scholarly journals COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

2021 ◽  
Author(s):  
Michele Simonetti ◽  
Ning Zhang ◽  
Luuk Harbers ◽  
Maria Grazia Milia ◽  
Thi Thu Huong Nguyen ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Protein A ◽  
Cost Effective ◽  
Mass Scale ◽  
Influenza Viruses ◽  
Spike Protein ◽  
Genome Coverage ◽  
Effective Manner ◽  
Geographical Regions ◽  
Different Populations

Abstract Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the spread and evolution of the virus across different populations, geographical regions and species. Here, we present a streamlined workflow—COVseq—based on the CUTseq method that we previously described, 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 validated COVseq on RNA extracted from the supernatant of a SARS-CoV-2 culture as well as from 85 left-over samples from nasopharyngeal swabs, demonstrating the ability of COVseq to achieve almost complete genome coverage, including the S region encoding the spike protein. A cost analysis showed that COVseq could be used to sequence thousands of samples per week at less than 20 USD per sample. COVseq is a versatile and scalable method that can be readily applied for genomic surveillance of the ongoing pandemic and easily adapted to other pathogens such as influenza viruses.

scholarly journals COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

2021 ◽  
Author(s):  
Michele Simonetti ◽  
Ning Zhang ◽  
Luuk Harbers ◽  
Maria Grazia Milia ◽  
Thi Nguyen ◽  
...  
Keyword(s):  
Protein A ◽  
Cost Effective ◽  
Mass Scale ◽  
Influenza Viruses ◽  
Spike Protein ◽  
Library Preparation ◽  
Genome Coverage ◽  
Effective Manner ◽  
Geographical Regions ◽  
Different Populations

Abstract Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the spread and evolution of the virus across different populations, geographical regions and species. Here, we present a streamlined workflow—COVseq—based on the CUTseq method that we previously described, 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 validated COVseq on RNA extracted from the supernatant of a SARS-CoV-2 culture as well as from 85 RNA samples from nasopharyngeal swabs, demonstrating the ability of COVseq to achieve near complete genome coverage, including the S region encoding the spike protein. A cost analysis showed that COVseq could be used to sequence thousands of samples per week at less than 10 USD per sample, including library preparation and sequencing costs. COVseq is a versatile and scalable method that can be readily applied for genomic surveillance of the ongoing pandemic and easily adapted to other pathogens such as influenza viruses.

scholarly journals COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

2021 ◽  
Author(s):  
Michele Simonetti ◽  
Ning Zhang ◽  
Luuk Harbers ◽  
Maria Grazia Milia ◽  
Silvia Brossa ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Cost Effective ◽  
Mass Scale ◽  
Influenza Viruses ◽  
Library Preparation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Effective Manner ◽  
Vaccination Campaigns ◽  
Standard Library

Abstract 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 benchmarked 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 demonstrated the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis showed 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.

scholarly journals COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

2021 ◽  
Author(s):  
Michele Simonetti ◽  
Ning Zhang ◽  
Luuk Harbers ◽  
Maria Grazia Milia ◽  
Silvia Brossa ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Cost Effective ◽  
Mass Scale ◽  
Influenza Viruses ◽  
Library Preparation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Effective Manner ◽  
Vaccination Campaigns ◽  
Standard Library

Abstract 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 benchmarked 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 demonstrated the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis showed 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.

scholarly journals COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michele Simonetti ◽  
Ning Zhang ◽  
Luuk Harbers ◽  
Maria Grazia Milia ◽  
Silvia Brossa ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Cost Effective ◽  
Mass Scale ◽  
Influenza Viruses ◽  
Library Preparation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Effective Manner ◽  
Vaccination Campaigns ◽  
Standard Library

AbstractWhile 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.

scholarly journals Development of a Colloidal Gold-Based Immunochromatographic Strip for Rapid Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein

2021 ◽  
Vol 12 ◽  
Author(s):  
Ge Li ◽  
Aiping Wang ◽  
Yumei Chen ◽  
Yaning Sun ◽  
Yongkun Du ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Colloidal Gold ◽  
Global Economy ◽  
Chinese Hamster ◽  
Influenza Viruses ◽  
Spike Protein ◽  
Disease Spread ◽  
Ovary Cell ◽  
Immunochromatographic Strip ◽  
Specific Reactions

The outbreak and worldwide pandemic of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have a significant impact on global economy and human health. In order to reduce the disease spread, 16 monoclonal antibodies (McAbs) again SARS-CoV-2 were generated by immunized mice with the spike protein receptor binding domain (RBD), which was expressed in Chinese hamster ovary cell (CHO). A colloidal gold-based immunochromatographic strip was developed with two McAbs to detect SARS-CoV-2 spike protein, which can play a potential role in monitoring vaccine quality. The strip is highly specific, detecting only SARS-CoV-2 spike protein, and does not show any non-specific reactions with syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and other coronavirus and influenza viruses. The strip detected subunit vaccine in our laboratory with a detection limit of spike protein of 62.5 ng/mL. This strip provides an effective method in monitoring vaccine quality by detecting the antigen content of spike protein.

Strategic planning in grassland farming: Principles andapplications

1997 ◽  
pp. 191-197
Author(s):  
W.J. Parker ◽  
N.M. Shadbolt ◽  
D.I. Gray
Keyword(s):  
Strategic Planning ◽  
Performance Indicators ◽  
Cost Effective ◽  
Key Performance Indicators ◽  
Strategic Plans ◽  
Effective Manner ◽  
Farm Business ◽  
Pastoral Farming ◽  
Financial Environment

Three levels of planning can be distinguished in grassland farming: strategic, tactical and operational. The purpose of strategic planning is to achieve a sustainable long-term fit of the farm business with its physical, social and financial environment. In pastoral farming, this essentially means developing plans that maximise and best match pasture growth with animal demand, while generating sufficient income to maintain or enhance farm resources and improvements, and attain personal and financial goals. Strategic plans relate to the whole farm business and are focused on the means to achieve future needs. They should be routinely (at least annually) reviewed and monitored for effectiveness through key performance indicators (e.g., Economic Farm Surplus) that enable progress toward goals to be measured in a timely and cost-effective manner. Failure to link strategy with control is likely to result in unfulfilled plans. Keywords: management, performance

scholarly journals Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry

Nanomaterials ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 186
Author(s):  
Jia-Huan Qu ◽  
Karen Leirs ◽  
Remei Escudero ◽  
Žiga Strmšek ◽  
Roman Jerala ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Fluorescent Protein ◽  
Cost Effective ◽  
Nitrilotriacetic Acid ◽  
Antibody Fragments ◽  
Rapid Screening ◽  
Red Fluorescent Protein ◽  
Effective Manner ◽  
Surface Regeneration ◽  
Sensitivity Specificity

To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.

scholarly journals Mass production of metal-doped graphene from the agriculture waste of Quercus ilex leaves for supercapacitors: inclusive DFT study

RSC Advances ◽  
2021 ◽  
Vol 11 (18) ◽  
pp. 10891-10901
Author(s):  
Gaurav Tatrari ◽  
Chetna Tewari ◽  
Manoj Karakoti ◽  
Mayank Pathak ◽  
Ritu Jangra ◽  
...  
Keyword(s):  
Effective Mass ◽  
Mass Production ◽  
Quercus Ilex ◽  
Cost Effective ◽  
Mass Scale ◽  
Graphene Sheets ◽  
Agriculture Waste ◽  
Doped Graphene ◽  
Metal Doped ◽  
Supercapacitor Applications

This work reports a facile, eco-friendly, and cost-effective mass-scale synthesis of metal-doped graphene sheets (MDGs) using agriculture waste of Quercus ilex leaves for supercapacitor applications.

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