Reassortant Cache Valley virus associated with acute febrile, non-neurologic illness, Missouri

2021 ◽  
Author(s):  
Molly Baker ◽  
Holly R Hughes ◽  
S Hasan Naqvi ◽  
Karen Yates ◽  
Jason O Velez ◽  
...  
Keyword(s):  
Renal Failure ◽  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Lactic Acidosis ◽  
Adult Male ◽  
Gastrointestinal Symptoms ◽  
Next Generation ◽  
Cache Valley Virus ◽  
Cache Valley ◽  
Generation Sequencing

Abstract An adult male from Missouri sought care for fever, fatigue, and gastrointestinal symptoms. He had leukopenia and thrombocytopenia and was treated for a presumed tickborne illness. His condition deteriorated with respiratory and renal failure, lactic acidosis, and hypotension. Next-generation sequencing and phylogenetic analysis identified a reassortant Cache Valley virus.

scholarly journals Investigation of neglected protists Blastocystis sp. and Dientamoeba fragilis in immunocompetent and immunodeficient diarrheal patients using both conventional and molecular methods

2021 ◽  
Vol 15 (10) ◽  
pp. e0009779
Author(s):  
Fakhriddin Sarzhanov ◽  
Funda Dogruman-Al ◽  
Monica Santin ◽  
Jenny G. Maloney ◽  
Ayse Semra Gureser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Symptoms ◽  
Molecular Methods ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Next Generation ◽  
Dientamoeba Fragilis ◽  
Significant Difference ◽  
Generation Sequencing ◽  
Immunocompetent Patients

Introduction The clinical significance of Blastocystis sp. and Dientamoeba fragilis in patients with gastrointestinal symptoms is a controversial issue. Since the pathogenicity of these protists has not been fully elucidated, testing for these organisms is not routinely pursued by most laboratories and clinicians. Thus, the prevalence of these organisms and the subtypes of Blastocystis sp. in human patients in Turkey are not well characterized. This study aimed to determine the prevalence of Blastocystis sp. and D. fragilis in the diarrheic stool samples of immunodeficient and immunocompetent patients using conventional and molecular methods and to identify Blastocystis sp. subtypes using next generation sequencing. Material and methods Individual stool specimens were collected from 245 immunodeficient and 193 immunocompetent diarrheic patients between March 2017 and December 2019 at the Gazi University Training and Research Hospital in Ankara, Turkey. Samples were screened for Blastocystis sp. and D. fragilis by conventional and molecular methods. Molecular detection of both protists was achieved by separate qPCRs targeting a partial fragment of the SSU rRNA gene. Next generation sequencing was used to identify Blastocystis sp. subtypes. Results The prevalence of Blastocystis sp. and D. fragilis was 16.7% and 11.9%, respectively as measured by qPCR. The prevalence of Blastocystis sp. and D. fragilis was lower in immunodeficient patients (12.7% and 10.6%, respectively) compared to immunocompetent patients (21.8% and 13.5%, respectively). Five Blastocystis sp. subtypes were identified and the following subtype distribution was observed: ST3 54.4% (n = 37), ST2 16.2% (n = 11), ST1 4.4% (n = 3), ST6 2.9% (n = 2), ST4 1.5% (n = 1), ST2/ST3 11.8% (n = 8) and ST1/ST3 8.8% (n = 6). There was no statistically significant difference in the distribution of Blastocystis sp. subtypes between immunocompetent and immunodeficient patients. Conclusion and recommendation Our findings demonstrated that Blastocystis sp. and D. fragilis are commonly present in immunocompetent and immunodeficient patients with diarrhea. This study is the first to use next generation sequencing to address the presence of Blastocystis sp. mixed subtypes and intra-subtype variability in clinical samples in Turkey.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7415
Author(s):  
An Huang ◽  
Shuo Liu ◽  
Haijun Li ◽  
Hongdi Luo ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Control Region ◽  
Evolutionary Process ◽  
Tree Frog ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mitogenome Sequence ◽  
Nd5 Gene ◽  
Generation Sequencing

The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

scholarly journals SAPROBITY IDENTIFICATION OF HYDROBIONT SPECIES OF VERHNIY KABAN LAKE OF KAZAN BY 18S rRNA MARKER GENE

2021 ◽  
Vol 6(72) (4) ◽  
pp. 127-142
Author(s):  
A. E. Sverdrup ◽  
L. L. Frolova
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Indicator Species ◽  
18S Rrna ◽  
Marker Gene ◽  
Ribosomal Genes ◽  
Molecular Phylogenetic Analysis ◽  
Next Generation ◽  
Molecular Phylogenetic ◽  
Generation Sequencing

The paper presents the results of a study of the hypothetical evolution of unicellular hydrobionts from Verhniy Kaban Lake of Kazan by 18S rRNA marker gene with aim of identifying species saprobity based on molecular phylogenetic analysis. Verhniy Kaban Lake is an isolated freshwater reservoir. Its coastline is relatively smooth except for the northern end, which forms swampy and overgrown bay. To the West of lake an urban settlement is situated and to the East are highway and garden plots. Lake length is about 1 km, average and maximum widths are 245 m and 370 m respectively. Deepest point is 15 m; average depth is 8 m; lake area – 25 hectares. Quality of lake water is classified as polluted. One of methods used for ecological assessment of water reservoirs is the bioindication method based on ability of indicator species to survive in water of certain pollution degree. At present, freshwater hydrobiont species from V.Sladechek’s list (1973) are used as indicators. Indicator species lists expand very slowly due to the long process of experimental observations. At the same time, price drop of the next-generation sequencing technologies allows to identify more organisms and run molecular phylogenetic analysis with aim of identifying species saprobity based on study of hypothetic evolution of hydrobionts by marker genes including 18S rRNA. The advantage of using 18S rRNA/16S rRNA ribosomal genes is that they are present in all organisms. Ribosomal genes are ones of the most conservative genes. Therefore, the systematic position of the organism and the time of divergence with closely related species can be determined via analysis of similarities and differences in rRNA sequences. Molecular phylogenetic trees were constructed by the neighbour joining (NJ) and maximal parsimony (MP) methods for Verhniy Kaban Lake hydrobionts identified with next-generation sequencing method (Illumina) by 18S rRNA marker gene (SRR7510986, SRR7465374, SRR7516513). Phylogenetic analysis of hydrobionts of Verhniy Kaban Lake by 18S rRNA marker gene revealed 12 clusters with a high bootstrap value (68–100 %), containing 12 existing indicator species of hydrobionts and 13 unicellular algae and ciliates – indicator species of different saprobity that did not previously have the status of bioindicators – algae: Diplosphaera mucosa (o-b-saprobity), Mucidosphaerium pulchellum (p-a-saprobity), Dinobryon pediforme (b-mesosaprobity), Gomphoneis minuta (b-mesosaprobity), Nitzschia amphibia (o-b-saprobity), Rhabdonema adriaticum (o-b-saprobity), Synura mammillosa (b-o-saprobity), Cryptomonas ozolini (b-mesosaprobity); ciliates: Astylozoon enriquesi (b-mesosaprobity), Blepharocorys curvigula (p-saprobity), Enchelys gasterosteus (p-saprobity), Monocoronella carnea (a-b-mesosaprobity), Plagiopogon loricatus (b-a-mesosaprobity). Most identified indicator species group near b-mesosaprobity. This indicates ecological state of Verhniy Kaban Lake as polluted by ecological assessments.

scholarly journals Cortinarius subgenus Leprocybe in Europe: expanded Sanger and Next Generation Sequencing unveil unexpected diversity in the Mediterranean

2021 ◽  
Author(s):  
A. Bidaud ◽  
M. Loizides ◽  
F. Armada ◽  
J. de Dios Reyes ◽  
X. Carteret ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Taxonomic Status ◽  
Next Generation ◽  
The Past ◽  
The Future ◽  
The Mediterranean ◽  
Molecular Phylogenies ◽  
Generation Sequencing

Molecular phylogenies in the past decade have demonstrated that the described diversity of Cortinarius is still underestimated, especially outside continental and boreal ecoregions where the genus has been historically investigated. We tackled this issue by revisiting the so far unresolved subgenus Leprocybe, and focused on the largely unexplored Mediterranean hotspot of biodiversity. The sequencing and phylogenetic analysis of 161 vouchered collections from Austria, Cyprus, France, Germany, Italy and Spain, including 16 types, allowed for the delineation of 11 species in this lineage, three of them recognised as new to science and formally introduced as C. jimenezianus, C. selinolens and C. viridans spp. nov., respectively. Interestingly, the newly described species exhibit a strict Mediterranean distribution, and one of them is putatively endemic to the island of Cyprus, highlighting the remarkable potential of this neglected ecoregion to uncover further undescribed diversity of Cortinarius in the future. The present work also unveils 23 synonymies in this subgenus, as well as previously undetected crypticism within C. venetus. Next Generation Sequencing carried out on three old and contaminated holotypes, successfully decrypts their phylogenetic identity, including that of C. leproleptopus, finally settling the long-standing controversy over the taxonomic status of this species. A brief overview of each species in the subgenus is lastly provided and a key is proposed to facilitate the identification of presently known European taxa of Leprocybe in the field.

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