SARS-CoV-2 variants of concern, Gamma (P.1) and Delta (B.1.617), sensitive detection and quantification in wastewater employing direct RT-qPCR

SARS-CoV-2 variants of concern present a worldwide threat. Demonstrating higher infection rate and durability to antibodies when compared to the original SARS-CoV-2 virus, the variants of concern are responsible for continuing global outbreaks. Prompt identification of the infecting SARS-CoV-2 variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive, time-consuming next generation sequencing. Rapid identification methodology for variants of concern is of great need and various variant-specific assays are being developed. Amongst the variants of concern that have recently appeared, the Gamma variant (P.1, Brazilian) and Delta variant (B.1.617, Indian) are the most prominent. Here we describe the development of a sensitive RT-qPCR assay for the quick direct detection of the Gamma and Delta variants as part of a methodical characterization and detection in municipal wastewater.

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Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Bloodstream Infection (BSI) Using the Karius Plasma Next Generation Sequencing (NGS) Test

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx163.1613 ◽

2017 ◽

Vol 4 (suppl_1) ◽

pp. S613-S613 ◽

Cited By ~ 4

Author(s):

Lisa Wanda ◽

Felicia Ruffin ◽

Jonathan Hill-Rorie ◽

Desiree Hollemon ◽

Hon Seng ◽

...

Keyword(s):

Next Generation Sequencing ◽

Bloodstream Infection ◽

Bacterial Cell ◽

Direct Detection ◽

Next Generation ◽

Cell Free Dna ◽

Free Dna ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Detection And Quantification

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Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

Frontiers in Zoology ◽

10.1186/1742-9994-10-45 ◽

2013 ◽

Vol 10 (1) ◽

pp. 45 ◽

Cited By ~ 138

Author(s):

Melissa E Carew ◽

Vincent J Pettigrove ◽

Leon Metzeling ◽

Ary A Hoffmann

Keyword(s):

Next Generation Sequencing ◽

Environmental Monitoring ◽

Rapid Identification ◽

Next Generation ◽

Bioindicator Species ◽

Generation Sequencing

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Teaching NeuroImage: Rapid Identification of Infectious Optic Neuritis by Next-Generation Sequencing

Neurology ◽

10.1212/wnl.0000000000013213 ◽

2021 ◽

pp. 10.1212/WNL.0000000000013213

Author(s):

Ying Huang ◽

Yulu Liu ◽

Yongguang Liu ◽

Qiang Li ◽

Xuejun Fu ◽

...

Keyword(s):

Next Generation Sequencing ◽

Optic Neuritis ◽

Rapid Identification ◽

Next Generation ◽

Generation Sequencing

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Laboratory diagnosis of bacterial meningitis by direct detection, serotyping and Next Generation Sequencing: How 10 years of testing in New York State has evolved to improve laboratory diagnosis and public health

Molecular and Cellular Probes ◽

10.1016/j.mcp.2021.101786 ◽

2021 ◽

pp. 101786

Author(s):

James R. Long ◽

Kara Mitchell ◽

Justine Edwards ◽

Danielle Wroblewski ◽

Elizabeth Luke ◽

...

Keyword(s):

Public Health ◽

New York ◽

Next Generation Sequencing ◽

Bacterial Meningitis ◽

Direct Detection ◽

New York State ◽

Laboratory Diagnosis ◽

Next Generation ◽

York State ◽

Generation Sequencing

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eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

Genetics in Medicine ◽

10.1038/s41436-018-0350-8 ◽

2018 ◽

Vol 21 (6) ◽

pp. 1407-1416 ◽

Cited By ~ 12

Author(s):

David Goudenège ◽

Celine Bris ◽

Virginie Hoffmann ◽

Valerie Desquiret-Dumas ◽

Claude Jardel ◽

...

Keyword(s):

Mitochondrial Dna ◽

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Sensitive Tool ◽

Dna Deletions ◽

Generation Sequencing ◽

Detection And Quantification

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Balamuthia mandrillaris-Related Primary Amoebic Encephalitis in China Diagnosed by Next Generation Sequencing and a Review of the Literature

Laboratory Medicine ◽

10.1093/labmed/lmz079 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yinan Yang ◽

Xiaobin Hu ◽

Li Min ◽

Xiangyu Dong ◽

Yuanlin Guan

Keyword(s):

Next Generation Sequencing ◽

Inflammatory Diseases ◽

Clinical Manifestations ◽

Infectious Agent ◽

Disease Diagnosis ◽

Rapid Identification ◽

Next Generation ◽

Balamuthia Mandrillaris ◽

Granulomatous Amoebic Encephalitis ◽

Generation Sequencing

Abstract Background Encephalitis is caused by infection, immune mediated diseases, or primary inflammatory diseases. Of all the causative infectious pathogens, 90% are viruses or bacteria. Granulomatous amoebic encephalitis (GAE), caused by Balamuthia mandrillaris, is a rare but life-threatening disease. Diagnosis and therapy are frequently delayed due to the lack of specific clinical manifestations. Method A healthy 2 year old Chinese male patient initially presented with a nearly 2 month history of irregular fever. We present this case of granulomatous amoebic encephalitis caused by B. mandrillaris. Next generation sequencing of the patient’s cerebrospinal fluid (CSF) was performed to identify an infectious agent. Result The results of next generation sequencing of the CSF showed that most of the mapped reads belonged to Balamuthia mandrillaris. Conclusion Next generation sequencing (NGS) is an unbiased and rapid diagnostic tool. The NGS method can be used for the rapid identification of causative pathogens. The NGS method should be widely applied in clinical practice and help clinicians provide direction for the diagnosis of diseases, especially for rare and difficult cases.

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Targeted Next Generation Sequencing improves detection and quantification of rare species from eDNA

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65075 ◽

2021 ◽

Vol 4 ◽

Author(s):

Kristen Westfall ◽

Thomas Therriault ◽

Cathryn Abbott

Keyword(s):

Next Generation Sequencing ◽

Spatial Variation ◽

Species Abundance ◽

Green Crab ◽

Great Promise ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Crab Abundance ◽

Generation Sequencing ◽

Detection And Quantification

Targeted species detection from eDNA is central to identifying and quantifying rare (i.e. invasive or endangered) species to inform conservation and resource management. Here we introduce a new targeted Next Generation Sequencing (tNGS) assay that shows improved detection relative to quantitative (q)PCR at low eDNA concentrations and increased precision to detect spatial variation in eDNA concentration related to species abundance. We compare the tNGS and qPCR methods using invasive European green crab (Carcinus maenas) in the northeast Pacific Ocean as a test case, and find that crab abundance measured by traditional trapping is significantly correlated with eDNA concentration across multiple sites for both methods. However, the tNGS assay outperformed qPCR in all tests: (1) increased precision of eDNA concentration estimation; (2) a 7-10% increase in detection probability at low abundance sites; and (3) greater power to detect spatial variation in eDNA concentration. The accuracy of predicting green crab abundance from eDNA concentration increased with the number of field replicates sampled and did not change appreciably over a tidal cycle. Green crab eDNA concentration behaving similarly to abundance measured from trapping demonstrates great promise for this tool to be implemented for early detection and routine monitoring surveys. The tNGS assay is easily accessible for surveying other species with existing qPCR assays and can thus be potentially important for detection and quantification of any species of high interest to management.

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