SARS-CoV-2

12 Articles

Coronavirus Testing: CRISPR Technology Set To Streamline Viral Testing

May 27, 2020 by 3 Comments

If we could run back 2020 to its beginning and get a do-over, chances are pretty good that we’d do a lot of things differently. There’s a ton of blame to go around on COVID-19, but it’s safe to say that one of the biggest failures of this whole episode has been the lack of cheap, quick, accurate testing for SARS-CoV-2, the virus behind the current pandemic. It’s not for lack of information; after all, Chinese scientists published the sequence of the viral genome very early in the pandemic, and researchers the world over did the same for all the information they gleaned from the virus as it rampaged around the planet.

But leveraging that information into usable diagnostics has been anything but a smooth process. Initially, the only method of detecting the virus was with reverse transcriptase-polymerase chain reaction (RT-PCR) tests, a fussy process that requires trained technicians and a well-equipped lab, takes days to weeks to return results, and can only tell if the patient has a current infection. Antibody testing has the potential for a quick and easy, no-lab-required test, but can only be used to see if a patient has had an infection at some time in the past.

What’s needed as the COVID-19 crisis continues is a test with the specificity and sensitivity of PCR combined with the rapidity and simplicity of an antibody test. That’s where a new assay, based on the latest in molecular biology methods and dubbed “STOPCovid” comes in, and it could play a major role in diagnostics now and in the future.

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Dr. Anthony Fauci, Infectious Disease Slayer

May 12, 2020 by 21 Comments

In the two months since the harsh realities of SARS-CoV-2 and COVID-19 have come into sharp focus, Americans have become increasingly familiar with a man who has been quietly serving the people since the days when Ronald Reagan was up for re-election. For many, Dr. Anthony Fauci is the national voice of reason in a sea of dubious information. He has arguably become the most trustworthy person the government has to offer in the face of this pandemic.

Officially, Dr. Fauci is the Director of the National Institute of Allergy and Infectious Diseases (NIAID), a position he was appointed to in 1984. He has worked under six presidents, advising them on every outbreak from the HIV/AIDS epidemic up through Zika and Ebola. Now, he is part of the White House’s coronavirus task force.

At 79 years old, he still works 18-hour days, sticking it to infectious diseases with one hand, and smoothing the feathers of the American people with the other. Dr. Fauci certainly feels like the right person at the right time. So how did he get to this point?

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Help Us Throw More Cycles At The Coronavirus Problem

May 10, 2020 by 45 Comments

The Hackaday community has answered the call and put their computers put to work folding proteins found in the coronavirus. Team_Hack-a-Day ranks #44 in the world so far this month, and I’ve seen us rank as high as #19 on 24-hour leaderboards.

Want to join the fight? Donate some of those computing cycles you’re not using to battling SARS‑CoV‑2. You’re probably not an epidemiologist or a vaccine researcher, but you can make their jobs easier by providing them with the data they need through the Folding@home Project.

As Dan Maloney explained in his excellent article on protein folding, understanding the incredibly complex folding behavior of the proteins in the virus will be key to finding treatments and possibly a vaccine. Folding@home connects countless computers via the internet and is now the largest supercomputer in the world, consisting of over 3.5 million CPUs and over half a million GPUs. The resulting data is freely available to researchers.

Let’s take a look at how easy it is to get up and running, how a GPU can supercharge a setup, and dip into the stats for Team_Hack-a-Day’s effort.

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Brainstorming COVID-19 Hack Chat

April 6, 2020 by 15 Comments

Join us on Wednesday, April 8 at noon Pacific for the Brainstorming COVID-19 Hack Chat!

The COVID-19 pandemic has been sweeping across the globe now for three months. In that time it has encountered little resistance in its advances, being a novel virus with just the right mix of transmissibility and virulence that our human immune systems have never encountered. The virus is racking up win after win across the world, crippling public health and medical systems, shutting down entire economies, and forcing billions of people into isolation for the foreseeable future.

While social distancing is certainly an effective way to limit the spread of the disease, it feels more like hiding than fighting. Bored and stuck at home, millions of fertile minds are looking for an outlet for this frustration, a more affirmative way to fight the good fight and build solutions that the world sorely needs. And thus we’ve seen the outpouring of designs, ideas, and prototypes of everything from social distancing helpers to personal protective equipment (PPE) hacks.

In this Hack Chat, we’ll try to provide a framework around which hackers can start to turn their ideas into COVID-19 solutions. There are a ton of problems right now, but the most acute and most approachable seem to revolve around making sure healthcare providers have the PPE they need to do their job safely. Hacking at the edges of managing social distancing seems doable, too, both in terms of helping people keep a healthy distance from each other and in managing the isolation that causes. And let’s not forget about managing boredom; idle hands lead to idle minds, and staying healthy mentally is just as important as good handwashing and nutrition.

Join us on Wednesday for this group-led Hack Chat and bring your best ideas for attacking COVID-19 head-on.

join-hack-chatOur Hack Chats are live community events in the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, April 8 at 12:00 PM Pacific time. If time zones have got you down, we have a handy time zone converter.

Click that speech bubble to the right, and you’ll be taken directly to the Hack Chat group on Hackaday.io. You don’t have to wait until Wednesday; join whenever you want and you can see what the community is talking about.

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Augmented Reality Aids In The Fight Against COVID-19

March 12, 2020 by 3 Comments

“Know your enemy” is the essence of one of the most famous quotes from [Sun Tzu]’s Art of War, and it’s as true now as it was 2,500 years ago. It also applies far beyond the martial arts, and as the world squares off for battle against COVID-19, it’s especially important to know the enemy: the novel coronavirus now dubbed SARS-CoV-2. And now, augmented reality technology is giving a boost to search for fatal flaws in the virus that can be exploited to defeat it.

The video below is a fascinating mix of 3D models of viral structures, like the external spike glycoproteins that give coronaviruses their characteristic crown appearance, layered onto live video of [Tom Goddard], a programmer/analysts at the University of California San Francisco. The tool he’s using is called ChimeraX, a molecular visualization program developed by him and his colleagues. He actually refers to this setup as “mixed reality” rather than “augmented reality”, to stress the fact that AR tends to be an experience that only the user can fully appreciate, whereas this system allows him to act as a guide on a virtual tour of the smallest of structures.

Using a depth-sensing camera and a VR headset, [Tom] is able to manipulate 3D models of the SARS virus — we don’t yet have full 3D structure data for the novel coronavirus proteins — to show us exactly how SARS binds to its receptor, angiotensin-converting enzyme-2 (ACE-2), a protein expressed on the cell surfaces of many different tissue types. It’s fascinating to see how the biding domain of the spike reaches out to latch onto ACE-2 to begin the process of invading a cell; it’s also heartening to watch [Tom]’s simulation of how the immune system responds to and blocks that binding.

It looks like ChimeraX and similar AR systems are going to prove to be powerful tools in the fight against not just COVID-19, but in all kinds of infectious diseases. Hats off to [Tom] and his team for making them available to researchers free of charge.

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