scholarly journals Molecular diversity of Giardia duodenalis in children under 5 years from the Manhiça district, Southern Mozambique enrolled in a matched case-control study on the aetiology of diarrhoea

2021 ◽  
Vol 15 (1) ◽  
pp. e0008987 ◽  
Author(s):  
Augusto Messa ◽  
Pamela C. Köster ◽  
Marcelino Garrine ◽  
Carol Gilchrist ◽  
Luther A. Bartelt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Genetic Recombination ◽  
Giardia Duodenalis ◽  
Paediatric Population ◽  
Nucleotide Polymorphisms ◽  
Symptomatic Infection ◽  
High Genetic Diversity ◽  
Pcr Targeting ◽  
Assemblage B

Giardia duodenalis is an enteric parasite commonly detected in children. Exposure to this organism may lead to asymptomatic or symptomatic infection. Additionally, early-life infections by this protozoan have been associated with impaired growth and cognitive function in poor resource settings. The Global Enteric Multicenter Study (GEMS) in Mozambique demonstrated that G. duodenalis was more frequent among controls than in diarrhoeal cases (≥3 loosing stools in the previous 24 hours). However, no molecular investigation was conducted to ascertain the molecular variability of the parasite. Therefore, we describe here the frequency and genetic diversity of G. duodenalis infections in children younger than five years of age with and without diarrhoea from the Manhiça district in southern Mozambique enrolled in the context of GEMS. Genomic DNA from 757 G. duodenalis-positive stool samples by immunoassay collected between 2007–2012, were reanalysed by multiplex PCR targeting the E1-HP and C1-P21 genes for the differentiation of assemblages A and B. Overall, 47% (353) of the samples were successfully amplified in at least one locus. Assemblage B accounted for 90% (319/353) of all positives, followed by assemblage A (8%, 29/353) and mixed A+B infections (1%, 5/353). No association between the presence of a given assemblage and the occurrence of diarrhoea could be demonstrated. A total of 351 samples were further analysed by a multi-locus sequence genotyping (MLSG) approach at the glutamate dehydrogenase (gdh), ß-giardin (bg) and triose phosphate isomerase (tpi) genes. Overall, 63% (222/351) of samples were genotyped and/or sub-genotyped in at least one of the three markers. Sequence analysis revealed the presence of assemblages A (10%; 23/222) and B (90%; 199/222) with high molecular diversity at the nucleotide level within the latter; no mixed infections were identified under the MLSG scheme. Assemblage A sequences were assigned to sub-assemblages AI (0.5%, 1/222), AII (7%, 15/222) or ambiguous AII/AIII (3%, 7/222). Within assemblage B, sequences were assigned to sub-assemblages BIII (13%, 28/222), BIV (14%, 31/222) and ambiguous BIII/BIV (59%, 132/222). BIII/BIV sequences accumulated the majority of the single nucleotide polymorphisms detected, particularly in the form of double peaks at chromatogram inspection. This study demonstrated that the occurrence of gastrointestinal illness (diarrhoea) was not associated to a given genotype of G. duodenalis in Mozambican children younger than five years of age. The assemblage B of the parasite was responsible for nine out of ten infections detected in this paediatric population. The extremely high genetic diversity observed within assemblage B isolates was compatible with an hyperendemic epidemiological scenario where infections and reinfections were common. The obtained molecular data may be indicative of high coinfection rates by different G. duodenalis assemblages/sub-assemblages and/or genetic recombination events, although the exact contribution of both mechanisms to the genetic diversity of the parasite remains unknown.

scholarly journals Molecular Characterization of Giardia duodenalis in Children and Adults Sampled in Algeria

2020 ◽  
Vol 9 (1) ◽  
pp. 54
Author(s):  
Salem Belkessa ◽  
Daniel Thomas-Lopez ◽  
Karim Houali ◽  
Farida Ghalmi ◽  
Christen Rune Stensvold
Keyword(s):  
Real Time ◽  
Molecular Characterization ◽  
Real Time Pcr ◽  
Intestinal Parasites ◽  
Giardia Duodenalis ◽  
Specific Pcr ◽  
Stool Samples ◽  
Pcr Targeting ◽  
Assemblage B

The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for Giardia. Molecular characterization of Giardia was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (tpi). Of the 119 samples, 80 (67%) were Giardia-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, tpi genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as tpi genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting Giardia in stool samples and that robust amplification and sequencing of the tpi gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on Giardia infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data.

scholarly journals Genetic Diversity and Recombination in the Plant Pathogen Sclerotinia sclerotiorum Detected in Sri Lanka

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 306
Author(s):  
Thirega Mahalingam ◽  
Weidong Chen ◽  
Chandima Shashikala Rajapakse ◽  
Kandangamuwa Pathirannahalage Somachandra ◽  
Renuka Nilmini Attanayake
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Sri Lanka ◽  
Sclerotinia Sclerotiorum ◽  
Genetic Recombination ◽  
Multiple Infections ◽  
Tropical Country ◽  
High Genetic Diversity ◽  
Principal Coordinates ◽  
Mycelial Compatibility

Sclerotinia sclerotiorum is an important fungal pathogen on many economically important crops including cabbage worldwide. Even though population structure and genetic diversity of S. sclerotiorum is well studied in temperate climatic conditions, only a few studies have been conducted in tropical countries. It is also not clear whether the populations are clonal or recombining in the tropics. In filling this information gap, 47 isolates of S. sclerotiorum were collected from commercial cabbage (Brassica oleracea L.) fields in Nuwara Eliya district of Sri Lanka, where the disease has been previously reported. All the isolates were subjected to genetic diversity study using mycelial compatibility grouping and microsatellite markers. Fourteen mycelial compatibility groups (MCGs) and 23 multilocus haplotypes (MLHs) were recorded. Mean expected heterozygosity of the population was 0.56. MLHs were weakly correlated with MCGs. Population genetic structure analysis and principal coordinates identified three genetic clusters. Genetic recombination was inferred within each genetic cluster when isolates were subjected to clone correction. There was evidence of multiple infections on single plant as detected by the presence of more than one MCG on each cabbage plant. However, multiple infections did not increase the disease severity in detached leaf assay. We found high genetic diversity and recombination of S. sclerotiorum population in a tropical country, Sri Lanka. Importance of detecting genetic structure when inferring recombination was also highlighted.

scholarly journals Molecular diversity analysis of genotypes from four Aegilops species based on retrotransposon–microsatellite amplified polymorphism (REMAP) markers

2020 ◽  
Author(s):  
Justyna Leśniowska-Nowak ◽  
Sylwia Okoń ◽  
Aleksandra Wieremczuk
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Crop Improvement ◽  
Diversity Analysis ◽  
Aegilops Species ◽  
Powerful Method ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Genetic Diversity Analysis ◽  
Valuable Source

Abstract Genetic diversity analysis is an important tool in crop improvement. Species with high genetic diversity are a valuable source of variation used in breeding programs. The aim of this study was to assess the genetic diversity of four species belonging to the genus Aegilops, which are often used to expand the genetic variability of wheat and triticale. Forty-five genotypes belonging to the genus Aegilops were investigated. Within- and among-species genetic diversity was calculated based on REMAP (retrotransposon–microsatellite amplified polymorphism) molecular markers. Obtained results showed that REMAP markers are a powerful method for genetic diversity analysis, which produces a high number of polymorphic bands (96.09% of total bands were polymorphic). Among tested genotypes, Ae. crassa and Ae. vavilovii showed the highest genetic diversity and should be chosen as a valuable source of genetic variation.

scholarly journals Genetics of Host Protection against Helicobacter pylori Infections

2021 ◽  
Vol 22 (6) ◽  
pp. 3192 ◽  
Author(s):  
Rosanna Capparelli ◽  
Domenico Iannelli
Keyword(s):  
Genetic Diversity ◽  
Helicobacter Pylori ◽  
T Regulatory Cells ◽  
Protective Role ◽  
Disease Genes ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Host Protection ◽  
High Level

This narrative review discusses the genetics of protection against Helicobacter pylori (Hp) infection. After a brief overview of the importance of studying infectious disease genes, we provide a detailed account of the properties of Hp, with a view to those relevant for our topic. Hp displays a very high level of genetic diversity, detectable even between single colonies from the same patient. The high genetic diversity of Hp can be evaded by stratifying patients according to the infecting Hp strain. This approach enhances the power and replication of the study. Scanning for single nucleotide polymorphisms is generally not successful since genes rarely work alone. We suggest selecting genes to study from among members of the same family, which are therefore inclined to cooperate. Further, extending the analysis to the metabolism would significantly enhance the power of the study. This combined approach displays the protective role of MyD88, TIRAP, and IL1RL1 against Hp infection. Finally, several studies in humans have demonstrated that the blood T cell levels are under the genetic control of the CD39+ T regulatory cells (TREGS).

scholarly journals Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

2021 ◽  
Author(s):  
Tao Zhang ◽  
Xue Li ◽  
Shuilian He
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Natural Populations ◽  
Environmental Parameters ◽  
Candidate Snps ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

scholarly journals Genetic Diversity and Prevalence of Giardia duodenalis in Qatar

2021 ◽  
Vol 11 ◽  
Author(s):  
Marwa Chourabi ◽  
Sonia Boughattas ◽  
Atiyeh M. Abdallah ◽  
Ahmed Ismail ◽  
Jerzy M. Behnke ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Genomic Dna ◽  
Intestinal Parasite ◽  
Demographic Data ◽  
Giardia Duodenalis ◽  
Comprehensive Understanding ◽  
Severity Of Disease ◽  
High Level ◽  
Assemblage B

BackgroundGiardia duodenalis is a common human intestinal parasite worldwide, and the causative agent of diarrhea, with the severity of disease ranging from asymptomatic to intense and debilitating infection. G. duodenalis is known to consist of eight genetically distinct assemblages, named from A to H. No data available on the genotypes and genetic diversity of G. duodenalis circulating in Qatar.MethodsWe genotyped 54 human Giardia isolates, collected from asymptomatic immigrants in Qatar, using a multilocus genotyping (MLGs) tool. We also investigated relationships between the subjects’ genotypes and their demographic data.ResultsGenomic DNA from 54 isolates were tested by PCR and sequence analysis at three loci: glutamate dehydrogenase (gdh), β-giardin (bg) and triose phosphate (tpi)). Assemblage A was identified in nine (16.67%), assemblage B in thirty (55.55%), and a mixture of assemblages A+B in fifteen (27.78%) isolates. All assemblage A isolates, genotyped in different loci, were assigned to sub-assemblage AII, and six of them had MLGs AII-1 while one new MLG was identified in two isolates. Sequences of assemblage B isolates have high level of genetic diversity and high presence of heterogeneous peaks, especially within the gdh gene. No significant associations between genotypes and the immigrants’ demographic data were found due to the extensive number of new variants.ConclusionsMLGs was used herein to genotype 54 immigrant Giardia isolates. The high level of genetic variability found in our isolates hampered MLGs determination, more investigations are now required to consolidate our findings, and to enable a comprehensive understanding of the diversity within G. duodenalis assemblage B isolates.

scholarly journals High genetic diversity of Anaplasma marginale infecting dairy cattle in northeastern Brazil

2021 ◽  
Vol 30 (4) ◽  
Author(s):  
José Gomes Pereira ◽  
Amanda Barbosa Garcia ◽  
Luiz Ricardo Gonçalves ◽  
Inalda Angélica de Souza Ramos ◽  
Maria do Socorro Costa Oliveira Braga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dairy Cattle ◽  
Anaplasma Marginale ◽  
The State ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Northeastern Brazil ◽  
High Genetic Diversity ◽  
Blood Samples ◽  
Pcr Targeting

Abstract Anaplasma marginale is an obligate intracellular Gram-negative bacterium found in ruminants’ erythrocytes and is the etiological agent of bovine anaplasmosis. The bacterium’s genetic diversity has been characterized based on sequences of major surface proteins (MSPs), such as MSP1α. The aim of the present study was to investigate the genetic diversity of A. marginale in cattle in the state of Maranhão, northeastern Brazil. To this end, 343 blood samples were harvested and subjected to iELISA assays using the recombinant surface protein MSP5. Out of 343 blood samples, 235 (68.5%) were randomly chosen and submitted to DNA extraction, qPCR and conventional PCR targeting the msp1α gene to determine amino acid sequences and classify the genotypes. The iELISA results showed 81.34% seropositivity (279/343), whereas qPCR revealed 224 positive samples (95.32%). Among these qPCR-positive samples, 67.4% (151/224) were also positive in the cPCR. Among the 50 obtained sequences, 21 strains had not been previously reported. Regarding the genotypes, H (26/50) and E (18/50) were identified most often, while genotypes F and C were only identified twice each and B and G once each. In conclusion, high prevalence and genetic diversity for A. marginale were observed in dairy cattle herds in the state of Maranhão.

High genetic diversity of Giardia duodenalis assemblage E in Chinese dairy cattle

2021 ◽  
pp. 104912
Author(s):  
Xueping Zhang ◽  
Jiaming Dan ◽  
Liqin Wang ◽  
Haifeng Liu ◽  
Ziyao Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dairy Cattle ◽  
Giardia Duodenalis ◽  
High Genetic Diversity

Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with Diversity Arrays Technology (DArT™)

2007 ◽  
Vol 58 (12) ◽  
pp. 1174 ◽  
Author(s):  
B. J. Stodart ◽  
M. C. Mackay ◽  
H. Raman
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Polymorphic Information Content ◽  
Ex Situ ◽  
Dart Markers ◽  
Strong Positive Correlation ◽  
High Genetic Diversity ◽  
Diversity Arrays Technology ◽  
Wheat Landraces ◽  
Landrace Accessions

Diversity Arrays Technology (DArT™) was evaluated as a tool for determining molecular diversity of wheat landraces held within the Australian Winter Cereals Collection (AWCC). Initially, a set of 44 wheat landraces was evaluated with 256 DArT markers. The dataset was compared with the results obtained using 16 amplified fragment length polymorphism (AFLP) primer combinations and 63 simple sequence repeat (SSR) markers, mapped on the 21 chromosomes, from a previous study. The DArT markers exhibited a strong positive correlation with AFLP and SSR, with each marker type distinguishing similar relationships among the 44 landrace accessions. The DArT markers exhibited a higher polymorphic information content than AFLP, and were comparable with that obtained with SSR. Three hundred and fifty-five DArT markers were then used to evaluate genetic diversity among 705 wheat landrace accessions from within the AWCC, chosen to represent 5 world regions. DArT analysis was capable of distinguishing accessions from different geographic regions, and suggested that accessions originating from Nepal represent a unique gene pool within the collection. A statistical resampling of DArT loci indicated that 10–20 loci were enough to distinguish the maximum molecular diversity present within the collection. This research demonstrates the efficacy of the DArT platform as a tool for efficient examination of wheat diversity. As an ex situ germplasm repository, the AWCC contains wheat accessions of high genetic diversity, from genetically differentiated collection sites, even though diversity was under-represented in some countries represented in the repository.

scholarly journals Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan

2014 ◽  
Vol 95 (9) ◽  
pp. 1945-1957 ◽  
Author(s):  
Asif Naeem ◽  
Takushi Hosomi ◽  
Yorihiro Nishimura ◽  
Muhammad Masroor Alam ◽  
Tomoichiro Oka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Diversity ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Full Genome Sequence ◽  
Emerging Viruses ◽  
High Genetic Diversity ◽  
Genotype Assignment ◽  
Pcr Targeting

Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5′ untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler’s murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41–56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.

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