The selection landscape of malaria parasites.

Malaria parasites have to survive and transmit within a highly selective and ever-changing host environment. Because immunity to malaria is nonsterilizing and builds up slowly through repeated infections, commonly the parasite invades a host that is immunologically and physiologically different from its previous host. During the course of infection, the parasite must also keep pace with changes in host immune responses and red-blood-cell physiology. Here, we describe the "selection landscape" of the most virulent of the human malaria parasites, Plasmodium falciparum, and the adaptive mechanisms it uses to navigate through that landscape. Taking a cost-benefit view of parasite fitness, we consider the evolutionary outcomes of the most important forces of selection operating on the parasite, namely immunity, host death, drugs, mosquito availability, and coinfection. Given the huge potential for malaria parasite evolution in the context of the recently renewed effort to eradicate malaria, a deeper understanding of P. falciparum adaptation is essential.

Virulence evolution in response to vaccination: the case of malaria.

One theory of why some pathogens are virulent (i.e., they damage their host) is that they need to extract resources from their host in order to compete for transmission to new hosts, and this resource extraction can damage the host. Here we describe our studies in malaria that test and support this idea. We go on to show that host immunity can exacerbate selection for virulence and therefore that vaccines that reduce pathogen replication may select for more virulent pathogens, eroding the benefits of vaccination and putting the unvaccinated at greater risk. We suggest that in disease contexts where wild-type parasites can be transmitted through vaccinated hosts, evolutionary outcomes need to be considered.

Drug resistance models for malaria.

The main factors affecting the evolution of drug resistance in malaria according to theoretical models are reviewed here. The overwhelming influence on the emergence and rate of spread of drug resistance is the proportion of infected hosts that are treated with drugs. A second important effect is drug efficacy in killing parasites. Factors such as average transmission rate, recombination, the biological cost of resistance, and the mode of gene action also influence the rate of spread but have relatively minor impacts. A simple population dynamics model that captures the epidemiological effects of drug treatment and resistance, as opposed to a population genetics model that does not, is presented in order to illustrate the main conclusions.

The effects of mosquito transmission and population bottlenecking on virulence, multiplication rate and rosetting in rodent malaria.

Malaria parasites vary in virulence, but the effects of mosquito transmission on virulence phenotypes have not been systematically analysed. Using six lines of malaria parasite that varied widely in virulence, three of which had been serially blood-stage passaged many times, we found that mosquito transmission led to a general reduction in malaria virulence. Despite that, the between-line variation in virulence remained. Forcing serially passaged lines through extreme population bottlenecks (<5 parasites) reduced virulence in only one of two lines. That reduction was to a level intermediate between that of the virulent parental and avirulent ancestral line. Mosquito transmission did not reverse the increased parasite replication rates that had accrued during serial passage, but it did increase rosetting frequencies. Re-setting of asexual stage genes during the sexual stages of the life cycle, coupled with stochastic sampling of parasites with variable virulence during population bottlenecks, could account for the virulence reductions and increased rosetting induced by mosquito transmission.

Rodent malaria parasites suffer from the presence of conspecific clones in three-clone Plasmodium chabaudi infections.

We studied infection dynamics of Plasmodium chabaudi in mice infected with 3 genetically distinct clones--1 less virulent than the other 2--either on their own or in mixtures. During the acute phase of infection, total numbers of asexual parasites in mixed-clone infections were equal to those produced by the 3 clones alone, suggesting strong in-host competition among clones. During the chronic phase of the infection, mixed-clone infections produced more asexual parasites than single-clone infections, suggesting lower levels of competition than during the acute phase, and indicating that a genetically diverse infection is harder to control by the host immune system. Transmission potential over the whole course of infection was lower from mixed-clone infections than from the average of the 3 single-clone infections. These results suggest that in-host competition reduces both growth rate and probability of transmission for individual parasite clones.

Local differentiation in Plasmodium falciparum drug resistance genes in Sudan.

Studies of population genetic structure of parasites can be used to infer which parasite genes are under selection. Here, the population structure of 4 genes associated with drug resistance of Plasmodium falciparum (the chloroquine resistance transporter, pfcrt, dihydrofolate reductase, dhfr, dihydropteroate synthase, dhps, and multi-drug resistance, pfmdr-1) were examined in parasite populations in 3 villages in eastern Sudan and in an urban area of Khartoum, the capital. In order to differentiate the effects of drug selection from neutral influences on population structure, parasites were also genotyped for 3 putatively neutral microsatellite loci (polyalpha, TA81 and pfg377), and for 2 antigenic loci that are either under balancing selection or neutral, merozoite surface protein 1 and 2, (MSP-1 and MSP-2). Cross-sectional surveys were carried out during the peak transmission (wet) season and in the ensuing dry season. No significant variation in frequencies of MSP-1 and MSP-2 alleles was seen among villages in the eastern region and between the villages and Khartoum, nor between the wet and dry season. However, the drug resistance genes, pfmdr-1, pfcrt and dhfr and to a lesser extent the microsatellite loci showed high FST values when comparing villages with Khartoum, indicating strong geographical differentiation at these loci. Moreover, variation in frequencies of the drug resistance genes, pfmdr-1, pfcrt and dhfr, was observed between the wet and dry season. These differences most probably reflect the variation in drug pressure between each region, and in drug usage between the wet and dry season in a given region.

The effects of host immunity on virulence-transmissibility relationships in the rodent malaria parasite Plasmodium chabaudi.

Here we examined the impact of host immunity on relationships between parasite virulence, transmission rate, intrinsic growth rate and host recovery rate in the rodent malaria parasite, Plasmodium chabaudi. Groups of naïve and immunized mice were infected with 1 of 10 cloned lines of parasites and their infection dynamics were monitored for 19 days. We found that (1) host immunity reduced the growth rate, virulence, transmission rate and infection length, with a consequent 3-fold reduction in life-time transmission potential, (2) clone means for these traits ranked similarly across naïve and immunized mice, (3) regression slopes of transmission potential on growth rate, virulence and infection length were similar in naive and immunized mice, (4) virulence and infection length were positively correlated in immunized but not naïve mice, and (5) for a similar level of parasite growth rate and virulence, transmission potential and infection length were lower in immunized than naïve mice. Thus host immunity reduced all these fitness traits in a manner consistent with direct parasite-driven biological links among them. These results support the basic assumption underlying our theory that predicts that anti-disease vaccines will select for higher virulence in those microparasites for which virulence is integrally linked to transmission.

Mosquito mortality and the evolution of malaria virulence.

Several laboratory studies of malaria parasites (Plasmodium sp.) and some field observations suggest that parasite virulence, defined as the harm a parasite causes to its vertebrate host, is positively correlated with transmission. Given this advantage, what limits the continual evolution of higher parasite virulence? One possibility is that while more virulent strains are more infectious, they are also more lethal to mosquitoes. In this study, we tested whether the virulence of the rodent malaria parasite P. chabaudi in the laboratory mouse was correlated with the fitness of mosquitoes it subsequently infected. Mice were infected with one of seven genetically distinct clones of P. chabaudi that differ in virulence. Weight loss and anemia in infected mice were monitored for 16-17 days before Anopheles stephensi mosquitoes were allowed to take a blood meal from them. Infection virulence in mice was positively correlated with transmission to mosquitoes (infection rate) and weakly associated with parasite burden (number of oocysts). Mosquito survival fell with increasing oocyst burden, but there was no overall statistically significant relationship between virulence in mice and mosquito mortality. Thus, there was no evidence that more virulent strains are more lethal to mosquitoes. Both vector survival and fecundity depended on parasite clone, and contrary to expectations, mosquitoes fed on infections more virulent to mice were more fecund. The strong parasite genetic effects associated with both fecundity and survival suggests that vector fitness could be an important selective agent shaping malaria population genetics and the evolution of phenotypes such as virulence in the vector.

Virulence in rodent malaria: host genotype by parasite genotype interactions.

In an effort to understand what limits the virulence of malaria parasites, we infected inbred mice of three genotypes (C57Bl/6J, CBA/Ca and DBA/2) with one of two parasite lines of the rodent malaria Plasmodium chabaudi. One of these parasite lines had been serially passaged through C57Bl/6J mice and had evolved higher asexual growth rate, virulence and transmission in the process. The other parasite line was the unadapted ancestral line which had low virulence. In all three host genotypes, the C57Bl/6J-adapted parasite line was more virulent than the ancestral line thus indicating that trade-offs in virulence between alternative host genotypes had not placed strong constraints on the evolution of high virulence in this system. By examining the infection dynamics for fitness-related components-asexual parasite population growth, transmission and virulence-we revealed alternative possible explanations for what sets the upper limit to virulence in nature. The total number of transmission forms (gametocytes) produced during the infection, a measure of parasite Darwinian fitness, was four-fold higher in mice that survived the infection than those which died. Among mice that survived, total gametocyte production was greatest in the host genotype that suffered intermediate levels of morbidity (anaemia and weight loss). Thus, there were transmission costs of high virulence that were partly due to host death (as most theoretical models of virulence evolution assume), but perhaps partly due to some factor related to high morbidity. Both mortality and morbidity-related factors might therefore influence the upper limit on virulence of malaria parasites.

Imperfect vaccines and the evolution of pathogen virulence.

Vaccines rarely provide full protection from disease. Nevertheless, partially effective (imperfect) vaccines may be used to protect both individuals and whole populations. We studied the potential impact of different types of imperfect vaccines on the evolution of pathogen virulence (induced host mortality) and the consequences for public health. Here we show that vaccines designed to reduce pathogen growth rate and/or toxicity diminish selection against virulent pathogens. The subsequent evolution leads to higher levels of intrinsic virulence and hence to more severe disease in unvaccinated individuals. This evolution can erode any population-wide benefits such that overall mortality rates are unaffected, or even increase, with the level of vaccination coverage. In contrast, infection-blocking vaccines induce no such effects, and can even select for lower virulence. These findings have policy implications for the development and use of vaccines that are not expected to provide full immunity, such as candidate vaccines for malaria.

Antimalarial drugs clear resistant parasites from partially immune hosts.

Circumstantial evidence in human malaria suggests that elimination of parasites by drug treatment meets higher success rates in individuals having some background immunity. In this study, using the rodent malaria model Plasmodium chabaudi, we show that drug-resistant parasites can be cleared by drugs when the host is partially immune.

Novel Plasmodium falciparum clones and rising clone multiplicities are associated with the increase in malaria morbidity in Ghanaian children during the transition into the high transmission season.

A survey of Plasmodium falciparum infection and clone multiplicity in Ghanaian children was carried out to study the effect of the onset of the malaria transmission season on disease incidence. Fortnightly blood samples were collected from 40 children living in the rural town of Dodowa, between February and August 1998. P. falciparum parasite densities were calculated and PCR genotyping was carried out using the polymorphic MSP-1 and MSP-2 genes as target loci for the estimation of the number of parasite clones in each sample. The average clone number was estimated using maximum likelihood techniques and the minimum number of clones per patient was analysed for the effects of age, sex, season, minimum number of clones per child, level of parasitaemia and parasite genotype. The statistical analysis indicated that the more clones a child carried, the more likely they were to have a clinical malaria episode. This was true after adjusting for age and season effects and for the measured circulating parasitaemia. The probability of clinical disease also increased if the MSP-1 MAD 20 and the MSP-2 FC 27 alleles were present. This longitudinal analysis thus indicates that the probability of a Ghanaian child having a symptomatic malaria episode is positively associated with both increasing numbers and novel types of P. falciparum clones.

Quantifying genetic and nongenetic contributions to malarial infection in a Sri Lankan population.

Explaining the causes of variation in the severity of malarial disease remains a major challenge in the treatment and control of malaria. Many factors are known to contribute to this variation, including parasite genetics, host genetics, acquired immunity, and exposure levels. However, the relative importance of each of these to the overall burden of malarial disease in human populations has not been assessed. Here, we have partitioned variation in the incidence of malarial infection and the clinical intensity of malarial disease in a rural population in Sri Lanka into its component causes by pedigree analysis of longitudinal data. We found that human genetics, housing, and predisposing systematic effects (e. g., sex, age, occupation, history of infections, village) each explained approximately 15% of the variation in the frequency of malarial infection. For clinical intensity of illness, 20% of the variation was explained by repeatable differences between patients, about half of which was attributable to host genetics. The other half was attributable to semipermanent differences among patients, most of which could be explained by known predisposing factors. Three percent of variation in clinical intensity was explained by housing, and an additional 7% was explained by current influences relating to infection status (e.g., parasitemia, parasite species). Genetic control of Plasmodium falciparum infections appeared to modulate the frequency and intensity of infections, whereas genetic control of Plasmodium vivax infections appeared to confer absolute susceptibility or refractoriness but not intensity of disease. Overall, the data show consistent, repeatable differences among hosts in their susceptibility to clinical disease, about half of which are attributable to host genes.

Population dynamics of Plasmodium falciparum in an unstable malaria area of eastern Sudan.

The Plasmodium falciparum population in Asar village, eastern Sudan, where malaria transmission is markedly seasonal, was monitored monthly over a period of 15 months. A cohort of infected patients was treated and then followed monthly throughout the dry season until the next transmission season. Parasitaemia detected by microscopy among the cohort reduced dramatically following treatment, but remained sporadic during the dry season, and reappeared following the onset of the next wet season. However between 40 and 50% of the cohort retained a persisting parasitaemia detectable by PCR throughout the dry season. These parasites were genetically complex, consisting of multiple clones with a large repertoire of alleles of the studied genes. While the number of clones per host dropped significantly following treatment of acute cases during the transmission season, drug treated people nevertheless maintained an average of one clone throughout the dry season. Allele frequencies of MSP-1, MSP-2 and GLURP showed slight, statistically insignificant, fluctuations between the dry and wet seasons. A higher frequency of inbreeding was estimated among the parasites that survived the dry season compared to the wet season.

Selection for high and low virulence in the malaria parasite Plasmodium chabaudi.

What stops parasites becoming ever more virulent? Conventional wisdom and most parasite-centred models of the evolution of virulence suppose that risk of host (and, hence, parasite) death imposes selection against more virulent strains. Here we selected for high and low virulence within each of two clones of the rodent malaria parasite Plasmodium chabaudi on the basis of between-host differences in a surrogate measure of virulence--loss of live weight post-infection. Despite imposing strong selection for low virulence which mimicked 50-75% host mortality, the low virulence lines increased in virulence as much as the high virulence lines. Thus, artificial selection on between-host differences in virulence was unable to counteract natural selection for increased virulence caused by within-host selection processes. The parasite's asexual replication rate and number of sexual transmission forms also increased in all lines, consistent with evolutionary models explaining high virulence. An upper bound to virulence, though not the asexual replication rate, was apparent, but this bound was not imposed by host mortality. Thus, we found evidence of the factors assumed to drive evolution of increased virulence, but not those thought to counter this selection.

The emergence of drug-resistant malaria.

Stochastic processes play a vital role in the early stages of the evolution of drug-resistant malaria. We present a simple and flexible method for investigating these processes and understanding how they affect the emergence of drug-resistant malaria. Qualitatively different predictions can be made depending on the biological and epidemiological factors which prevail in the field. Intense intra-host competition between co-infecting clones, low numbers of genes required to encode resistance, and high drug usage all encourage the emergence of drug resistance. Drug-resistant forms present at the time drug application starts are less likely to survive than those which arise subsequently; survival of the former largely depends on how rapidly malaria population size stabilizes after drug application. In particular, whether resistance is more likely to emerge in areas of high or low transmission depends on malaria intra-host dynamics, the level of drug usage, the population regulation of malaria, and the number of genes required to encode resistance. These factors are discussed in relation to the practical implementation of drug control programmes.

The evolution of multiple drug resistance in malaria parasites.

Forces determining the rate of spread of drug resistance in malaria were explored using a genetics transmission model which took account of the strong population structure of these parasites. The rate of change of frequency of drug resistant mutants in the parasite population is primarily a function of the proportion of hosts treated with drugs, and parasite transmission rates. With high transmission rates, selection by drugs is more effective than with lower rates because the resistant mutant passes on more copies of itself to the next generation of hosts. Thus reducing transmission rates, either at the overall population level or from drug-treated individuals, should be effective in curbing the spread of resistance. An exception to this is when 2 unlinked genes act jointly (not independently) to confer resistance, when the prevailing transmission rate is already low, drug use is minimal, and resistance genes are rare. Reductions in fitness of the mutant in the absence of drugs (i.e., a fitness cost to resistance) and the degree of epistasis and the mode of gene action of the drugs do not alter these conclusions.

Usefulness of antinuclear antibody testing to screen for rheumatic diseases.

OBJECTIVE: To assess the usefulness of the indirect immunofluorescence antinuclear antibody test (FANA) using human laryngeal epithelial carcinoma cells as nuclear substrate, to screen for childhood rheumatic diseases. STUDY DESIGN: A review of all FANA tests performed on children at British Columbia's Children's Hospital between 7 March 1991 and 31 July 1995. RESULTS: FANA tests were positive at titres of 1:20 or greater in 41% of all subjects tested, and in 65% of all subjects in whom the diagnosis was obtained. FANA positivity occurred in 67% of those with a rheumatic disease, compared with 64% of those with a non-rheumatic disease (p = 0.4). More girls had high titre FANA positivity than boys independent of whether or not they had a rheumatic disease (p = 0.05). At a screening serum dilution of 1:40 a positive test has a sensitivity of only 0.63, and a positive predictive value of only 0.33 for any rheumatic disease. For systemic lupus erythematosus (SLE), mixed connective tissue disease (MCTD), or overlap syndrome at a screening dilution of 1:40 the test has a very high sensitivity of 0.98, but a very low positive predictive value of only 0.10, the test having slightly better characteristics for boys than girls. CONCLUSION: Although a negative FANA test makes a diagnosis of SLE or MCTD extremely unlikely, a positive test even at moderately high titres of 1:160 or higher is found so frequently in children without a rheumatic disease that a positive result has little or no diagnostic value. It is suggested that a screening serum dilution of 1:160 or 1:320 would increase the usefulness of the test, by decreasing false positive tests, without significantly increasing false negative tests for SLE or MCTD, and would have the potential for considerable cost savings.

Survival probability of drug resistant mutants in malaria parasites.

This study predicts the ultimate probability of survival of a newly arisen drug resistant mutant in a population of malaria parasites, with a view to understanding what conditions favour the evolution of drug resistance. Using branching process theory and a population genetics transmission model, the probabilities of survival of one- and two-locus new mutants are calculated as functions of the degree of drug pressure, the mean and variation in transmission rate, and the degree of natural selection against the mutant. Probability of survival increases approximately linearly with drug pressure, the slope of the line increasing with mean transmission rate. Thus increased drug pressure, especially in combination with high transmission rates, strongly favours the evolution of drug resistance. These conclusions also hold for the case of multiple drug resistance where it is coded for by two unlinked loci: the greater effective recombination breakdown in high transmission areas is counteracted by greater effective selection so that the net effect of higher transmission rates is to favour the evolution of multiple drug resistance. High variability in transmission rate and natural selection against the mutants are unfavourable to mutant survival, though these are relatively weak forces.

Use of deterministic sampling for exploring likelihoods in linkage analysis for quantitative traits.

Deterministic sampling was used to numerically evaluate the expected log-likelihood surfaces of QTL-marker linkage models in large pedigrees with simple structures. By calculating the expected values of likelihoods, questions of power of experimental designs, bias in parameter estimates, approximate lower-bound standard errors of estimates and correlations among estimates, and suitability of statistical models were addressed. Examples illustrated that bracket markers around the QTL approximately halved the standard error of the recombination fraction between the QTL and the marker, although they did not affect the standard error of the QTL's effect, that overestimation of the distance between the markers caused overestimation of the distance between the QTL and marker, that more parameters in the model did not affect the accuracy of parameter estimates, that there was a moderate positive correlation between the estimates of the QTL effect and its recombination distance from the marker, and that selective genotyping did not introduce bias into the estimates of the parameters. The method is suggested as a useful tool for exploring the power and accuracy of QTL linkage experiments, and the value of alternative statistical models, whenever the likelihood of the model can be written explictly.