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
January 26,2020

High-protein diets may help people lose weight and build muscle, but there is a downside to it --a greater heart attack risk. Researchers now report that high-protein diets boost artery-clogging plaque.

The research in mice showed that high-protein diets spur unstable plaque -- the kind most prone to rupturing and causing blocked arteries.

More plaque buildup in the arteries, particularly if it's unstable, increases the risk of heart attack.

"There are clear weight-loss benefits to high-protein diets, which has boosted their popularity in recent years," said senior author Babak Razani, associate professor at Washington University School of Medicine in St. Louis, Missouri.

"But animal studies and some large epidemiological studies in people have linked high dietary protein to cardiovascular problems. We decided to take a look at whether there is truly a causal link between high dietary protein and poorer cardiovascular health," Razani added.

The researchers studied mice who were fed a high-fat diet to deliberately induce atherosclerosis, or plaque buildup in the arteries.

Some of the mice received a high-fat diet that was also high in protein. And others were fed a high-fat, low-protein diet for comparison.

The mice on the high-fat, high-protein diet developed worse atherosclerosis -- about 30 per cent more plaque in the arteries -- than mice on the high-fat, normal-protein diet, despite the fact that the mice eating more protein did not gain weight, unlike the mice on the high-fat, normal-protein diet.

"A couple of a scoop of protein powder in a milkshake or smoothie adds something like 40 grams of protein -- almost equivalent to the daily recommended intake," Razani said.

"To see if protein has an effect on cardiovascular health, we tripled the amount of protein that the mice receive in the high-fat, high-protein diet -- keeping the fat constant. Protein went from 15 per cent to 46 per cent of calories for these mice".

Plaque contains a mix of fat, cholesterol, calcium deposits and dead cells. Past work by Razani's team and other groups has shown that immune cells called macrophages work to clean up plaque in the arteries.

But the environment inside plaque can overwhelm these cells, and when such cells die, they make the problem worse, contributing to plaque buildup and increasing plaque complexity.

"In mice on the high-protein diet, their plaques were a macrophage graveyard," Razani informed.

To understand how high dietary protein might increase plaque complexity, Razani and his colleagues also studied the path protein takes after it has been digested -- broken down into its original building blocks, called amino acids.

"This study is not the first to show a telltale increase in plaque with high-protein diets, but it offers a deeper understanding of the impact of high protein with the detailed analysis of the plaques," said Razani.

"This work not only defines the critical processes underlying the cardiovascular risks of dietary protein but also lays the groundwork for targeting these pathways in treating heart disease," he added.

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Agencies
June 20,2020

The World Health Organisation has warned that the COVID-19 pandemic is entering a "new and dangerous" phase. Thursday saw the most cases in a single day reported to the WHO.

Tedros Adhanom Ghebreyesus said the day had seen 150,000 new cases with half of those coming from the Americas and large numbers also from the Middle East and South Asia, the BBC reported.

He said the virus was still spreading fast and the pandemic accelerating.

He acknowledged people might be fed up with self-isolating and countries were eager to open their economies but he said that now was a time for extreme vigilance.

Maria van Kerkhove, technical lead of the WHO's COVID-19 response, told a press conference the pandemic is "accelerating in many parts of the world".

"While we have seen countries have some success in suppressing transmission and bringing transition down to a low level, every country must remain ready," she said.

Mike Ryan, the head of the WHO's Health Emergencies Programme, said that some countries had managed to flatten the peak of infections without bringing them down to a very low level.

"You can see a situation in some countries where they could get a second peak now, because the disease has not been brought under control," he said.

"The disease will then go away and reduce to a low level, and they could then get a second wave again in the autumn or later in the year."

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Agencies
July 7,2020

The World Health Organization (WHO) is reviewing a report that suggested its advice on the novel coronavirus needs updating after some scientists told the New York Times there was evidence the virus could be spread by tiny particles in the air.

The WHO says the Covid-19 disease spreads primarily through small droplets, which are expelled from the nose and mouth when an infected person breaths them out in coughs, sneezes, speech or laughter and quickly sink to the ground.

In an open letter to the Geneva-based agency, 239 scientists in 32 countries outlined the evidence they say shows that smaller exhaled particles can infect people who inhale them, the newspaper said on Saturday.

Because those smaller particles can linger in the air longer, the scientists - who plan to publish their findings in a scientific journal this week - are urging WHO to update its guidance, the Times said.

"We are aware of the article and are reviewing its contents with our technical experts," WHO spokesman Tarik Jasarevic said in an email reply on Monday to a Reuters request for comment.

The extent to which the coronavirus can be spread by the so-called airborne or aerosol route - as opposed to by larger droplets in coughs and sneezes - remains disputed.

Any change in the WHO's assessment of the risk of transmission could affect its current advice on keeping one-metre physical distancing. Governments, which also rely on the agency for guidance policy, may also have to adjust public health measures aimed at curbing the spread of the virus.

"Especially in the last couple of months, we have been stating several times that we consider airborne transmission as possible but certainly not supported by solid or even clear evidence," Benedetta Allegranzi, the WHO's technical lead for infection prevention and control, was quoted as saying in the New York Times.

WHO guidance to health workers, dated June 29, says that SARS-CoV-2, the virus that causes Covid-19, is primarily transmitted between people through respiratory droplets and on surfaces.

But airborne transmission via smaller particles is possible in some circumstances, such as when performing intubation and aerosol-generating procedures, it says.

Medical workers performing such procedures should wear heavy-duty N95 respiratory masks and other protective equipment in an adequately ventilated room, the WHO says.

Officials at South Korea's Centers for Disease Control said on Monday they were continuing to discuss various issues about Covid-19, including the possible airborne transmission. They said more investigations and evidence were needed.

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