Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection

ABSTRACT: Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection

PROVIDER: PRJNA735451 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR14742501.fastq.gz	Fastqsanger.gz
	SRR14742502.fastq.gz	Fastqsanger.gz
	SRR14742503.fastq.gz	Fastqsanger.gz
	SRR14742504.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection

Project description:The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing worldwide has led to major issues in scaling the efforts of diagnostic labs and even in securing basic supplies for collection and processing of samples. This has in turn led to worldwide efforts by the scientific community to establish improved protocols that are cheaper, more scalable, and not as resource intensive. One such effort resulted in an assay called “Swab-Seq”, which was so named because it was originally developed to work with dry nasal swab samples, but is actually flexible in terms of the sample type it can accommodate for testing. The assay adapts the existing gold standard (RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction, “qRT-PCR”) to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques it is possible to achieve high scalability at low cost per sample, and a reasonable turnaround time for reporting results. We evaluated the effectiveness of this assay both on samples collected from asymptomatic individuals using the traditional NP swab and using alternative extraction-free sampling techniques, including saliva and a saline mouth gargle protocol, and found the assay to be highly sensitive (comparable to the standard qRT-PCR assay), flexible (adaptable to saliva and gargle samples stored at room temperature up to a week), and scalable (easily accommodating hundreds of samples at a time). Continued development in the future will lead to more effective testing regimes that reduce the burden of transmissible respiratory infections on the global community.

2022-02-23 | GSE176224 | GEO

Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection.

Project description:The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples. This has motivated efforts by the scientific community to establish improved protocols that are more scalable, less resource intensive, and less expensive. One such developmental effort has resulted in an assay called "Swab-Seq", so named because it was originally developed to work with dry nasal swab samples. The existing gold standard test consists of RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR). Swab-Seq adapts this method to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques, Swab-Seq achieves high scalability, low cost per sample, and a reasonable turnaround time. We evaluated the effectiveness of this assay in a community surveillance setting by testing samples collected from both symptomatic and asymptomatic individuals using the traditional NP swab. In addition, we evaluated extraction-free sampling techniques (both saliva and saline mouth gargle samples). We found the assay to be as clinically sensitive as the qRT-PCR assay, adaptable to multiple sample types, and able to easily accommodate hundreds of samples at a time. We thus provide independent validation of Swab-Seq and extend its utility regarding sample type and sample stability. Assays of this type greatly expand the possibility of routine, noninvasive, repeated testing of asymptomatic individuals suitable for current and potential future needs.

| S-EPMC8866503 | biostudies-literature

A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)

Project description:A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)

| PRJNA632978 | ENA

Single-cell RNA sequencing of human nasal swab from healthy donors

Project description:Understanding on pathogenesis of COVID-19 is rapidly growing, but primary target cells of SARS-CoV-2 infection is still not known. Here, we performed single cell RNA sequencing on human nasal swab from healthy donors to investigate the expression patterns of host cell entry factors of SARS-CoV-2.

2021-04-06 | GSE171488 | GEO

Single-cell RNA sequencing of human nasal swab from COVID-19 patient

Project description:Understanding on pathogenesis of COVID-19 is rapidly growing, but primary target cells of SARS-CoV-2 infection is still not known. Here, we performed single cell RNA sequencing on human nasal swab from COVID-19 patient to investigate the expression patterns of host cell entry factors of SARS-CoV-2.

2021-01-12 | GSE164547 | GEO

Metabolome and exposome profiling of the biospecimens from COVID-19 patients in India (Nasopharyngeal swab assay)

Project description:INTRODUCTION: COVID-19 has become a global impediment by bringing everything to a halt starting from January 2020. India underwent the lockdown starting from 22nd March 2020 with the sudden spike in the number of COVID-19 patients in major cities and states. This study focused on how metabolites play a crucial role in SARSCoV-2 prognosis.MATERIALS AND METHODS: Metabolome profiling of 106 plasma samples and 24 swab samples from symptomatic patients in the Indian population of the Mumbai region was done. COVID-19 positive samples were further segregated under the non-severe COVID-19 and severe COVID-19 patient cohort for both plasma and swab.RESULTS: After analyzing the raw files, total 7,949 and 12,871 metabolites in plasma and swab were found. 11 and 35 significantly altered metabolites were found in COVID-19 positive compared to COVID-19 negative plasma and swab samples, respectively. Also, 9 and 23 significantly altered metabolites were found in severe COVID-19 positive to non-severe COVID-19 positive plasma and swab samples, respectively. The majorly affected pathways in COVID-19 patients were found to be the amino acid metabolism pathway, sphingosine metabolism pathway, and bile salt metabolism pathway.CONCLUSION: This study facilitates identification of potential metabolite-based biomarker candidates for rapid diagnosis and prognosis for clinical applications. Nasopharyngeal swab assay is reported in the current study MTBLS2349.Blood plasma assay is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS2291' rel='noopener noreferrer' target='_blank'>MTBLS2291</a>.

2022-01-13 | MTBLS2349 | MetaboLights

Scalable pooled CRISPR screens with single cell chromatin accessibility profiling.

Project description:A scalable, cost-effective method that combines CRISPR perturbations with a single-cell indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). This method links genome-wide chromatin accessibility to genetic perturbations through simultaneous capture of ATAC-seq fragments and CRISPR guide RNAs from single cells using a 96-well plate combinatorial indexing approach.

2020-11-07 | GSE161002 | GEO

Transcription profiling of human primary ALL cells (B-lineage) sensitive to daunorubicin by the MTT in vitro sensitivity assay

Project description:primary ALL cells (B-lineage) sensitive to daunorubicin by the MTT in vitro sensitivity assay

2008-06-15 | E-GEOD-659 | biostudies-arrayexpress

Transcription profiling of human primary ALL cells (B-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay

Project description:primary ALL cells (B-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay

2008-06-15 | E-GEOD-657 | biostudies-arrayexpress

Transcription profiling of human primary ALL cells (B-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay

Project description:primary ALL cells (B-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay

2008-06-15 | E-GEOD-655 | biostudies-arrayexpress