scholarly journals Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients

2020 ◽  
Author(s):  
Anthony Levasseur ◽  
Jeremy Delerce ◽  
Aurelia Caputo ◽  
Ludivine Brechard ◽  
Philippe Colson ◽  
...  
Keyword(s):  
Stop Codon ◽  
Genomic Diversity ◽  
The Novel ◽  
Viral Isolate ◽  
Mutational Signatures ◽  
Phylogenetic Origin ◽  
Substitution Mutations ◽  
Novel Coronavirus ◽  
Shed Light ◽  
French Cohort

ABSTRACTThe novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

scholarly journals Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9576
Author(s):  
Arohi Parlikar ◽  
Kishan Kalia ◽  
Shruti Sinha ◽  
Sucheta Patnaik ◽  
Neeraj Sharma ◽  
...  
Keyword(s):  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
The Novel ◽  
Origin And Evolution ◽  
Pan Genome ◽  
Mutational Hotspots ◽  
Evolutionary Studies ◽  
Low Probability ◽  
Shed Light ◽  
Country Specific

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.

scholarly journals Detection techniques aiding in the diagnosis of the novel coronavirus SARS-Cov-2 induced infections

2021 ◽  
Vol 2 (2) ◽  
pp. 112-115
Author(s):  
Chateen Izaddin Ali Pambuk ◽  
Fatma Mustafa Muhammad
Keyword(s):  
Elisa Test ◽  
The Novel ◽  
Virus Infections ◽  
Detection Techniques ◽  
Corona Virus ◽  
Polymerase Chain ◽  
Antigen Tests ◽  
Novel Coronavirus ◽  
Antibody Tests ◽  
Shed Light

Some people may not be able to distinguish between the symptoms of the emerging corona virus 2019 and other respiratory diseases, and some individuals may be infected with the virus without symptoms, or without noticeable symptoms, so it is important to conduct a corona examination to diagnose the disease. To monitor the new Corona virus infections, many tests have been developed since the SARS-Cov 2 virus first appeared at the end of last year until today. About 350 types of detection techniqes are currently used in all laboratories of the world. They can be divided into three pivotal sections: the [PCR] examination, which is also known as the "polymerase chain reaction" examination, then the [antigen-tests] known as antibody tests, and finally the ELISA test. The aim of this descriptive minireview, generally, is to shed light on the main detection techniques used in Covid 19 diagnosis.

scholarly journals Risk, mourning, politics: Toward a transnational critical conception of grief for COVID-19 deaths in Iran

2021 ◽  
pp. 001139212110071
Author(s):  
Zohreh Bayatrizi ◽  
Hajar Ghorbani ◽  
Reza Taslimi Tehrani
Keyword(s):  
Mixed Methods ◽  
Social Stigma ◽  
Biological Agent ◽  
Mixed Methods Study ◽  
The Novel ◽  
Disenfranchised Grief ◽  
Political Risks ◽  
Novel Coronavirus ◽  
Shed Light

This article examines the case of COVID-19 deaths and grief in Iran in order to shed light on how the biological, social and political ‘risks of contagion’ combine to impact mourning and grief. As a contagious biological agent, the novel coronavirus causes people to suffer, die and grieve alone. But this loneliness is deepened due to social stigma and political abandonment. Conceptually guided by Mary Douglas’s work on the socio-cultural and political constructions of ‘contagion’, Judith Butler’s notion of ‘ungrievable lives’ and Kenneth Doka’s concept of ‘disenfranchised grief’, the authors of this article have undertaken a preliminary mixed-methods study that explores the possibility of a transnational, decolonial understanding of grief in a time of contagion.

Comparative docking of SARS-CoV-2 receptors antagonists from repurposing drugs

2020 ◽  
Author(s):  
Micael Davi Lima de Oliveira ◽  
Kelson Mota Teixeira de Oliveira
Keyword(s):  
World Health Organisation ◽  
World Health ◽  
Lung Cells ◽  
The Novel ◽  
High Modulation ◽  
Main Protease ◽  
The World ◽  
Novel Coronavirus ◽  
Viral Receptors ◽  
Theoretical Results

According to the World Health Organisation, until 16 June, 2020, the number of confirmed and notified cases of COVID-19 has already exceeded 7.9 million with approximately 434 thousand deaths worldwide. This research aimed to find repurposing antagonists, that may inhibit the activity of the main protease (Mpro) of the SARS-CoV-2 virus, as well as partially modulate the ACE2 receptors largely found in lung cells, and reduce viral replication by inhibiting Nsp12 RNA polymerase. Docking molecular simulations were performed among a total of 60 structures, most of all, published in the literature against the novel coronavirus. The theoretical results indicated that, in comparative terms, paritaprevir, ivermectin, ledipasvir, and simeprevir, are among the most theoretical promising drugs in remission of symptoms from the disease. Furthermore, also corroborate indinavir to the high modulation in viral receptors. The second group of promising drugs includes remdesivir and azithromycin. The repurposing drugs HCQ and chloroquine were not effective in comparative terms to other drugs, as monotherapies, against SARS-CoV-2 infection.

SARS-COV2 virus and Coronavirus disease (COVID-19)

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 977-982
Author(s):  
Mohamed J. Saadh ◽  
Bashar Haj Rashid M ◽  
Roa’a Matar ◽  
Sajeda Riyad Aldibs ◽  
Hala Sbaih ◽  
...  
Keyword(s):  
Close Contact ◽  
Antiviral Agents ◽  
Health Concern ◽  
The Novel ◽  
Global Public Health ◽  
Fatal Disease ◽  
Mild Disease ◽  
Life Threatening ◽  
Novel Coronavirus

SARS-COV2 virus causes Coronavirus disease (COVID-19) and represents the causative agent of a potentially fatal disease that is of great global public health concern. The novel coronavirus (2019) was discovered in 2019 in Wuhan, the market of the wet animal, China with viral pneumonia cases and is life-threatening. Today, WHO announces COVID-19 outbreak as a pandemic. COVID-19 is likely to be zoonotic. It is transmitted from bats as intermediary animals to human. Also, the virus is transmitted from human to human who is in close contact with others. The computerized tomographic chest scan is usually abnormal even in those with no symptoms or mild disease. Treatment is nearly supportive; the role of antiviral agents is yet to be established. The SARS-COV2 virus spreads faster than its two ancestors, the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), but has lower fatality. In this article, we aimed to summarize the transmission, symptoms, pathogenesis, diagnosis, treatment, and vaccine to control the spread of this fatal disease.

Coronavirus: Towards controlling of the pandemic - Indian scenario

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 462-468
Author(s):  
Latika kothari ◽  
Sanskruti Wadatkar ◽  
Roshni Taori ◽  
Pavan Bajaj ◽  
Diksha Agrawal
Keyword(s):  
Control Measures ◽  
The Novel ◽  
Medical Treatments ◽  
Health Crisis ◽  
The Public ◽  
Infection Control Measures ◽  
The Social ◽  
Asking Questions ◽  
The Government ◽  
Novel Coronavirus

Coronavirus disease 2019 (COVID-19) is a communicable infection caused by the novel coronavirus resulting in severe acute respiratory syndrome coronavirus 2 (SARS-CoV). It was recognized to be a health crisis for the general population of international concern on 30th January 2020 and conceded as a pandemic on 11th March 2020. India is taking various measures to fight this invisible enemy by adopting different strategies and policies. To stop the COVID-19 from spreading, the Home Affairs Ministry and the health ministry, of India, has issued the nCoV 19 guidelines on travel. Screening for COVID-19 by asking questions about any symptoms, recent travel history, and exposure. India has been trying to get testing kits available. The government of India has enforced various laws like the social distancing, Janata curfew, strict lockdowns, screening door to door to control the spread of novel coronavirus. In this pandemic, innovative medical treatments are being explored, and a proper vaccine is being hunted to deal with the situation. Infection control measures are necessary to prevent the virus from further spreading and to help control the current situation. Thus, this review illustrates and explains the criteria provided by the government of India to the awareness of the public to prevent the spread of COVID-19.

Association and treatment of diabetes in patients affected by Covid-19

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 1198-1201
Author(s):  
Syed Yasir Afaque
Keyword(s):  
Diabetes Mellitus ◽  
Prognostic Value ◽  
Heart Diseases ◽  
The Novel ◽  
The World ◽  
Treatment Of Diabetes ◽  
Coronavirus Infection ◽  
Composite Outcomes ◽  
Novel Coronavirus ◽  
The Impact

In December 2019, a unique coronavirus infection, SARS-CoV-2, was first identified in the province of Wuhan in China. Since then, it spread rapidly all over the world and has been responsible for a large number of morbidity and mortality among humans. According to a latest study, Diabetes mellitus, heart diseases, Hypertension etc. are being considered important risk factors for the development of this infection and is also associated with unfavorable outcomes in these patients. There is little evidence concerning the trail back of these patients possibly because of a small number of participants and people who experienced primary composite outcomes (such as admission in the ICU, usage of machine-driven ventilation or even fatality of these patients). Until now, there are no academic findings that have proven independent prognostic value of diabetes on death in the novel Coronavirus patients. However, there are several conjectures linking Diabetes with the impact as well as progression of COVID-19 in these patients. The aim of this review is to acknowledge about the association amongst Diabetes and the novel Coronavirus and the result of the infection in such patients.

The role and relationship of mindreading and social attunement in HRI – position statements of interdisciplinary researchers. Workshop HRI'20

2020 ◽  
Author(s):  
Agnieszka Wykowska ◽  
Jairo Pérez-Osorio ◽  
Stefan Kopp
Keyword(s):  
Mental States ◽  
Human Robot Interaction ◽  
Human Interaction ◽  
Artificial Agents ◽  
The Novel ◽  
Robot Interaction ◽  
Novel Coronavirus ◽  
Relationship Of ◽  
The Relationship

This booklet is a collection of the position statements accepted for the HRI’20 conference workshop “Social Cognition for HRI: Exploring the relationship between mindreading and social attunement in human-robot interaction” (Wykowska, Perez-Osorio & Kopp, 2020). Unfortunately, due to the rapid unfolding of the novel coronavirus at the beginning of the present year, the conference and consequently our workshop, were canceled. On the light of these events, we decided to put together the positions statements accepted for the workshop. The contributions collected in these pages highlight the role of attribution of mental states to artificial agents in human-robot interaction, and precisely the quality and presence of social attunement mechanisms that are known to make human interaction smooth, efficient, and robust. These papers also accentuate the importance of the multidisciplinary approach to advance the understanding of the factors and the consequences of social interactions with artificial agents.

The Political Impact of Affective Polarization: How Partisan Animus Shapes COVID-19 Attitudes

2020 ◽  
Author(s):  
James Druckman ◽  
Samara Klar ◽  
Yanna Krupnikov ◽  
Matthew Levendusky ◽  
John B. Ryan
Keyword(s):  
21St Century ◽  
American Politics ◽  
The Other ◽  
Policy Discourse ◽  
The Political ◽  
The Novel ◽  
Political Impact ◽  
Novel Coronavirus ◽  
Citizens Attitudes

Affective polarization is a defining feature of 21st century American politics—partisans harbor considerable dislike and distrust of those from the other party. Does this animus have consequences for citizens’ opinions? Such effects would highlight not only the consequences of polarization, but also shed new light onto how citizens form preferences more generally. Normally, this question is intractable, but the outbreak of the novel coronavirus allows us to answer it. We find that affective polarization powerfully shapes citizens’ attitudes about the pandemic, as well as the actions they have taken in response to it. However, these effects are conditional on the local severity of the outbreak, as the effects decline in areas with high caseloads—threat vitiates partisan reasoning. Our results clarify that closing the divide on important issues requires not just policy discourse but also attempts to reduce inter-partisan hostility.

Curve Estimation Modeling for Predictions of the Novel Coronavirus (Covid-19) Epidemic in Nigeria

2020 ◽  
Vol 4 (1) ◽  
pp. 1
Author(s):  
Christian Ebere Enyoh ◽  
Andrew Wirnkor Verla ◽  
Chidi Edbert Duru ◽  
Emmanuel Chinedu Enyoh ◽  
Budi Setiawan
Keyword(s):  
State Governments ◽  
The Novel ◽  
Curve Estimation ◽  
Exponential Models ◽  
Inverse Models ◽  
Forward Prediction ◽  
S Curve ◽  
Novel Coronavirus ◽  
Best Fit ◽  
Official Data

Based on the official Nigeria Centre for Disease Control (NCDC) data, the current research paper modeled the confirmed cases of the novel coronavirus disease 2019 (COVID-19) in Nigeria. Ten different curve regression models including linear, logarithmic, inverse, quadratic, cubic, compound, power, S-curve, growth, and exponential were used to fit the obtained official data. The cubic (R2 = 0.999) model gave the best fit for the entire country. However, the growth and exponential had the lowest standard error of estimate (0.958) and thus may best be used. The equations for these models were e0.78897+0.0944x and 2.2011e0.0944x respectively. In terms of confirmed cases in individual State, quadratic, cubic, compound, growth, power and exponential models generally best describe the official data for many states except for the state of Kogi which is best fitted with S-curve and inverse models.  The error between the model and the official data curve is quite small especially for compound, power, growth and exponential models. The computed models will help to realized forward prediction and backward inference of the epidemic situation in Nigeria, and the relevant analysis help Federal and State governments to make vital decisions on how to manage the lockdown in the country.

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