BackgroundThe new SARS-CoV-2 variant VUI (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit).MethodsTo control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to SARS-CoV-2 variant VUI (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile.ResultsOur results emphasized that all S-negative samples harbored the mutations Δ69/Δ70 and Δ106/Δ107/Δ108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene.ConclusionsThis technique may allow to identify patients carrying the VUI (202012/01) variant or a closely related variant, in case of shortage in sequencing.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a rapid spread emerging disease. Recently, a new variant of this virus called SARS-CoV-2 VOC 202012/01 (or B.1.1.7 lineage), described in the United Kingdom (UK), has become highly prevalent in several countries. Its rate of transmission has been estimated to be greatly higher. B.1.1.7 lineage harbors 23 mutations co-existed for the first time in the same variant. Herein, we are interested only by the deletion mutation ΔH69/ΔV70 in the spike protein.In the UK they were able to identify the increase of this new variant through the increase in the false negative result for the spike target of a three-target RT-PCR assay from Thermo Fisher Scientific (TaqPath kit). Later, the manufacturer announced that this false negative result is because of the deletion ΔH69/ΔV70 in the area targeted by the TaqPath Kit. Furthermore, The European CDC recommended that the use of this kit help to track the new variant.Genome sequencing is the gold method to confirm the new variant, but observational studies provide also stronger evidence if similar models are observed in multiple countries, especially when randomized studies are not possible. In Lebanon, the highest number of confirmed cases were reported in first week of 2021. In the present study, we show the emergence and the fast spreading of the new variant in Lebanon and a relationship between SARS-CoV-2 transmission intensity and the frequency of the new variant during the first twelve days of January.
Recently, a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) designated VOC 202012/01 (or B.1.1.7 lineage) has become highly prevalent in several countries, after first being described in the United Kingdom (UK). Its rate of transmission has been estimated to be increased compared to other lineages. In the present study, we show the emergence, dominance and the rapid spread of the B.1.1.7 lineage in Lebanon.
BackgroundThe new SARS-CoV-2 variant VOC (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit). Methods To control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to the VOC (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, detected by using the Applied Biosystems TaqPath RT-PCR COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile. Results Our results emphasized that all S-negative samples harbored the mutations Δ69/Δ70 and Δ106/Δ107/Δ108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene. Conclusions This technique may allow to identify patients carrying the VOC (202012/01) or a closely related variant, in case of shortage in sequencing.
Although seemingly benign, the presence of a patent foramen ovale (PFO) may play an important role in the pathophysiology of disease, specifically a paradoxical embolism leading to cryptogenic stroke. The European Society of Cardiology recently published guidelines detailing how PFOs are associated with paradoxical embolism and how they are diagnosed and managed. This review guides physicians in the diagnostic and referral process to a multidisciplinary team involved in PFO closure. It reviews the clinical trials comparing device closure with medical therapy and highlights the current NHS England commissioning process on PFO management. Finally, we give an overview of other conditions where PFO device closure may need to be considered.
The transport planning is essential to meeting passengers’ needs for fast, safe, and reliable transport. The research goals of this study are to determine the most suitable mode of transport between predetermined alternatives according the criteria related to the transport planning. The research method combines GIS analysis, SWOT analysis, BEM method, and PROMETHEE II method in an integrated approach for decision-making. The methodology is applied to the city of Peshawar city. It includes six steps. First, a passenger questionnaire is used to establish passenger preferences when making a trip in the city. Secondly, alternative modes of urban transportation are defined. In the case of Peshawar, the following alternatives are considered: a new BRT service, BRT with five additional stops, old bus service, wagon, carpooling, and Careem/Uber. Thirdly, there is GIS analysis to investigate the stops of the BRT alternative transportation. GIS and satellite analysis have been completed for each stop. Fourthly, criteria for the assessment of urban transport modes are determined based on SWOT analysis. A total of twenty four subcriteria are proposed. Fifthly, the best-worst method (BWM) which is based on linear programming method is applied to determine the weightings that should be given to the main criteria and subcriteria. Sixthly, alternative modes of transportation are ranked by applying preference ranking organization method for enrichment evaluations’ (PROMETHEE II) method. The results show that the main important criteria greater than 5% are small movement interval: S4 (6%), security: S7 (13%), reliability: S8 (8%), accessibility:O1 (15%), possibility of special services: O2 (5%), possibility of including insurance in the travel tariff: O3 (8%), possibility of the modernization of the infrastructure: O4 (7%), and environmental pollution: T3 (5%). The implications of this study propose a BRT service with five additional stops is the best urban transport plan for Peshawar. The originality of this research consists in integration of a strategic planning technique SWOT analysis, GIS analysis, and multicriteria analysis in complete methodology to evaluate traveler’s modes priority. The methodology used in this research can be applied to evaluate different transport alternatives for transport networks worldwide.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.