Hamza A. Babiker

High-Level Chloroquine Resistance in Sudanese Isolates of Plasmodium falciparum Is Associated with Mutations in the Chloroquine Resistance Transporter Gene pfcrt and the Multidrug Resistance Gene pfmdr1

Polymorphisms were examined in 2 Plasmodium falciparum genes, as were chloroquine responses of clones and isolates from a village in eastern Sudan. There was a significant association between an allele of the P. falciparum chloroquine resistance transporter gene (pfcrt-T76) and both in vitro and in vivo resistance. There was a less significant association with the multidrug resistance gene pfmdr1-Y86 allele. A significant association between pfmdr1-Y86 and pfcrt-T76 was apparent among resistant isolates, which suggests a joint action of the 2 genes in high-level chloroquine resistance.

Random mating in a natural population of the malaria parasite Plasmodium falciparum

The genetic structure of a population of the malaria parasite Plasmodium falciparum has been examined in a village in Tanzania. Seventeen alleles of the merozoite surface protein MSP-1 and 23 of MSP-2 were detected by the polymerase chain reaction (PCR) among the blood parasites of the inhabitants. Most infections contained mixtures of genetically distinct parasite clones. PCR was then used to examine individual P. falciparum oocysts, the products of fertilization events, in wild-caught mosquitoes. Forty-five out of 71 oocysts were heterozygous for one or both genes, showing that crossing between clones was taking place frequently, following uptake of mixtures of gametocytes by the mosquitoes. The frequency of heterozygous forms showed that random mating events probably occurred within mosquito bloodmeals between gametes belonging to different parasite clones.

Genotyping of Plasmodium falciparum infections by PCR: a comparative multicentre study

Genetic diversity of malaria parasites represents a major issue in understanding several aspects of malaria infection and disease. Genotyping of Plasmodium falciparum infections with polymerase chain reaction (PCR)-based methods has therefore been introduced in epidemiological studies. Polymorphic regions of the msp1, msp2 and glurp genes are the most frequently used markers for genotyping, but methods may differ. A multicentre study was therefore conducted to evaluate the comparability of results from different laboratories when the same samples were analysed. Analyses of laboratory-cloned lines revealed high specificity but varying sensitivity. Detection of low-density clones was hampered in multiclonal infections. Analyses of isolates from Tanzania and Papua New Guinea revealed similar positivity rates with the same allelic types identified. The number of alleles detected per isolate, however, varied systematically between the laboratories especially at high parasite densities. When the analyses were repeated within the laboratories, high agreement was found in getting positive or negative results but with a random variation in the number of alleles detected. The msp2 locus appeared to be the most informative single marker for analyses of multiplicity of infection. Genotyping by PCR is a powerful tool for studies on genetic diversity of P. falciparum but this study has revealed limitations in comparing results on multiplicity of infection derived from different laboratories and emphasizes the need for highly standardized laboratory protocols.

Current views on the population structure of plasmodium falciparum: Implications for control

In recent years there has been a considerable debate on the population genetic structure of malaria parasites. Work on this subject has been revolutionized by the advent of the polymerase chain reaction (PCR) technique, which has made it feasible to study the genetic diversity of parasites in small samples of infected blood, allowing extensive surveys of natural parasite populations to be made. In addition, the technique can be applied to the mosquito stages of the malaria parasite, allowing direct assessments to be trade of the frequency of crossing between parasite clones in Nature. Studies on Plasmodium falcjparum in a wide range of malaria-endemic regions are now revealing the relationship between parasite population structure and malaria epidemiology. In this article, Hamza Babiker and David Walliker review recent work in this field, and discuss how such knowledge might be used to advise on the future deployment of control measures such as antimalarial drugs and possible malaria vaccines.

Estimation of inbreeding coefficients from genotypic data on multiple alleles, and application to estimation of clonality in malaria parasites

Methods for estimating probability of identity by descent (f) are derived for data on numbers of genotypes at single loci and at pairs of loci with many alleles at each locus. The methods are general, but are specifically applied to data on genotype frequencies in zygotes of the malaria parasite sampled from its mosquito host in order to find the extent of outcrossing in the parasite and the degree of clonality in populations. It is assumed that zygotes are the outcome either of gametes of the same clone, in which they are identical at all loci, or are products of two random, unrelated clones. From the estimate of f an effective number of clones per human host can also be derived. For Plasmodium falciparum from a Tanzanian village, estimates of f are 0.33 from data on zygote frequencies at two multiallelic loci, indicating that two-thirds of zygotes produce recombinant type.

Identification of a Conserved Plasmodium falciparum var Gene Implicated in Malaria in Pregnancy

The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family is a highly polymorphic class of variant surface antigens encoded by var genes that play an important role in malaria pathogenesis. This report describes the unexpected finding that 1 of the var genes encoding a PfEMP1 variant that binds to the host receptor chondroitin sulfate A (CSA) and is implicated in malaria in pregnancy is well conserved among P. falciparum isolates worldwide. The N-terminal domains of this PfEMP1 variant are especially highly conserved, whereas the functional CSA binding domain is more variable. Analysis of var gene expression in placental parasites from primigravid women in Malawi did not support a role for this conserved gene in placental infection but identified a second commonly occurring var gene. These results indicate the need for reevaluation of previous assumptions of a minimal overlap between var gene repertoires from different parasite isolates.

Molecular analysis of recrudescent parasites in a Plasmodium falciparum drug efficacy trial in Gabon.

Recrudescent Plasmodium falciparum parasites were sampled from 108 children taking part in a drug efficacy trial in Gabon. A finger-prick blood sample was taken from each child before treatment, and a post-treatment sample taken of the recrudescent parasites. Sample deoxyribonucleic acid was amplified by the polymerase chain reaction using primers specific to the P. falciparum antigen genes MSP-1, MSP-2 and GLURP. Seventy-seven children had identical parasites in their pre- and post-treatment samples, indicating genuine recrudescences of resistant parasites. Fourteen children had completely different parasites in their pre- and post-treatment samples, indicating either a fresh infection from a mosquito or growth of a population of parasites not detected in the pre-treatment sample, perhaps due to sequestration. The remaining 17 children had a mixture of pre-treatment and new parasites in their post-treatment samples. This study demonstrated the use of polymorphic markers to confirm whether parasites in patients with clinical recrudescences after drug treatment are genuinely resistant.

3. Genetic structure and dynamics of Plasmodium falciparum infections in the Kilombero region of Tanzania

Plasmodium falciparum parasites exist as genetically distinct haploid clones in infected people. In the Kilombero valley in south-east Tanzania, at least 85% of the inhabitants of Michenga village harbour more than one clone. Using 2 highly polymorphic unlinked markers, it has been estimated that each infected person harbours between one and 6 P. falciparum clones at any one time, with a mean of 3.5 clones. When mosquitoes acquire gametocytes of 2 different clones in a blood meal, crossing generates recombinant clones differing from their parental genotypes. The inbreeding coefficient of the parasite population has been estimated as 0.33.

Dynamics of gametocytes among Plasmodium falciparum clones in natural infections in an area of highly seasonal transmission

The dynamics of gametocyte production in Plasmodium falciparum clones were studied in inhabitants of an area of highly seasonal malaria transmission in eastern Sudan. Reverse-transcriptase polymerase chain reaction was used to detect expression of 2 genes that encode gametocyte-specific proteins, pfs25 and pfg377, in parasites sampled from individuals throughout one year. Some patients who acquired infections during the wet season were found to harbor subpatent gametocytemia through the following dry season in the apparent absence of mosquito transmission. Genotyping of parasites in multiclonal infections showed considerable fluctuation of gametocyte production by individual clones. The gametocytes present at the end of the dry season provide the most probable source of the genetically complex cyclical malaria outbreaks following the rainy season in this region.

Estimation of Numbers of Malaria Clones in Blood Samples

Methods are derived for estimating the mean number of clones of the haploid malaria parasite Plasmodium falciparum from samples of blood of infected hosts which have been tested for the presence of alleles at marker loci. For example, at a locus with three alleles the sample might contain only A1 or A1 and A2, or A1, A2 and A3, with multiple allele classes being more common at high infection rates. Assuming either a Poisson or negative binomial distribution of numbers of infections per host, formulae are derived for the frequency of different classes of blood samples, and maximum likelihood methods are used to estimate the mean number of clones and allele frequencies. Two data sets, each on two loci, are analysed. One data set was from the same locality in Tanzania from which oocysts of the parasite in mosquito vectors were tested for clonality (i. e. diploid unions of gametes from the same clone) using genetic markers. Good agreement was obtained between the observed clonality in oocysts and that expected from the number of infections per host (mean approximately three).