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Genetics and Genomics of Malaria Parasites
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Genetics and Genomics of Malaria Parasites

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 16315

Special Issue Editors

Prof. Dr. Eugenia Lo

E-Mail Website
Guest Editor
Biological Sciences, University of North Carolina Charlotte, Charlotte, NC 28262, USA
Interests: malaria parasites; spatial epidemiology; host-pathogen interactions; invasion mechanism; population genomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Liwang Cui

E-Mail Website
Guest Editor
Department of Internal Medicine, University of South Florida, Tampa, FL 33620, USA
Interests: malaria; developmental biology; epigenetics; translation regulation; drug resistance; functional genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In 2016, the World Health Organization estimated that 3.4 billion people were at risk of malaria, with approximately 80% of malaria cases and 90% of deaths occurring in sub-Saharan Africa. In non-human primates, approximately 25 malaria parasite species have been described. Among them, six species including Plasmodium falciparum, P. vivax. P. malariae, P. ovale, P. knowlesi, and P. simium are known to infect humans, causing malaria. Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills about half a million annually. While P. falciparum causes most malaria mortality, P. vivax can also cause severe disease and, rarely, death.

The genetics and genomics of malaria parasites reveal evolutionary processes/mechanisms and inheritance patterns. Genetic information helps track the movement of infectious pathogens as well as the response to malaria interventions over time. The advent and accessibility of high-throughput sequencing technologies and bioinformatic tools in the last decade provides remarkable insights into the global genetic structure, genomic composition, and recombination rates, as well as genetic variants associated with antimalarial drug resistance of Plasmodium. Global malaria elimination programs focus primarily on P. falciparum. Nevertheless, non-P. falciparum malaria still presents a major challenge for malaria elimination. Recent research efforts and control programs have drawn resources to P. vivax malaria. In contrast, other Plasmodium species receive little attention, and malaria caused by these organisms is among the most neglected tropical diseases.

This Special Issue will cover the genetic and/or genomic features of the various malaria parasite species in the context of disease epidemiology, evolution, functions of genes or gene products, and host–pathogen interactions. We cordially invite researchers working in these areas to contribute to this Special Issue with original research or reviews.

Prof. Eugenia Lo
Prof. Liwang Cui
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Plasmodium
  • Functional genomics
  • Population genomics
  • Epigenetics
  • Antimalarial drug resistance
  • Gene functions and products
  • Host-pathogen interactions
  • Malaria epidemiology

Published Papers (4 papers)

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Research

13 pages, 1013 KiB  
Article
Contrasting Asymptomatic and Drug Resistance Gene Prevalence of Plasmodium falciparum in Ghana: Implications on Seasonal Malaria Chemoprevention
by Cheikh Cambel Dieng, Lauren Gonzalez, Kareen Pestana, Shittu B. Dhikrullahi, Linda E. Amoah, Yaw A. Afrane and Eugenia Lo
Genes 2019, 10(7), 538; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10070538 - 16 Jul 2019
Cited by 14 | Viewed by 4202
Abstract
Malaria is a significant public health problem in Ghana. Seasonal Malaria Chemoprevention (SMC) using a combination of sulfadoxine-pyrimethamine and amodiaquine has been implemented since 2015 in northern Ghana where malaria transmission is intense and seasonal. In this study, we estimated the prevalence of [...] Read more.
Malaria is a significant public health problem in Ghana. Seasonal Malaria Chemoprevention (SMC) using a combination of sulfadoxine-pyrimethamine and amodiaquine has been implemented since 2015 in northern Ghana where malaria transmission is intense and seasonal. In this study, we estimated the prevalence of asymptomatic P. falciparum carriers in three ecological zones of Ghana, and compared the sensitivity and specificity of different molecular methods in identifying asymptomatic infections. Moreover, we examined the frequency of mutations in pfcrt, pfmdr1, pfdhfr, and pfdhps that relate to the ongoing SMC. A total of 535 asymptomatic schoolchildren were screened by microscopy and PCR (18s rRNA and TARE-2) methods. Among all samples, 28.6% were detected as positive by 18S nested PCR, whereas 19.6% were detected by microscopy. A high PCR-based asymptomatic prevalence was observed in the north (51%) compared to in the central (27.8%) and south (16.9%). The prevalence of pfdhfr-N51I/C59R/S108N/pfdhps-A437G quadruple mutant associated with sulfadoxine-pyrimethamine resistance was significantly higher in the north where SMC was implemented. Compared to 18S rRNA, TARE-2 serves as a more sensitive molecular marker for detecting submicroscopic asymptomatic infections in high and low transmission settings. These findings establish a baseline for monitoring P. falciparum prevalence and resistance in response to SMC over time. Full article
(This article belongs to the Special Issue Genetics and Genomics of Malaria Parasites)
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26 pages, 7715 KiB  
Article
Novel Molecular Synapomorphies Demarcate Different Main Groups/Subgroups of Plasmodium and Piroplasmida Species Clarifying Their Evolutionary Relationships
by Rahul Sharma and Radhey S. Gupta
Genes 2019, 10(7), 490; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10070490 - 28 Jun 2019
Cited by 4 | Viewed by 4270
Abstract
The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study [...] Read more.
The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except B. microti and two CSIs are specific for the genus Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the Plasmodium subgenera Haemamoeba, Laverania, Vinckeia and Plasmodium (excluding P. ovale and P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-Plasmodium species in comparison to the mammalian-infecting groups of Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera Plasmodium and Vinckeia and three CSIs each that reliably group P. malariae with members of the subgenus Plasmodium and P. ovale within the subgenus Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms. Full article
(This article belongs to the Special Issue Genetics and Genomics of Malaria Parasites)
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9 pages, 1386 KiB  
Article
Distribution of Duffy Phenotypes among Plasmodium vivax Infections in Sudan
by Musab M.A. Albsheer, Kareen Pestana, Safaa Ahmed, Mohammed Elfaki, Eiman Gamil, Salma M. Ahmed, Muntaser E. Ibrahim, Ahmed M. Musa, Eugenia Lo and Muzamil M. Abdel Hamid
Genes 2019, 10(6), 437; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10060437 - 08 Jun 2019
Cited by 14 | Viewed by 3280
Abstract
Negative Duffy expression on the surface of human red blood cells was believed to be a barrier for Plasmodium vivax infection in most Africans. However, P. vivax has been demonstrated to infect Duffy-negative individuals in several Central and East African countries. In this [...] Read more.
Negative Duffy expression on the surface of human red blood cells was believed to be a barrier for Plasmodium vivax infection in most Africans. However, P. vivax has been demonstrated to infect Duffy-negative individuals in several Central and East African countries. In this study, we investigated the distribution of Duffy blood group phenotypes with regard to P. vivax infection and parasitemia in Sudan. Out of 992 microscopic-positive malaria samples, 190 were identified as P. vivax positive infections. Among them, 186 were P. vivax mono-infections and 4 were mixed P. vivax and Plasmodium falciparum infections. A subset of 77 samples was estimated with parasitemia by quantitative real-time PCR. Duffy codons were sequenced from the 190 P. vivax positive samples. We found that the Duffy Fy(a-b+) phenotype was the most prevalent, accounting for 67.9% of all P. vivax infections, while homozygous Duffy-negative Fy(a-b-) accounted for 17.9% of the P. vivax infections. The prevalence of infection in Fy(a-b+) and Fy(a+b-)were significantly higher than Fy(a-b-) phenotypes (p = 0.01 and p < 0.01, respectively). A significantly low proportion of P. vivax infection was observed in Duffy negative individuals Fy(a-b-). This study highlights the prevalence of P. vivax in Duffy-negatives in Sudan and indicates low parasitemia among the Duffy-negative individuals. Full article
(This article belongs to the Special Issue Genetics and Genomics of Malaria Parasites)
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14 pages, 2388 KiB  
Article
The Diversity, Multiplicity of Infection and Population Structure of P. falciparum Parasites Circulating in Asymptomatic Carriers Living in High and Low Malaria Transmission Settings of Ghana
by Zakaria Abukari, Ruth Okonu, Samuel B. Nyarko, Aminata C. Lo, Cheikh C. Dieng, Samson P. Salifu, Ben A. Gyan, Eugenia Lo and Linda E. Amoah
Genes 2019, 10(6), 434; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10060434 - 07 Jun 2019
Cited by 29 | Viewed by 3946
Abstract
Background: Diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. This study utilized 12 polymorphic microsatellite (MS) markers and the Msp2 marker to examine diversity, multiplicity of infection (MOI) as well as the population structure of parasites circulating [...] Read more.
Background: Diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. This study utilized 12 polymorphic microsatellite (MS) markers and the Msp2 marker to examine diversity, multiplicity of infection (MOI) as well as the population structure of parasites circulating in two sites separated by about 92 km and with varying malaria transmission intensities within the Greater Accra Region of Ghana. Methods: The diversity and MOI of P. falciparum parasites in 160 non-symptomatic volunteers living in Obom (high malaria transmission intensity) and Asutsuare (low malaria transmission intensity) aged between 8 and 60 years was determined using Msp2 genotyping and microsatellite analysis. Results: The prevalence of asymptomatic P. falciparum carriers as well as the parasite density of infections was significantly higher in Obom than in Asutsuare. Samples from Asutsuare and Obom were 100% and 65% clonal, respectively, by Msp2 genotyping but decreased to 50% and 5%, respectively, when determined by MS analysis. The genetic composition of parasites from Obom and Asutsuare were highly distinct, with parasites from Obom being more diverse than those from Asutsuare. Conclusion: Plasmodium falciparum parasites circulating in Obom are genetically more diverse and distinct from those circulating in Asutsuare. The MOI in samples from both Obom and Asutsuare increased when assessed by MS analysis relative to MSP2 genotyping. The TA40 and TA87 loci are useful markers for estimating MOI in high and low parasite prevalence settings. Full article
(This article belongs to the Special Issue Genetics and Genomics of Malaria Parasites)
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