fitness by allowing colonization of different host tissues. For example, certain antigenic variants of the blood-borne spirochete Borrelia turicatae sequester in the brain, protected from immune pressure. Antigenic variants of Plasmodium falciparum affect cytoadherence to capillary endothelia, which influences the tendency of the parasite to be hidden from sites of powerful immune activity. Sequestered variants may prolong infection or provide a source for reestablishing infection after the majority of parasites have been cleared from other body compartments. Many antigenic variants of B. turicatae and P. falciparum arise during a single infection because both species change surface antigens by switching gene expression between loci in a genomic archive of variants. Those surface variants stimulate strong antibody responses, suggesting that both immune escape and variable tissue tropism can provide important benefits for antigenic variation.

The fifth section describes how some antigenic variants interfere with the immune response to other variants. For example, a host may first encounter a particular antigenic type and then later become infected by a cross-reacting variant. The second infection sometimes stimulates a host memory response to the first variant rather than a new, specific response to the second variant. The memory response to the first variant may not clear the second variant effectively. Thus, hosts' memory profiles can benefit certain cross-reacting variants. In other cases, one variant may interfere with a host's ability to respond to another variant. This antagonism may cause the interacting variants to occur together because one or both variants enjoy the protection created by the presence of the other variant.

The final section outlines promising topics of study for future research.

3.1. Extend Length of Infection

Many parasites follow a simple pattern of infection and clearance. The measles virus, for example, multiplies and develops a large population in the host upon first infection (Griffin 2001). As the initial parasitemia builds, the host develops a specific immune response that eventually clears the infection. That same host rapidly clears later measles reinfections by specific immunity against the measles virus. Immunity that protects against reinfection develops from special memory components of the immune system. The immune system attacks conserved epitopes of the measles virus that do not vary significantly between viruses. Thus, measles does not escape immunity by changing its dominant antigens.

Other parasites begin their infection cycle in the same way—a large initial parasitemia followed by reduction when the host mounts a specific immune response against a dominant epitope. But some parasites can alter their dominant epitope. Antigenic variants escape recognition by the first wave of specific host defense against the initial antigenic type, extending the length of infection.

Trypanosoma brucei changes its dominant antigenic surface glycoprotein at a rate of 10−3 to 10−2 per cell division (Turner 1997). The trypanosome changes to another surface coat by altering expression between different genes already present in the genome. Infections lead to successive waves of parasitemia and clearance as novel antigenic types spread and are then checked by specific immunity.

Some viruses, such as HIV, escape immune attack by mutating their dominant epitopes (McMichael and Phillips 1997). Mutational changes to new, successful epitopes may be rare in each replication of the virus. But the very large population size of viruses within a host means that mutations, rare in each replication, often occur at least once in the host in each parasite generation.

For parasites that produce antigenic variants within hosts, the infection continues until the host controls all variants, raises an immune response against a nonvarying epitope, or clears the parasite by non-specific defenses.

Antigenic variation can extend the total time before clearance (Moxon et al. 1994; Deitsch et al. 1997; Fussenegger 1997). Extended infection benefits the parasite by increasing the chances for transmission to new hosts.

3.2. Infect Hosts with Prior Exposure

Hosts often maintain memory against antigens from prior infections. Host memory of particular antigens blocks reinfection by parasites carrying those antigens. Parasites can escape host memory by varying their antigens.

Cross-reaction between antigenic variants occurs when a host can use its specific recognition from exposure to a prior variant to fight against a later, slightly different variant. Cross-reactive protection may provide only partial defense, allowing infection but clearing the parasite more rapidly than in naive hosts.

In the simplest case, each antigenic type acts like a separate parasite that does not cross-react with other variants. The distribution of antigenic variants will be influenced by the rate at which new variants arise and spread and the rate at which old variants are lost from the population. As host individuals age, they become infected by and recover from different antigenic variants. Thus, the host population can be classified by resistance profiles based on the past infection and recovery of each individual (Andreasen et al. 1997).

Two extreme cases define the range of outcomes. On the one hand, each variant may occasionally spread epidemically through the host population. This leaves a large fraction of the hosts resistant upon recovery, driving that particular variant down in frequency because it has few hosts it can infect. The variant can spread again only after many resistant hosts die and are replaced by young hosts without prior exposure to that antigen. In this case, three factors set the temporal pacing for each antigenic variant: host age structure, the rapidity with which variants can spread and be cleared, and the waiting time until a potentially successful variant arises.

Variants may, on the other hand, be maintained endemically in the host population. This requires a balance between the rate at which infections lead to host death or recovery and the rate at which new susceptible hosts enter the population. The parasite population maintains as many variants as arise and do not cross-react, subject to "birth-death" processes governing the stochastic origin of new variants and the loss of existing variants.

These extreme cases set highly simplified end points. In reality, variants may differ in their ability to transmit between hosts and to grow within hosts. Nonspecific immunity or partial resistance to nonvarying or secondary epitopes also complicate the dynamics. Nonetheless, the epidemiology of the parasite, the host age structure and resistance profiles, and the processes that generate new variants drive many aspects of the dynamics.

Cross-reactivity between variants adds another dimension (Andreasen et al. 1997; Lin et al. 1999). The resistance profiles of individual hosts can still be described by history of exposure. However, a new variant's ability to infect a particular host depends on the impedance to the variant caused by the host's exposure profile and the cross-reactivity between antigens.

3.3. Infect Hosts with Genetically Variable Resistance

Host genotype can influence susceptibility to different parasite variants. For example, MHC genotype determines the host's efficiency in presenting particular epitopes to T cells. From the parasite's point of view, a particular antigenic variant may be able to attack some host genotypes but not others.

Hill (1998) pointed out that hepatitis B virus provides a good model for studying the interaction between MHC and parasite epitopes. Preliminary reports found associations between MHC genotype and whether infections were cleared or became persistent (van Hattum et al. 1987; Almarri and Batchelor 1994; Thursz et al. 1995; Hohler et al. 1997). The hepatitis B virus genome is very small (about 3,000 base pairs, or bp), which should allow direct study of how variation in viral epitopes interacts with the host's MHC genotype.

Host genotype can also affect the structure of the cellular receptors to which parasites attach. For example, the human CCR5 gene encodes a coreceptor required for HIV-1 to enter macrophages. A 32bp deletion of this gene occurs at a frequency of 0.1 in European populations. This deletion prevents the virus from entering macrophages (Martinson et al. 1997; O'Brien and Dean 1997; Smith et al. 1997).

It is not clear whether minor variants of cellular receptors occur sufficiently frequently to favor widespread matching variation of parasite surface antigens. Several cases of this sort may eventually be found, but in vertebrate hosts genetic variation of cellular receptors may be a relatively minor cause of parasite diversity.

3.4. Vary Attachment Characters

Parasite surface antigens often play a role in attachment and entry into host cells or attachment to particular types of host tissue. Varying these attachment characters allows attack of different cell types or adhesion to various tissues. Such variability can provide the parasite with additional resources or protection from host defenses.

Several species of the spirochete genus Borrelia cause relapsing fever (Barbour and Hayes 1986; Barbour 1987, 1993). Relapses occur because the parasite switches expression between different genetic copies of the major surface antigen. The host develops fever and then clears the initial parasitemia, but suffers a few rounds of relapse as the antigenic variants rise and fall. A subset of antigenic variants of these blood-borne bacteria have a tendency to accumulate in the brain, where they can avoid the host's immune response (Cadavid et al. 2001). Those bacteria in the brain may cause later relapses after the host has cleared the pathogens from the blood. The differing tissue tropisms of the antigenic variants may combine to increase the total parasitemia.

Protozoan parasites of the genus Plasmodium cause malaria in a variety of vertebrate hosts. Several Plasmodium species switch antigenic type (Brannan et al. 1994). Switching has been studied most extensively in P. falciparum (Reeder and Brown 1996). Programmed mechanisms of gene expression choose a single gene from among many archival genetic copies for the P. falciparum erythrocyte membrane protein 1 (PfEMP1) (Chen et al. 1998). As its name implies, the parasite expresses this antigen on the surface of infected erythrocytes. PfEMP1 induces an antibody response, which likely plays a role in the host's ability to control infection (Reeder and Brown 1996).

PfEMP1 influences cytoadherence of infected erythrocytes to capillary endothelia (Reeder and Brown 1996). This adherence may help the parasite to avoid clearance in the spleen. Thus, antigenic variants can influence the course of infection by escaping specific recognition and by hiding from host defenses (Reeder and Brown 1996). Full understanding of the forces that have shaped the archival repertoire, switching process, and course of infection requires study of both specific immune recognition and cytoadherence properties of the different antigenic variants.

The bacteria that cause gonorrhea and a type of meningitis have antigenically varying surface molecules. The variable Opa proteins form a family that influences the colony opacity (Malorny et al. 1998). Neisseria gonorrhoeae has eleven to twelve opa loci in its genome, and N. meningitidis has three to four opa loci. Any particular bacterial cell typically expresses only one or two of the opa loci; cellular lineages change expression in the opa loci (Stern et al. 1986). Both conserved and hypervariable regions occur among the loci. The bacteria expose the hypervariable regions on the cell surface (Malorny et al. 1998; Virji et al. 1999). The exposed regions contain domains that affect binding to host cells and to antibody epitopes.

The different antigenic variants within the Opa of proteins family affect tropism for particular classes of host cells (Gray-Owen et al. 1997; Virji et al. 1999). For N. gonorrhoeae, some Opa proteins have an affinity for the host cell surface protein CD66e found on the squamous epithelium of the uterine portio. Other Opa variants bind more effectively to CD66a found on the epithelium of the cervix, uterus, and colon tissues. Thus, the CD66-specific Opa variants may mediate the colonization of different tissues encountered during gonococcal infection (Gray-Owen et al. 1997).

HIV provides the final example for this section. This virus links its surface protein gp120 to two host-cell receptors before it enters the cell (O'Brien and Dean 1997). One host-cell receptor, CD4, appears to be required by most HIV variants (but see Saha et al. 2001). The second host-cell receptor can be CCR5 or CXCR4. Macrophages express CCR5. A host that lacks functional CCR5 proteins apparently can avoid infection by HIV, suggesting that the initial invasion requires infection of macrophages. HIV isolates with tropism for CCR5 can be found throughout the infection; this HIV variant is probably the transmissive form that infects new hosts.

As an infection proceeds within a host, HIV variants with tropism for CXCR4 emerge (O'Brien and Dean 1997). This host-cell receptor occurs on the surface of the CD4+ (helper) T lymphocytes. The emergence of viral variants with tropism for CXCR4 coincides with a drop in CD4+ T cells and onset of the immunosuppression that characterizes AIDS.

These examples show that variable surface antigens may sometimes occur because they provide alternative cell or tissue tropisms rather than, or in addition to, escape from immune recognition.

3.5. Antigenic Interference

Prior exposure of the host to particular epitopes sometimes reduces the host's ability to raise an immune response against slightly altered parasite variants. This interference was first observed in influenza (Fazekas de St. Groth and Webster 1966a, 1966b). In this case, if a host first encounters a variant, x, then a later cross-reacting variant, y, restimulates an antibody response against x rather than stimulating a specific response against y. This phenomenon is called original antigenic sin because the host tends to restimulate antibodies against the first antigen encountered. A similar pattern has been observed for the cytotoxic T cell response of mice against lymphocytic choriomeningitis virus (Klenerman and Zinkernagel 1998).

In some cases, antibodies from a first infection appear to enhance the success of infection by later, cross-reacting strains (see references in Ferguson et al. 1999). The mechanisms are not clear for many of these cases, but the potential consequences are important. If cross-reactive strains interfere with each other's success, then populations of parasites tend to become organized into nonoverlapping antigenic variants that define strains (Gupta et al. 1998). By contrast, if similar epitopes enhance each other's success, then well-defined strain clustering is less likely (Ferguson et al. 1999).

Simultaneous infection by two related epitopes sometimes interferes with binding by cytotoxic T cells. This interference, called altered peptide ligand antagonism, has been observed in HIV, hepatitis B virus, and Plasmodium falciparum (Bertoletti et al. 1994; Klenerman et al. 1994; Gilbert et al. 1998). In P. falciparum, the MHC molecule HLA-B35 binds two common epitopes of the circumsporozoite protein, cp26 and cp29, but does not bind two other epitopes, cp27 and cp28 (Gilbert et al. 1998). In hosts with HLA-B35, simultaneous infection with cp26 and cp29 appears to limit T cell responsiveness. In natural infections, hosts harbored both cp26 and cp29 variants more often than expected if epitopes were distributed randomly between hosts. Gilbert et al. (1998) suggest that the excess cp26-cp29 infections may have occurred because these two epitopes act synergistically to interfere with T cell response.

3.6. Problems for Future Research

1. Measures of parasite fitness

The first section of this chapter described how antigenic variation potentially extends the length of infection within a single host. Longer infections probably increase the transmission of the parasites to new hosts, increasing the fitness of the parasites. Other attributes of infection dynamics may also contribute to transmission and fitness. For example, the density of parasites in the host may affect the numbers of parasites transmitted by vectors. If so, then a good measure of fitness may be the number of parasites in the host summed over the total length of infection. It would be interesting to study experimentally the relations between infection length, parasite abundance, and transmission success. These relations between parasite characters and fitness strongly influence how selection shapes antigenic variation within hosts.

2. Interference between antigens in archival libraries of variants

Reports of original antigenic sin and altered peptide ligand antagonism have come from observations of antigenic variants generated by mutation. It would be interesting to learn whether parasites with archival variants also induce these phenomena. One might, for example, find that some variants induce a memory response that interferes with the host's ability to generate a specific response to other variants. Thus, the antigenic repertoire in archival libraries may be shaped both by the tendency to avoid cross-reaction and by the degree to which variants can interfere with the immune response to other variants.