First open source all-atom models of COVID-19 protein developed

Agencies
June 22, 2020

A team of scientists has produced first open source all-atom models of full-length COVID-19 Spike protein that facilitates viral entry into host cells – a discovery that can facilitate a faster vaccine and antiviral drug development.

The group from Seoul National University in South Korea, University of Cambridge in the UK and Lehigh University in the US produced the first open-source all-atom models of a full-length S protein.

The researchers say this is of particular importance because the S protein plays a central role in viral entry into cells, making it a main target for vaccine and antiviral drug development.

"Our models are the first full-length SARS-CoV-2 spike (S) protein models that are available to other scientists," said Wonpil Im, a professor in Lehigh University.

"Our team spent days and nights to build these models very carefully from the known cryo-EM structure portions. Modeling was very challenging because there were many regions where simple modeling failed to provide high-quality models," he wrote in a paper published in The Journal of Physical Chemistry B.

Scientists can use the models to conduct innovative and novel simulation research for the prevention and treatment of Covid-19.

Though the coronavirus uses many different proteins to replicate and invade cells, the Spike protein is the major surface protein that it uses to bind to a receptor.

The total number of global COVID-19 cases was nearing 9 million, while the deaths have increased to over 467,000, according to the Johns Hopkins University.

With 2,279,306 cases and 119,967 deaths, the US continues with the world's highest number of COVID-19 infections and fatalities, according to the CSSE.

Brazil comes in the second place with 1,083,341 infections and 50,591 deaths.

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Agencies
June 11,2020

The World Health Organisation (WHO) Director-General Tedros Adhanom Ghebreyesus said that more research needs to be done to better understand the extent to which COVID-19 is being spread by people who don't show symptoms.

"Since early February, we have said that asymptomatic people can transmit COVID-19, but that we need more research to establish the extent of asymptomatic transmission," the WHO chief said at a virtual press conference from Geneva on Wednesday, Xinhua news agency reported.

"That research is ongoing, and we're seeing more and more research being done," he added.

Saying that the world has been achieving a lot in knowing the new virus, the WHO chief told reporters that "there's still a lot we don't

"WHO's advice will continue to evolve as new information becomes available," he said.

Tedros stressed that the most critical way to stop transmission is to find, isolate and test people with symptoms, and trace and quarantine their contacts.

"Many countries have succeeded in suppressing transmission and controlling the virus doing exactly this," Tedros said.

Meanwhile, Michael Ryan, executive director of WHO Health Emergencies Program, said Wednesday that the COVID-19 pandemic is still evolving.

"If we look at the numbers... this pandemic is still evolving. It is growing in many parts of the world," he said. "We have deep concerns that health systems of some countries are struggling, under a huge strain and require our support, our help and our solidarity."

He said "each and every country has a different combination of risks and opportunities, and it's really down to national authorities to carefully consider where they are in the pandemic."

In Europe, the risk issue now are about travels and the opening of the schools, around risk management, mass gathering, surveillance and contact tracing, said the WHO official.

In Southeast Asian countries, where to a great extent transmissions have been under control, governments are more concerned about the re-emergence of clusters, while in South America, the issue of PPE for health workers has not gone away, said Ryan.

As regards Africa, Ryan said the death rates have been very low in the past week, but the health system can be overwhelmed, as it would have to cope with other diseases such as malaria.

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Agencies
May 18,2020

China, where the novel coronavirus originated, has reported 111 cases since beginning of May, which shows the infection rate has dipped, and 3 deaths since April 27, according to the WHO. A Shanghai-based Noida doctor says China is close to winning the battle against COVID-19, and the combination of zinc, hydroxychloroquine (HCQ) and antibiotic azithromycin has been able to save the lives of coronavirus patients.

Speaking to media persons, Dr Sanjeev Choubey, Medical Director Internal Medicine at St. Michael Hospital said this combination has been adopted as a line of treatment for patients infected with coronavirus, and as a result patients are recovering, decreasing their need for intensive care.

What is the line of treatment for COVID-19 patients, which also include asymptomatic patients?

The combination of zinc, hydroxychloroquine and antibiotic azithromycin has produced positive results, and it helped in the recovery of many COVID-19 patients. The combination -- Ascorbic Acid, B-complex, Zinc, Selenium, L-carnitine, Vitamin B-12 and Glutathione normal saline should be administered on patients twice a week for at least 6 weeks. This is COVID-19 treatment protocol for prophylaxis, and it implies both asymptomatic and symptomatic along with other medicine support.

Based on your experience on COVID-19 in China, after how many tests, is it safe to call a person coronavirus free?

The coronavirus should be performed at least 9 times, before terming a patient COVID-19 free. It is a standard in China. This procedure has worked in China and it will also work in India. Minimum five tests should be mandatory through RT-PCR.

Does coronavirus majorly attack the respiratory system or it could lead to organ failure too?

Line of treatment should not be just looking at the respiratory system, as the problem lies somewhere else. COVID-19 attacks many vital organs in the body. In China, a coronavirus patient died from a stroke. In the autopsy it was found that the innermost layer in the arteries was swollen. It was concluded that coronavirus had inflamed the layer of the arteries leading to clotting, which was a factor in generating a heart attack. Therefore, COVID-19 is not just a respiratory problem.

Amid the coronavirus pandemic, should autopsy be made mandatory in the case of unpredictable death or where reasons for death are not unknown?

Patients below 50 years, who die suddenly and the reasons are not known, then it should be mandatory to conduct the autopsy. After death, coronavirus is active in the body for five days, and it fades away on day 6. Therefore, if an autopsy is done then it will help in understanding this disease. In China, we have seen young COVID-19 patients, aged 22 and 28, succumbed to strokes.

Since the beginning of May, India has recorded more than 2,000 cases everyday in the first week, then it jumped past 3,000 mark in the second week. Finally, the tally is 4,987 on May 17. At 90,927 cases, has India progressed into community transmission or Stage3?

Yes, India has moved into Stage 3. The data suggests that 3,000 to 4,000 active COVID-19 cases, who are asymptomatic, are moving around and spreading the infection. The research has indicated that COVID-19 from an infected person spreads in 30 minutes to non-infected persons. The relaxation on the lockdown will certainly contribute to a high infection rate.

Do you think India has reached its peak in COVID-19 cases, or the sharp rise will continue till July end?

It seems India has already reached its peak and cases will begin to come down from June end or beginning of July first week. If social distancing norms are followed then certainly things can improve, but if not followed then it may get worse. High population density is a major contributor for the increase in cases. The government should continue to focus on finding hotspots, and urge people to follow the rules, eventually it is for people’s own benefit.

Has China won the battle against COVID-19?

It seems China has won the battle by not opening up Wuhan. The Chinese are following a COVID-19 patient’s engagement program, where the authorities continuously interact with people infected with the disease. The Government of India should reward people who follow the guidelines; it will help in setting up a positive trend in the society.

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Agencies
March 3,2020

Taking multiple courses of antibiotics within a short span of time may do people more harm than good, suggests new research which discovered an association between the number of prescriptions for antibiotics and a higher risk of hospital admissions.

Patients who have had 9 or more antibiotic prescriptions for common infections in the previous three years are 2.26 times more likely to go to hospital with another infection in three or more months, said the researchers.

Patients who had two antibiotic prescriptions were 1.23 times more likely, patients who had three to four prescriptions 1.33 times more likely and patients who had five to eight 1.77 times more likely to go to hospital with another infection.

"We don't know why this is, but overuse of antibiotics might kill the good bacteria in the gut (microbiota) and make us more susceptible to infections, for example," said Professor Tjeerd van Staa from the University of Manchester in Britain.

The study, published in the journal BMC Medicine, is based on the data of two million patients in England and Wales.

The patient records, from 2000 to 2016, covered common infections such as upper respiratory tract, urinary tract, ear and chest infections and excluded long term conditions such as cystic fibrosis and chronic lung disease.

The risks of going to hospital with another infection were related to the number of the antibiotic prescriptions in the previous three years.

A course is defined by the team as being given over a period of one or two weeks.

"GPs (general physicians) care about their patients, and over recent years have worked hard to reduce the prescribing of antibiotics,""Staa said.

"But it is clear GPs do not have the tools to prescribe antibiotics effectively for common infections, especially when patients already have previously used antibiotics.

"They may prescribe numerous courses of antibiotics over several years, which according to our study increases the risk of a more serious infection. That in turn, we show, is linked to hospital admissions," Staa added.

It not clear why hospital admissions are linked to higher prescriptions and research is needed to show what or if any biological factors exist, said the research team.

"Our hope is that, however, a tool we are working for GPs, based on patient history, will be able to calculate the risks associated with taking multiple courses of antibiotics," said Francine Jury from the University of Manchester.

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