scholarly journals Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

EcoHealth ◽  
2021 ◽  
Author(s):  
Julie Teresa Shapiro ◽  
Sarah Mollerup ◽  
Randi Holm Jensen ◽  
Jill Katharina Olofsson ◽  
Nam-phuong D. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Full Length ◽  
Metagenomic Analysis ◽  
Human Settlements ◽  
Fecal Samples ◽  
Potential Risks ◽  
Bat Coronavirus

AbstractWe investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

scholarly journals Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

2013 ◽  
Vol 44 (2) ◽  
pp. 597-603 ◽  
Author(s):  
Christian E. Busse ◽  
Irina Czogiel ◽  
Peter Braun ◽  
Peter F. Arndt ◽  
Hedda Wardemann
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Light Chain ◽  
High Throughput Sequencing ◽  
Full Length

scholarly journals Full-length immunoglobulin high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome

2019 ◽  
Author(s):  
Sébastien Bender ◽  
Vincent Javaugue ◽  
Alexis Saintamand ◽  
Maria Victoria Ayala ◽  
Mehdi Alizadeh ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Plasma Cell ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Clinical Manifestations ◽  
Diagnostic Value ◽  
Poems Syndrome ◽  
Full Length ◽  
Plasma Cell Dyscrasia ◽  
Multisystem Disease

AbstractPOEMS syndrome is a rare multisystem disease due to an underlying plasma cell (PC) dyscrasia. The pathophysiology of the disease remains unclear but the role of the monoclonal immunoglobulin (Ig) light chain (LC) is strongly suspected, due to the highly restrictive usage of two λ variable (V) domains (IGLV1-40 and IGLV1-44) and the general improvement of clinical manifestations following PC clone-targeted treatment. However, the diagnostic value of Ig LC sequencing, especially in case of incomplete forms of the disease, remains to be determined. Using a sensitive high-throughput Ig repertoire sequencing on RNA (RACE-RepSeq), we detected a λ LC monoclonal expansion in the bone marrow (BM) of 85% of patients with POEMS syndrome, including some in whom bone marrow tests routinely performed to diagnose plasma cell dyscrasia failed to detect λ+ monoclonal PCs. Twenty-four of the 30 LC clonal sequences found (80%) were derived from the IGLV1-40 and IGLV1-44 germline genes, two from the closely related IGLV1-36 gene, and all were associated with an IGLJ3*02 junction (J) gene, confirming the high restriction of VJ region usage in POEMS syndrome. RACE-RepSeq VJ full-length sequencing additionally revealed original mutational patterns, the strong specificity of which might crucially help establish or eliminate the diagnosis of POEMS syndrome in uncertain cases. Thus, RACE-RepSeq appears as a sensitive, rapid and specific tool to detect low-abundance PC clones in BM, and assign them to POEMS syndrome, with all the consequences for therapeutic options hereby.

scholarly journals DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses

Evaluating high‐throughput sequencing as a method for metagenomic analysis of nematode diversity

2009 ◽  
Vol 9 (6) ◽  
pp. 1439-1450 ◽  
Author(s):  
DOROTA L. PORAZINSKA ◽  
ROBIN M. GIBLIN‐DAVIS ◽  
LINA FALLER ◽  
WILLIAM FARMERIE ◽  
NATSUMI KANZAKI ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Metagenomic Analysis ◽  
Nematode Diversity

scholarly journals Access COI barcode efficiently using high throughput Single-End 400 bp sequencing

2018 ◽  
Author(s):  
Chentao Yang ◽  
Shangjin Tan ◽  
Guangliang Meng ◽  
David G. Bourne ◽  
Paul A. O’Brien ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Full Length ◽  
List Type ◽  
Sequencing Data ◽  
Test Plate ◽  
Function Modules ◽  
Sequencing Platforms

SummaryOver the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, constraints in barcoding costs led to unbalanced efforts which prevented accurate taxonomic identification for biodiversity studies.We present a high throughput sequencing approach based on the HIFI-SE pipeline which takes advantage of Single-End 400 bp (SE400) sequencing data generated by BGISEQ-500 to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons. HIFI-SE was written in Python and included four function modules of filter, assign, assembly and taxonomy.We applied the HIFI-SE to a test plate which contained 96 samples (30 corals, 64 insects and 2 blank controls) and delivered a total of 86 fully assembled HIFI COI barcodes. By comparing to their corresponding Sanger sequences (72 sequences available), it showed that most of the samples (98.61%, 71/72) were correctly and accurately assembled, including 46 samples that had a similarity of 100% and 25 of ca. 99%.Our approach can produce standard full-length barcodes cost efficiently, allowing DNA barcoding for global biomes which will advance DNA-based species identification for various ecosystems and improve quarantine biosecurity efforts.

scholarly journals METAGENOMIC ANALYSIS TO IDENTIFY THE CAUSATIVE AGENTS OF ATYPICAL UROGENITAL TRACT INFECTIONS

2021 ◽  
Author(s):  
D. Kutilin
Keyword(s):  
Chronic Inflammation ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Urogenital Tract ◽  
Metagenomic Analysis ◽  
Healthy Individuals ◽  
Microbiological Methods ◽  
Wide Range ◽  
Tract Infections ◽  
Apparently Healthy

Importance. Research in recent decades has shown that classical microbiological methods can only detect a small, cultivable portion of microorganisms. One of the modern approaches to detect a wide range of bacteria and archaea is presented as a type of metagenomic analysis performed by high-throughput sequencing of ribosomal operon fragment libraries.Objective. Metagenomic analysis of samples from the urogenital tract of patients with chronic inflammation to identify pathogens not detected by other methods.Methods. Taxonomic analysis of the bacterial community was performed by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by using the Illumina HiSeq 3000 platform.Results. The study allowed to identify the taxonomic diversity of microorganisms in samples from the urogenital tract (from 197 to 794 different microorganisms belonging to the Bacteria were identified), as well as to establish differential differences concerning members of the genera Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phobormidium, Sphing Temperatibacter, Oxobacter, Georgenia, Actinobaculum, Varibaculum, Mycobacterium, Rhodococcus, Sediminihabitans, Actinobacter, Actinoplanes, Spirochaeta, Enhydrobacter, Thermacetogenium, Bdellovibrio, Oleibacter, Porphyrom, Klebsiella, Lachnoclostridium, Caulobacter, Xanthomonas, Novispirillum, Marvinbryantia, afipia, Shinella, Tepidimonas, Faecalibacterium, Paludibacterium, Aerococcus, Campylobacter, Pasteurella, Rumen, Psychrobacter, Haemophilus, Brevibacillus, Sporosarcina, Yaniella and Lactobacillus between samples from patients with chronic inflammation and apparently healthy individuals.Conclusion. Differential differences were found in the composition of the microbiome from the samples of patients with chronic inflammation and apparently healthy individuals, concerning members of 44 genera, including Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phormidium and Lactobacillus. The inflammatory processes observed in the patient urogenital tract can be associated with imbalanced microflora such as decreased level of typical members of the genera Staphylococcus, Streptococcus and Lactobacillus, but increased number of members from of the genera Klebsiella and Citrobacter.

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