Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies.

BACKGROUND: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. RESULTS: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. CONCLUSION: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Yellow fever (YF) vaccination does not increase dengue severity: A retrospective study based on 11,448 dengue notifications in a YF and dengue endemic region.

BACKGROUND: We study the association between prior yellow fever immunization and clinical outcomes of dengue infections in individuals of varying sexes and ages. Serological interactions between dengue virus and other flaviviruses could drive antibody dependent enhancement, which is associated with disease severity in dengue infections. This effect may influence disease severity in individuals subsequently affected by related flaviviruses, such as dengue. We compare the severity of dengue episodes between patients vaccinated and non-vaccinated against yellow fever. METHODS: We evaluated the severity of 11,448 lab-confirmed dengue cases reported in São José do Rio Preto, Brazil, in 7370 YF vaccinated patients compared to 4043 unvaccinated patients. We regressed dengue severity against YF vaccine status and a number of demographic, clinical, and laboratory variables as controls. We also evaluated the association between YF vaccination status and the clinical and laboratory symptoms of dengue patients. RESULTS: We did not find any evidence of increased risk for severe dengue in patients vaccinated against YF (odds ratio = 1.00; 95% confidence interval = 0.87-1.14). Most of the variables analyzed did not have a statistically significant association with YF vaccination status. CONCLUSIONS: We found no evidence that YF vaccination in dengue-endemic areas increases the risk of severe dengue fever.

Epidemiology and control of frontier malaria in Brazil: lessons from community-based studies in rural Amazonia.

We describe the epidemiology of malaria in a frontier agricultural settlement in Brazilian Amazonia. We analysed the incidence of slide-confirmed symptomatic infections diagnosed between 2001 and 2006 in a cohort of 531 individuals (2281.53 person-years of follow-up) and parasite prevalence data derived from four cross-sectional surveys. Overall, the incidence rates of Plasmodium vivax and P. falciparum were 20.6/100 and 6.8/100 person-years at risk, respectively, with a marked decline in the incidence of both species (81.4 and 56.8%, respectively) observed between 2001 and 2006. PCR revealed 5.4-fold more infections than conventional microscopy in population-wide cross-sectional surveys carried out between 2004 and 2006 (average prevalence, 11.3 vs. 2.0%). Only 27.2% of PCR-positive (but 73.3% of slide-positive) individuals had symptoms when enrolled, indicating that asymptomatic carriage of low-grade parasitaemias is a common phenomenon in frontier settlements. A circular cluster comprising 22.3% of the households, all situated in the area of most recent occupation, comprised 69.1% of all malaria infections diagnosed during the follow-up, with malaria incidence decreasing exponentially with distance from the cluster centre. By targeting one-quarter of the households, with selective indoor spraying or other house-protection measures, malaria incidence could be reduced by more than two-thirds in this community.

A community-based survey of human toxoplasmosis in rural Amazonia: seroprevalence, seroconversion rate, and associated risk factors.

IgG antibodies to Toxoplasma gondii were detected in, March-April 2004, in 65.8% (95% confidence interval, 60.8-70.8%) of 342 systematically sampled subjects 5-90 years of age (87.5% of the eligible) living in a rural settlement in Amazonia, with a seroconversion rate of 9% over 1 year of follow-up of 99 seronegative subjects. Multiple logistic regression analysis identified age as the only significant independent predictor of seropositivity at the baseline. Each additional year of age increases the odds of being seropositive by 6%, and 76.8% of the subjects are expected to be seropositive at 30 years of age. A single high-prevalence spatial cluster, comprising 11.9% of the seropositive subjects, was detected in the area; households in the cluster were less likely to have dogs as pets and their heads had a lower education level, when compared with households located outside the cluster. The challenges for preventing human toxoplasmosis in tropical rural settings are discussed.

Malaria on the Amazonian frontier: transmission dynamics, risk factors, spatial distribution, and prospects for control.

Little follow-up data on malaria transmission in communities originating from frontier settlements in Amazonia are available. Here we describe a cohort study in a frontier settlement in Acre, Brazil, where 509 subjects contributed 489.7 person-years of follow-up. The association between malaria morbidity during the follow-up and individual, household, and spatial covariates was explored with mixed-effects logistic regression models and spatial analysis. Incidence rates for Plasmodium vivax and Plasmodium falciparum malaria were 30.0/100 and 16.3/100 person-years at risk, respectively. Malaria morbidity was strongly associated with land clearing and farming, and decreased after five years of residence in the area, suggesting that clinical immunity develops among subjects exposed to low malaria endemicity. Significant spatial clustering of malaria was observed in the areas of most recent occupation, indicating that the continuous influx of nonimmune settlers to forest-fringe areas perpetuates the cycle of environmental change and colonization that favors malaria transmission in rural Amazonia.

Risk factors for dengue virus infection in rural Amazonia: population-based cross-sectional surveys.

A comparison of dengue virus (DENV) antibody levels in paired serum samples collected from predominantly DENV-naive residents in an agricultural settlement in Brazilian Amazonia (baseline seroprevalence, 18.3%) showed a seroconversion rate of 3.67 episodes/100 person-years at risk during 12 months of follow-up. Multivariate analysis identified male sex, poverty, and migration from extra-Amazonian states as significant predictors of baseline DENV seropositivity, whereas male sex, a history of clinical diagnosis of dengue fever, and travel to an urban area predicted subsequent seroconversion. The laboratory surveillance of acute febrile illnesses implemented at the study site and in a nearby town between 2004 and 2006 confirmed 11 DENV infections among 102 episodes studied with DENV IgM detection, reverse transcriptase-polymerase chain reaction, and virus isolation; DENV-3 was isolated. Because DENV exposure is associated with migration or travel, personal protection measures when visiting high-risk urban areas may reduce the incidence of DENV infection in this rural population.

Population structure and transmission dynamics of Plasmodium vivax in rural Amazonia.

Understanding the genetic structure of malaria parasites is essential to predict how fast some phenotypes of interest originate and spread in populations. In the present study, we used highly polymorphic microsatellite markers to analyze 74 Plasmodium vivax isolates, which we collected in cross-sectional and longitudinal surveys performed in an area of low malaria endemicity in Brazilian Amazonia, and to explore the transmission dynamics of genetically diverse haplotypes or strains. P. vivax populations are more diverse and more frequently comprise multiple-clone infections than do sympatric Plasmodium falciparum isolates, but these features paradoxically coexist with high levels of inbreeding, leading to significant multilocus linkage disequilibrium. Moreover, the high rates of microsatellite haplotype replacement that we found during 15 months of follow-up most likely do not result from strong diversifying selection. We conclude that the small-area genetic diversity in P. vivax populations under low-level transmission is not severely constrained by the low rates of effective meiotic recombination, with clear public health implications.