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.

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.

scholarly journals Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Adelaide Milani ◽  
Gianpiero Zamperin ◽  
Alice Fusaro ◽  
Annalisa Salviato ◽  
Luca Bano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Full Genome Sequence ◽  
Full Genome ◽  
High Genetic Diversity ◽  
Content Type ◽  
First Time

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.

scholarly journals Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1476
Author(s):  
Lester J. Perez ◽  
Gavin A. Cloherty ◽  
Michael G. Berg
Keyword(s):  
Genetic Diversity ◽  
Sequence Comparison ◽  
Complete Resolution ◽  
Pairwise Distance ◽  
Pairwise Sequence Comparison ◽  
Double Stranded Rna ◽  
Phylogenetic Marker ◽  
High Degree ◽  
Phylogenetic Noise

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

scholarly journals Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

2022 ◽  
Author(s):  
Pablo Villarreal ◽  
Carlos Villarroel ◽  
Samuel O’Donnell ◽  
Nicolas Agier ◽  
Julian Quintero-Galvis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Diversity ◽  
Divergence Time ◽  
Glacial Refugia ◽  
Ecological Niches ◽  
Natural Environments ◽  
South American ◽  
The South ◽  
Adaptive Genetic Variation ◽  
High Genetic Diversity

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles, which explains its ecological versatility. The yeast Lachancea cidri is an ideal model for exploring the interplay between genetics, ecological function and evolution. L. cidri is a species that diverged from the Saccharomyces lineage before the whole-genome duplication and exhibits a broad distribution across the South Hemisphere, thus displaying an important ecological success. Here, we applied phylogenomics to investigate the adaptive genetic variation of L. cidri isolates obtained from natural environments in Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggest that South American and Australian lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA), consistent with the presence of multiple glacial refugia. Interestingly, we found that the French reference strain belongs to the Australian lineage, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, species delimitation analysis identified different evolutionary units within the South American lineage and, together with parameters like Pi (π) and FST, revealed that Patagonia contains most of the genetic diversity of this species. These results agree with phenotypic characterizations, demonstrating a greater phenotypic diversity in the South American lineage. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favored the extensive distribution of L. cidri in Patagonia.

scholarly journals Genetic and chemical differentiation ofCampylobacter coliandCampylobacter jejunilipooligosaccharide pathways

2016 ◽  
Author(s):  
Alejandra Culebro ◽  
Joana Revez ◽  
Ben Pascoe ◽  
Yasmin Friedmann ◽  
Matthew D Hitchings ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lipid A ◽  
Phenotypic Diversity ◽  
Outer Core ◽  
Mass Spectrometry Analysis ◽  
High Genetic Diversity ◽  
Spectrometry Analysis ◽  
Structure Heterogeneity ◽  
Species Specific ◽  
First Time

ABSTRACTDespite the importance of lipooligosaccharides (LOS) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS inC. coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelatedC. coliisolates sampled from several different host species. Furthermore, we pairedC. coligenomic information and LOS chemical composition for the first time to identify mechanisms consistent with the generation of LOS phenotypic heterogeneity. After classifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structure heterogeneity. Mass spectrometry analysis of the LOS of nine isolates, representing four different LOS classes, identified two features distinguishingC. coliLOS fromC. jejuni’s. GlcN-GlcN disaccharides were present in the lipid A backbone in contrast to the GlcN3N-GlcN backbone observed inC. jejuni. Moreover, despite that many of the genes putatively involved in Qui3pNAcyl were absence in the genomes of various isolates, this rare sugar was found in the outer core of allC. coli. Therefore, regardless the high genetic diversity of LOS biosynthes is locus inC. coli, we identified species-specific phenotypic features ofC. coliLOS which might explain differences betweenC. jejuniandC. coliin terms of population dynamics and host adaptation.Depositories (where applicable)The whole genome sequences ofC. coliare publicly available on the RAST server (http://rast.nmpdr.org) with guest account (login and password ‘guest’) under IDs: 195.91, 195.96-195.119, 195.124-195.126, 195.128-195.130, 195.133, 195.134, 6666666.94320

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 Genetic diversity of farmer-preferred cowpea (Vigna unguiculata L. Walp) landraces in Turkey and evaluation of their relationships based on agromorphological traits

Genetika ◽  
2017 ◽  
Vol 49 (3) ◽  
pp. 935-957 ◽  
Author(s):  
Mehmet Bozokalfa ◽  
Aşçioğul Kaygisiz ◽  
Dursun Eşiyok
Keyword(s):  
Genetic Diversity ◽  
Vigna Unguiculata ◽  
Phenotypic Diversity ◽  
Plant Genetic Resources ◽  
Geographic Origin ◽  
Conservation Strategies ◽  
Eye Color ◽  
Components Analysis ◽  
The Tropics

Cowpea (Vigna unguiculata L. Walp) is one of the important vegetable, grain, and fodder legume species grown in the tropics and subtropics. Cowpea is grown on small farms, and locally adapted landraces or populations are cultivated, and genetic improvements are limited by the lack of knowledge of genetic diversity of the indigenous and cultivated germplasm. Characterization and classification of diversity of the germplasm is valuable for both plant breeders and germplasm curators in the development of conservation strategies and identification of plant genetic resources. In the present study, 36 qualitative and quantitative agromorphological traits were used to characterize and assess the genetic diversity of 32 farmer preferred cowpea genotypes collected from diverse cultivated locations. Genetic variation was highly significant, and phenotypic diversity was observed for agromorphological traits. Agromorphological traits were classified by principal components analysis (PCA) into 10 components, which explained 81.18% of the total variation. PCA revealed that seed properties such as weight, diameter, width, length, eye color and immature pod pigmentation, leaf and pod color properties were the primary characteristics to discriminate cowpea genotypes. The hierarchical analysis grouped the genotypes into five clusters, and significant association was not apparent between geographic origin and agromorphological traits. The promising germplasm was identified to improve the landraces for fresh pod, grain, and fodder.

scholarly journals Complete Genome Sequence of a Representative New Jersey Vesiculovirus Strain, NJ03CPB, from a Region of Endemicity in Southern Mexico

2019 ◽  
Vol 8 (25) ◽  
Author(s):  
Lauro Velazquez-Salinas ◽  
Steven J. Pauszek ◽  
Luis L. Rodriguez
Keyword(s):  
Genetic Diversity ◽  
New Jersey ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Full Genome Sequence ◽  
Full Genome ◽  
High Genetic Diversity ◽  
Southern Mexico ◽  
Vesicular Stomatitis ◽  
Epithelial Lesion

We report the full-genome sequence of a New Jersey vesiculovirus strain, commonly referred to as vesicular stomatitis New Jersey virus (VSNJV), obtained from an epithelial lesion of a naturally infected cow in Chiapas, Mexico. This genome is a representative from the zone of endemicity in Mexico, a region of high genetic diversity.

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