scholarly journals Genetic diversity of Giardia isolates from patients in Chandigarh region: India

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Shabnam Thakur ◽  
Upninder Kaur ◽  
Rakesh Sehgal
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Glutamate Dehydrogenase ◽  
Nested Pcr ◽  
Epidemiological Studies ◽  
Nucleotide Sequences ◽  
Neighbor Joining ◽  
Pcr Targeting ◽  
Assemblage B

Abstract Objective The aim of study was to characterize Giardia isolates genetically among patients in Chandigarh region, India. For this, nested PCR targeting fragment of the glutamate dehydrogenase (GLUD1 earlier named as GDH) gene was used. Phylogenetic analysis was done by constructing neighbor-joining tree made out of the nucleotide sequences of G. intestinalis isolates obtained in this study and with the known sequences published in GenBank. Results Out of 40 samples, GLUD1 gene was amplified in 33 samples (82.5%). The product of GLUD1 gene was successfully sequenced only in 32 samples. In these samples, assemblage B was found in 27 (84.37%) samples whereas 5 (15.6%) samples had assemblage A. Among assemblage B most of them were of BIII. Therefore, genotyping of Giardia would be helpful in conducting epidemiological studies.

scholarly journals Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters

2003 ◽  
Vol 69 (10) ◽  
pp. 5782-5786 ◽  
Author(s):  
Tomoko Nishida ◽  
Hirokazu Kimura ◽  
Mika Saitoh ◽  
Michiyo Shinohara ◽  
Masahiko Kato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Virus Type ◽  
Reverse Transcription ◽  
Real Time Pcr ◽  
The Other ◽  
Capsid Gene ◽  
Neighbor Joining ◽  
Norwalk Virus ◽  
Reverse Transcription Pcr

ABSTRACT Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 102 copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.

Polymorphism and Genetic Diversity among Cassava Cultivars based on ITS1-5.8S-ITS2 Sequences of rDNA

2017 ◽  
Vol 6 (6) ◽  
pp. 220-227
Author(s):  
Djirabaye Nadjiam ◽  
Aliou Guisse ◽  
Mbacké Sembéne ◽  
Fatimata Mbaye
Keyword(s):  
Genetic Diversity ◽  
Bayesian Approach ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Sequences ◽  
Its2 Region ◽  
Neighbor Joining ◽  
High Haplotype Diversity ◽  
The Bayesian Approach

Cassava is an important crop in the southern area of the Chad and it is char- acterized by many cultivars. But these cultivars have never been evaluated at the molecular level. Therefore, the objective of this study was to analyze their genetic diversity and their phylogenetic relationships. After DNA extraction, amplification and sequencing, the nucleotide sequences of the ITS1- 5.8S-ITS2 region of the ribosomal DNA of 12 selected cultivars have been analyzed. The Neighbor-Joining method, Maximum Parsimony, Maximum Likelihood and the Bayesian approach allowed studying the ancestral links. The identified nucleotide sequences have 542 bp. The targeted genes showed 468 conserved sites and 59 polymorphic sites. The nucleotide frequency was 18.64% for Adenine, 14.01% for Thymine, 34.46% for Cytosine and 32.89% for Guanine. The (G + C) content was 67.35% compared to 32.65% for the (A+T). The substitution rate was in favor of the transversions (67.46%) against the transitions (32.54%). The analysis revealed high haplotype diversity (Hd=0.954) and low nucleotide diversity (π=0.026) with an average number of pairwise nucleo de di erences (k=14.045). On the all popula on, 9 haplotypes, including 6 individual and 3 double, were identified. Gene c di eren a on is medium (FST=0.314) with a low number of migrants (Nm=0.55) and a medium genetic distance (0.028). Phylogenetic analysis based on the Bayesian approach revealed three groups of cul vars with the existence of two strongly supported clades. The cultivars studied are characterized by demographic stability or moderate population growth.They will be incorporated in the breeding program in order to limit their genetic erosion and to select the interesting characters. 

scholarly journals Genetic diversity of Plasmodium falciparum populations in three malaria transmission settings in Madagascar

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fanomezantsoa Ralinoro ◽  
Tovonahary Angelo Rakotomanga ◽  
Rianasoambolanoro Rakotosaona ◽  
Danielle A. Doll Rakoto ◽  
Didier Menard ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Malaria Transmission ◽  
Nested Pcr ◽  
Drug Efficacy ◽  
Control Measures ◽  
Epidemiological Strata ◽  
Allele Specific ◽  
The Impact ◽  
Pcr Targeting

Abstract Background Assessment of the genetic diversity of Plasmodium falciparum parasites from various malaria transmission settings could help to define tailored local strategies for malaria control and elimination. Such assessments are currently scarce in Madagascar. The study presented here aimed to bridge this gap by investigating the genetic diversity of P. falciparum populations in three epidemiological strata (Equatorial, Tropical and Fringes) in Madagascar. Methods Two-hundred and sixty-six P. falciparum isolates were obtained from patients with uncomplicated malaria enrolled in clinical drug efficacy studies conducted at health centres in Tsaratanana (Equatorial stratum), Antanimbary (Tropical stratum) and Anjoma Ramartina (Fringes) in 2013 and 2016. Parasite DNA was extracted from blood samples collected before anti-malarial treatment. Plasmodium species were identified by nested PCR targeting the 18 S rRNA gene. The genetic profiles of P. falciparum parasites were defined by allele-specific nested PCR on the polymorphic regions of the msp-1 and msp-2 genes. Results Fifty-eight alleles were detected in the P. falciparum samples tested: 18 alleles for msp-1 and 40 for msp-2. K1 (62.9%, 139/221) and FC27 (69.5%, 114/164) were the principal msp-1 and msp-2 allele families detected, although the proportions of the msp-1 and msp-2 alleles varied significantly between sites. Polyclonal infections were more frequent at sites in the Equatorial stratum (69.8%) than at sites in the Tropical stratum (60.5%) or Fringes (58.1%). Population genetics analyses showed that genetic diversity was similar between sites and that parasite flow within sites was limited. Conclusions This study provides recent information about the genetic diversity of P. falciparum populations in three transmission strata in Madagascar, and valuable baseline data for further evaluation of the impact of the control measures implemented in Madagascar.

scholarly journals Detection of assemblages A and B of Giardia duodenalis in water and sewage from São Paulo state, Brazil

2011 ◽  
Vol 9 (2) ◽  
pp. 361-367 ◽  
Author(s):  
Licia Natal Fernandes ◽  
Patrícia Pereira de Souza ◽  
Ronalda Silva de Araújo ◽  
Maria Tereza Pepe Razzolini ◽  
Rodrigo Martins Soares ◽  
...  
Keyword(s):  
Public Health ◽  
Phylogenetic Analysis ◽  
Water Samples ◽  
Nested Pcr ◽  
Giardia Duodenalis ◽  
Spring Water ◽  
Human Faeces ◽  
Paulo State ◽  
Treated Sewage ◽  
Assemblage B

Giardia duodenalis is a protozoan that parasitizes humans and other mammals and causes giardiasis. Although its isolates have been divided into seven assemblages, named A to G, only A and B have been detected in human faeces. Assemblage A isolates are commonly divided into two genotypes, AI and AII. Even though information about the presence of this protozoan in water and sewage is available in Brazil, it is important to verify the distribution of different assemblages that might be present, which can only be done by genotyping techniques. A total of 24 raw and treated sewage, surface and spring water samples were collected, concentrated and purified. DNA was extracted, and a nested PCR was used to amplify an 890 bp fragment of the gdh gene of G. duodenalis, which codes for glutamate dehydrogenase. Positive samples were cloned and sequenced. Ten out of 24 (41.6%) samples were confirmed to be positive for G. duodenalis by sequencing. Phylogenetic analysis grouped most sequences with G. duodenalis genotype AII from GenBank. Only two raw sewage samples presented sequences assigned to assemblage B. In one of these samples genotype AII was also detected. As these assemblages/genotypes are commonly associated to human giardiasis, the contact with these matrices represents risk for public health.

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 Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Insights into the genetic diversity and the phylogenetic analysis of Tunisian isolates of Tomato chlorosis virus

2014 ◽  
Vol 43 (1) ◽  
pp. 87-96 ◽  
Author(s):  
Charfeddine Gharsallah ◽  
Amina Ben Halima ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Tomato Chlorosis Virus

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

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