scholarly journals HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene

2022 ◽  
Vol 8 ◽  
Author(s):  
Ephraim Fass ◽  
Gal Zizelski Valenci ◽  
Mor Rubinstein ◽  
Paul J. Freidlin ◽  
Shira Rosencwaig ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Cost Effective ◽  
Developed Countries ◽  
Spike Protein ◽  
Medical Community ◽  
Effective Vaccine ◽  
Gene Variants ◽  
Spike Gene ◽  
Field Samples

The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.

scholarly journals HiSpike: A high-throughput cost effective sequencing method for the SARS-CoV-2 spike gene

2021 ◽  
Author(s):  
Ephraim Fass ◽  
Gal Zizelski Valenci ◽  
Mor Rubinstein ◽  
Paul J Freidlin ◽  
Shira Rosencwaig ◽  
...  
Keyword(s):  
Real Time ◽  
South African ◽  
High Throughput ◽  
Spike Protein ◽  
Medical Community ◽  
Effective Vaccine ◽  
Gene Variants ◽  
Spike Gene ◽  
Field Samples ◽  
The Uk

ABSTRACTThe changing nature of the corona virus of the SARS-CoV-2 pandemic poses unprecedented challenges to the world’s health systems. New and virulent emerging spike gene variants, such as the UK 20I/501Y.V1 and South African 20H/501Y.V2, could jeopardize global efforts to produce immunity and reduce mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and therefore, it is most susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is also the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Therefore, tight monitoring of the spike protein gene variants is key to mitigating COVID-19 spread and vaccine escape mutants. Currently, the ARTIC method for SARS-CoV-2 whole genome sequencing is applied worldwide. However, this method commonly requires more than 96 hours (4-5 days) from start to finish and at present high sample sequence demands, sequencing resources are quickly exhausted. In this work, we present HiSpike, a method for high-throughput targeted next generation sequencing (NGS) of the spike gene. This simple three-step method can be completed in less than 30 hours and can sequence 10-fold more samples compared to the conventional ARTIC method and at a fraction of the cost. HiSpike was proven valid, and has identified, at high quality, multiple spike variants from real-time field samples, such as the UK and the South African variants. This method will certainly be effective in discovering future spike mutations. Therefore, running HiSpike for full sequencing of the spike gene of all positive SARS-CoV-2 samples could be considered for near real-time detection of known and emerging spike mutations as they evolve. HiSpike provides affordable sequencing options to help laboratories conserve resources, hence it provides a tool for widespread monitoring, that can support critical knowledge-based decisions.

scholarly journals HiSpike: A high-throughput cost effective sequencing method for the SARS-CoV-2 spike gene

2021 ◽  
Author(s):  
Ephraim Fass ◽  
Gal Valenci Zizelski ◽  
Mor Rubinstein ◽  
Paul Freidlin ◽  
Shira Rosencwaig ◽  
...  
Keyword(s):  
Real Time ◽  
South African ◽  
High Throughput ◽  
Spike Protein ◽  
Medical Community ◽  
Effective Vaccine ◽  
Gene Variants ◽  
Spike Gene ◽  
Field Samples ◽  
The Uk

Abstract The changing nature of the corona virus of the SARS-CoV-2 pandemic poses unprecedented challenges to the world’s health systems. New and virulent emerging spike gene variants, such as the UK 20I/501Y.V1 and South African 20H/501Y.V2, could jeopardize global efforts to produce immunity and reduce mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and therefore, it is most susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is also the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Therefore, tight monitoring of the spike protein gene variants is key to mitigating COVID-19 spread and vaccine escape mutants. Currently, the ARTIC method for SARS-CoV-2 whole genome sequencing is applied worldwide. However, this method commonly requires more than 96 hours (4–5 days) from start to finish and at present high sample sequence demands, sequencing resources are quickly exhausted. In this work, we present HiSpike, a method for high-throughput targeted next generation sequencing (NGS) of the spike gene. This simple three-step method can be completed in less than 30 hours and can sequence 10-fold more samples compared to the conventional ARTIC method and at a fraction of the cost. HiSpike was proven valid, and has identified, at high quality, multiple spike variants from real-time field samples, such as the UK and the South African variants. This method will certainly be effective in discovering future spike mutations. Therefore, running HiSpike for full sequencing of the spike gene of all positive SARS-CoV-2 samples could be considered for near real-time detection of known and emerging spike mutations as they evolve. HiSpike provides affordable sequencing options to help laboratories conserve resources, hence it provides a tool for widespread monitoring, that can support critical knowledge-based decisions.

scholarly journals High-throughput Mutational Surveillance of the SARS-CoV-2 Spike Gene

2021 ◽  
Author(s):  
Ezgi Özkan ◽  
Marcus Martin Strobl ◽  
Maria Novatchkova ◽  
Ramesh Yelagandula ◽  
Tanino Giuseppe Albanese ◽  
...  
Keyword(s):  
Immune Escape ◽  
Viral Evolution ◽  
Cost Effective ◽  
Spike Protein ◽  
Successful Implementation ◽  
Close Monitoring ◽  
Gene Encoding ◽  
Spike Gene ◽  
S Gene ◽  
Specific Pcr

SARS-CoV-2 has evolved rapidly towards higher infectivity and partial immune escape over the course of the pandemic. This evolution is driven by the enormous virus population, that has infected close to 200 million people by now. Therefore, cost effective and scalable methods are needed to monitor viral evolution globally. Mutation-specific PCR approaches have become inadequate to distinguish the variety of circulating SARS-CoV-2 variants and are unable to detect novel ones. Conversely, whole genome sequencing protocols remain too labor- and cost-intensive to monitor SARS-CoV-2 at the required density. By adapting SARSeq we present a simple, fast, and scalable S-gene tiling pipeline for focused sequencing of the S-gene encoding for the spike protein. This method reports on all sequence positions with known importance for infectivity and immunity, yet scales to >20K samples per run. S-gene tiling is used for nationwide surveillance of SARS-CoV-2 at a density of 10% to 50% of all cases of infection in Austria. SARSeq S-tiling uncovered several infection clusters with variants of concern such as the biggest known cluster of Beta/B.1.351 outside Africa and successfully informed public health measures in a timely manner, allowing their successful implementation. Our close monitoring of mutations further highlighted evolutionary constraints and freedom of the spike protein ectodomain and sheds light on foreseeable evolutionary trajectories.

scholarly journals Design of a High-Throughput Real-Time PCR System for Detection of Bovine Respiratory and Enteric Pathogens

2021 ◽  
Vol 8 ◽  
Author(s):  
Nicole B. Goecke ◽  
Bodil H. Nielsen ◽  
Mette B. Petersen ◽  
Lars E. Larsen
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Real Time Pcr ◽  
Negative Impact ◽  
Animal Health ◽  
Simultaneous Detection ◽  
Individual Sample ◽  
Vast Number ◽  
Positive Individual ◽  
Field Samples

Bovine respiratory and enteric diseases have a profound negative impact on animal, health, welfare, and productivity. A vast number of viruses and bacteria are associated with the diseases. Pathogen detection using real-time PCR (rtPCR) assays performed on traditional rtPCR platforms are costly and time consuming and by that limit the use of diagnostics in bovine medicine. To diminish these limitations, we have developed a high-throughput rtPCR system (BioMark HD; Fluidigm) for simultaneous detection of the 11 most important respiratory and enteric viral and bacterial pathogens. The sensitivity and specificity of the rtPCR assays on the high-throughput platform was comparable with that of the traditional rtPCR platform. Pools consisting of positive and negative individual field samples were tested in the high-throughput rtPCR system in order to investigate the effect of an individual sample in a pool. The pool tests showed that irrespective of the size of the pool, a high-range positive individual sample had a high influence on the cycle quantification value of the pool compared with the influence of a low-range positive individual sample. To validate the test on field samples, 2,393 nasal swab and 2,379 fecal samples were tested on the high-throughput rtPCR system as pools in order to determine the occurrence of the 11 pathogens in 100 Danish herds (83 dairy and 17 veal herds). In the dairy calves, Pasteurella multocida (38.4%), rotavirus A (27.4%), Mycoplasma spp. (26.2%), and Trueperella pyogenes (25.5%) were the most prevalent pathogens, while P. multocida (71.4%), Mycoplasma spp. (58.9%), Mannheimia haemolytica (53.6%), and Mycoplasma bovis (42.9%) were the most often detected pathogens in the veal calves. The established high-throughput system provides new possibilities for analysis of bovine samples, since the system enables testing of multiple samples for the presence of different pathogens in the same analysis test even with reduced costs and turnover time.

scholarly journals Rapid Detection of Enteroviruses in Small Volumes of Natural Waters by Real-Time Quantitative Reverse Transcriptase PCR

2005 ◽  
Vol 71 (8) ◽  
pp. 4523-4530 ◽  
Author(s):  
Jed A. Fuhrman ◽  
Xiaolin Liang ◽  
Rachel T. Noble
Keyword(s):  
Los Angeles ◽  
Reverse Transcriptase ◽  
Real Time ◽  
Natural Waters ◽  
Cost Effective ◽  
Environmental Water ◽  
Viral Contamination ◽  
Reverse Transcriptase Pcr ◽  
Qrt Pcr ◽  
Field Samples

ABSTRACT Despite viral contamination of recreational waters, only bacterial, not viral, indicators are monitored routinely, due to a lack of rapid and cost-effective assays. We used negatively charged filters to capture enteroviruses from seawater and freshwater. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (qRT-PCR). Poliovirus (6.6 to 330,000 virus particles/ml) was added to samples from watersheds in Los Angeles, California, and analysis showed that with 50-ml samples, a cellulose acetate/nitrate (HA) filter yielded final recovery of 51% (r 2 = 0.99) in fresh water and 23% (r 2 = 0.90) in seawater. However, for additions of low levels of virus (more likely to represent field samples; <104 enterovirus particles/ml), the recovery was lower and more variable, with HA being best in freshwater (17%, r 2 = 0.97) and the type GF/F glass filter having higher average recovery in seawater (GF/F, 17%; r 2 = 0.93; HA 12%, r 2 = 0.87). The optimized method was used with 1-liter field samples from two very different freshwater “creeks” that drain into Santa Monica Bay, California: Topanga Creek (TC), a relatively pristine mountain creek, and Ballona Creek (BC), a concrete-lined urban storm drain. One TC site out of 10 and 2 BC sites out of 7 tested significantly positive for enteroviruses, with higher enterovirus concentrations in BC than in TC (ca. 10 to 25 versus 1 equivalent enterovirus particle/ml). The presented filtration-qRT-PCR approach is fast (<8 h from sampling to results), sensitive, and cost efficient and is promising for monitoring viral contamination in environmental water samples.

Isolation and identification of Marek’s disease virus (MDV) from feather follicle epithelium and internal organs of diseased chickens in Dakahlia Governorate, Egypt

2019 ◽  
Vol 20 (2) ◽  
pp. 6-11
Author(s):  
Aly El-Kenawy ◽  
Mohamed El-Tholoth ◽  
Emad A
Keyword(s):  
Real Time ◽  
Disease Virus ◽  
Real Time Pcr ◽  
Marek's Disease Virus ◽  
Marek's Disease ◽  
Marek’S Disease Virus ◽  
Marek’S Disease ◽  
Field Samples ◽  
Feather Follicle ◽  
Positive Results

In the present study, a total of 16 samples including feather follicle epithelium, ovary, spleen and kidney (4 samples for each organ) were collected from diseased chicken flocks suspected to be infected with Marek’s disease virus (MDV) at Dakahlia Governorate, Egypt during the period from October 2016 to October 2017. Each sample was pooled randomly from three to five birds (90 to 360 days old). The isolation of the suspected virus from the collected samples was carried out via chorioallantoic membranes (CAMs) of 12 days old embryonated chicken eggs (ECEs). Three egg passages were carried out for each sample. Hyperimmune serum was prepared against standard MDV. MDV in both field and egg passaged samples (after 3rd passage) was identified by agar gel precipitation test (AGPT) and indirect fluorescence antibody test (IFAT). Molecular identification of virus was carried out by conventional polymerase chain reaction (PCR) and real- time PCR in four selected samples. The results revealed that 14 samples (87.5%) including 4 (100%) samples from feather follicle epithelium, ovary and kidney and 2 (50%) samples from spleen, showed positive results in virus isolation after 3rd passage. The positive results percentage by AGPT for field samples were 50% (8 out of 16 samples), while after the 3rd passage in ECEs were 37.5% (6 out of 16 samples) and the positive results percentage by IFAT for field samples were 62.5% (10 out of 16 samples), while after the 3rd passage in ECEs were 81.25 % (13 out of 16 samples). Viral nucleic acid was detected in all selected samples by conventional and real- time PCR. The results indicate that feather follicle epithelium is the best organ for MDV detection. IFAT is superior over AGPT in virus detection. Conventional and real - time PCR could be efficiently used for molecular detection of the virus.

scholarly journals Modeling Fused Filament Fabrication using Artificial Neural Networks

2021 ◽  
Author(s):  
Paul Oehlmann ◽  
Paul Osswald ◽  
Juan Camilo Blanco ◽  
Martin Friedrich ◽  
Dominik Rietzel ◽  
...  
Keyword(s):  
Real Time ◽  
Large Scale ◽  
Cost Effective ◽  
Print Quality ◽  
Ann Model ◽  
Production Environment ◽  
Fused Filament Fabrication ◽  
Artificial Neural ◽  
Using Data ◽  
Artificial Neural Network Ann

AbstractWith industries pushing towards digitalized production, adaption to expectations and increasing requirements for modern applications, has brought additive manufacturing (AM) to the forefront of Industry 4.0. In fact, AM is a main accelerator for digital production with its possibilities in structural design, such as topology optimization, production flexibility, customization, product development, to name a few. Fused Filament Fabrication (FFF) is a widespread and practical tool for rapid prototyping that also demonstrates the importance of AM technologies through its accessibility to the general public by creating cost effective desktop solutions. An increasing integration of systems in an intelligent production environment also enables the generation of large-scale data to be used for process monitoring and process control. Deep learning as a form of artificial intelligence (AI) and more specifically, a method of machine learning (ML) is ideal for handling big data. This study uses a trained artificial neural network (ANN) model as a digital shadow to predict the force within the nozzle of an FFF printer using filament speed and nozzle temperatures as input data. After the ANN model was tested using data from a theoretical model it was implemented to predict the behavior using real-time printer data. For this purpose, an FFF printer was equipped with sensors that collect real time printer data during the printing process. The ANN model reflected the kinematics of melting and flow predicted by models currently available for various speeds of printing. The model allows for a deeper understanding of the influencing process parameters which ultimately results in the determination of the optimum combination of process speed and print quality.

scholarly journals Anti-meningococcal B vaccination in Italian adolescents: a cost-effective health opportunity

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
D Panatto ◽  
P Landa ◽  
D Amicizia ◽  
P L Lai ◽  
E Lecini ◽  
...  
Keyword(s):  
Large Scale ◽  
Public Health Problem ◽  
Vaccination Strategy ◽  
Cost Effective ◽  
Dose Schedule ◽  
Developed Countries ◽  
Invasive Disease ◽  
International Setting ◽  
The Impact

Abstract Background Invasive disease due to Neisseria meningitidis (Nm) is a serious public health problem even in developed countries, owing to its high lethality rate (8-15%) and the invalidating sequelae suffered by many (up to 60%) survivors. As the microorganism is transmitted via the airborne route, the only available weapon in the fight against Nm invasive disease is vaccination. Our aim was to carry out an HTA to evaluate the costs and benefits of anti-meningococcal B (MenB) vaccination with Trumenba® in adolescents in Italy, while also considering the impact of this new vaccination strategy on organizational and ethics aspects. Methods A lifetime Markov model was developed. MenB vaccination with the two-dose schedule of Trumenba® in adolescents was compared with 'non-vaccination'. Two perspectives were considered: the National Health Service (NHS) and society. Three disease phases were defined: acute, post-acute and long-term. Epidemiological, economic and health utilities data were taken from Italian and international literature. The analysis was conducted by means of Microsoft Excel 2010®. Results Our study indicated that vaccinating adolescents (11th year of life) with Trumenba® was cost-effective with an ICER = € 7,912/QALY from the NHS perspective and € 7,758/QALY from the perspective of society. Vaccinating adolescents reduces the number of cases of disease due to meningococcus B in one of the periods of highest incidence of the disease, resulting in significant economic and health savings. Conclusions This is the first study to evaluate the overall impact of free MenB vaccination in adolescents both in Italy and in the international setting. Although cases of invasive disease due to meningococcus B are few, if the overall impact of the disease is adequately considered, it becomes clear that including anti-meningococcal B vaccination into the immunization program for adolescents is strongly recommended from the health and economic standpoints. Key messages Free, large-scale MenB vaccination is key to strengthening the global fight against invasive meningococcal disease. Anti-meningococcal B vaccination in adolescents is a cost-effective health opportunity.

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