Multilocus genotyping of microbial pathogens has revealed a range of population structures, with some bacteria showing extensive recombination and others showing almost complete clonality. The population structure of the protozoan parasite Plasmodium falciparum has been harder to evaluate, since most studies have used a limited number of antigen-encoding loci that are known to be under strong selection. We describe length variation at 12 microsatellite loci in 465 infections collected from 9 locations worldwide. These data reveal dramatic differences in parasite population structure in different locations. Strong linkage disequilibrium (LD) was observed in six of nine populations. Significant LD occurred in all locations with prevalence <1% and in only two of five of the populations from regions with higher transmission intensities. Where present, LD results largely from the presence of identical multilocus genotypes within populations, suggesting high levels of self-fertilization in populations with low levels of transmission. We also observed dramatic variation in diversity and geographical differentiation in different regions. Mean heterozygosities in South American countries (0.3-0.4) were less than half those observed in African locations (0. 76-0.8), with intermediate heterozygosities in the Southeast Asia/Pacific samples (0.51-0.65). Furthermore, variation was distributed among locations in South America (F:(ST) = 0.364) and within locations in Africa (F:(ST) = 0.007). The intraspecific patterns of diversity and genetic differentiation observed in P. falciparum are strikingly similar to those seen in interspecific comparisons of plants and animals with differing levels of outcrossing, suggesting that similar processes may be involved. The differences observed may also reflect the recent colonization of non-African populations from an African source, and the relative influences of epidemiology and population history are difficult to disentangle. These data reveal a range of population structures within a single pathogen species and suggest intimate links between patterns of epidemiology and genetic structure in this organism.

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.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads, the susceptible subpopulation declines causing the rate at which new infections occur to slow down. Variation in individual susceptibility or exposure to infection exacerbates this effect. Individuals that are more susceptible or more exposed tend to be infected and removed from the susceptible subpopulation earlier. This selective depletion of susceptibles intensifies the deceleration in incidence. Eventually, susceptible numbers become low enough to prevent epidemic growth or, in other words, the herd immunity threshold is reached. Here we fit epidemiological models with inbuilt distributions of susceptibility or exposure to SARS-CoV-2 outbreaks to estimate basic reproduction numbers (R_0) alongside coefficients of individual variation (CV) and the effects of containment strategies. Herd immunity thresholds are then calculated as 1-(1⁄R_0 )^(1⁄((1+〖CV〗^2 ) )) or 1-(1⁄R_0 )^(1⁄((1+〖2CV〗^2 ) )), depending on whether variation is on susceptibility or exposure. Our inferences result in herd immunity thresholds around 10-20%, considerably lower than the minimum coverage needed to interrupt transmission by random vaccination, which for R_0 higher than 2.5 is estimated above 60%. We emphasize that the classical formula, 1-1⁄R_0 , remains applicable to describe herd immunity thresholds for random vaccination, but not for immunity induced by infection which is naturally selective. These findings have profound consequences for the governance of the current pandemic given that some populations may be close to achieving herd immunity despite being under more or less strict social distancing measures.

Five community-based cross-sectional surveys of malaria morbidity and associated risk factors in remote riverine populations in northwestern Brazil showed average parasite rates of 4.2% (thick-smear microscopy) and 14.4% (polymerase chain reaction [PCR]) in the overall population, with a spleen rate of 13.9% among children 2-9 years of age. Plasmodium vivax was 2.8 times more prevalent than P. falciparum, with rare instances of P. malariae and mixed-species infections confirmed by PCR; 9.6% of asymptomatic subjects had parasitemias detected by PCR. Low-grade parasitemia detected by PCR only was a risk factor for anemia, after controlling for age and other covariates. Although clinical and subclinical infections occurred in all age groups, the risk of infection and disease decreased significantly with increasing age, after adjustment for several covariates in multilevel logistic regression models. These findings suggest that the continuous exposure to hypo- or mesoendemic malaria may induce significant anti-parasite and anti-disease immunity in native Amazonians.

Resumo ObjetivoEstimar a prevalência e a distribuição social das parasitoses intestinais na infância, estabelecer a tendência secular dessas enfermidades e analisar sua determinação, com base em dois inquéritos domiciliares, realizados na cidade de São Paulo, SP, em 1984/85 e 1995/96. Métodos Os inquéritos estudaram amostras probabilísticas da população residente na cidade com idades entre zero e 59 meses (1.016 em 1984/85 e 1.280 em 1995/96). Amostras de fezes foram coletadas nos dois inquéritos e submetidas a exame parasitológico pela técnica de sedimentação, realizando-se leituras de preparações simples e de preparações coradas com lugol para exame de cistos de protozoários. O estudo da distribuição social das parasitoses levou em conta tercis da renda familiar per capita em cada um dos inquéritos. A estratégia analítica para estudar os determinantes da evolução da prevalência das parasitoses na população empregou modelos hierárquicos de causalidade, análises multivariadas de regressão e procedimentos análogos aos utilizados para calcular riscos atribuíveis populacionais. Resultados/ConclusõesHouve entre os inquéritos reduções expressivas na prevalência das parasitoses em geral (de 30,9% para 10,7%), das helmintoses (22,3% para 4,8%), da giardíase (14,5% para 5,5%) e do poliparasitismo intestinal (13,1% para 0,5%). Embora declínios intensos tenham sido observados em todos os estratos sociais, manteve-se inalterada no período a forte relação inversa entre nível de renda e ocorrência de parasitismo. Mudanças positivas em determinantes distais (renda familiar e escolaridade materna) e intermediários (moradia, saneamento do meio e acesso a serviços de saúde) das helmintoses, justificaram parte substancial da redução de sua prevalência. A redução da giardíase foi atribuída a melhorias na escolaridade materna e nas condições de moradia e saneamento. A duplicação da freqüência a creches refreou o declínio da giardíase. Abstract ObjectiveData from two consecutive household surveys undertaken in mid-80s and mid-90s allow to characterize and analyse secular trends in infant and child intestinal parasitic diseases in the city of S. Paulo, Brazil.

The article presents prevalence rates for malnutrition, intestinal parasitic infections, anemia, and iron deficiency in under-five children in a population-based cross-sectional survey performed in the urban area of two counties in the Western Brazilian Amazon, Assis Brasil (n = 200) and Acrelandia (n = 477). Available data included: (a) weight and height measurements, standardized as z-scores using the 1977 NCHS reference population, (b) diagnosis of current intestinal parasitic infection, (c) blood hemoglobin levels, and (d) plasma ferritin and soluble transferrin receptor levels. Overall prevalence rates of low weight-for-height, low weight-for-age, and low height-for-age were 3.7%, 8.7%, and 7.5%, respectively, with similar figures in the two towns. Intestinal parasites were detected in 32.5% children; helminths were uncommon. Anemia and iron deficiency were diagnosed in 30.6% and 43.5% of the children, respectively. Evidence of anemia was found in only 47.6% of the children with depleted iron reserves, indicating that hemoglobin measurement alone would severely underestimate the magnitude of iron deficiency in this population. In both towns, anemia and malnutrition were significantly more prevalent among children in the lowest socioeconomic stratum.

Sequence analyses of six isolates from Southeast Asia supports dividing species into types

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