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germinate_love germinate_love
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4 years ago
I'm learning how to do PCR in my home lab and coincidentally, I encountered several pieces of key information which have prompted some questions about testing of the virus.

First, the CDC has published the following:
* Complete Genome of the Virus
* Complete RT-PCR Testing Protocol
* PCR Probes and Primers
* There's also a regular, non-RT PCR protocol published - still looking for it

There are also at least seven different countries which have developed test kit manufacturing pipeline that appears to have made it to the marker much quicker than in the US.

One of the earliest test protocols (maybe the first published) created by a German bio startup has been able to create a PCR-based test for under $5 per person. Once they got a working test protocol, they partnered with a local big pharma and have been working night/day to package and ship out the tests.

In simplistic terms, I believe the test works by using PCR to amplify a segment of DNA of the virus from a respiratory sample and then detecting the presence of the viral DNA from the specimen.

If it really is that simple, and I think it is, then why aren't tests more readily available in the US? Is it purely a regulatory / FDA backlog? I know the creation of the primers is something you def. can't do easily at home so is that the bottleneck? They use a modified COVID-19 virus in the master mix as a control - that might also be hard to get a hold of - is that the bottleneck?

I just feel like this is exactly why I think we need Citizen Scientists and indie biohackers because collectively, we can work on these sort of problems and move on these kinds of issues much quicker than behemoth govt and big pharma. I'm aware of the need for regulation and a proper process, but in times of crisis, I think people should have the freedom to of taking a test or treatment so long as they assume full responsibility for the outcome and it doesn't hurt others.

What haven't more biolabs figured out how to get a simple cheap test to market quicker? I don't understand why even local universities and biolabs aren't more engaged in working on this problem. Maybe they are and I'm just out of the loop?

tldr; If the Covid-19 virus testing protocol is cheap, easy and accessible to saavy home biohackers who can do PCR, why isn't the test more accessible to the public?
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wrote...
Educator
4 years ago Edited: 4 years ago, bio_man
Very cool, thanks for sharing the genome!

If it really is that simple, and I think it is, then why aren't tests more readily available in the US? Is it purely a regulatory / FDA backlog? I know the creation of the primers is something you def. can't do easily at home so is that the bottleneck? They use a modified COVID-19 virus in the master mix as a control - that might also be hard to get a hold of - is that the bottleneck?

It's preparedness. Once it got declared a pandemic, more people began taking it seriously, and only then did citizens begin to apply pressure on their government representatives to start taking action. I remember 2 weeks ago watching Pres. Trump presume it to be no different than the flu.

Preparing these kits in theory is easy, but administering them and producing them in high numbers isn't. Furthermore, most blood test requires lab technicians to isolate the components of the blood, and perform the interpret the tests correctly - unfortunately, they're currently swamped with test requests.

If it were are as easy as a pregnancy test, then it can be done at home, but the technology isn't there yet. Take, for example, an HIV self-testing kit. Since its discovery in the 80s, we're only seeing this technology available to the public relatively recently. That being said, I don't see a home kit being mass-produced any time soon simply due to the logistics. But I can assure you every major player in the pharmaceutical industry is working endlessly to be the first to release something -- it's only a matter of time.
wrote...
Staff Member
4 years ago Edited: 4 years ago, duddy
What does think of this post made by Dr. Paul Offit:

Which will do more harm, the virus or the fear of the virus?

Why are we so scared of the novel coronavirus, COVID-19?

People are usually scared of viruses for three reasons:

  • One: the virus causes gruesome, disfiguring, permanent symptoms. Smallpox, for example, not only caused life-long facial scarring, it also was a frequent cause of blindness in those who survived.
  • Two: the virus has a predilection for children. Polio paralyzed tens of thousands of young children every year until a vaccine finally eliminated the disease from the United States.
  • Three: the virus is likely to kill you. Rabies kills virtually 100 percent of people who develop symptoms after a bite from a rabid animal.

The novel coronavirus currently circulating in the United States—the one that has caused us to shut down schools, restaurants, sporting events, and virtually every aspect of our culture—falls into none of these categories.

Nonetheless, people are scared. Really scared. The reason is they think that if they catch COVID-19, they have a high likelihood of dying from the disease. Most public health officials have done little to lessen this fear, arguing that people are ten times more likely to die from this novel coronavirus than from influenza. Unfortunately, these officials haven’t made clear the difference between relative risk and absolute risk. Although people are more likely to die from COVID-19 than from influenza, they are far more likely to catch influenza. Therefore, they are far more likely to die from influenza.

According to the Centers for Disease Control and Prevention, as of March 7, 2020, 36 million to 51 million people have suffered from influenza, 370,000 to 670,000 have been hospitalized, and 22,000 to 55,000 have died from the disease. To put these numbers in perspective, let’s look at countries that have dealt with COVID-19.

China, where COVID-19 originated, has reported roughly 3,000 deaths. The population of China is about 1.4 billion, three times greater than ours. If we suffer an equivalent proportion of deaths, then 1,000 Americans will die from COVID-19, one-twentieth to one-fiftieth of the number who have died from influenza.

Italy has reported roughly 2,000 deaths from COVID-19 and, as a result, has shut down the country; only grocery stores and pharmacies remain open. Italy has a population of 60 million, about one-fifth of the U.S. population. If we suffer an equivalent proportion of deaths, then 10,000 Americans will die of COVID-19, about one-half to one-fifth of the number of deaths from influenza
.
Not everyone, however, is at equal risk of dying. The virus primarily kills the elderly and those suffering from chronic diseases, which explains the situation in Italy, where 25 percent of its population is more than 65 years of age; in the U.S. it’s 16 percent. Wouldn’t it make more sense, then, to ask people who are elderly and infirm to stay away from crowds, thus lessening their chances of contracting the disease. Also, to ask people who are sick with respiratory symptoms to stay home. Focus on common sense things like washing hands several times a day and standing clear of people who are coughing or sneezing. The federal government can also help by making it easier for businesses to allow people who are ill to stay home.

In 2009-2010, the world suffered an influenza pandemic caused by swine flu; about 203,000 people were killed by the virus; 12,000 in the United States. The novel coronavirus has killed about 6,000 people to date; 62 in the United States. It doesn’t make sense to shut down our entire way of life to try and stop a virus that is unlikely to harm healthy people and will be far less devastating than the influenza epidemics that we experience every winter and the influenza pandemic we experienced ten years ago. Let’s take common sense measures to stop the spread. The precautionary principle dictates caution to prevent harm. But the precautionary principle also dictates that you don’t cause harm in the name of preventing harm. It will take years to recover from the draconian measures that we are currently instituting.
- Master of Science in Biology
- Bachelor of Science
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Donated
4 years ago Edited: 4 years ago, germinate_love
Very cool, thanks for sharing the genome!
If it really is that simple, and I think it is, then why aren't tests more readily available in the US? Is it purely a regulatory / FDA backlog? I know the creation of the primers is something you def. can't do easily at home so is that the bottleneck? They use a modified COVID-19 virus in the master mix as a control - that might also be hard to get a hold of - is that the bottleneck?
It's preparedness. Once it got declared a pandemic, more people began taking it seriously, and only then did citizens begin to apply pressure on their government representatives to start taking action. I remember 2 weeks ago watching Pres. Trump presume it to be no different than the flu. Preparing these kits in theory is easy, but administering them and producing them in high numbers isn't. Furthermore, most blood test requires lab technicians to isolate the components of the blood, and perform the interpret the tests correctly - unfortunately, they're currently swamped with test requests. If it were are as easy as a pregnancy test, then it can be done at home, but the technology isn't there yet. Take, for example, an HIV self-testing kit. Since its discovery in the 80s, we're only seeing this technology available to the public relatively recently. That being said, I don't see a home kit being mass-produced any time soon simply due to the logistics. But I can assure you every major player in the pharmaceutical industry is working endlessly to be the first to release something -- it's only a matter of time.

I'm of the mindset to ask, "why do we need our centralized government to solve this problem to begin with?" If a German biotech startup with 12 people can develop a test and then manage to ramp up to 10,000+ tests a week in the matter of days - why couldn't one of our great American companies do the same?

Is it regulation? Do we need to allow more citizens to assume more risk and liability if it means getting quicker access to experimental tests and treatment? Many folks would happily accept the possibility of a false test as a data point vs having no data at all.

Since PCR is getting cheaper to do at home, I see no reason why we can't open source a DNA-based viral infection test kit that can be easily adapted to the infection de jour. I'm certain the ingenuity of our people can work to overcome the risks in exchange for access to something that is otherwise is in the hands of controlling interests which may have competing objectives.

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But I can assure you every major player in the pharmaceutical industry is working endlessly to be the first to release something -- it's only a matter of time.

I'm aware of at least three US companies, including the CDC, which have already released and are manufacturing their tests; though, they have not yet been widely administered.

I'm wondering what specifically created this delay in the US system vs. Germany which made it to market, at-scale super fast and by a startup no less.
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4 years ago
@duddy I can't argue those facts; there are a confluence of factors leading towards the overreaction, not the least of which is a dying media that thrives on keeping consumers in constant fear in order stay in business, self-serving politicians vying for power, and probably the most influential factor of all - the lack of emotional resilience among a generation of people who have spent the majority of their lives living a relatively easy life with a wealth of incredible benefits that were unavailable throughout 99.9% of human history.

So far, there's no indication this virus is anymore deadly than of recent past. Regular flu kills 40K+ a year. Heck, 500K people die a year from heart disease in the US. Where's the panic there? Los Angeles recently had a typhus outbreak in the homeless community - I didn't see the mayor or governor declare a state of emergency then. It makes you wonder.

All that said, I think there's opportunity in using this moment to assess and uncover potential improvements across the board.
wrote...
Educator
4 years ago
I'm of the mindset to ask, "why do we need our centralized government to solve this problem to begin with?" If a German biotech startup with 12 people can develop a test and then manage to ramp up to 10,000+ tests a week in the matter of days - why couldn't one of our great American companies do the same?

Believe it or not, people trust the government in Washington to do what is right. When an idea is officially endorsed or promoted through legislation, it's correlated with safety and security, and those are the primary concerns for most citizens.

As you can see, it only takes a small team to produce a viable testing kit, but the government has the responsibility of making sure it works properly for the masses. It needs to be tested a lot more before it can be sold, and I don't think the biotech team has done that yet. The government has this luxury to test a product at large scale due to endless resources, but still very little is known about the pathogen. At the end of the day, institutions were unprepared for this pandemic, and most government officials let it fly under their radar.

Quote
Is it regulation? Do we need to allow more citizens to assume more risk and liability if it means getting quicker access to experimental tests and treatment? Many folks would happily accept the possibility of a false test as a data point vs having no data at all.

The tax-paying public is unforgiving whenever their government lets them down, especially with such a polarized population we have today. Personally, if I purchased a kit that tested negative, only to know I really had it, and subsequently infected others in my family that later succumbed because of my negligence, the company that sold me the product and the FDA would definitely be part of the blame. Most of these companies are massive, so losing customer trust and other stakeholders would just devastate their reputation.

@Duddy

The media has played a big part in propagating the fear most people are experiencing. All I've heard and read for the past two weeks has been about the virus, yet "safe sex" is encouraged in our movies, commercials, and by our friends. The media is doing its part in getting people to tune in more each day, can't blame them for doing what they're good at doing. The doctor makes some great points, but it's the uncertainty of it all that's creating this visceral reaction. Hence why we're more afraid of it than the flu, or even eating bugs.
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Donated
4 years ago
I will come back and respond, but I wanted to share this article that literally just came out:

Biohackers team up online to help develop coronavirus solutions
https://www.theguardian.com/world/2020/mar/18/biohacking-online-forums-coronavirus-vaccines-testing

Quote
The ultimate goal of the JOGL challenge was initially to develop an open source (publicly shared) methodology to safely test for the virus “using tools as common as possible.

That is exactly what I was suggesting in my previous post! Here I am in isolation thinking why aren't people doing this - how can I make it happen - and sure enough, there's a whole community of people like myself already working on it.

Here's where the open source viral test kit is being organized and discussed: https://diybio.org/global/

Side note, might want to add a DYI Bio forum here at some point. I can't help but believe the interest and growth of biohacking will only continue to grow in the coming decade.

OK will read and come back to your prior post shortly! Just had to share my excitement on that article.
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Donated
4 years ago Edited: 4 years ago, germinate_love
Quote from: bio_man
Believe it or not, people trust the government in Washington to do what is right. When an idea is officially endorsed or promoted through legislation, it's correlated with safety and security, and those are the primary concerns for most citizens.

I believe you and I don't disagree with the sentiment. I do; however, think that there are many folks, myself included, who would be OK with taking on more risks and responsibility in exchange for more access and freedom to choose. I also think many people can point to the many failures over history of the large central government and huge corporate interests in their failure to protect the people.

So like with most things, there needs to be a balance and I think we're just bantering ideas to figure out where it might be.

Quote from: bio_man
The tax-paying public is unforgiving whenever their government lets them down, especially with such a polarized population we have today.

Amen to that. This is exactly why we need to shift some of our reliance on government to protect us, tell us what to think and do, etc to self-reliance, self-organization, and the development of emotional resilience.

To tie it back to the topic at hand, the biohacking community or DIYbio or citizen scientists - whatever you want to call them - are in a sense exhibiting this attitude of, OK - we're going to take care of this ourselves and remove some of the power these huge entities have over our well-being. A great example of this is the Open Insulin project. They've modified a yeast to generate an insulin synthesizing protein and are now working to increase the yield. It could bring the cost of insulin for a person from $1200 /month to $1 for life. Incredible. And they started with a measily $20K budget.

I see more of this happening, not less in the future. The availability of amazing learning resources, such as you and this forum, for virtually no cost (btw - how do I make a donation to you or this site?) are in part why this is even a possibility.
wrote...
Educator
4 years ago
Holy Moly! Didn't realize how expensive it was to produce insulin.

Reading through this link (and this one, it looks like they're on the hunt for COVID-19 antibodies. I suppose once that code is cracked, an ELISA test would be all that's needed to begin packaging this up into kits, and releasing to the public.

Check this out - a great example of bioinformatics; this is how technology was intended to be used. Apparently it's free to join, have you decided to take the plunge and actually check it out?

Quote
Side note, might want to add a DYI Bio forum here at some point. I can't help but believe the interest and growth of biohacking will only continue to grow in the coming decade.

Something similar was in the works a year ago, where we thought to have a section exclusive to lab protocols that would be organized into categories and accessed free by our members. Unfortunately, the member who proposed the idea lost interest, and the whole project went to zero. I don't mind restarting it.

Donations can be made via this link.
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4 years ago Edited: 4 years ago, germinate_love
Quote from: bio_man
Check this out - a great example of bioinformatics; this is how technology was intended to be used. Apparently it's free to join, have you decided to take the plunge and actually check it out?

Yea, I signed up, did the survey and dropped my info on the public Slack room. We'll see if it goes anywhere as far as my involvement.

I'm in the Los Angeles area and to my dismay, we have no community biology labs where people like me can do independent research in a real lab or take hands-on classes.

I just got off the phone with a lab that I cold-called and they weren't interested in helping at all. Surprised they didn't even seem empathetic to the cause.

Quote from: bio_man
Something similar was in the works a year ago, where we thought to have a section exclusive to lab protocols that would be organized into categories and accessed free by our members. Unfortunately, the member who proposed the idea lost interest, and the whole project went to zero. I don't mind restarting it. Donations can be made via this link.

Hmm. It has already crossed my mind to create my own learning resource center - blogging and adding real hands-on DYI protocols for all the projects I'm pursing, starting with basic techniques (ex: sterile technique, pippetting, etc) to more complex tasks like PCR, gene editing, plasmid design. Lot's of pics and videos.

Since there are quite a bit of supplies and equipment needed, the business model would just be to use affiliate links for the equipment lists to start and then maybe create premium content for a fee later. I'm sort of envisioning a mix between instructables and ifixit.

The dream would be get enough revenue to rent physical space and begin public outreach and education, with the hopes that ultimately the lab can make a real contribution to the sciences.

I know we don't know each other that well but if there's an opportunity to explore collaborating on this, I'd certainly be open to it.

Donation made.
wrote...
Educator
4 years ago
I just got off the phone with a lab that I cold-called and they weren't interested in helping at all. Surprised they didn't even seem empathetic to the cause.

Out of curiosity, did you speak to someone important? Thinking optimistically, it may have just been some random payroll technician. On a side note, most lead researchers I've dealt with do come across as pricks. Not sure why, it could be a lack of social skills or an ego thing -- maybe a mix of both, doesn't matter.

Given your background in technology, starting a website shouldn't be a problem. There's definitely a need for what's you've outlined above, you'd target a ton of college sophomores enrolled in science programs each year. Check if something like that already exists though, and access whether there's still a need for what you're proposing. If you can make a list of those sites, we can start to analyze them here.

Making your own videos is probably the bread and butter here. The website would then be used as a vessel to deliver those videos to a larger audience. Making short 1 to 3 minute videos could be used in schools and shown to students preparing for a lab; it won't be easy to do, but as long as you enjoy doing it, that's an incentive in itself.

I don't mind collaborating with you on this project, but the question is how? How can Biology Forums help propel your business idea forward? If you're interested, I could ask our admin to dedicate some server space and a sub-domain to help you get started. You could install Wordpress, and start from there... Just throwing an idea out there, unless you had something else in mind.
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Donated
4 years ago
Out of curiosity, did you speak to someone important? Thinking optimistically, it may have just been some random payroll technician.

It was the COO, unfortunately.

Quote from: bio_man link=topic=1943334.msg5029935
On a side note, most lead researchers I've dealt with do come across as pricks. Not sure why, it could be a lack of social skills or an ego thing -- maybe a mix of both, doesn't matter.

Yea. This is quite a common phenomena in highly intellectual fields and I have a wealth of experience with it in my past career in software engineering.

Quote from: bio_man
Given your background in technology, starting a website shouldn't be a problem. There's definitely a need for what's you've outlined above, you'd target a ton of college sophomores enrolled in science programs each year.

I'd like to target a much broader audience, but no doubt some subset of the population would be traditional students. My aim would be make the information accessible to savvy and intellectually inclined self-learners. Part of the benefit, again in my humble opinion, is that we educate and motivate people from outside the field to participate. The diversity of ideas from those who haven't been indoctrinated or biased by the exiting power and knowledge structures might eventually yield some creative and clever ideas for solving hard problems that would have otherwise gone unnoticed or unattended. In essence, DIYers have the ability to disrupt existing markets and/or create new ones altogether.

BinomicaLabs (mentioned below) describes an almost identical goal as mine:

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Binomica Labs is a small non-profit (pending) research laboratory in New York City, run by a dedicated international group of volunteers with the goal of creating educational materials enabling attributable scientific research. We work by closely collaborating with experts and educators on chosen research topics, creating the necessary tools and frameworks to help students generate new knowledge. Along with fellow scientists, early-stage researchers are furtherly invited to provide feedback and participate as fully attributed partners, building up towards publication-quality research in peer-reviewed journals or pre-print servers (bioRxiv).

Here are some sites to check out:
https://amino.bio/ (diy bio kits, equipment and classes)
https://www.the-odin.com/ (paid classes, genetic engineering kits, equipment, merch)
https://binomicalabs.org/ (non-profit dedicated to creating diy biology education)
https://www.youtube.com/channel/UCV5vCi3jPJdURZwAOO_FNfQ (wonderful diy bioengineering videos, but not singularly focused)
https://biobricks.org/freegenes/ (free sequencing for diyers)
https://www.bento.bio/product/bento-lab/ ($1200 portable dna lab for diyers)

None are exactly like what I'm thinking, but even if there were, there's no clear market leader and I think there's room for another player to enter the space.

Quote
Making your own videos is probably the bread and butter here. The website would then be used as a vessel to deliver those videos to a larger audience. Making short 1 to 3 minute videos could be used in schools and shown to students preparing for a lab; it won't be easy to do, but as long as you enjoy doing it, that's an incentive in itself.

Yea, a real possibility for sure. The website and videos would complement each other since the website would be the place to go for the protocols/procedures, links to dive into deeper topics or links to parts list (equipment, reagents, etc) and suppliers.

Quote from: bio_man
I don't mind collaborating with you on this project, but the question is how? How can Biology Forums help propel your business idea forward? If you're interested, I could ask our admin to dedicate some server space and a sub-domain to help you get started. You could install Wordpress, and start from there... Just throwing an idea out there, unless you had something else in mind.

That's kind of you. Thank you for being open to the idea. Let me just think aloud here...

I'm good on the tech-side - I've got access to hosting and WP and all that. Tech won't be the limiting factor for moving ahead. Maybe we might want to have a person to deal with WP config, template setup, design, etc but that will work itself once confidence in the content creation strategy is nailed down.

What I think you guys bring to the table is an actual biology background and teaching mindset. I'm actually more like the customer. That's good because I think something like this needs both to work. I can't even begin to pretend that I'm far enough in my learning that I'd be able to publish a guide for "How to Genetically Engineer Yeast to Glow in the Dark" (as an example), but I could certainly facilitate the process of building the guide by going through the steps, asking questions, simplifying, and finding ways to take really complex ideas and simplifying them into something more approachable to the masses.

 As my own skills advance in the process, I'd be more equipped to take on more of the curriculum development if needed. I also have no shortage of project, experiment and technique related guides that I wish existed for myself.

I could even have a go at the video and photo content creation if we can get one specific enough that it's clear what each video would need to convey. Having your eyes validating the accuracy and safety of the information is also valuable.

Thoughts? How to make all that happen, I'm not sure yet. Let's think on it.


wrote...
Staff Member
4 years ago Edited: 4 years ago, duddy
Hey fellas, I think this might peak your interests https://www.the-scientist.com/news-opinion/monkeys-develop-protective-antibodies-to-sars-cov-2-67281

Apparently one of the reasons the virus hasn't subsided is due to re-infections. The article mentions how there have been cases of COVID-19 survivors who recovered and were discharged upon testing negative for the virus, only to then developed another infection.

Monkeys though have better immunity the second time around, suggesting plasma may be a better way to treat infections. I know i'm a little off topic here, but what do you think?
- Master of Science in Biology
- Bachelor of Science
wrote...
Educator
4 years ago
@duddy

The study is still in its preliminary phase, no peer-reviews, and relatively few subjects to conclude anything. TBH I don't see any reputable journal accepting their work. Surprised that you of all people didn't catch that Face with Stuck-out Tongue

Quote
The diversity of ideas from those who haven't been indoctrinated or biased by the exiting power and knowledge structures might eventually yield some creative and clever ideas for solving hard problems that would have otherwise gone unnoticed or unattended.

Who's someone you think falls in this category?

Honestly, looking at BinomicaLabs website, it's not that popular. Its Alexa rank is in the millions, so they're probably not getting the traffic and attention they deserve. It's a little concerning, but a positive for you nonetheless because that suggests there aren't any major player in this industry.

But I'm curious as to why there isn't a greater following? My hypothesis is that the brightest and enthusiastic scientists are snatched up by major research companies, and hence have very little time to do leisurely stuff on the side.

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Having your eyes validating the accuracy and safety of the information is also valuable.

So you'd need us on the sidelines, acting as a buffer of some sort to validate misinformation, etc. Would be glad to, and probably wouldn't mind endorsing your work if it all checks out.

When you're ready, let us know how you move forward
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