Prevalence of G6PD deficiency and associated haematological parameters in children from Botswana

The ethnogeographic variability of genetic factors underlying G6PD deficiency

Glucose-6-phosphate dehydrogenase (G6PD) deficiency caused by genetic variants in the G6PD gene, constitutes the most common enzymopathy worldwide, affecting approximately 5% of the global population. While carriers are mostly asymptomatic, they are at substantial risk of acute hemolytic anemia upon certain infections or exposure to various medications. As such, information about G6PD activity status in a given patient can constitute an important parameter to guide clinical decision-making. Here, we leveraged whole genome sequencing data from 142,069 unrelated individuals across seven human populations to provide a global comprehensive map of G6PD variability. By integrating established functional classifications with stringent computational predictions using 13 partly orthogonal algorithms for uncharacterized and novel variants, we reveal the large extent of ethnogeographic variability in G6PD deficiency and highlight its population-specific genetic composition. Overall, estimated disease prevalence in males ranged between 12.2% in Africans, 2.7-3.5% across Asia and 2.1% in Middle Easterners to < 0.3% in Europeans, Finnish and Amish. In Africans, the major deficient alleles were A-^202A/376 G (minor allele frequency 11.6%) and A-^{968 C/376 G} (0.5%). In contrast, G6PD deficiency in Middle Easterners was primarily due to the Mediterranean allele (1.3%) and the population-specific Cairo variant (0.4%). In South Asia, the most prevalent deficient alleles were Mediterranean (1.7%), Kerala (1.1%), Gond (0.9%) and Orissa (0.2%), whereas in East Asian populations the Canton (1.1%), Kaiping (0.7%) and Viangchan (0.3%) variants were predominant. Combined, our analyses provide a large dataset of G6PD variability across major ethnogeographic groups and can instruct population-specific genotyping strategies to optimize genetically guided therapeutic interventions.

Similar Ferroportin Q248H polymorphism prevalence in patients with Plasmodium falciparum malaria and control subjects in the low-endemic setting of Botswana

INTRODUCTION

Recent evidence suggests that ferroportin (FPN) Q248H may confer a survival advantage against malaria by reducing erythrocytic intracellular iron in Africans. We investigated if FPN Q248H mutation, that is prevalent in Batswana, is a factor in limiting the susceptibility to Plasmodium falciparum malaria.

METHODS

264 archived dried blood spot samples (183 P. falciparum malaria cases and 81 controls, matched for geographical region and season for equal exposure) were genotyped. Human and P. falciparum DNA was extracted using Chelex-100 resin and P. falciparum molecular confirmation performed. Ferroportin Q248H mutation was identified by restriction fragment length polymorphism. The prevalence of the FPN Q248H mutation and allele frequency and the accompanying 95% confidence interval were calculated. A qPCR method was employed to estimate P. falciparum parasitaemia. Association between FPN and malaria susceptibility was tested using Pearson Chi-square test and Mood's median test was used to compare P. falciparum parasitaemias according to FPN Q248H mutation.

RESULTS

All samples were successfully genotyped. The FPN Q248H allele frequency was 0.08 (95% CI: 0.05-0.11) in cases and 0.08 (95% CI: 0.02-0.14) in controls, consistent with Hardy-Weinberg equilibrium. The prevalence of FPN Q248H phenotype was comparable in patients with P. falciparum malaria and in un-infected individuals, 16.4% (95% CI: 11.0-21.8) vs 14.8% (95% CI: 7.1-22.5), P = 0.746. In addition, no association of presence of FPN Q248H with reduced parasitaemia was recorded, P = 0.837.

CONCLUSION

In this small study, FPN Q248H polymorphism prevalence was comparable between patients with P. falciparum malaria and control subjects in the low-endemic setting of Botswana.

Recent Molecular Assessment of Plasmodium vivax and Plasmodium falciparum Asymptomatic Infections in Botswana

In 2016, we reported the presence of Plasmodium vivax in Botswana through active case detection. A real-time PCR was used during a similar study in 10 districts to assess changes in the P. vivax prevalence. We assessed 1,614 children (2–13 years of age) for hemoglobin (Hb; g/dL) and Plasmodium parasites. The median age of all participants was 5.0 years (25^th percentile, 3 years; 75^th percentile, 8 years). The median Hb (g/dL) level was 12.1, but 18.3% of the participants had anemia (Hb < 11.0 g/dL); these participants were clustered in the younger than 5 years age group in all districts (P < 0.001). The risk of anemia decreased with age 5 years or older (odds ratio [OR], 0.26; 95% confidence interval [CI], 0.197–0.34; P < 0.001). The prevalence rates of Plasmodium parasites were as follows: P. vivax, 12.7%; P. falciparum, 12.7%; P. malariae, 0.74%; and P. ovale (P. ovale curtisi), 0.68%. Mixed infection rates were as follows: P. falciparum and P. vivax, 2.35%; P. falciparum and P. ovale curtisi, 0.56%; P. vivax and P. malariae, 0.06%; and P. falciparum and P. malariae, 0.68%. The infections were largely asymptomatic (99.6%). Using logistic regression, the risk of infection with P. vivax was highest in Kweneng East (OR, 6.2; 95% CI, 2.9–13.1), followed by South East (OR, 5.6; 95% CI, 2.5–12.3) and Ngami (OR, 5.1; 95% CI, 2.2–12.0). Compared to the risk of infection for children younger than 5 years, the risk of infection decreased for children 5 years or older in regions with high rates of P. vivax and P. falciparum infections. P. vivax and P. falciparum have expanded within the asymptomatic population in Botswana; therefore, careful attention is required for their elimination.

G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19

Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identified nine variants, of which four are potentially deleterious to G6PD function, and one (rs1050828) that is known to cause G6PD deficiency. We supplemented data for the rs1050828 variant with genotype array data from over 11,000 Africans. Although this variant is common in Africans overall, large allele frequency differences exist between sub-populations. African sub-populations in the same country can show significant differences in allele frequency (e.g. 16.0% in Tsonga vs 0.8% in Xhosa, both in South Africa, p = 2.4 × 10^-3). The high prevalence of variants in the G6PD gene found in this analysis suggests that it may be a significant interaction factor in clinical trials of chloroquine and hydroxychloroquine for treatment of COVID-19 in Africans.

Past and current biological factors affecting malaria in the low transmission setting of Botswana: A review

Malaria continues to be one of the top infectious agents contributing to morbidity and mortality in sub-Saharan Africa. Annually, Botswana accounts only for a small proportion of cases (<<1%). Despite significantly reduced incidence rate, the country still experiences sporadic outbreaks that hamper the goal of malaria elimination. This review evaluated previous and current biological factors that impact malaria in Botswana, specifically focussing on the vectors, the parasite and the host. This was accomplished via a literature review evaluating these variables in Botswana. Current literature suggests that Anopheles arabiensis is the main malaria vector in the country. Several other potential vectors have been found widely distributed throughout Botswana in high numbers, yet remain largely unstudied with regards to their contribution to the country's malaria burden. We also report the most up to date list of all Anopheles species that have been found in Botswana. Plasmodium falciparum is responsible for the vast majority of symptomatic malaria in the country and some drug resistance markers have been documented for this species. Plasmodium vivax has been reported in asymptomatic subjects, even though a large proportion of the Botswana population appears to be Duffy antigen negative. Very little is known about the true distribution of P. vivax and no point of care testing infrastructure for this species exists in Botswana, making it difficult to tailor treatment to address possible recrudescence or relapse. Due to a genetically diverse population with a substantial Khoisan contribution into the Bantu genetic background, several phenotypes that potentially impact prevalence and severity of malaria exist within the country. These include sickle cell trait, Glucose-6-Phosphate Dehydrogenase deficiency, and Duffy negativity. This review highlights the information that currently exists on malaria in Botswana. It also postulates that a comprehensive understanding of these aforementioned biological factors may help to explain malaria persistence in Botswana.

Glucose-6-phosphate dehydrogenase deficiency genotypes and allele frequencies in the Kavango and Zambezi regions of northern Namibia

BACKGROUND

Namibia has made significant gains in the fight against malaria, with a target of elimination by 2023. We examined the genotype and allele frequencies of glucose-6-phosphate dehydrogenase (G6PD) deficiency to inform decisions on primaquine use, as we recently detected clusters of Plasmodium ovale curtisi in Kavango.

METHODS

A multistaged cross-sectional sampling method was used to enrol 212 children 2-9 y of age from schools and clinics in the Okavango and Zambezi regions of northern Namibia. Genotypes for the 202 G→A and 376 A→G mutations were assigned by polymerase chain reaction restriction fragment length polymorphism.

RESULTS

Of the 212 subjects enrolled, genotypes were available for 210, made up of 61 males and 149 females. G6PD-deficient males (hemizygotes) and females (homozygotes) constituted 3.27% (2/61) and 0.0% (0/149), respectively. Female heterozygotes (AA- and BA-) constituted 10.07% (15/149), while G6PD wild-type males (with A or B haplotype) and females (with AA, BB or AB haplotypes) consisted of 96.72% (59/61) and 89.93% (134/149), respectively. The A-, A and B allele frequencies were 0.0474, 0.3036 and 0.6490, respectively. Hardy-Weinberg equilibrium tests for female genotype frequencies did not show deviation (p=0.29).

CONCLUSIONS

The frequency of G6PD deficiency alleles in males in the Kavango and Zambezi regions of northern Namibia constitute 3.27%, a first report to inform policy on primaquine role out.

Molecular Characterization of Glucose-6-Phosphate Dehydrogenase: Do Single Nucleotide Polymorphisms Affect Hematological Parameters in HIV-Positive Patients?

This descriptive, cross-sectional study aimed at evaluating the prevalence of G6PD deficiency and the 376A ⟶ G, 202G ⟶ A single nucleotide polymorphisms (SNPs) among HIV patients attending care at a teaching hospital in Ghana and determine how the SNPs affect haematological profile in HIV. A total of 200 HIV-positive Ghanaians were recruited. Venous blood samples were obtained and complete blood count, and G6PD screening and genotyping for the 376A ⟶ G, 202G ⟶ A SNPs were performed. Out of the 200 participants, 13.0% (26/200) were G6PD-deficient based on the methemoglobin reductase technique, with 1.5% (3/200) and 11.5% (23/200) presenting with partial and full enzyme defect, respectively. Among the 13.0% participants with G6PD deficiency, 19.2% (5/26), 30.8% (8/26), and 19.2% (5/26) presented with 376A ⟶ G only (enzyme activity (EA): 1.19 U/g Hb), 202G ⟶A only (EA: 1.41 U/g Hb), and G202/A376 SNPs (EA: 1.14 U/g Hb), respectively. Having the 376A ⟶ G mutation was associated not only with lower red blood cell (RBC) count (3.38 × 106/µL (3.16-3.46) vs 3.95 × 106/µL (3.53-4.41), p = 0.010) but also with higher mean cell volume (MCV) (102.90 (99.40-113.0) vs 91.10 fL (84.65-98.98), p = 0.041) and mean cell haemoglobin (MCH) (33.70 pg (32.70-38.50) vs 30.75 pg (28.50-33.35), p = 0.038), whereas possessing the 202G ⟶ A mutation was associated with higher MCV only (98.90 fL (90.95-102.35) vs 91.10 fL (84.65-98.98), p = 0.041) compared to G6PD nondeficient participants. The prevalence of G6PD deficiency among HIV patients in Kumasi, Ghana, is 13.0% prevalence, comprising 1.5% and 11.5% partial and full enzyme defect, respectively, based on the methemoglobin reductase technique among HIV patients in Ghana. Among G6PD-deficient HIV patients, the prevalence of G202/A376 SNPs is 19.2%. The 376A ⟶ G mutation is associated not only with lower RBC count but also with higher MCV and MCH, whereas the 202G ⟶ A mutation is associated with higher MCV compared to the normal G6PD population.

G6PD variant distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19

Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole-genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identified nine variants, of which four are potentially deleterious to G6PD function, and one (rs1050828) that is known to cause G6PD deficiency. We supplemented data for the rs1050828 variant with genotype array data from over 11,000 Africans. Although this variant is common in Africans overall, large allele frequency differences exist between sub-populations. African sub-populations in the same country can show significant differences in allele frequency (e.g. 16.0% in Tsonga vs 0.8% in Xhosa, both in South Africa, ρ=2.4×10 -3 ). The high prevalence of variants in the G6PD gene found in this analysis suggests that it may be a significant interaction factor in clinical trials of chloroquine and hydrochloroquine for treatment of COVID-19 in Africans.

Growing evidence of Plasmodium vivax across malaria-endemic Africa

Effective malaria control strategies require an accurate understanding of the epidemiology of locally transmitted Plasmodium species. Compared to Plasmodium falciparum infection, Plasmodium vivax has a lower asexual parasitaemia, forms dormant liver-stages (hypnozoites), and is more transmissible. Hence, treatment and diagnostic policies aimed exclusively at P. falciparum are far less efficient against endemic P. vivax. Within sub-Saharan Africa, malaria control programmes justly focus on reducing the morbidity and mortality associated with P. falciparum. However, the recent emphasis on malaria elimination and increased accessibility of more sensitive diagnostic tools have revealed greater intricacies in malaria epidemiology across the continent. Since 2010, the number of studies identifying P. vivax endemic to Africa has expanded considerably, with 88 new scientific reports published since a review of evidence in 2015, approximately doubling the available data. There is evidence of P. vivax in all regions of Africa, apparent from infected vectors, clinical cases, serological indicators, parasite prevalence, exported infections, and P. vivax-infected Duffy-negative individuals. Where the prevalence of microscopic parasitaemia is low, a greater proportion of P. vivax infections were observed relative to P. falciparum. This evidence highlights an underlying widespread presence of P. vivax across all malaria-endemic regions of Africa, further complicating the current practical understanding of malaria epidemiology in this region. Thus, ultimate elimination of malaria in Africa will require national malaria control programmes to adopt policy and practice aimed at all human species of malaria.