Recent insights into COVID-19 binding epitopes

  

The novel coronavirus, COVID-19, has been declared a pan- demic by the world health organization (WHO). As it spreads, researchers are mobilizing to understand the virus’s binding mechanisms as a first step in the development of a vaccine. Below are examples of recent publications highlighting insights into these binding mechanisms.

CASE 1

Just two weeks after receiving the genome sequence of the virus from Chinese researchers, a team from the University of Texas at Austin and the National Institutes of Health made a critical breakthrough by creating the 3-D atomic scale map of the virus that binds to and infects human cells. The paper was published in the journal Science1.

Bio-Layer Interferometry (BLI) played a vital role, allowing scien- tist to rapidly determine virus binding mechanisms. The Octet RED96e system was utilized in this research as well as the Anti-Human Capture (AHC) biosensors.

Two experiments, one to determine binding affinity and the other to check for cross-reactivity were quickly performed using Fc-tagged 2019-nCoV RBD-SD1 and ACE2 (binding affinity studies and SARS-CoV RBD-directed mAbs S230, m396 and 80R (cross-reactivity assessment). The Fc epitope binding anti-human capture (AHC) biosensors from ForteBio were used for the studies.

The scientists found that despite the relatively high degree of similarity between 2019-nCoV RBD and SARS-CoV RBD, no binding to the 2019-nCoV RBD could be detected for any of the three mAbs tested. Although the epitopes of these three anti- bodies represent a relatively small percentage of the surface area of the 2019-nCoV RBD, the lack of binding implies that SARS-directed mAbs may not be cross-reactive. Thus, thera- peutic design utilizing 2019-nCoV S proteins as probes could show promise.

SPR data showed in the same article that ACE2 bound to 2019-nCoV S with an affinity of (KD=14.7 nM). Both BLI and SPR demonstrated that new coronavirus and cell ACE2 affinity is much higher than SARS (KD = 325.8 nM). The atomic-resolution structure of 2019-nCoV S should enable rapid development and evaluation of medical countermeasures to address the ongoing public health crisis.

CASE 2

Scientists from Fudan University and Wuhan Institute of Virolo- gy, Chinese Academy of Sciences identified a SARS antibody that binds to the coronavirus. The Octet RED96 system, with selected biosensors, was used to quickly determine the binding affinity of several SARS-CoV-specific neutralizing antibodies with 2019-nCoV. The binding epitope of CR3022 was confirmed by performing a short (10 min) cross-competition study.

The scientists expressed and purified 2019-nCoV RBD protein and predicted the structure. Next, they expressed and purified several representative SARS-CoV-specific antibodies that target RBD and possess potent neutralizing activities.

One SARS-CoV-specific antibody, CR3022, was found to bind potently with 2019-nCoV RBD as determined by ELISA and BLI. CR3022 demonstrated a fast-on (kon = 1.84×105 Ms-1) and slow-off (k  = 1.16×10-3 s-1) binding kinetics, resulting in a K  = 6.3 nM. To

off D

confirm the binding result, they further measured the binding kinetics using BLI. The whole binding kinetics assay of BLI took only 10 min. Researchers concluded that CR3022 has the po- tential for development into a therapeutic candidate2.

Conclusion

Target binding characterization is an essential analytical step for the selection of high affinity and highly specific therapeutics regardless of the types of molecules. Kinetic analysis further describes the components of association and dissociation that comprise the overall affinity interaction.

BLI technology is helping to address real-world research questions and complete projects faster.

References

1 Daniel Wrapp, Nianshuang Wang, Kizzmekia S. Corbett, Jory A. Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S. Graham, Jason S. McLellan, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 2020 Feb 19, pii: eabb2507, 10.1126/science.abb2507, [Epub ahead of print].

2 Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, Lu L, Jiang S, Yang Z, Wu Y, Ying T. Potent binding of 2019 novel coronavirus spike protein by a SARS corona- virus-specific human monoclonal antibody, Emerg Microbes Infect., 2020 Dec;9(1):382-385, doi: 10.1080/22221751.2020.1729069.

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Coronavirus:Arthritis drug seems to work

A commonly used arthritis drug has shown "excellent results" in two coronavirus patients and a national protocol for its extensive use against the virus should be drawn up, oncologist Paolo Ascierto of Naples' Pascale Hospital said Wednesday. The drug, tocilizumab, "has shown it is effective against pneumonia caused by COVID-29," he said. One of the two patients will be taken off life support Thursday because of the improvement in his condition, Ascierto said.
    He called for a "national protocol to immediately extend the use of tocilizumab in an emergency that has killed 631 people and infected over 10,000 in Italy".
    Ascierto said the hospital had started treating two other patients with the virus on Tuesday and will begin treating another two Wednesday.
   

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Why does the coronavirus spread so easily between people

Researchers have identified microscopic features that could make the pathogen more infectious than the SARS virus — and serve as drug targets.

An image of the new coronavirus taken with an electron microscope.Credit: U.S. National Institutes of Health/AP/Shutterstock

As the number of coronavirus infections approaches 100,000 people worldwide, researchers are racing to understand what makes it spread so easily. 

A handful of genetic and structural analyses have identified a key feature of the virus — a protein on its surface — that might explain why it infects human cells so readily. 

Other groups are investigating the doorway through which the new coronavirus enters human tissues — a receptor on cell membranes. Both the cell receptor and the virus protein offer potential targets for drugs to block the pathogen, but researchers say it is too early to be sure.

“Understanding transmission of the virus is key to its containment and future prevention,” says David Veesler, a structural virologist at the University of Washington in Seattle, who posted his team’s findings about the virus protein on the biomedical preprint server bioRxiv on 20 February1. 

The new virus spreads much more readily than the one that caused severe acute respiratory syndrome, or SARS (also a coronavirus), and has infected more than ten times the number of people who contracted SARS.

Spiky invader

To infect a cell, coronaviruses use a ‘spike’ protein that binds to the cell membrane, a process that's activated by specific cell enzymes. Genomic analyses of the new coronavirus have revealed that its spike protein differs from those of close relatives, and suggest that the protein has a site on it which is activated by a host-cell enzyme called furin. 

This is significant because furin is found in lots of human tissues, including the lungs, liver and small intestines, which means that the virus has the potential to attack multiple organs, says Li Hua, a structural biologist at Huazhong University of Science and Technology in Wuhan, China, where the outbreak began. The finding could explain some of the symptoms observed in people with the coronavirus, such as liver failure, says Li, who co-authored a genetic analysis of the virus that was posted on the ChinaXiv preprint server on 23 February2. SARS and other coronaviruses in the same genus as the new virus don't have furin activation sites, he says.

The furin activation site “sets the virus up very differently to SARS in terms of its entry into cells, and possibly affects virus stability and hence transmission”, says Gary Whittaker, a virologist at Cornell University in Ithaca, New York. His team published another structural analysis of the coronavirus’s spike protein on bioRxiv on 18 February3.

Several other groups have also identified the activation site as possibly enabling the virus to spread efficiently between humans4. They note that these sites are also found in other viruses that spread easily between people, including severe strains of the influenza virus. On these viruses, the activation site is found on a protein called haemagglutinin, not on the spike protein.

Urging caution

But some researchers are cautious about overstating the role of the activation site in helping the coronavirus to spread more easily. “We don’t know if this is going to be a big deal or not,” says Jason McLellan, a structural biologist at the University of Texas at Austin, who co-authored another structural analysis of the coronavirus, which was published in Science on 20 February5.

Other scientists are wary of comparing furin activation sites on flu viruses to those on the new coronavirus. The haemagglutinin protein on the surface of flu viruses isn’t similar or related to the spike protein in coronaviruses, says Peter White, a virologist at the University of New South Wales in Sydney, Australia.

And the flu virus that caused the deadliest recorded pandemic, the 1918 Spanish flu pandemic, doesn’t even have a furin activation site, says Lijun Rong, a virologist at the University of Illinois in Chicago.

Whittaker says studies in cell or animal models are needed to test the activation site’s function. “Coronaviruses are unpredictable, and good hypotheses often turn out to be wrong,” he says. His team is currently testing how removing or modifying the site affects the spike protein’s function.

Drug targets

Li's team are also looking at molecules that could block furin, which could be investigated as possible therapies. But their progress is slow because of the outbreak. Li lives on campus and is currently the only member able to access his team's laboratory.

McLellan’s group in Texas has identified another feature that could explain why the new coronavirus infects human cells so successfully. Their experiments have shown that the spike protein binds to a receptor on human cells — known as angiotensin-converting enzyme 2 (ACE2) — at least ten times more tightly than does the spike protein in the SARS virus. Veesler’s team has also found this, which suggests that the receptor is another potential target for vaccines or therapies. For example, a drug that blocks the receptor might make it harder for coronavirus to enter cells.

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STUDENT ANXIETY

Part I.

Study anxiety: A havoc on youngsters.

What is study anxiety?

Anxiety is a common problem among children and is one of the largest groups of mental health problems especially during the period of childhood. This problem not only has an impact on developmental functioning but also has an impact on every day functioning including educational endeavors (Stallard, 2009). School students commonly experience anxiety issues related to studies and this phenomenon is called study anxiety (Cummings, Caporino & Kendall, 2004). This problem has been the focus of the attention of professionals around the world but unfortunately, it is not being addressed in Asian countries.

Understanding the anxiety

Anxiety is an emotional state of mind that includes having feelings of tension, distress thoughts along with physical changes like increased blood pressure, sweating, and nervousness. Children avoid studies and school activities to get rid of anxious feelings. Children may have many physical indications such as sweating, trembling, dizziness or a rapid heartbeat as well as a psychological disturbance in the form of intrusive and fearful thoughts. These feelings of anxiousness can interfere with the children's daily activities such as school performance, school work, and relationships (Spielberg, 1983). Furthermore, when a feeling of anxiousness persistently occurs in mind, a person cannot do what they want to do (Stallard, 2009).

The decline in academic performance

 Study anxiety is not only due to the learning issues, but it is due to habitual anxiety feelings and corresponding past negative experiences. Studies have confirmed that anxiety levels directly affect a student’s academic performance. For example, high levels of anxiety cause lower classroom performance and inwardly cause more anxiety (Hembree, 1988). Study anxiety is a condition that is associated with some particular situation which provokes anxious behavior and severely hampers the student’s academics (Zeidner, 1998). The concept of “study anxiety” is adapted from the general idea of anxiety and applied in the educational field, as is used to describe and explore the possibility of anxiety among students as well as its effects.

Symptoms

The psychological symptoms  experienced by students is the inability to maintain a flow of thoughts, feelings of helplessness, frightening behavior, and lack of interest in particularly difficult subjects (Spielberger, 1980). Furthermore, these children feel nervous before a class tutorial, freaking, going blank during an oral test, feeling helpless while doing homework, or lack of interest in that subject which is difficult to understand (Ruffins, 2007). There are also frequently associated physical symptoms, which include sweaty palms, accelerated breathing, a racing heartbeat, and nausea or general discomfort (Spielberger, 1980). Additionally feeling panic, uncontrolled breathing, irregular heartbeat, or a distressed stomach (Ruffins, 2007). The children are suffering from negative thinking patterns such as: “If I don’t pass this test, exam, and class I will not get a good job” and won’t be able to become an educated person. Due to study anxiety, children squirm in his/her seats and do not pay attention to classroom activities. Study anxiety also leady to truancy problems, breaking the school and classroom rules, avoiding the vocational activities, and taking too many sick leaves. Mostly school-going children break eye contact, low pitch of speech, avoid the connection with the teacher to hide their anxiousness (Child Mind Institution, 2018).

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MODE OF ACTION OF EBOLA VIRUS

MODE OF ACTION OF EBOLA VIRUS

INTRODUCTION TO EBOLA:

          It was seen in Congo the very first time that’s why it is also known as the Congo virus. Later it was also seen that it affects some of the African countries.it becomes a very hot topic for scientists when an amazing fact was known about it that it has the death rate of 90%.there is a large number of Ebola virus types known till now but the most dangerous one is the Zaire virus. [MODE OF ACTION OF EBOLA VIRUS].

TRANSFORMATION OF EBOLA VIRUS:

        There are many ways of transformation of the Ebola virus as other viruses but mainly thus viruses spread by the aerosol transformation. With the help of air. Another method which it uses is direct contact with the contaminated agents. Or it may spread by the feces of the Ebola-infected person.

SYMPTOMS OF EBOLA VIRUS INFECTION:

       Symptoms of Ebola virus is very much hard to define because it has very much similar symptoms of infection as other viruses have. Such as vomiting, chest pain, headache, are the major ones. All these symptoms may appear in any case of a viral infection is it is very hard to differentiate between Ebola and other virus infections.

STRUCTURE OF EBOLA VIRUS:

       Diameter of Ebola virus is about 80nm. And the length of Ebola is 800nm. A nucleocapsid is located at the center of Ebola virus. Ebola(Zaire) virus has an ssRNA genome on both sides of which NP, VP30, VP35, and L proteins are present. All this structure is wrapped by the envelope.

EBOLA PLAYS WITH OUR IMMUNE SYSTEM:

      Ebola dodges our immune system in a very great way. When our immune system is scanning our body about a problem in the meantime Ebola has done its work and our body has destroyed. When our body comes to know about the Ebola virus till that time our body is damaged till such a level that it is not possible to recover it.

MODE OF ACTION OF EBOLA VIRUS:

        Ebola actually uses our immune system to proceed infection cycle. Its infectivity is enhanced in the presence of antibodies produced by the immune response. A virus starts its activity after the attachment with the receptor on the cell. A ligand C1q helps the antibody-virus complex to bind with the receptor present on the cell. This ligand supports the Ebola to bind with the cell.

       Once the virus bind with the receptor it enters the host cell. After entering the body, the very first target of Ebola is macrophages and monocytes which are the immune cells Ebola destroy them by using the immune system, complement system of the host. Now white blood cells play their role against the virus and release the proinflammatory cytokines in a very large amount these cytokines, these cytokines enhance the permeability vascular endothelium.
Now because of these cytokines, the action virus can easily approach its secondary target or inner components of the cell which are the main target of the virus. The second task performed by the cytokine is to bring the new large number of the macrophages, and as the number of macrophages increases the virus has much more target to attack so due to a large amount of the macrophage the Ebola spread in a very large surface area. And have very much potential to cause disease. When cytokines are bringing new macrophages in the meantime virus destroy the hepatocytes. due to the hepatocytes destruction, the cell signal cannot be passed into the bloodstream.

ENTRY INTO ENDOTHELIAL:

         Now with the help of GP-mediated receptors the Ebola get entry into the endothelial cell. by using macro pinocytosis. With the help of micro pinocytosis, the small vesicle structure is formed which is known as macropinosomes. Now finally by using these macropinosomes viruses move into the acidic area of the cell at these compartments of the cell the PH dependent fusion of the virus takes place into endothelial cells among various viral and cell membranes. So as a result of this fusion and invagination the cell become totally disconnected from its neighbor cells as well as from its base. And completely loses its function as well as stability. Now Ebola replicates itself and made particles. These particles leave the cell with the help of lipids rafts and leave behind the destabilized vascular system. This system causes a huge blood loss which is the main characteristic of the patient affected by Ebola.

WHAT IS FUNCTION OF IMMUNE SYSTEM WHEN EBOLA TAKES CONTROL ON THE HOST BODY?

      At the time when Ebola takes control on the body, the immune system is completely out of control.

ACTION OF VP35 VIRAL PROTEIN:

       At the mean while the protein vp35 of the virus take command on the production of the interferon

And regulate their production

ACTION OF GP VIRAL PROTEIN:

       The GP protein takes control of the white blood cells regulation and trap the white blood cell into the circulatory system. That they could not perform their function.

      Now the remaining immune cells such as macrophages and monocytes release the cytokines these cytokines which are the proinflammatory due release of these cytokines virus take control over the vascular endothelium efficiently and damage it.

PARADOXICAL STATE:

            This state of the body is the paradoxical state it is the condition in which the patient dies because of hypovolemic shock from a huge hemorrhage and. Formation of huge clots of blood occur around the all body.
Keywords: [ ebola outbreak, ebola virus china, Ebola virus cure, ebola virus deaths, Ebola virus uk, Mode of action of ebola virus ]

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FULLY FUNDED Exchange Program for Pakistani Students in USA

FULLY FUNDED Exchange Program for Pakistani Students

SUSI 2020 Summer Exchange Program in the United States *NO IELTS/TOEFL Required.*
Students from any field of study can apply. *Undergraduates of (2,3,4,5,6,7) Semester are Eligible*

Type of scholarship: Fully funded by the Department of the United States
Duration: 5-6 Weeks

*SUSI Student Leaders 2020:* Male & Female Students Apply
Link: https://bit.ly/2OVQKMK
*Deadline*: December 17, 2019.

*SUSI Women Leaders 2020:*
Female Students Can Apply
Link: http://bit.ly/2DVZjlL
*Deadline*: December 10, 2019

*SUSI TIPS* https://bit.ly/2qWTuRZ

*Videos sessions* for your proper guidance and the preparation of the statement of purpose to increase the chances of your selection:

http://bit.ly/Video_Session_01
http://bit.ly/Video_Session_02
http://bit.ly/Video_Session_03
http://bit.ly/Video_Session_04

You can also visit  : Japanese scholarships 

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Japanese and Chinese fully funded Scholarship Updates for December 2020

Scholarship Updates

Ritsumeikan University

Japan Fully Funded MEXT Scholarships 2020 
under Japanese Government for International Students from all over the world.
Apply Website: https://scholarships365.info/ritsumeikan-university-scholarship

Offers: Airfare, Tuition, and Monthly Allowance

Programs: MS and Ph.D. Programs.

Deadline: 8th Jan 2020
Scholarships365, No Agent,
Direct Apply toUniversity. Shanghai Jiao Tong University Scholarship 2020
Fully Funded for International Students
(All Countries Students Can Apply).

Apply Website: https://scholarships365.info/Shanghai-Jiaotong-University-Scholarship
Programs: 100+ Masters and Ph.D.
Programs Offers: Full Tuition, Accommodation, Monthly Stipend, and Medical. Deadline: 15th December 2019 No Agent, Direct Apply.

Japanese fully funded Scholarship Updates for December 2020

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World Youth forum 2019 Sharm El-Sheikh, Egypt

World Youth forum 2019, Sharm El-Sheikh, Egypt is Now Back.* Fully Funded International Conference 2019

Biggest International Conference for all International Students & Egyptians. This Year in 2019 More than 5000 Participants will Participate.

Participants with *any academic disciplines* are eligible to apply. There are *No Academic or CGPA Requirements.* It’s not an academic program. It’s a Leadership Program

The aim of the WYF is to send a message of Peace & Make World Better.

Round Airfare Tickets, Meals, Full Accommodation, Local Transportation will be provided.

How to Apply Online *Link:* https://youtu.be/YjlVwnSxrJ8

Official Website Link: https://wyfegypt.com/index.php

*Deadline:* 10th November 2019

Keep Support & Share this Post in all your Facebook and WhatsApp groups for others Help. For More latest Upcoming Opportunities Stay Tuned. If you need any guidance Comments Or Inbox.

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Registrations for *KPITB's Digital Internship Program 2019-20 are open now

Registrations for *KPITB's Digital Internship Program 2019-20* are open now.

*Apply Now:* http://assami.kp.gov.pk/

Last date to apply: September 20, 2019

*SALIENT FEATURES:*

- Monthly stipend of PKR 14000/-

- ICT capacity building of KP youth to enable them to compete in Global ICT markets

- Skill ready workforce to ensure speedy expansion of ICT industry in KP

*ELIGIBILITY CRITERIA FOR SOFTWARE HOUSES:*

- 16 years of Education in IT, CS or ICT
FOR CALL CENTERS

- 14 years of Education (BA or equivalent)

*TERMS & CONDITIONS:*

- Applicants must have domicile of Khyber Pakhtunkhwa or Newly Merged Districts of Khyber Pakhtunkhwa (Former F.A.T.A)

- Applicants that graduated in the last 3 years (after 30th July 2016) are eligible to apply

- Fresh graduates may also apply by submitting final year transcript

- Applicants that already have Post-qualification work experience are not eligible

- Applicants that have already availed KPITB’s Digital Internship are not eligible

*Admin*

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Admissions open in Universities

*ADMISSION ALERT*

UET Lahore announces Admissions for BSc Engineering Programs
*Deadline:* 16-09-2019
*Level*: Bachelor

VIRTUAL UNIVERSITY OF PAKISTAN, LAHORE
*Deadline:* 14-09-2019
*Level*: PhD, Bachelor, MA/MSc, MS

UNIVERSITY OF THE PUNJAB, LAHORE
*Deadline:* 06-09-2019
*Level*: MS

LAHORE COLLEGE FOR WOMEN UNIVERSITY, LAHORE
*Deadline:* 13-09-2019
*Level*: Bachelor, MS, PhD, MA/MSc

GOVERNMENT COLLEGE UNIVERSITY, LAHORE
*Deadline:* 04-09-2019
*Level*: MS

RACHNA COLLEGE OF ENGINEERING AND TECHNOLOGY, GUJRANWALA
*Deadline:* 16-09-2019
*Level*: Bachelor
ZIA-UD-DIN MEDICAL UNIVERSITY, KARACHI
*Deadline:* 10-09-2019
*Level*: MS

DHA SUFFA UNIVERSITY(MAIN CAMPUS), KARACHI
*Deadline:* 14-09-2019
Admissions open in Universities

*Level*: Bachelor, MS, PhD

THE GOVERNMENT SADIQ COLLEGE WOMEN UNIVERSITY, BAHAWAL PUR
*Deadline:* 20-09-2019
*Level*: Bachelor, MS, MA/MSc, PhD

UNIVERSITY OF HARIPUR, HARIPUR
*Deadline:* 10-09-2019
*Level*: Bachelor, MS, MA/MSc

MUHAMMAD NAWAZ SHARIF UNIVERSITY OF AGRICULTURE, MULTAN
*Deadline:* 20-09-2019
*Level*: Bachelor

NATIONAL UNIVERSITY OF MODERN LANGUAGES ( FAISALABAD CAMPUS ), FAISALABAD
*Deadline:* 30-08-2019
*Level*: MS, Bachelor, MA/MSc

SARHAD UNIVERSITY OF SCIENCE & INFORMATION TECHNOLOGY, PESHAWAR
*Deadline:* 30-08-2019
*Level*: Bachelor, MA/MSc

ABBOTTABAD UNIVERSITY OF SCIENCE AND TECHNOLOGY, ABBOTTABAD
*Deadline:* 02-09-2019
*Level*: Bachelor

IMPERIAL COLLEGE OF BUSINESS STUDIES, LAHORE
*Deadline:* 05-09-2019
*Level*: Bachelor

BZU Multan
*Deadline* : 25-9-19
*LeveL*: BS and MS

RIPHAH INTERNATIONAL UNIVERSITY, ISLAMABAD
*Deadline:* 08-09-2019
*Level*: Bachelor

ABBOTTABAD UNIVERSITY OF SCIENCE AND TECHNOLOGY, ABBOTTABAD
*Deadline:* 13-09-2019
*Level*: MS, MA/MSc

CITY UNIVERSITY OF SCIENCE & INFORMATION TECHNOLOGY, PESHAWAR
*Deadline:* 16-09-2019
*Level*: Bachelor, MS, PhD, MA/MSc

LAHORE LEADS UNIVERSITY, LAHORE
*Deadline:* 17-09-2019
*Level*: Bachelor, MS, MA/MSc

THE UNIVERSITY OF LAHORE ( ISLAMABAD CAMPUS ), ISLAMABAD
*Deadline:* 06-09-2019
*Level*: Bachelor

NATIONAL TEXTILE UNIVERSITY FAISALABAD, SUB CAMPUS, KARACHI
*Deadline:* 14-09-2019
*Level*: Bachelor

THE UNIVERSITY OF LAHORE ( ISLAMABAD CAMPUS ), ISLAMABAD
*Deadline:* 15-09-2019
*Level*: Bachelor

*Admin*

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