scholarly journals Optimizing SARS-CoV-2 molecular diagnostic using N gene target: insights about reinfection

2020 ◽  
Author(s):  
Raphael Contelli Klein ◽  
Mary Hellen Fabres Klein ◽  
Larissa Gomes Barbosa ◽  
Lívia Vasconcelos Gonzaga Knnup ◽  
Larissa Paola Rodrigues Venâncio ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Molecular Test ◽  
Gene Target ◽  
Infected People ◽  
Remote Locations ◽  
The World ◽  
The Cost ◽  
Huge Challenge

AbstractIntroductionMolecular diagnosis of SARS-CoV-2 is a huge challenge to many countries around the world. The cost of tests to check infected people is inaccessible since specialized teams and equipment are not disposable in remote locations. Herein, we compared the fitness of two primers sets to the SARS-CoV-2 N gene in the molecular diagnosis of COVID-19.Materials and MethodsThe 1029 patient samples were tested to presense/abscence molecular test using in house US CDC protocol. We compared the fitness of two primers sets to two different regions of N gene targets.ResultsBoth targets, N1 and N2 displayed similar fitness during testing with no differences between Ct or measurable viral genome copies. In addition, we verified security ranges Cts related to positive diagnostic with Ct above 35 value failuring in 66,6% after retesting of samples.Main conclusionOur data suggest that it is secure to use just one primer set to the N gene to identify SARS-CoV-2 in samples and the labs should be careful to set positive samples in high Ct values using high cutoffs.

scholarly journals Clinical Performance of the Luminex NxTAG CoV Extended Panel for SARS-CoV-2 Detection in Nasopharyngeal Specimens from COVID-19 Patients in Hong Kong

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Jonathan Hon-Kwan Chen ◽  
Cyril Chik-Yan Yip ◽  
Jasper Fuk-Woo Chan ◽  
Rosana Wing-Shan Poon ◽  
Kelvin Kai-Wang To ◽  
...  
Keyword(s):  
Hong Kong ◽  
High Throughput ◽  
Clinical Performance ◽  
Diagnostic System ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Gene Target ◽  
E Gene

ABSTRACT In December 2019, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first reported in the Hubei province of China and later spread all over the world. There was an urgent need of a high-throughput molecular test for screening the COVID-19 patients in the community. The Luminex NxTAG CoV extended panel is a high-throughput FDA emergency use-authorized molecular diagnostic assay for SARS-CoV-2 detection. This system targets three genes (ORF1ab, N, and E genes) of SARS-CoV-2, the ORF1ab region of SARS-CoV, and the ORF5 region of MERS-CoV. In this study, we evaluated the diagnostic performance of this system with nasopharyngeal swab specimens of 214 suspected COVID-19 patients in Hong Kong. The results were compared with our routine COVID-19 reverse transcription-PCR (RT-PCR) protocol with a LightMix SarbecoV E-gene kit and an in-house RdRp/Hel RT-PCR assay. The NxTAG CoV extended panel demonstrated 97.8% sensitivity and 100% specificity to SARS-CoV-2 in nasopharyngeal specimens. On low-viral load specimens, the sensitivity of the NxTAG panel could still maintain at 85.71%. Strong agreement was observed between the NxTAG panel and the routine COVID-19 RT-PCR protocol (kappa value = 0.98). Overall, the E gene target of the NxTAG panel demonstrated the highest sensitivity among the three SARS-CoV-2 targets, while the N gene targets demonstrated the least. In conclusion, the NxTAG CoV extended panel is simple to use, and it has high diagnostic sensitivity and specificity to SARS-CoV-2 in nasopharyngeal specimens. We recommend this diagnostic system for high-throughput COVID-19 screening in the community.

Optimizing SARS-CoV-2 Molecular Diagnostic Using N Gene Target

2020 ◽  
Author(s):  
Raphael Contelli Klein ◽  
Mary Hellen Fabres-Klein ◽  
Larissa Gomes Barbosa ◽  
Lívia Vasconcelos Gonzaga Knnup ◽  
Larissa Paola Rodrigues Venâncio ◽  
...  
Keyword(s):  
Molecular Diagnostic ◽  
N Gene ◽  
Gene Target

scholarly journals Molecular Diagnosis of COVID-19: An Update and Review

2020 ◽  
Vol 56 (03) ◽  
pp. 126-137 ◽  
Author(s):  
Ketan Priyadarshi ◽  
Vijaya Lakshmi Nag ◽  
Sarika P. Kombade ◽  
Ravi Sekhar Gadepalli ◽  
Sanjeev Misra ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Correct Diagnosis ◽  
Public Health Problem ◽  
N Gene ◽  
Diagnostic Tools ◽  
Family Welfare ◽  
Global Public Health ◽  
Molecular Assays ◽  
Ssrna Virus ◽  
The World

AbstractSARS-CoV-2 belongs to genus Betacoronavirus subgenus Sarbecovirus of the family Coronaviridae, which originated as a global public health problem. The disease caused is termed as Coronavirus Disease (COVID-19). The virus spread in more than 213 countries and territories all over the world and disease was declared as a pandemic. SARS-CoV-2 is an enveloped positive-sense single- stranded ribonucleic acid (ssRNA) virus. Severe infection and high-mortality are seen in patients with comorbid conditions like diabetes, hypertension, cancer, old age, malnutrition, children, and pregnancy. In India, strategy for testing of COVID-19 has been framed and revised over the course of time by the Indian Council of Medical Research (ICMR), Department of Health Research (DHR), Ministry of Health and Family Welfare (MOHFW), Government of India. ICMR has created a network of viral research and diagnostic laboratories (VRDLs) all over the country, and COVID-19 testing has also been undertaken by ICMR. AIIMS Jodhpur is a regional level VRDL, mentoring 38 government and private laboratories for molecular diagnosis of COVID-19 in the states of Rajasthan and Gujarat. Currently, real-time reverse transcription polymerase chain reaction (rRT-PCR) assay is used all over the country for diagnosis of COVID-19. It uses the TaqMan fluorogenic probe-based chemistry and 5′- nuclease activity of Taq DNA polymerase. It targets specific genes like the RdRp gene, HKU-Orf1ab gene, E gene, and N gene. Apart from rRT-PCR, other isothermal nucleic acid test (NAT)-like transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), etc. are emerging diagnostic tools to detect COVID-19. Cepheid Xpert Xpress SARS- CoV-2 test and Truenat betaCoV are point-of-care molecular assays which gives results in less than 1 hour, and helps to provide rapid and accurate results. Automated molecular assays like Cobas SARS-CoV-2 and Multiplex NAAT BioFire Respiratory Panel 2.1 (RP2.1) are newer techniques to curb the disease. Sherlock CRISPR SARS-CoV-2 kit is a highly specific and sensitive assay developed to diagnose COVID-19. rRT-PCR has been combined with techniques like bead hybridization, digital droplet PCR, microarray, etc. for improving the correct diagnosis. Recent molecular assays are the future pillars for containment of COVID-19 outbreaks all over the world.

scholarly journals Comparison of genes as target for molecular diagnosis of peste des petits ruminants in goats

2013 ◽  
Vol 29 (2) ◽  
pp. 56-62 ◽  
Author(s):  
AR Bhuiyan ◽  
MM Rahman ◽  
JA Begum ◽  
MR Islam ◽  
EH Chowdhury
Keyword(s):  
Viral Disease ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Peste Des Petits Ruminants ◽  
Gene Target ◽  
Field Samples ◽  
Successful Control ◽  
Primer Sets ◽  
Molecular Diagnostic Test ◽  
Np Gene

Peste des petits ruminants (PPR) are an acute viral disease of sheep and goats. Rapid and accurate diagnosis is essential for successful control. Reverse transcriptase polymerase chain reaction (RT-PCR), a molecular diagnostic test based on amplification of the gene target is more sensitive than other tests. The study was to find an efficient primer set and structural gene, which would be more specific and sensitive for detecting PPR virus (PPRV) in field samples. Six primer sets for six structural genes of PPR were used. Primer against NP gene (np3/np4) was specific and sensitive. To ensure efficient amplification and detection of viruses in field samples, more than one set of primers should be used and F and N gene specific primers were the most suitable. DOI: http://dx.doi.org/10.3329/bvet.v29i2.14343 Bangl. vet. 2012. Vol. 29, No. 2, 56-62

Glembotskaya G.T., Eremin S.Yu. Scientific and practical approach to optimizing costs on development and promotion of drugs

2019 ◽  
Vol 2019 (3) ◽  
pp. 47-53
Author(s):  
Галина Глембоцкая ◽  
Galina Glembockaya ◽  
Станислав Еремин ◽  
Stanislav Eremin
Keyword(s):  
Scientific Literature ◽  
Pharmacological Action ◽  
Pharmaceutical Market ◽  
Pharmaceutical Companies ◽  
Strategic Development ◽  
The World ◽  
The Russian Federation ◽  
The Cost ◽  
Further Development ◽  
Registration Phase

In order to identify promising strategic development possibilities for the pharmaceutical industry in the Russian Federation, a pilot study was conducted, which has analyzed the main trends in the development of innovative medicines. As a result of the content analysis of available sources of scientific literature, the characteristics of options used in the world practice for increasing the innovative activity of individual subjects and the pharmaceutical market as a whole are presented. Possible reserves for the further development of the innovative component of the pharmaceutical market within the framework of the concept of personalized medicine according to the P4 principle (predictive - personalized - preventive - participatory) are identified and structured. The results of use by individual pharmaceutical companies of scientifically and practically justified approaches to optimizing the costs of development and promoting drugs are presented. The advantages and real prospects of a generally accepted method to reduce the cost of development by «expanding the pharmacological effect» (label expansion) of already existing drugs with a known safety profile in the world practice are shown. A scientific generalization and structuring of the goals and results of the post-registration phase of clinical trials to expand the pharmacological action of a number of drugs already existed at the market have been carried out.

What Every Neuropathologist Needs to Know: Practical Aspects and Pitfalls in Molecular Diagnosis of Brain Tumors

2021 ◽  
Author(s):  
J Stephen Nix ◽  
Cristiane M Ida
Keyword(s):  
Brain Tumors ◽  
Molecular Diagnosis ◽  
Genetic Alterations ◽  
Genetic Alteration ◽  
Molecular Testing ◽  
Test Results ◽  
Molecular Test ◽  
Molecular Tests ◽  
Clinically Significant ◽  
Selection Of

Abstract Molecular testing has become part of the routine diagnostic workup of brain tumors after the implementation of integrated histomolecular diagnoses in the 2016 WHO classification update. It is important for every neuropathologist to be aware of practical preanalytical, analytical, and postanalytical factors that impact the performance and interpretation of molecular tests. Prior to testing, optimizing tumor purity and tumor amount increases the ability of the molecular test to detect the genetic alteration of interest. Recognizing basic molecular testing platform analytical characteristics allows selection of the optimal platform for each clinicopathological scenario. Finally, postanalytical considerations to properly interpret molecular test results include understanding the clinical significance of the detected genetic alteration, recognizing that detected clinically significant genetic alterations are occasionally germline constitutional rather than somatic tumor-specific, and being cognizant that recommended and commonly used genetic nomenclature may differ. Potential pitfalls in brain tumor molecular diagnosis are also discussed.

scholarly journals The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases

2021 ◽  
Vol 22 (8) ◽  
pp. 4274
Author(s):  
Dèlia Yubero ◽  
Daniel Natera-de Benito ◽  
Jordi Pijuan ◽  
Judith Armstrong ◽  
Loreto Martorell ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Clinical Symptoms ◽  
Neuromuscular Diseases ◽  
Genomic Analysis ◽  
Molecular Diagnostic ◽  
Diagnostic Process ◽  
Targeted Analysis ◽  
Whole Exome ◽  
Referral Hospitals ◽  
Uncertain Significance

The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.

scholarly journals Punishment Strategies across Societies: Conventional Wisdoms Reconsidered

Games ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 63
Author(s):  
Ramzi Suleiman ◽  
Yuval Samid
Keyword(s):  
Public Goods ◽  
Strong Predictor ◽  
Social Environments ◽  
Public Goods Game ◽  
The Public ◽  
Free Riders ◽  
The World ◽  
Emergence Of Cooperation ◽  
Using Data ◽  
The Cost

Experiments using the public goods game have repeatedly shown that in cooperative social environments, punishment makes cooperation flourish, and withholding punishment makes cooperation collapse. In less cooperative social environments, where antisocial punishment has been detected, punishment was detrimental to cooperation. The success of punishment in enhancing cooperation was explained as deterrence of free riders by cooperative strong reciprocators, who were willing to pay the cost of punishing them, whereas in environments in which punishment diminished cooperation, antisocial punishment was explained as revenge by low cooperators against high cooperators suspected of punishing them in previous rounds. The present paper reconsiders the generality of both explanations. Using data from a public goods experiment with punishment, conducted by the authors on Israeli subjects (Study 1), and from a study published in Science using sixteen participant pools from cities around the world (Study 2), we found that: 1. The effect of punishment on the emergence of cooperation was mainly due to contributors increasing their cooperation, rather than from free riders being deterred. 2. Participants adhered to different contribution and punishment strategies. Some cooperated and did not punish (‘cooperators’); others cooperated and punished free riders (‘strong reciprocators’); a third subgroup punished upward and downward relative to their own contribution (‘norm-keepers’); and a small sub-group punished only cooperators (‘antisocial punishers’). 3. Clear societal differences emerged in the mix of the four participant types, with high-contributing pools characterized by higher ratios of ‘strong reciprocators’, and ‘cooperators’, and low-contributing pools characterized by a higher ratio of ‘norm keepers’. 4. The fraction of ‘strong reciprocators’ out of the total punishers emerged as a strong predictor of the groups’ level of cooperation and success in providing the public goods.

Hospitality at community wells: The life-giving waters of John 4:7–15

2020 ◽  
Vol 117 (4) ◽  
pp. 526-535
Author(s):  
Cindy Bolden
Keyword(s):  
North Carolina ◽  
God's Love ◽  
The World ◽  
The Cost ◽  
The Church ◽  
Samaritan Woman

Jesus’s encounter with the Samaritan woman at the well is a paradigmatic text for the Church, showing new possibilities for how the Church can engage the world, specifically engagement through invitational conversation and acts of charity at modern-day community wells. A Place at the Table is a pay-what-you-can café in Raleigh, North Carolina. Patrons can pay the suggested price, less than the suggested price, redeem a token worth the cost of a meal, or pay by volunteering at the café. Patrons who are able to “pay it forward” can further support the mission by tipping or buying meal tokens for others. At this café, a space reminiscent of an ancient “community well,” thirsty travelers receive the life-giving waters of acceptance, connection, and sustenance. The custom of hospitality is a life-giving and transformational practice for the Church, a viable and tangible way to connect with its neighbor and draw all persons into the experience of God’s love.

India–Myanmar Relations

2012 ◽  
Vol 19 (1) ◽  
pp. 79-99
Author(s):  
Gaurav Kumar Jha ◽  
Amrita Banerjee
Keyword(s):  
Cold War ◽  
Structural Changes ◽  
Prime Minister ◽  
World Order ◽  
Post Cold War ◽  
Post Colonial ◽  
The World ◽  
The Cost ◽  
Market Interdependence

Despite long historical ties, post-colonial relations between India and Myanmar have fluctuated between magnanimity and mistrust. While India often stood for high moral grounds and promotion of democracy, it did so at the cost of losing Myanmar to China. This affected both India and Myanmar adversely: while New Delhi’s economic, energy and security interests were hurt, isolated Yangon became more China-dependent. However, since the early 1990s, domestic developments in Myanmar and post-Cold War structural changes in the world order necessitated conditions for cooperation and mutual gains. It appears that blatant domestic suppression in, and international seclusion of, Myanmar is not desirable. Having witnessed two eras of magnanimity and mistrust, Prime Minister Manmohan Singh’s visit to Myanmar in 2012 heralds a prospective era of market interdependence while opening Pandora’s box: can India get a better share of Myanmar’s commercial possibilities without compromising its core interests in promoting democracy, development and diaspora protection?

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