scholarly journals Novel Insights for Biosurveillance of Bat-Borne Viruses

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 47
Author(s):  
Adrian C. Paskey ◽  
Justin H. J. Ng ◽  
Gregory K. Rice ◽  
Wan Ni Chia ◽  
Casandra W. Philipson ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Temporal Patterns ◽  
Population Level ◽  
The Body ◽  
Population Persistence ◽  
Target Enrichment ◽  
Species Barrier ◽  
Future Directions ◽  
New Knowledge

Bats are rich reservoirs of viruses, including several high consequence zoonoses. In this study, high throughput sequencing was used to characterize the virome through a longitudinal study of a captive colony of lesser dawn bats, species Eonycteris spelaea, in Singapore. This study utilized viral RNA extracted from swabs of four body sites per bat per timepoint. Swabs of the exterior of the bat (head and body) were used to evaluate virus populations and demonstrate utility as a sample site for future surveillance to extrapolate population-level infection. Through unbiased shotgun and target-enrichment sequencing, we identified both the known and previously unknown viruses of zoonotic relevance and defined the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. We observed the population persistence of three zoonotic-related viral families that are known to be associated with spillover from bats to humans: Paramyxoviridae, Reoviridae, and Coronaviridae. To our knowledge, this is the first study that combines probe-based viral enrichment with high-throughput sequencing or that creates a viral profile from multiple swab sites on individual bats and their cohorts. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Noninvasive surveillance methods that target the body of bats not only detect viruses shed within the colony but can also represent viral populations dispersed throughout the entire colony. New knowledge of persistent viral families should inform future directions for the biosurveillance of viruses that have the potential to cross the species barrier from bats to humans or other amplifying hosts.

scholarly journals INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. eabe5054
Author(s):  
Qianxin Wu ◽  
Chenqu Suo ◽  
Tom Brown ◽  
Tengyao Wang ◽  
Sarah A. Teichmann ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Population Level ◽  
Reaction Products ◽  
Testing Strategy ◽  
Asymptomatic Patients ◽  
Testing Stage ◽  
Population Scale

We present INSIGHT [isothermal NASBA (nucleic acid sequence–based amplification) sequencing–based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing–based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.

Analysis of the effects of nanosilver on bacterial community in the intestinal fluid of silkworms using high-throughput sequencing

2019 ◽  
Vol 110 (3) ◽  
pp. 309-320
Author(s):  
Chen Lin ◽  
Zhou Wei ◽  
Zhou Yi ◽  
Tan Tingting ◽  
Du Huamao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Intestinal Bacteria ◽  
Illumina Miseq ◽  
The Body ◽  
Dependent Manner ◽  
Negative Effects ◽  
Silkworm Larvae ◽  
Intestinal Bacterial Community

AbstractNanosilver is an environment-friendly, harmless alternative of traditional disinfectants which can be potentially applied in the sericulture industry. However, the effects of nanosilver on the intestinal bacterial community of the silkworms (Bombyx mori L.) are unclear. In this study, Illumina MiSeq high-throughput sequencing technology was used to assess the intestinal bacterial community in both male and female silkworms while treated with different concentrations of nanosilver. We found that nanosilver significantly influenced the composition of silkworm intestinal bacterial community on the different taxonomic levels. Most conspicuously, the abundance of Firmicutes was increased by the treatment of 20 mg L−1 nanosilver but decreased by that of 100 mg L−1 nanosilver at the phylum level. The same trend was observed in Bacilli at the class level and in Enterococcus at the genus level. In some extreme cases, application of nanosilver eliminated the bacterium, e.g., Brevibacillus, but increased the population of several other bacteria in the host intestine, such as Blautia, Terrisporobacter, Faecalibacterium, and some bacteria could only be found in nanosilver treatment groups, e.g., Dialister. In addition, although nanosilver generally showed negative effects on the cocooning rate in a dose-dependent manner, we found that 20 mg L−1 nanosilver treatment significantly increased the body weight of silkworms and did not show negative effects on the survival rate. These results indicated that the intestinal bacteria community of silkworm larvae was significantly changed after nanosilver treatment which might consequently influence host growth and development.

Emulsion PCR-coupled target enrichment: An effective fishing method for high-throughput sequencing of poorly preserved ancient DNA

Gene ◽  
2013 ◽  
Vol 528 (2) ◽  
pp. 347-351 ◽  
Author(s):  
Makio Kihana ◽  
Fuzuki Mizuno ◽  
Rikai Sawafuji ◽  
Li Wang ◽  
Shintaroh Ueda
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Sequencing ◽  
Target Enrichment ◽  
Emulsion Pcr

scholarly journals Current impact and future directions of high throughput sequencing in plant virus diagnostics

2014 ◽  
Vol 188 ◽  
pp. 90-96 ◽  
Author(s):  
Sebastien Massart ◽  
Antonio Olmos ◽  
Haissam Jijakli ◽  
Thierry Candresse
Keyword(s):  
High Throughput ◽  
Plant Virus ◽  
High Throughput Sequencing ◽  
Future Directions ◽  
Virus Diagnostics ◽  
Current Impact

scholarly journals Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Lasse Vinner ◽  
Tobias Mourier ◽  
Jens Friis-Nielsen ◽  
Robert Gniadecki ◽  
Karen Dybkaer ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Enrichment ◽  
Human Cancers

scholarly journals How Do We Define the Genomic Landscape?

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. SCI-13-SCI-13
Author(s):  
Sandeep S. Dave
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Conflicts Of Interest ◽  
Genomic Analysis ◽  
Future Directions ◽  
Tissue Samples ◽  
Genomic Landscape ◽  
Fresh Frozen ◽  
Definition Of ◽  
Formalin Fixed

High throughput sequencing is a revolutionary technology for the definition of the genomic features of tumors. This talk will provide a review of the relevant methodologies for non-experts in the field. The presentation will include a discussion of how high throughput sequencing is performed, its relative strengths and weaknesses, and how it is applicable to formalin-fixed and fresh/frozen tissue samples. The talk will also describe future directions in the genomic analysis of tumors. Disclosures No relevant conflicts of interest to declare.

scholarly journals Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

2019 ◽  
Vol 63 (4) ◽  
pp. 471-479
Author(s):  
Anna Orłowska ◽  
Ewelina Iwan ◽  
Marcin Smreczak ◽  
Jerzy Rola
Keyword(s):  
High Throughput ◽  
Deep Sequencing ◽  
High Throughput Sequencing ◽  
De Novo ◽  
High Reliability ◽  
Rna Extraction ◽  
Genetic Material ◽  
Target Enrichment ◽  
Red Foxes ◽  
Field Samples

AbstractIntroductionHigh-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).Material and MethodsThe material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.ResultsTesting RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.ConclusionDirect metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.

scholarly journals The temporal RNA virome patterns of a lesser dawn bat (Eonycteris spelaea) colony revealed by deep sequencing

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Adrian C Paskey ◽  
Justin H J Ng ◽  
Gregory K Rice ◽  
Wan Ni Chia ◽  
Casandra W Philipson ◽  
...  
Keyword(s):  
Department Of Defense ◽  
Disease Surveillance ◽  
High Throughput Sequencing ◽  
Temporal Patterns ◽  
Asia Pacific ◽  
Asia Pacific Region ◽  
Species Barrier ◽  
Infectious Disease Surveillance ◽  
And Control ◽  
Regional Public Health

Abstract The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat–human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.

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