Duffy Blood Group System and the malaria adaptation process in humans

Detection of Duffy Blood Group Genotypes and Submicroscopic Plasmodium Infections Using Molecular Diagnostic Assays in Febrile Malaria Patients

Background

Malaria remains a severe parasitic disease, posing a significant threat to public health and hindering economic development in sub-Saharan Africa. Ethiopia, a malaria endemic country, is facing a resurgence of the disease with a steadily rising incidence. Conventional diagnostic methods, such asmicroscopy, have become less effective due to low parasite density, particularly among Duffy-negative human populations in Africa. To develop comprehensive control strategies, it is crucial to generate data on the distribution and clinical occurrence of Plasmodium vivax and P. falciparum infections in regions where the disease is prevalent. This study assessed Plasmodium infections and Duffy antigen genotypes in febrile patients in Ethiopia.

Methods

Three hundred febrile patients visiting four health facilities in Jimma town of southwestern Ethiopia were randomly selected during the malaria transmission season (Apr-Oct). Sociodemographic information was collected, and microscopic examination was performed for all study participants. Plasmodiumspecies and parasitemia as well as the Duffy genotype were assessed by quantitative polymerase chain reaction (qPCR) for all samples. Data were analyzed using Fisher's exact test and kappa statistics.

Results

The Plasmodium infection rate by qPCR was 16% (48/300) among febrile patients, of which 19 (39.6%) were P. vivax, 25 (52.1%) were P. falciparum, and 4 (8.3%) were mixed (P. vivax and P. falciparum) infections. Among the 48 qPCR-positive samples, 39 (13%) were negative by microscopy. The results of bivariate logistic regression analysis showed that agriculture-related occupation, relapse and recurrence were significantly associated withPlasmodium infection (P<0.001). Of the 300 febrile patients, 85 (28.3%) were Duffy negative, of whom two had P. vivax, six had P. falciparum, and one had mixed infections.Except for one patient with P. falciparum infection, Plasmodium infections in Duffy-negative individuals were all submicroscopic with low parasitemia.

Conclusions

The present study revealed a high prevalence of submicroscopic malaria infections. Plasmodium vivax infections in Duffy-negative individuals were not detected due to low parasitemia. Here, we recommend an improved molecular diagnostic tool to detect and characterize plasmodium infections, with the goal of quantifyingP. vivax infection in Duffy-negative individuals.

Unraveling the Complexity of Imported Malaria Infections by Amplicon Deep Sequencing

Imported malaria and recurrent infections are becoming an emerging issue in many malaria non-endemic countries. This study aimed to determine the molecular patterns of the imported malaria infections and recurrence. Blood samples were collected from patients with imported malaria infections during 2016-2018 in Guangxi Zhuang Autonomous Region, China. Next-generation amplicon deep-sequencing approaches were used to assess parasite genetic diversity, multiplexity of infection, relapse, recrudescence, and antimalarial drug resistance. A total of 44 imported malaria cases were examined during the study, of which 35 (79.5%) had recurrent malaria infections within 1 year. The majority (91.4%) had one recurrent malaria episode, whereas two patients had two recurrences and one patient had three recurrences. A total of 19 recurrence patterns (the species responsible for primary and successive clinical episodes) were found in patients returning from malaria epidemic countries. Four parasite species were detected with a higher than usual proportion (46.2%) of non-falciparum infections or mixed-species infections. An increasing trend of recurrence infections and reduced drug treatment efficacy were observed among the cases of imported malaria. The high recurrence rate and complex patterns of imported malaria from Africa to non-endemic countries have the potential to initiate local transmission, thereby undermining efforts to eliminate locally acquired malaria. Our findings highlight the power of amplicon deep-sequencing applications in molecular epidemiological studies of the imported malaria recurrences.

High frequency of the Duffy-negative genotype and absence of Plasmodium vivax infections in Ghana

Background

Recent studies from different malaria-endemic regions including western Africa have now shown that Plasmodium vivax can infect red blood cells (RBCs) and cause clinical disease in Duffy-negative people, though the Duffy-negative phenotype was thought to confer complete refractoriness against blood invasion with P. vivax. The actual prevalence of P. vivax in local populations in Ghana is unknown and little information is available about the distribution of Duffy genotypes. The aim of this study was to assess the prevalence of P. vivax in both asymptomatic and symptomatic outpatients and the distribution of Duffy genotypes in Ghana.

Methods

DNA was extracted from dried blood spots (DBS) collected from 952 subjects (845 malaria patients and 107 asymptomatic persons) from nine locations in Ghana. Plasmodium species identification was carried out by nested polymerase chain reaction (PCR) amplification of the small-subunit (SSU) rRNA genes. For P. vivax detection, a second PCR of the central region of the Pvcsp gene was carried out. Duffy blood group genotyping was performed by allele-specific PCR to detect the presence of the FY^ES allele.

Results

No cases of P. vivax were detected in any of the samples by both PCR methods used. Majority of infections (542, 94.8%) in the malaria patient samples were due to P. falciparum with only 1 infection (0.0017%) due to Plasmodium malariae, and 2 infections (0.0034%) due to Plasmodium ovale. No case of mixed infection was identified. Of the samples tested for the FY^ES allele from all the sites, 90.5% (862/952) had the FY^ES allele. All positive samples were genotyped as FY*B-33/FY*B-33 (Duffy-negative homozygous) and therefore classified as Fy(a−b−).

Conclusions

No cases of P. vivax were detected by both PCRs and majority of the subjects tested carried the FY^ES allele. The lack of P. vivax infections observed can be attributed to the high frequency of the FY^ES allele that silences erythroid expression of the Duffy. These results provide insights on the host susceptibility for P. vivax infections that had not been investigated in Ghana before.

The Duffy T-33C is an insightful marker of human history and admixture

A contrasting genotype and allele frequency pattern between Africans and non-Africans in the Duffy (T-33C) locus is reported. Its near fixation in various populations suggest is no longer under natural selection, and that current distribution is possibly a relic of distant extreme selection combined with genetic drift during the out of Africa. We put this difference into the utility to infer the ancestral state of ambiguous loci in different populations.

Presence of additional Plasmodium vivax malaria in Duffy negative individuals from Southwestern Nigeria

Background

Malaria in sub-Saharan Africa (sSA) is thought to be mostly caused by Plasmodium falciparum. Recently, growing reports of cases due to Plasmodium ovale, Plasmodium malariae, and Plasmodium vivax have been increasingly observed to play a role in malaria epidemiology in sSA. This in fact is due to the usage of very sensitive diagnostic tools (e.g. PCR), which have highlighted the underestimation of non-falciparum malaria in this sub-region. Plasmodium vivax was historically thought to be absent in sSA due to the high prevalence of the Duffy negativity in individuals residing in this sub-continent. Recent studies reporting detection of vivax malaria in Duffy-negative individuals from Mali, Mauritania, Cameroon challenge this notion.

Methods

Following previous report of P. vivax in Duffy-negative individuals in Nigeria, samples were further collected and assessed RDT and/or microscopy. Thereafter, malaria positive samples were subjected to conventional PCR method and DNA sequencing to confirm both single/mixed infections as well as the Duffy status of the individuals.

Results

Amplification of Plasmodium gDNA was successful in 59.9% (145/242) of the evaluated isolates and as expected P. falciparum was the most predominant (91.7%) species identified. Interestingly, four P. vivax isolates were identified either as single (3) or mixed (one P. falciparum/P. vivax) infection. Sequencing results confirmed all vivax isolates as truly vivax malaria and the patient were of Duffy-negative genotype.

Conclusion

Identification of additional vivax isolates among Duffy-negative individuals from Nigeria, substantiate the expanding body of evidence on the ability of P. vivax to infect RBCs that do not express the DARC gene. Hence, such genetic-epidemiological study should be conducted at the country level in order to evaluate the true burden of P. vivax in Nigeria.

Analyses of genome wide association data, cytokines, and gene expression in African-Americans with benign ethnic neutropenia

BACKGROUND

Benign ethnic neutropenia (BEN) is a hematologic condition associated with people of African ancestry and specific Middle Eastern ethnic groups. Prior genetic association studies in large population showed that rs2814778 in Duffy Antigen Receptor for Chemokines (DARC) gene, specifically DARC null red cell phenotype, was associated with BEN. However, the mechanism of this red cell phenotype leading to low white cell count remained elusive.

METHODS

We conducted an extreme phenotype design genome-wide association study (GWAS), analyzed ~16 million single nucleotide polymorphisms (SNP) in 1,178 African-Americans individuals from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study and replicated from 819 African-American participants in the Atherosclerosis Risk in Communities (ARIC) study. Conditional analyses on rs2814778 were performed to identify additional association signals on chromosome 1q22. In a separate cohort of healthy individuals with and without BEN, whole genome gene expression from peripheral blood neutrophils were analyzed for DARC.

RESULTS

We confirmed that rs2814778 in DARC was associated with BEN (p = 4.09×10-53). Conditioning on rs2814778 abolished other significant chromosome 1 associations. Inflammatory cytokines (IL-2, 6, and 10) in participants in the Howard University Family Study (HUFS) and Multi-Ethnic Study in Atherosclerosis (MESA) showed similar levels in individuals homozygous for the rs2814778 allele compared to others, indicating cytokine sink hypothesis played a minor role in leukocyte homeostasis. Gene expression in neutrophils of individuals with and without BEN was also similar except for low DARC expression in BEN, suggesting normal function. BEN neutrophils had slightly activated profiles in leukocyte migration and hematopoietic stem cell mobilization pathways (expression fold change <2).

CONCLUSIONS

These results in humans support the notion of DARC null erythroid progenitors preferentially differentiating to myeloid cells, leading to activated DARC null neutrophils egressing from circulation to the spleen, and causing relative neutropenia. Collectively, these human data sufficiently explained the mechanism DARC null red cell phenotype causing BEN and further provided a biologic basis that BEN is clinically benign.

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants. Therefore, Sasquatch uses an unbiased approach, independent of known transcription factor binding sites and motifs. Sasquatch only requires a single DNase-seq data set per cell type, from any genotype, and produces consistent predictions from data generated by different experimental procedures and at different sequence depths. Here we demonstrate the effectiveness of Sasquatch using previously validated functional SNPs and benchmark its performance against existing approaches. Sasquatch is available as a versatile webtool incorporating publicly available data, including the human ENCODE collection. Thus, Sasquatch provides a powerful tool and repository for prioritizing likely regulatory SNPs in the noncoding genome.

Atypical Chemokine Receptor 1 Polymorphism can not Affect Susceptibility to Hepatitis C Virus

Background:

Hepatitis C virus has infected 130 to 150 million individuals globally. Atypical chemokine receptor 1 has become a focus of research because of its diverse roles in different diseases. However, little is known regarding the association of atypical chemokine receptor 1 polymorphism with susceptibility to hepatitis C virus.

Aims:

To determine the association of an atypical chemokine receptor 1 polymorphism (rs12075) with hepatitis C virus susceptibility.

Study Design:

Case-control study.

Methods:

We collected blood samples from 231 patients infected with hepatitis C virus and 239 blood donors as control subjects. Genotyping of atypical chemokine receptor 1 was performed using a 5ˊ-nuclease assay with TaqMan-minor groove binding probes. Comparisons between hepatitis C virus-infected patients and control subjects were assessed using Fisher’s exact test.

Results:

The genotype frequencies of FY*A/FY*A, FY*A/FY*B and FY*B/FY*B were 86.1%, 13.9% and 0% in the patient group, and 86.2%, 13.4% and 0.4% in the control group, respectively. The difference in atypical chemokine receptor 1 genotype frequencies between hepatitis C virus-infected patients and control group was not significant (p=1.00, OR=1.004, 95% CI=0.594-1.695). FY*A and FY*B allele frequencies were 93.1% and 6.9% in the patient group, and 92.9% and 7.1% in the control group, respectively. The difference in atypical chemokine receptor 1 allele frequencies between hepatitis C virus-infected patients and the control group was not significant (p=1.00, OR=0.972, 95% CI=0.589-1.603).

Conclusion:

Our result indicates that atypical chemokine receptor 1 polymorphism (rs12075) does not affect susceptibility to hepatitis C virus.

Is there malaria transmission in urban settings in Colombia?

Background

Colombia contributes a significant proportion of malaria cases in the Americas, which are predominantly rural. However, in the last 8 years ~ 10 % of the endemic municipalities have also reported urban and peri-urban malaria cases, a growing concern for health authorities. This study focused on the characterization of the officially reported urban malaria cases.

Methods

A descriptive retrospective study based on secondary information provided by the Colombian National Surveillance System-SIVIGILA for the 2008–2012 period was conducted. A total of 17 municipalities with consistent and persistent reports of urban and peri-urban malaria were selected for analysis, which included site of origin and of residence, age, gender and ethnicity of patients, health system affiliation, Plasmodium species and the presence of malaria vectors.

Results

A total of 18,113 malaria cases were reported from urban and peri-urban areas of 17 endemic municipalities. Almost 70 % of the reports originated in localities in the departments of Chocó and Nariño, located on the Pacific Coast where a predominantly Afro-Colombian population, of individuals of under 30 years of age, was the most affected (80.7 %), mainly with Plasmodium falciparum infections (52.1 %). Median annual parasite index (API) was 6.4 per 1000 inhabitants (3.4 in 2008; 10.8 in 2010 and 6.0 in 2012). Between 2011 and 2012 complicated cases (2.4 %) and malaria in pregnant women (1.4 %) were reported. Study areas reported the presence of at least seven Anopheles species considered malaria vectors. These analyses did not allow ascertaining the presumable origin of the recorded urban cases due to the lack of a consensus on a definition of urban, peri-urban and rural limits and the lack of proper verification of the geographical source of infection.

Conclusions

The study indicates the probable presence of endemic, unstable and low-intensity malaria transmission in Colombian urban and peri-urban areas of a group of municipalities located mainly on the Pacific coast region and a few others in the eastern region. There is a need to unequivocally confirm the urban or peri-urban origin of the malaria cases reported and the transmission conditions, as well as to develop and implement new strategies for urban and peri-urban malaria control and elimination.

Malaria and vascular endothelium

Involvement of the cardiovascular system in patients with infectious and parasitic diseases can result from both intrinsic mechanisms of the disease and drug intervention. Malaria is an example, considering that the endothelial injury by Plasmodium-infected erythrocytes can cause circulatory disorders. This is a literature review aimed at discussing the relationship between malaria and endothelial impairment, especially its effects on the cardiovascular system. We discuss the implications of endothelial aggression and the interdisciplinarity that should guide the malaria patient care, whose acute infection can contribute to precipitate or aggravate a preexisting heart disease.

A New Method for Analyzing the Duffy Blood Group Genotype by TaqMan Minor Groove Binding Probes

BACKGROUND

Duffy blood group genotyping is useful to ensure transfusion safety and determine the association of Duffy blood group polymorphism with diseases, and therefore has its clinical significance. In order to improve the existing methods for genotyping of Duffy blood group, which normally require post-PCR manipulation, a new method was developed by using 5'-nuclease assay (NA) with TaqMan minor groove binding (MGB) probes.

METHODS

Primers and TaqMan-MGB probes were designed and synthesized to genotype FY*A and FY*B alleles at Duffy blood group locus on a real-time PCR platform. A total of 120 samples were genotyped by using the new 5'-NA and conventional polymerase chain reaction with allele-specific primers (PCR-ASP). The results obtained by the two methods were compared.

RESULTS

There was a complete concordance of results for all samples genotyped by 5'-NA and PCR-ASP. The retesting results of 5'-NA were consistent with those of the initial testing. The detection limit of 5'-NA was determined as 100 pg per reaction. The FY*A and FY*B allelic frequencies were 93.3% and 6.7% respectively in the Chinese Han population in Dalian.

CONCLUSIONS

The 5'-NA for genotyping of Duffy blood group is simple, rapid, reliable, reproducible, sensitive, and high-throughput and is superior to PCR-ASP used in routine genotyping.