Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure

Genetic variants of TLR4, including the novel variant, rs5030719, and related genes are associated with susceptibility to clinical malaria in African children

BACKGROUND

Malaria is a deadly disease caused by Plasmodium spp. Several blood phenotypes have been associated with malarial resistance, which suggests a genetic component to immune protection.

METHODS

One hundred and eighty-seven single nucleotide polymorphisms (SNPs) in 37 candidate genes were genotyped and investigated for associations with clinical malaria in a longitudinal cohort of 349 infants from Manhiça, Mozambique, in a randomized controlled clinical trial (RCT) (AgeMal, NCT00231452). Malaria candidate genes were selected according to involvement in known malarial haemoglobinopathies, immune, and pathogenesis pathways.

RESULTS

Statistically significant evidence was found for the association of TLR4 and related genes with the incidence of clinical malaria (p = 0.0005). These additional genes include ABO, CAT, CD14, CD36, CR1, G6PD, GCLM, HP, IFNG, IFNGR1, IL13, IL1A, IL1B, IL4R, IL4, IL6, IL13, MBL, MNSOD, and TLR2. Of specific interest, the previously identified TLR4 SNP rs4986790 and the novel finding of TRL4 SNP rs5030719 were associated with primary cases of clinical malaria.

CONCLUSIONS

These findings highlight a potential central role of TLR4 in clinical malarial pathogenesis. This supports the current literature and suggests that further research into the role of TLR4, as well as associated genes, in clinical malaria may provide insight into treatment and drug development.

Prevalence and changes of anemia among young children and women in 47 low- and middle-income countries, 2000-2018

BACKGROUND

Anemia remains a major public health issue, particularly for children and women in low- and middle-income countries (LMICs). However, the current prevalence and recent changes of anemia among young children and women of reproductive age, particularly for pregnant women in different trimesters are unclear. We examined the current prevalence of anemia among children aged less than 5 years by age (6-35 months vs. 36-59 months) and women of reproductive age by pregnant status (pregnant vs. non-pregnant) and trimesters (the third vs. the second vs. the first trimester) between 2010 and 2018 and further examined changes in the prevalence from 2000-2009 to 2010-2018.

METHODS

Data were from the cross-sectional Demographic and Health Surveys performed between 2000 and 2018. A total of 47 countries were included to examine the current prevalence of anemia (weighted prevalence and 95% confidence interval [CI]) among young children aged less than 5 years (N = 459,785) and 46 countries among women of reproductive age (N = 1,079,805) between 2010 and 2018. To examine changes in the prevalence of anemia, a total of 29 countries with at least two Demographic and Health Surveys performed between 2000 and 2009 (children: N = 130,772; women: N = 371,845) and 2010-2018 (children: N = 386,202; women: N = 928,889) were included. Modified Poisson regression analyses with robust error variance were used to examine changes in anemia between 2000-2009 and 2010-2018 in participants by child age (6-5 months vs. 36-59 months), women pregnant status (pregnant vs. non-pregnant), trimesters (the second or third trimester vs. the first trimester) with the adjustment for potential covariates.

FINDINGS

In 47 LMICs for children aged less than 5 years between 2010 and 2018, the total prevalence of anemia was 56.5% (95% CI 56.2, 56.8). Younger children aged 6-35 months were more likely to have anemia than older children aged 36-59 months (adjusted odds ratio [OR] 1.38, 95% CI 1.36-1.39, P < 0.001). In 46 LMICs for women of reproductive age, the total prevalence was 40.4% (95% CI 40.1, 40.7). Pregnant women were more likely to have anemia than non-pregnant women (adjusted OR 1.14, 1.12-1.16, P < 0.001). Moreover, pregnant women in the third trimester (adjusted OR 1.55, 1.48-1.62, P < 0.001) and the second trimester (adjusted OR 1.51, 1.45-1.58, P < 0.001) were more likely to have anemia than those in the first trimester. Among 29 included countries, although there was a decreasing change (absolute change, relative change, and average annual rate of reduction) in young children and women between 2000-2009 and 2010-2018 in a majority of countries, the current prevalence of anemia remained at a high level.

INTERPRETATION

The prevalence of anemia among children aged less than 5 years and women of reproductive age was still high in LMICs, particularly for younger children and pregnant women. The relative change among women of reproductive age was far away from the WHO goal of reduction of anemia by 50% by 2025 (i.e., prevalence reduction to about 15.2% by 2025 from 30.3% at 2012 baseline). Continued and effective efforts, particularly for high-risk populations, are needed to improve the general health of the population.

FUNDING

Innovation Team of "Climbing" Program of Shandong University, and the Youth Team of Humanistic and Social Science of Shandong University (20820IFYT1902).

Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa

Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease. We also inferred a deep time to coalescence of variation at IFN-γ (~ 0.8 million years ago) and ancient ages for common polymorphisms predating the evolution of modern humans. Taken together, these results are congruent with a model of positive selection on standing variation in African populations. Furthermore, we inferred that common variants in intron 3 of IFN-γ are the likely targets of selection. In addition, we observed a paucity of non-synonymous substitutions relative to synonymous changes in the exons of IFN-γ in African and non-African populations, suggestive of strong purifying selection. Therefore, we contend that positive and purifying selection have influenced levels of diversity in different regions of IFN-γ, implying that these distinct genic regions are, or have been, functionally important. Overall, this study provides additional insights into the evolutionary events that have contributed to the frequency and distribution of alleles having a role in human health and disease.

Genetic variation and adaptation in Africa: implications for human evolution and disease

Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.