COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
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ABSTRACT:
PROVIDER: PRJEB42601 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5779560.fastq.gz | Fastqsanger.gz | |||
| ERR5779570.fastq.gz | Fastqsanger.gz | |||
| ERR5779580.fastq.gz | Fastqsanger.gz | |||
| ERR5779590.fastq.gz | Fastqsanger.gz | |||
| ERR5779590_1.fastq.gz | Fastqsanger.gz |
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Project description:While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
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| S-EPMC8703000 | biostudies-literature
Project description:Objectives: The provision of high-quality personal protective equipment (PPE) has been a critical challenge during the COVID-19 pandemic. We evaluated an alternative strategy, mass deployment of a powered air-purifying respirator (PeRSo), in a large university hospital. Methods: We performed prospective user feedback via questionnaires sent to healthcare workers (HCWs) issued PeRSos, economic analysis, and evaluated the real-world impact. Results: Where paired responses were available, PeRSo was preferred over droplet precautions for comfort, patient response, overall experience, and subjective feeling of safety. For all responses, more participants reported the overall experience being rated "Very good" more frequently for PeRSo. The primary limitation identified was impairment of hearing. Economic simulation exercises revealed that the adoption of PeRSo within ICU is associated with net cost savings in the majority of scenarios and savings increased progressively with greater ITU occupancy. In evaluation during the second UK wave, over 3,600 respirators were deployed, all requested by staff, which were associated with a low staff absence relative to most comparator hospitals. Conclusions: Health services should consider a widespread implementation of powered reusable respirators as a safe and sustainable solution for the protection of HCWs as SARS-CoV-2 becomes an endemic viral illness.
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Project description:BackgroundThe global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries.ResultsHere we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach.ConclusionsThe tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.
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Project description:DNA microarrays are two-dimensional arrangements of specific probes deposited on a substrate that have been widely used in gene expression analysis by measuring mRNA accumulation. The use of this type of microarrays involves the synthesis of cDNA, which has to be double stranded (ds) if the microarray probes are of the positive strand. We have used a custom-synthesized non-commercial NimbleGen microarray from melon to evaluate an alternative method of ds cDNA synthesis, which differs substantially in its economical cost relative to a widely recommended method. The results suggested that both methods produce cDNA representative of the melon transcriptome to a similar extent, indicating that the alternative technique provides a cheaper method of ds cDNA synthesis for microarray gene expression assays. Recently, we have analyzed the transcriptome of melon in response to WMV infection. Cotyledons of two genotypes of melon were virus inoculated and transcriptomic responses to the infection were analyzed by comparing infected and mock inoculated samples at 1, 3, and 7 days post-inoculation (dpi). Three biological replicates were performed for each sample. Double stranded cDNA was obtained with the Double stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA), based on the nick translation approach (Mol. Cell. Biol (1982) 2:161-170; Gene (1983) 25:263-269). Raw and processed microarray data are freely available from GEO database under the accession number GSE30111. By using this set of microarray hybridizations as a reference, RNA corresponding to infected cotyledons replicate 3 at 1 dpi (A1) and replicate 1 at 3 dpi (A2) (GEO accession numbers GSM745566 and GSM745567) were used to perform cDNA synthesis by the alternative method (samples B1 and B2, respectively), based on the SMART approach (BioTechniques (2001) 30:892-897), and microarray data were compared.
2012-03-07 | E-GEOD-30693 | biostudies-arrayexpress
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2012-03-07 | GSE30693 | GEO