Sexual recombination is a signature of a persisting malaria epidemic in Peru

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to consider the impact that multi-clone, complex infections have on a parasite population structure in a low transmission setting. In general, complexity of infection (minimum number of clones within an infection) and the overall population level diversity is expected to be minimal in low transmission settings. Additionally, the parasite population structure is predicted to be clonal, rather than sexual due to infrequent parasite inoculation and lack of recombination between genetically distinct clones. However, in this low transmission of the Peruvian Amazon, complex infections are becoming more frequent, in spite of decreasing infection prevalence. In this study, it was hypothesized that sexual recombination between distinct clonal lineages of <it>Plasmodium falciparum </it>parasites were altering the subpopulation structure and effectively maintaining the population-level diversity.</p> <p>Methods</p> <p>Fourteen microsatellite markers were chosen to describe the genetic diversity in 313 naturally occurring <it>P. falciparum </it>infections from Peruvian Amazon. The population and subpopulation structure was characterized by measuring: clusteredness, expected heterozygosity (H_e), allelic richness, private allelic richness, and linkage disequilibrium. Next, microsatellite haplotypes and alleles were correlated with <it>P. falciparum </it>merozoite surface protein 1 Block 2 (<it>Pf</it>msp1-B2) to examine the presence of recombinant microsatellite haplotypes.</p> <p>Results</p> <p>The parasite population structure consists of six genetically diverse subpopulations of clones, called "clusters". Clusters 1, 3, 4, and 6 have unique haplotypes that exceed 70% of the total number of clones within each cluster, while Clusters 2 and 5 have a lower proportion of unique haplotypes, but still exceed 46%. By measuring the H_e, allelic richness, and private allelic richness within each of the six subpopulations, relatively low levels of genetic diversity within each subpopulation (except Cluster 4) are observed. This indicated that the number of alleles, and not the combination of alleles, are limited. Next, the standard index of association (I_A^S) was measured, which revealed a significant decay in linkage disequilibrium (LD) associated with Cluster 6, which is indicative of independent assortment of alleles. This decay in LD is a signature of this subpopulation approaching linkage equilibrium by undergoing sexual recombination. To trace possible recombination events, the two most frequent microsatellite haplotypes observed over time (defined by either a K1 or Mad20) were selected as the progenitors and then potential recombinants were identified in within the natural population.</p> <p>Conclusions</p> <p>Contrary to conventional low transmission models, this study provides evidence of a parasite population structure that is superficially defined by a clonal backbone. Sexual recombination does occur and even arguably is responsible for maintaining the substructure of this population.</p

The Plasmodium falciparum merozoite surface protein-1 19 KD antibody response in the Peruvian Amazon predominantly targets the non-allele specific, shared sites of this antigen

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>re-emerged in Iquitos, Peru in 1994 and is now hypoendemic (< 0.5 infections/person/year). Purportedly non-immune individuals with discrete (non-overlapping) <it>P. falciparum </it>infections can be followed using this population dynamic. Previous work demonstrated a strong association between this population's antibody response to <it>Pf</it>MSP1-19KD and protection against febrile illness and parasitaemia. Therefore, some selection for <it>Pf</it>MSP1-19KD allelic diversity would be expected if the protection is to allele-specific sites of <it>Pf</it>MSP1-19KD. Here, the potential for allele-specific polymorphisms in this population is investigated, and the allele-specificity of antibody responses to <it>Pf</it>MSP1-19KD are determined.</p> <p>Methods</p> <p>The 42KD region in <it>Pf</it>MSP1 was genotyped from 160 individual infections collected between 2003 and 2007. Additionally, the polymorphic block 2 region of <it>Pfmsp1 </it>(<it>Pfmsp1</it>-B2) was genotyped in 781 infection-months to provide a baseline for population-level diversity. To test whether <it>Pf</it>MSP1-19KD genetic diversity had any impact on antibody responses, ELISAs testing IgG antibody response were performed on individuals using all four allele-types of <it>Pf</it>MSP1-19KD. An antibody depletion ELISA was used to test the ability of antibodies to cross-react between allele-types.</p> <p>Results</p> <p>Despite increased diversity in <it>Pfmsp1</it>-B2, limited diversity within <it>Pfmsp1</it>-42KD was observed. All 160 infections genotyped were Mad20-like at the <it>Pfmsp1</it>-33KD locus. In the <it>Pfmsp1</it>-19KD locus, 159 (99.4%) were the Q-KSNG-F haplotype and 1 (0.6%) was the E-KSNG-L haplotype. Antibody responses in 105 individuals showed that Q-KNG and Q-TSR alleles generated the strongest immune responses, while Q-KNG and E-KNG responses were more concordant with each other than with those from Q-TSR and E-TSR, and vice versa. The immuno-depletion ELISAs showed all samples responded to the antigenic sites shared amongst all allelic forms of <it>Pf</it>MSP1-19KD.</p> <p>Conclusions</p> <p>A non-allele specific antibody response in <it>Pf</it>MSP1-19KD may explain why other allelic forms have not been maintained or evolved in this population. This has important implications for the use of <it>Pf</it>MSP1-19KD as a vaccine candidate. It is possible that Peruvians have increased antibody responses to the shared sites of <it>Pf</it>MSP1-19KD, either due to exposure/parasite characteristics or due to a human-genetic predisposition. Alternatively, these allelic polymorphisms are not immune-specific even in other geographic regions, implying these polymorphisms may be less important in immune evasion that previous studies suggest.</p

Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru

<p>Abstract</p> <p>Background</p> <p>Several of the intended <it>Plasmodium falciparum </it>vaccine candidate antigens are highly polymorphic and could render a vaccine ineffective if their antigenic sites were not represented in the vaccine. In this study, characterization of genetic variability was performed in major B and T-cell epitopes within vaccine candidate antigens in isolates of <it>P. falciparum </it>from Peru.</p> <p>Methods</p> <p>DNA sequencing analysis was completed on 139 isolates of <it>P. falciparum </it>collected from endemic areas of the Amazon basin in Loreto, Peru from years 1998 to 2006. Genetic diversity was determined in immunological important regions in circumsporozoite protein (CSP), merozoite surface protein-1 (MSP-1), apical membrane antigen-1 (AMA-1), liver stage antigen-1 (LSA-1) and thrombospondin-related anonymous protein (TRAP). Alleles identified by DNA sequencing were aligned with the vaccine strain 3D7 and DNA polymorphism analysis and FST study-year pairwise comparisons were done using the DnaSP software. Multilocus analysis (MLA) was performed and average of expected heterozygosity was calculated for each loci and haplotype over time.</p> <p>Results</p> <p>Three different alleles for CSP, seven for MSP-1 Block 2, one for MSP-1 Block 17, three for AMA-1 and for LSA-1 each and one for TRAP were identified. There were 24 different haplotypes in 125 infections with complete locus typing for each gene.</p> <p>Conclusion</p> <p>Characterization of the genetic diversity in <it>Plasmodium </it>isolates from the Amazon Region of Peru showed that <it>P. falciparum </it>T and B cell epitopes in these antigens have polymorphisms more similar to India than to Africa. These findings are helpful in the formulation of a vaccine considering restricted repertoire populations.</p

Antibody response dynamics to the Plasmodium falciparum conserved vaccine candidate antigen, merozoite surface protein-1 C-terminal 19kD (MSP1-19kD), in Peruvians exposed to hypoendemic malaria transmission

<p>Abstract</p> <p>Background</p> <p>In high-transmission areas, developing immunity to symptomatic <it>Plasmodium falciparum </it>infections requires 2–10 years of uninterrupted exposure. Delayed malaria-immunity has been attributed to difficult-to-develop and then short-lived antibody responses.</p> <p>Methods</p> <p>In a study area with <0.5 <it>P. falciparum </it>infections/person/year, antibody responses to the MSP1-19kD antigen were evaluated and associations with <it>P. falciparum </it>infections in children and adults. In months surrounding and during the malaria seasons of 2003–2004, 1,772 participants received ≥6 active visits in one study-year. Community-wide surveys were conducted at the beginning and end of each malaria season, and weekly active visits were completed for randomly-selected individuals each month. There were 79 <it>P. falciparum </it>infections with serum samples collected during and approximately one month before and after infection. Anti-MSP1-19kD IgG levels were measured by ELISA.</p> <p>Results</p> <p>The infection prevalence during February-July was similar in children (0.02–0.12 infections/person/month) and adults (0.03–0.14 infections/person/month) and was negligible in the four-month dry season. In children and adults, the seroprevalence was maintained in the beginning (children = 28.9%, adults = 61.8%) versus ending malaria-season community survey (children = 26.7%, adults = 64.6%). Despite the four-month non-transmission season, the IgG levels in <it>Plasmodium</it>-negative adults were similar to <it>P. falciparum</it>-positive adults. Although children frequently responded upon infection, the transition from a negative/low level before infection to a high level during/after infection was slower in children. Adults and children IgG-positive before infection had reduced symptoms and parasite density.</p> <p>Conclusion</p> <p>Individuals in low transmission areas can rapidly develop and maintain αMSP1-19kD IgG responses for >4 months, unlike responses reported in high transmission study areas. A greater immune capacity might contribute to the frequent asymptomatic <it>P. falciparum </it>infections in this Peruvian population.</p

Walls talk: Microbial biogeography of homes spanning urbanization.

Westernization has propelled changes in urbanization and architecture, altering our exposure to the outdoor environment from that experienced during most of human evolution. These changes might affect the developmental exposure of infants to bacteria, immune development, and human microbiome diversity. Contemporary urban humans spend most of their time indoors, and little is known about the microbes associated with different designs of the built environment and their interaction with the human immune system. This study addresses the associations between architectural design and the microbial biogeography of households across a gradient of urbanization in South America. Urbanization was associated with households' increased isolation from outdoor environments, with additional indoor space isolation by walls. Microbes from house walls and floors segregate by location, and urban indoor walls contain human bacterial markers of space use. Urbanized spaces uniquely increase the content of human-associated microbes-which could increase transmission of potential pathogens-and decrease exposure to the environmental microbes with which humans have coevolved

A Positive Correlation between Atypical Memory B Cells and Plasmodium falciparum Transmission Intensity in Cross-Sectional Studies in Peru and Mali

transmission intensity correlates with atypical memory B cell expansion.. In Peru, the mean level of atypical memory B cells, as a percent of total B cells, was higher than U.S. adults (Peru mean: 5.4% [95% CI: 3.61–7.28]; U.S. mean: 1.4% [95% CI: 0.92–1.81]; p<0.0001) but lower than Malian adults (Mali mean 13.1% [95% CI: 10.68–15.57]; p = 0.0001). In Peru, individuals self-reporting ≥1 prior malaria episodes had a higher percentage of atypical memory B cells compared to those reporting no prior episodes (≥1 prior episodes mean: 6.6% [95% CI: 4.09–9.11]; no prior episodes mean: 3.1% [95% CI: 1.52–4.73]; p = 0.028). infection could contribute to our understanding of naturally-acquired malaria immunity

Perfiles hematológicos en pacientes infectados con malaria en un área endémica del Perú [Hematological profiles of malaria-infected patients in an endemic area of Peru]

OBJECTIVES.: To evaluate the variation of hematological profiles of patients infected with uncomplicated Plasmodium vivax (Pv) and P. falciparum (Pf) malaria before, during and after treatment in a population of the Loreto region. MATERIALS AND METHODS.: This study was conducted between 2010 and 2012, in Zungarococha (Iquitos). The 425 participants had three visits (visit 1-day 0-before treatment, visit 2-day 7-during treatment, visit 3-day 28-after treatment), complete blood count, microscopic and molecular diagnosis (PCR). RESULTS.: At the first visit, 93 (21.9%) participants were found positive for Pv and 34 (8.0%) for Pf. All positives showed a reduction in hematocrit, white blood cell count (WBC), ablated and segmented neutrophils, eosinophils and platelets (p<0.001) compared to the negative group. A higher percentage of ablated neutrophils was found in Pf and segmented neutrophils in Pv compared to the negative group. Variations in hematological profiles were observed after treatment for both species; ablated neutrophils decreased, platelets increased, eosinophils increased at day 7 and declined at day 28, hematocrit and segmented neutrophils decreased at day 7 and normalized at day 28. Interspecies differences over time showed a bigger daily decrease in ablated neutrophils in Pv-infected when compared to Pf. CONCLUSIONS.: The hematological profile in uncomplicated malaria-positive patients varies over time during and after treatment. These are indicators of disease progression and help in the therapeutic surveillance of Plasmodium-infected patients

Population Structure Shapes Copy Number Variation in Malaria Parasites.

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen