Coronavirus

[ifly4fun]

Glad you posted that - I just emailed our IT guy to ask him if we've run that scenario.

We just load tested ours yesterday, Made everyone who has a laptop WFH... 800 users. no issues. I'm sure its only a matter of time before we're told to stay home - especially with schools closing eminent.

 

[anmut]

I was out in NYC two weeks ago. Today home in WI with a fever and a sick 5 year old that’s the same. Talk about paranoia... 99% this is flu B (wife was sick weeks ago, but not sick this time and I’m pretty sure I know who the sick d*ck that gave it to me at work). But still...

 

[AboveTheBest]

Toilet Paper Crisis

 

[Ronnie]

World’s shortest horror movie.

 

[tabbibus]

@swatski I can't believe all primers have the same color. That is high level BS right there. It also gave me PTSD from my days as a fellow working in the lab trying to design an assay

 

[Peelz]

I've been listening to that JRE podcast off and on today. That's good stuff, and well worth the listen in my pea-brained opinion. I can describe to you how a pressurized water nuclear reactor works, but I can't tell you shit about this Roni virus......Other than I want to jump off a bridge when I see my 401k balance!

yeah im not going to look for at least a couple months.

thanks for the reminder.

 

[Julian]

I looked at my retirement assets yesterday....ouch.

Our company just announced formal work from home policy for the next month.

 

[swatski]

@swatski I can't believe all primers have the same color. That is high level BS right there. It also gave me PTSD from my days as a fellow working in the lab trying to design an assay

It really is... The CDC calls it a "kit", but it is just a set of 4 primer pairs and probes from IDT (a major oligo supplier they partnered with). Because they are labeled the same, the reactions need to be run separately, basically - no internal controls. Then, if the reactions for N1, N2, sars, and loading are all positive - you have a positive, and if the first three are negative with a positive loading - it's reported as a negative.
Now, the fun starts if loading is negative but the first three are positive - CDC allows for a "presumed positive" sign out but it is, along with every other combination, really up to a lab director discretion. We have collaborative agreements with UW and other centers to use sequence "tracks" that will flag any mutations within the templated regions, but none of it is automated at this point.

Hopefully the Roche Cobas system will be approved and harnessed soon, that would be the end of the ridiculous, unnecessary, low throughput LDT nightmare. At least in the big centers where those systems are available (and used for routine screening for HIV, HPV, etc.)

--

 

[Julian]

It really is... The CDC calls it a "kit", but it is just a set of 4 primer pairs and probes from IDT (a major oligo supplier they partnered with). Because they are labeled the same, the reactions need to be run separately, basically - no internal controls. Then, if the reactions for N1, N2, sars, and loading are all positive - you have a positive, and if the first three are negative with a positive loading - it's reported as a negative.
Now, the fun starts if loading is negative but the first three are positive - CDC allows for a "presumed positive" sign out but it is, along with every other combination, really up to a lab director discretion. We have collaborative agreements with UW and other centers to use sequence "tracks" that will flag any mutations within the templated regions, but none of it is automated at this point.

Hopefully the Roche Cobas system will be approved and harnessed soon, that would be the end of the ridiculous, unnecessary, low throughput LDT nightmare. At least in the big centers where those systems are available (and used for routine screening for HIV, HPV, etc.)

--

Is this the test that will work better?

Roche Gets Emergency FDA OK to Make Coronavirus Test Kits

Roche says it received FDA ‘Emergency Use Authorization’ to begin mass-producing coronavirus testing kits, and processing results.

www.thestreet.com

 

[Scottintexas]

@swatski I realize you have other priorities so don't feel like you have to answer me directly or immediately as I sit and waste time on corona, I'm asking these out of ignorance so please correct any wrong assumptions,

1. Are other countries having a hard time creating test kits? if not why aren't we copying theirs or why aren't they sharing theirs?

2. If you or your family (healthy wife and kids, I'm assuming) would get symptoms, fever, chills, would you go to the doctor/hospital to get tested ?

if my family ( wife and kids 20,18,15) exhibited any symptoms I think we would just self quarantine and treat symptoms as such unless something became unmanageable.
Now if my 83 year old mom or in-laws exhibited symptoms I would be a lot faster in telling them to go for professional treatment.

3. this virus was "unknown" 6 months ago and it wasn't until aprox. Jan 1 that China told us what the "sequence" or whatever the key is to detecting it. In your semi-informed professional opinion, What would be an acceptable time frame for scientist to come up with a A. Test B. test kits for public use at least by each states Health department C. Vaccine D. Cure



.

 

[swatski]

Is this the test that will work better?

Roche Gets Emergency FDA OK to Make Coronavirus Test Kits

Roche says it received FDA ‘Emergency Use Authorization’ to begin mass-producing coronavirus testing kits, and processing results.

www.thestreet.com

Yes sir!
that’s the test that runs on big bad Cobas instruments, fully automated, a few thousand cases a day - high throughout. Few local hospitals have those but most regional centers do.

—

 

[swatski]

@swatski I realize you have other priorities so don't feel like you have to answer me directly or immediately as I sit and waste time on corona, I'm asking these out of ignorance so please correct any wrong assumptions,

1. Are other countries having a hard time creating test kits? if not why aren't we copying theirs or why aren't they sharing theirs?

2. If you or your family (healthy wife and kids, I'm assuming) would get symptoms, fever, chills, would you go to the doctor/hospital to get tested ?

if my family ( wife and kids 20,18,15) exhibited any symptoms I think we would just self quarantine and treat symptoms as such unless something became unmanageable.
Now if my 83 year old mom or in-laws exhibited symptoms I would be a lot faster in telling them to go for professional treatment.

3. this virus was "unknown" 6 months ago and it wasn't until aprox. Jan 1 that China told us what the "sequence" or whatever the key is to detecting it. In your semi-informed professional opinion, What would be an acceptable time frame for scientist to come up with a A. Test B. test kits for public use at least by each states Health department C. Vaccine D. Cure



.

Please keep in mind I’m not an expert.
1. Generally speaking our FDA and CDC rule here and in this case they did not manage to get in front of the problem, to say the least. Not the agencies’ fault. They are like Pentagon, get their marching orders from above. On the other hand private labs and hospitals are bound by the emergency use authorization - by the above.
no further comment, lol. I don’t want to be banned.

2. At this time only the state epidemiologist on duty can order the testing, but rules are not clear, and because of the scarcity of the available test kits this is a contentious issue at the moment. Moreover the LIS systems are not set up for ordering and processing these test results, so everything is manual going into your EHRs (electronic health records).
3. The test and the vaccine is conceptually easy but the logistics, testing of the vaccine for safety, and production and delivery simply takes time. As far as cure, there are some antivirals that work to some extent just like Tamiflu. I wouldn’t expect there to be any true targeted therapeutics for this in the near future. Just like flu, treating the symptoms, and the key is to have access to hospital beds and respirators for people who need it. The symptoms tend to be more severe than flu, especially more mild influenza B, with respiratory distress that can be pretty bad.

—

 

[GTBRMC]

Please keep in mind I’m not an expert.
1. Generally speaking our FDA and CDC rule here and in this case they did not manage to get in front of the problem, to say the least. Not the agencies’ fault. They are like Pentagon, get their marching orders from above. On the other hand private labs and hospitals are bound by the emergency use authorization - by the above.
no further comment, lol. I don’t want to be banned.

2. At this time only the state epidemiologist on duty can order the testing, but rules are not clear, and because of the scarcity of the available test kits this is a contentious issue at the moment. Moreover the LIS systems are not set up for ordering and processing these test results, so everything is manual going into your EHRs (electronic health records).
3. The test and the vaccine is conceptually easy but the logistics, testing of the vaccine for safety, and production and delivery simply takes time. As far as cure, there are some antivirals that work to some extent just like Tamiflu. I wouldn’t expect there to be any true targeted therapeutics for this in the near future. Just like flu, treating the symptoms, and the key is to have access to hospital beds and respirators for people who need it. The symptoms tend to be more severe than flu, especially more mild influenza B, with respiratory distress that can be pretty bad.

—

Per President Trump's speech (now ongoing), the Roche test is approved and being distributed in large numbers (sounded like order of magnitude hundreds of thousands) over the next few days. Google, Thermo Fisher, Wal-Mart, Walgreens, Target, CVS (and other companies and organizations) named as involved in automating testing and/or other coordinated efforts. Drive through testing sites going already, will be available soon in hot spots across the country "soon."

Anyway, appears there is a heavy effort to address this particular issue at the federal level. Importantly, they (briefly) acknowledged mistakes previously made in testing.

 

[biglar155]

Today we were given official marching orders to work from home unless absolutely necessary. I still need to run in and grab another big monitor and the correct power supply for my docking station but other than that I'm home for a while.

My Middle School and High School kids will be doing classes "remotely" until at least April 13th. I'm not sure how The Boy is supposed to weld remotely for his metals class, but he can sure change my oil and rotate my tires. (Maybe it's finally time to buy a welder and have my kid teach me something for a change.)

As mentioned, University of Wisconsin is doing remote classes until at least the 10th.

So for the next few weeks my wife will have all four kids and her husband home. I'm hiding the key to the gun cabinet.

We're also canceling a planned visit to the In-Laws in Lower MI. 1) We don't want to spread anything to them or pick up anything from them and 2) We feel that part of being a responsible citizen right now is to minimize travel to reduce the possibility of spreading something.

 

[MattFX4]

Honest question here... what happens at the end of these 2-3 week shutdowns if the virus is still present? Won’t it just flair right back up again and we will be back to square one? Unless completely irradiated it only takes one person to start the whole process over again right? What am I missing?

 

[Scottintexas]

I think the idea is that the shutdown will slow the spread while a test is made Available to the masses once the mass testing is Available we can identify carriers to help control the spread, i dunno???

 

[BigN8]

 

[zipper]

Anybody wanting to ski Jay Peak in Northern Vermont, today is their last day of the Winter season. Not closing due to lack of snow.

 

[fireflymedic]

They just shut down all Florida schools for 2 weeks. In my part of Florida 1 of those weeks is spring break so not as bad.

 

[Julian]

Sanjay Gupta on the testing issues. @swatski Is the german test the one you referenced or is that another test? Let's hope we really can ramp up testing now!