scholarly journals Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 52 ◽  
Author(s):  
Veljko Veljkovic ◽  
Júlia Vergara-Alert ◽  
Joaquim Segalés ◽  
Slobodan Paessler

A novel coronavirus recently identified in Wuhan, China (2019-nCoV) has expanded the number of highly pathogenic coronaviruses affecting humans. The 2019-nCoV represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging 2019-nCoV is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of 2019-nCoV; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the 2019-nCoV, and that domain 288-330 of S1 protein from the 2019-nCoV represents promising therapeutic and/or vaccine target.

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 52 ◽  
Author(s):  
Veljko Veljkovic ◽  
Júlia Vergara-Alert ◽  
Joaquim Segalés ◽  
Slobodan Paessler

A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.


F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 52
Author(s):  
Veljko Veljkovic ◽  
Júlia Vergara-Alert ◽  
Joaquim Segalés ◽  
Slobodan Paessler

A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.


F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 52 ◽  
Author(s):  
Veljko Veljkovic ◽  
Júlia Vergara-Alert ◽  
Joaquim Segalés ◽  
Slobodan Paessler

A novel coronavirus recently identified in Wuhan, China (2019-nCoV) has expanded the number of highly pathogenic coronaviruses affecting humans. The 2019-nCoV represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging 2019-nCoV is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the 2019-nCoV, and that domain 288-330 of S1 protein from the 2019-nCoV represents promising therapeutic and/or vaccine target.


2020 ◽  
pp. CLINLACT-D-20-00008
Author(s):  
Dena Duran ◽  
Jarold T. Johnston

ObjectivesSome hospitals have instituted separation of mothers and their newborn(s) when SARS-CoV-2 is suspected or confirmed in the mother. Limited data are available for SARS-CoV-2 vertical transmission, including studies on breast milk. This article looks at SARS CoV-2 case studies and data to date as well as prior pertinent research.MethodsInformal searches of PUBMED, CINAHL and Ovid Emcare were used to identify early reports of vertical transmissions of the novel Coronavirus, case reports, and population based reports of early evolving protocols and their outcomes. As this is a novel virus the authors used previously identified anti-infectivity and antiviral mechanisms of human milk on other similar viruses to guide analysis. Further this article reviewed the well established literature regarding the risks of undue infant separation which negatively affect nearly every aspect of infant and maternal health.ResultsInformal searches conducted in the spring and early summer of 2020 identified 14 early reports attempting to analyze the initial and evolving global response to SARS-CoV-2 and the effects of the virus on the maternal-infant dyad.ConclusionThe feasibility of single-family rooms and support for breastfeeding as an alternative approach that addresses many of the risks favorably and reduces economic cost, both in lifetime disease burden and direct care are discussed. Initial reports seem to indicate that immediate separation of the mother from her newborn is likely to increase the risk to both mother and infant.


Author(s):  
Yanyan Zhu ◽  
Miaomiao Jiang ◽  
Liang Gao ◽  
Xiaoyun Huang

ACE2, the putative receptor for the novel coronavirus (2019-nCoV), played an important role in cell entry of 2019-nCoV. However, it is not yet clear what cell types within the human body express ACE2. Here, a systematic analysis was undertaken using published single cell datasets. In total, our study analyzed 229652 cells, from five different organs, derived from 88 donors. The top ACE2 expressing cells include proximal tubule cells in the kidney and enterocytes in the intestine. Other major ACE2 expressing cells in the kidney include podocytes, intercalated cells and endothelial cells. Our results offer a comprehensive atlas of ACE2 expression at the single cell level and unravel the enormous potential targets of 2019-nCoVinfection beyond the lung.


2020 ◽  
Author(s):  
Alessandra Oliva ◽  
Guido Siccardi ◽  
Ambra Migliarini ◽  
Francesca Cancelli ◽  
Martina Carnevalini ◽  
...  

Abstract The novel coronavirus SARS-CoV-2 has spread all over the world causing a global pandemic and representing a great medical challenge. Nowadays, there is limited knowledge on the rate of co-infections with other respiratory pathogens, with viral co-infection being the most representative agents. Co-infection with Mycoplasma pneumoniae has been described both in adults and pediatrics whereas only 2 cases of Chlamydia pneumoniae have been reported in a large US study so far. In the present report, we describe a series of 7 patients where co-infection with C. pneumoniae (n=5) or M. pneumoniae (n=2) and SARS-CoV-2 was detected in a large teaching hospital in Rome. An extensive review of the updated literature regarding the co-infection between SARS-CoV-2 and these atypical pathogens is also performed.


Author(s):  
Tieying Hou ◽  
Weiqi Zeng ◽  
Minling Yang ◽  
Wenjing Chen ◽  
Lili Ren ◽  
...  

BackgroundThe recent outbreak of infections by the 2019 novel coronavirus (2019-nCoV), the third zoonotic CoV has raised great public health concern. The demand for rapid and accurate diagnosis of this novel pathogen brought significant clinical and technological challenges. Currently, metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) are the most widely used molecular diagnostics for 2019-nCoV.Methods2019-nCoV infections were confirmed in 52 specimens by mNGS. Genomic information was analyzed and used for the design and development of an isothermal, CRISPR-based diagnostic for the novel virus. The diagnostic performance of CRISPR-nCoV was assessed and also compared across three technology platforms (mNGS, RT-PCR and CRISPR)Results2019-nCoVs sequenced in our study were conserved with the Wuhan strain, and shared certain genetic similarity with SARS-CoV. A high degree of variation in the level of viral RNA was observed in clinical specimens. CRISPR-nCoV demonstrated a near single-copy sensitivity and great clinical sensitivity with a shorter turn-around time than RT-PCR.ConclusionCRISPR-nCoV presents as a promising diagnostic option for the emerging pathogen.


2020 ◽  
Vol 148 ◽  
Author(s):  
Eduardo Massad ◽  
Marcos Amaku ◽  
Annelies Wilder-Smith ◽  
Paulo Cesar Costa dos Santos ◽  
Claudio Jose Struchiner ◽  
...  

Abstract We present two complementary model-based methods for calculating the risk of international spread of the novel coronavirus SARS-CoV-2 from the outbreak epicentre. One model aims to calculate the number of cases that would be exported from an endemic country to disease-free regions by travellers. The second model calculates the probability that an infected traveller will generate at least one secondary autochthonous case in the visited country. Although this paper focuses on the data from China, our methods can be adapted to calculate the risk of importation and subsequent outbreaks. We found an average R0 = 5.31 (ranging from 4.08 to 7.91) and a risk of spreading of 0.75 latent individuals per 1000 travellers. In addition, one infective traveller would be able to generate at least one secondary autochthonous case in the visited country with a probability of 23%.


2020 ◽  
Vol 10 (4) ◽  
pp. 303-311
Author(s):  
Gundu H. R. Rao

The first human case of COVID-19, caused by the novel coronavirus, was reported by health officials in the city of Wuhan, China, in December of 2019. The virus was identified as a novel coronavirus in early January 2020, and its genetic sequence was shared publicly on January 11, 2020. The novel virus, previously called 2019-novel coronavirus (2019-nCoV), is currently designated as the severe respiratory syndrome coronavirus-2 (SARS-CoV-2). On January 23, Wuhan was locked down, and the World Health Organization (WHO) declared a “public health emergency of international concern.” The viral genome of SARS-CoV-2 is around 29.8 kilobase, containing six major open reading frames. The most common clinical symptoms were fever, cough, fatigue, shortness of breath, dyspnea, muscle ache, headache, chest pain, vomiting, sore throat, and sputum production. The main mode of transmission is through respiratory particles. The incubation period is 3 to 7 days. Both asymptomatic and symptomatic patients seem to be infectious. Spike (S) proteins of SARS-CoV-2 seem to have a 10- to 20-fold higher affinity to the human angiotensin enzyme 2 (ACE2) receptor than that of SARS-CoV. The high affinity of S protein to theACE2 receptor, and the additional advantages offered by the transfection facilitators Furin and Neutropilin-1, likely, contributes to the rapid spreading of this novel virus. Since these receptors are highly expressed on a variety of cells, including vascular endothelial cells and adipose tissue, individuals with compromised function of these tissues drive greater infection and severity in patients with COVID-19. Global health experts estimate that one in five individuals worldwide could be at risk for severe COVID-19, due to underlying health conditions. There is a great need for a rapid, specific, cost-effective test for monitoring the infected individuals. Even though a 15- minute, antigen test was made available by Abbott recently, it seems that the schools, colleges, and business establishments lack the ability to use these tests effectively to keep their businesses open safely. Management of the infected individuals seems to be based on clinical symptoms that manifest as the disease progresses. The US Food & Drug Administration (FDA), has created a special emergency program for possible therapies, the Coronavirus Treatment Acceleration Program (CTAP). The program uses every available method to move new and emerging treatments as quickly as possible, keeping in mind the safety and efficacy of such therapies. According to the WHO report, there are currently more than 150 COVID-19 vaccine candidates under development. Several vaccines are in Phase 3 clinical trials. In an unprecedented effort, one of the experimental monoclonal antibody cocktails of Regeneron was used for therapeutic purposes when the US president was tested positive for COVID-19. There are no drugs or other therapeutics approved by the US FDA to prevent or treat COVID-19. The National Institutes of Health (NIH) have published interim guidelines for the medical management of COVID-19. In the absence of a cure, the only choice we all have is to follow the best practices recommended by the public health experts—use of face masks (coverings), frequent hand washing with soap, contact tracing of infected individuals, and quarantining COVID-19 positive individuals, till they are free of the highly infectious virus.


2021 ◽  
Vol 19 ◽  
pp. 205873922110029
Author(s):  
Areeg M Dabbish ◽  
Nouran Yonis ◽  
Mohamed Salama ◽  
Musthafa M Essa ◽  
M Walid Qoronfleh

The public health crisis of the novel coronavirus disease (COVID-19) is alarming since January 2020. COVID-19 genome (SARS-CoV-2) is related to other highly pathogenic coronaviruses SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS-CoV (Middle East respiratory syndrome coronavirus). Amino acid substitutions in some of SARS-CoV-2 proteins resulted in mutations proposing more virulent and contagious properties for this novel virus. Coronavirus penetrates the host cell via endocytosis and once infected, immune responses are triggered to fight against the pathogen. Innate immune response activates major transcription factors to secrete proinflammatory cytokines and type 1 interferon response (T1INF) to induce antiviral immunity. While adaptive immunity initiates cascade of B-cells antibody mediated and T-cells cellular mediate immunities, several mechanisms are raised by SARS-CoV-2 to evade host immune response. Consequently, a surge of proinflammatory cytokines, known as cytokine storm (CS) are released. Failure to manage CS results in several pathological complications as acute respiratory distress syndrome (ARDS). Although researches have not discovered an effective treatment against SARS-CoV-2, recent therapeutic approaches recommending the use of anti-inflammatories in combination with antivirals and some repurposed drugs for COVID-19 patients. Future medications should be designed to target essential hallmarks in the CS to improve clinical outcomes.


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