Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants

In Silico ◽

The Other ◽

Viral Rna ◽

Potential Threat ◽

For 1 year now, the world is undergoing a coronavirus disease-2019 (COVID-19) pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method for COVID-19 diagnosis is the detection of viral RNA by RT-qPCR with a specific set of primers and probe. It is important to frequently evaluate the performance of these tests and this can be done first by an in silico approach. Previously, we reported some mismatches between the oligonucleotides of publicly available RT-qPCR assays and SARS-CoV-2 genomes collected from GISAID and NCBI, potentially impacting proper detection of the virus. In the present study, 11 primers and probe sets investigated during the first study were evaluated again with 84,305 new SARS-CoV-2 unique genomes collected between June 2020 and January 2021. The lower inclusivity of the China CDC assay targeting the gene N has continued to decrease with new mismatches detected, whereas the other evaluated assays kept their inclusivity above 99%. Additionally, some mutations specific to new SARS-CoV-2 variants of concern were found to be located in oligonucleotide annealing sites. This might impact the strategy to be considered for future SARS-CoV-2 testing. Given the potential threat of the new variants, it is crucial to assess if they can still be correctly targeted by the primers and probes of the RT-qPCR assays. Our study highlights that considering the evolution of the virus and the emergence of new variants, an in silico (re-)evaluation should be performed on a regular basis. Ideally, this should be done for all the RT-qPCR assays employed for SARS-CoV-2 detection, including also commercial tests, although the primer and probe sequences used in these kits are rarely disclosed, which impedes independent performance evaluation.

Does the novel coronavirus 2019 like heart more than the other family members of coronaviruses?

Journal of Cardiovascular and Thoracic Research ◽

10.34172/jcvtr.2020.27 ◽

2020 ◽

Vol 12 (2) ◽

pp. 156-157

Author(s):

Mohammad Mostafa Ansari Ramandi ◽

Mohammadreza Baay ◽

Nasim Naderi

Keyword(s):

Middle East ◽

Family Members ◽

Middle East Respiratory Syndrome ◽

The Other ◽

The Novel ◽

The World ◽

Future Challenges ◽

Novel Coronavirus ◽

Coronavirus Infections

The disaster due to the novel coronavirus disease 2019 (COVID-19) around the world has made investigators enthusiastic about working on different aspects of COVID-19. However, although the pandemic of COVID-19 has not yet ended, it seems that COVID-19 compared to the other coronavirus infections (the Middle East Respiratory Syndrome [MERS] and Severe Acute Respiratory Syndrome [SARS]) is more likely to target the heart. Comparing the previous presentations of the coronavirus family and the recent cardiovascular manifestations of COVID-19 can also help in predicting possible future challenges and taking measures to tackle these issues.

In silico Studies of Novel Synthetic Compounds as Potential Drugs to Inhibit Coronavirus (SARS-CoV-2): A Systematic Review

Biointerface Research in Applied Chemistry ◽

10.33263/briac124.42934306 ◽

2021 ◽

Vol 12 (4) ◽

pp. 4293-4306

Keyword(s):

Systematic Review ◽

In Silico ◽

Drug Target ◽

Computational Studies ◽

Pharmacological Treatments ◽

Synthetic Compounds ◽

In Silico Studies ◽

The World ◽

Molecule Interaction

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), detected first in China, spread out fast to other parts of the world, and was soon recognized as a pandemic in March 2020. According to WHO, 179.686.071 confirmed cases and 3.899.172 deaths due to new coronavirus were reported worldwide on 26th June 2021. Despite countless efforts in searching for repositioned drugs to treat this disease, the results are still modest. Thus, the search for new molecular entities in the treatment of COVID-19 is an essential field in medicinal chemistry. Since the pandemic's beginning, several studies have reported the synthesis of novel organic compounds and their in silico interactions with the new coronavirus. Such computational studies are currently being applied to unveil the complexities of drug-target molecule interaction and also helping in developing new pharmacological treatments. This systematic review aims to provide an overview of studies describing the utilization of novel compounds as prospective drugs in the treatment of COVID-19.

Potential specific therapies in COVID-19

Therapeutic Advances in Respiratory Disease ◽

10.1177/1753466620926853 ◽

2020 ◽

Vol 14 ◽

pp. 175346662092685 ◽

Cited By ~ 7

Author(s):

Muhammad Hamdan Gul ◽

Zin Mar Htun ◽

Nauman Shaukat ◽

Muhammad Imran ◽

Ahmad Khan

Keyword(s):

Clinical Trials ◽

Randomized Clinical Trials ◽

Middle Eastern ◽

The Other ◽

Potential Treatment ◽

Blood Products ◽

Material Section ◽

Global Pandemic ◽

COVID-19 has grown into a global pandemic that has strained healthcare throughout the world. There is a sense of urgency in finding a cure for this deadly virus. In this study, we reviewed the empiric options used in common practice for COVID-19, based on the literature available online, with an emphasis on human experiences with these treatments on severe acute respiratory syndrome-associated coronavirus (SARS-COV-1) and other viruses. Convalescent blood products are the most promising potential treatment for use in COVID-19. The use of chloroquine or hydroxychloroquine (HCQ), remdesivir, and tocilizumab are some of the other promising potential therapies; however, they are yet to be tested in randomized clinical trials (RCTs). The use of lopinavir-ritonavir did not prove beneficial in a large RCT. The use of corticosteroids should be avoided in COVID-19 pneumonia unless used for other indications, based on the suggestion of harm in patients with SARS-COV-1 and Middle Eastern Respiratory Syndrome (MERS) infection. The reviews of this paper are available via the supplemental material section.

An Overview on Covid-19: Clinical Features, Treatment and Prevention

Coronaviruses ◽

10.2174/2666796701999200818145609 ◽

2020 ◽

Vol 01 ◽

Author(s):

Shahid Ud Din Wani ◽

Surya Prakash Gautam ◽

Zulfkar Latief Qadrie

Keyword(s):

Clinical Trials ◽

Viral Disease ◽

Pharmaceutical Products ◽

The Other ◽

Wuhan City ◽

Treatment And Prevention ◽

The World ◽

Control And Prevention ◽

Respiratory Droplets

Background: The Coronavirus disease 2019 (COVID-19) is a transmissible illness produced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has now quickly expanded since its outbreak in Wuhan City of Hubei region of China to the other parts of the world. In accordance with the Centers for Disease Control and Prevention (CDC), the spread of COVID-19 emerges typically human-to-humans through respiratory droplets within an area of 1-2 meters. Aim/ Objective: In the present perspective, we have discussed some of the measures taken to prevent and treat the patient suffering from COVID-19, and how to restrict the further spread of COVID-19 due to SARS-CoV-2. Findings/results: The general clinical properties are fever, cough, sore throat, headache, tiredness, myalgia and difficulty in breathing. Presently no approved treatments for COVID-19, as of now no pharmaceutical products have been revealed to be harmless & efficient for the management of COVID-19. Various anti-viral medicines e.g. ribavirin, lopinavir, and ritonavir have been utilized supported on the familiarity with SARS and MERS. Many drugs and vaccines are currently being studied in clinical trials, jointly with the (Solidarity trial) co-sponsored by the WHO. Conclusion: The use of a mask by fit people in community areas to guard against respiratory viral disease is presently recommended by WHO. Patients must be kept in individual rooms, the rooms, surfaces and equipment should go through standard sanitization possibly with sodium hypochlorite. Consequently, apart from restricting this epidemic, efforts should be made to plan wide-ranging procedures to thwart potential outbreaks of the zoonotic sources.

Point mutation of COVID-19 proteins: A study on noval corona virus (nCov) correlation with MERS and H1N1 viruses and in silico investigation of nCoV proteins for future applications

Journal of Cellular Biotechnology ◽

10.3233/jcb-210037 ◽

2021 ◽

pp. 1-14

Author(s):

Akansha Kaushik ◽

Swati Kasana ◽

Priyanka Verma ◽

Anuj Kumar Singh

Keyword(s):

Phylogenetic Tree ◽

Point Mutation ◽

Mutation Analysis ◽

In Silico ◽

Respiratory Diseases ◽

Point Mutations ◽

H1n1 Influenza ◽

Influenza Viruses ◽

Coronavirus disease (COVID 19) which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) was first reported in Wuhan, China in December 2019. The disease transformed to a pandemic and affected people’s lives all over the world. It caused death to millions of people all over the world. In this project we focused on finding out the correlation of SARS-CoV2 with other respiratory diseases causing viruses like MERS and H1N1 influenza viruses. We further investigated to understand the mutations that occur in the sequences of the SARS-CoV2 during the spread of the disease and correlated it with the functional domains of proteins. The resulted phylogenetic tree indicated that SARS-CoV2 is closely related to the MERS and H1N1 viruses are distantly related. The mutation analysis of 10 different proteins of the SARS-CoV2 shows that there were more than 50 point-mutations among 34 countries sequences for six proteins. Interestingly, four proteins did not any mutation during the analysis. Therefore, these four proteins may be taken into consideration during the development of the diagnostics or therapeutics against this disease.

Indonesian Literature’s Position in World Literature

TEKNOSASTIK ◽

10.33365/ts.v14i2.55 ◽

2018 ◽

Vol 14 (2) ◽

pp. 1

Author(s):

Dina Amelia

Keyword(s):

World Literature ◽

The Other ◽

National Literature ◽

Western World ◽

The World ◽

The One ◽

The Voice

There are two most inevitable issues on national literature, in this case Indonesian literature. First is the translation and the second is the standard of world literature. Can one speak for the other as a representative? Why is this representation matter? Does translation embody the voice of the represented? Without translation Indonesian literature cannot gain its recognition in world literature, yet, translation conveys the voice of other. In the case of production, publication, or distribution of Indonesian Literature to the world, translation works can be very beneficial. The position of Indonesian literature is as a part of world literature. The concept that the Western world should be the one who represent the subaltern can be overcome as long as the subaltern performs as the active speaker. If the subaltern remains silent then it means it allows the “representation” by the Western.

Scientific collections of the Lviv National Music Academy named after M V Lysenko ◽

Experiment role in the world music (based on the «The Road» album of the Ukrainian «Dakha Brakha» band)

10.33398/2310-0583.2018.4243.215.227 ◽

2018 ◽

pp. 215-227

Author(s):

Iia Fedorova

Keyword(s):

Folk Music ◽

World Music ◽

The Other ◽

Modern Music ◽

Musical Practice ◽

The Road ◽

Music Practice ◽

The World ◽

Binary Oppositions ◽

Musical Practices

The main objective of this study is the substantiation of experiment as one of the key features of the world music in Ukraine. Based on the creative works of the brightest world music representatives in Ukraine, «Dakha Brakha» band, the experiment is regarded as a kind of creative setting. Methodology and scientific approaches. The methodology was based on the music practice theory by T. Cherednychenko. The author distinguishes four binary oppositions, which can describe the musical practice. According to one of these oppositions («observance of the canon or violation of the canon»), the musical practices, to which the Ukrainian musicology usually classifies the world music («folk music» and «minstrel music»), are compared with the creative work of «Dakha Brakha» band. Study findings. A lack of the setting to experiment in the musical practices of the «folk music» and «minstrel music» separates the world music musical practice from them. Therefore, the world music is a separate type of musical practice in which the experiment is crucial. The study analyzed several scientific articles of Ukrainian musicologists on the world music; examined the history of the Ukrainian «Dakha Brakha» band; presented a list of the folk songs used in the fifth album «The Road» by «Dakha Brakha» band; and showed the degree of the source transformation by musicians based on the example of the «Monk» song. The study findings can be used to form a comprehensive understanding of the world music musical practice. The further studies may be related to clarification of the other parameters of the world music musical practice, and to determination of the experiment role in creative works of the other world music representatives, both Ukrainian and foreign. The practical study value is the ability to use its key provisions in the course of modern music in higher artistic schools of Ukraine. Originality / value. So far, the Ukrainian musicology did not consider the experiment role as the key one in the world music.

Does Literature Matter Today? Thoughts of the Outside

CounterText ◽

10.3366/count.2018.0118 ◽

2018 ◽

Vol 4 (1) ◽

pp. 98-113

Author(s):

Shaobo Xie

Keyword(s):

Aesthetic Education ◽

The Other ◽

Human Values ◽

Literary Texts ◽

Lost Cause ◽

Western Tradition ◽

The paper celebrates the publication of Ranjan Ghosh and J. Hillis Miller's Thinking Literature across Continents as a significant event in the age of neoliberalism. It argues that, in spite of the different premises and the resulting interpretative procedures respectively championed by the two co-authors, both of them anchor their readings of literary texts in a concept of literature that is diametrically opposed to neoliberal rationality, and both impassionedly safeguard human values and experiences that resist the technologisation and marketisation of the humanities and aesthetic education. While Ghosh's readings of literature offer lightning flashes of thought from the outside of the Western tradition, signalling a new culture of reading as well as a new manner of appreciation of the other, Miller dedicatedly speaks and thinks against the hegemony of neoliberal reason, opening our eyes to the kind of change our teaching or reading of literature can trigger in the world, and the role aesthetic education should and can play at a time when the humanities are considered ‘a lost cause’.

Simone de Beauvoir's Philosophy of Individuation

10.3366/edinburgh/9781474418874.001.0001 ◽

2017 ◽

Cited By ~ 2

Author(s):

Laura Hengehold

Keyword(s):

Lived Experience ◽

20Th Century ◽

Sexual Difference ◽

Gilles Deleuze ◽

The Other ◽

Simone De Beauvoir ◽

Second Sex ◽

Other Hand ◽

Most studies of Simone de Beauvoir situate her with respect to Hegel and the tradition of 20th-century phenomenology begun by Husserl, Heidegger, and Merleau-Ponty. This book analyzes The Second Sex in light of the concepts of becoming, problematization, and the Other found in Gilles Deleuze. Reading Beauvoir through a Deleuzian lens allows more emphasis to be placed on Beauvoir's early interest in Bergson and Leibniz, and on the individuation of consciousness, a puzzle of continuing interest to both phenomenologists and Deleuzians. By engaging with the philosophical issues in her novels and student diaries, this book rethinks Beauvoir’s focus on recognition in The Second Sex in terms of women’s struggle to individuate themselves despite sexist forms of representation. It shows how specific forms of women’s “lived experience” can be understood as the result of habits conforming to and resisting this sexist “sense.” Later feminists put forward important criticisms regarding Beauvoir’s claims not to be a philosopher, as well as the value of sexual difference and the supposedly Eurocentric universalism of her thought. Deleuzians, on the other hand, might well object to her ideas about recognition. This book attempts to address those criticisms, while challenging the historicist assumptions behind many efforts to establish Beauvoir’s significance as a philosopher and feminist thinker. As a result, readers can establish a productive relationship between Beauvoir’s “problems” and those of women around the world who read her work under very different circumstances.

Modernism, Empiricism, and Rationalism

Irish University Review ◽

10.3366/iur.2016.0199 ◽

2016 ◽

Vol 46 (1) ◽

pp. 38-47

Author(s):

Geoffrey Squires

Keyword(s):

Twentieth Century ◽

The Other ◽

Modern Poetry ◽

Philosophical Perspective ◽

Irish Poetry ◽

Dimensional Spectrum ◽

Culture History ◽

The World ◽

The Impact ◽

Rule Out

Modernism is usually defined historically as the composite movement at the beginning of the twentieth century which led to a radical break with what had gone before in literature and the other arts. Given the problems of the continuing use of the concept to cover subsequent writing, this essay proposes an alternative, philosophical perspective which explores the impact of rationalism (what we bring to the world) on the prevailing empiricism (what we take from the world) of modern poetry, which leads to a concern with consciousness rather than experience. This in turn involves a re-conceptualisation of the lyric or narrative I, of language itself as a phenomenon, and of other poetic themes such as nature, culture, history, and art. Against the background of the dominant empiricism of modern Irish poetry as presented in Crotty's anthology, the essay explores these ideas in terms of a small number of poets who may be considered modernist in various ways. This does not rule out modernist elements in some other poets and the initial distinction between a poetics of experience and one of consciousness is better seen as a multi-dimensional spectrum that requires further, more detailed analysis than is possible here.