Claude_Verret
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Posts posted by Claude_Verret
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If anyone is interested (or really, really bored) here is a good video on the nitty gritty of running a covid19 PCR reaction. Some of the early steps that she goes through for viral RNA extraction can be more automated for higher throughput, but the steps and process of setting up the RT-PCR reaction itself is going to closely resemble what is being done in labs throughout the world for covid19 diagnostics.
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For those who like to pass the time reading, a relevant but perhaps anxiety inducing read would be this:
I read it years ago and I remember it being a fascinating story for all audiences...not too technical.
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I was already in between gigs when this all started so I was filling some extra free time with working around the house etc. But now my kids are home all damn day with me and needless to say that creates a whole new dynamic. My sons school actually has a good online classroom learning program in place that started this week, but my daughter at a different school has no plan in place yet for online learning. So Im filling time with doddering around the house and trying to not let my kids drive me nuts. Today I'm thinking about making multiple runs to the dump with my truck to clean out clutter from the attic and garage.
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2 minutes ago, shrader said:
Compared to most of the people up there at those press conferences each day, yeah, 54 is a young adult. They may want to consider finding someone younger to throw up there. I typically hate all the celebrity worship, but so many of these kids are so dumb that we may actually need to get a Kardashian up there with them. That's the only thing they listen to these days.
Someone please feel free to replace that with a more relevant name. I have no idea what they are watching now.
At 48 I have zero clue when my 15 and 11 year olds name the current celebrities. In a world where short social media snippets from unverified sources rules the day, especially for millennials, it didn't take very long for the concept that this is only a problem for the old and sick to go viral, pardon the pun. Meanwhile, in the constantly evolving situation it seems like we are now seeing increased hospitilizations among younger people that was linked upthread, early data did seem to suggest that symptom severity correlates with viral dose received.
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12 hours ago, SwampD said:
I find myself clicking on this thread hoping for a post from @Claude_Verret, @North Buffalo, or @Wyldnwoody44.
Three stars of the game in no particular order and my barometer on this matter.
Appreciate that man. Although I have dumped on the CDC for dropping the ball here, and they have, I must say that I have worked with good people in that and other government organizations who work solely on pandemic preparedness. The project I was working on at my former company in conjunction with the government was a test for flu antiviral susceptibility. It was around the 2013-2014 time frame and I remember there were reported cases of H7N9 flu in China. When this happened the small team of people in the government that we would communicate with daily went silent for a few weeks. It was all hands on deck to deal with that potential outbreak. Fortunately, it ended up that strain did not readily transmit human to human. Based on my experience I have little doubt that things would have gone way better on the testing front if this was another flu pandemic, they just got caught with their pants down with this novel coronavirus.
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10 hours ago, Wyldnwoody44 said:
What happened today was concerning a bit. We are ordered to no longer test for influenza and rsv as it uses the same medium that we use to test for covid-19, this is because we simply don't have enough media and tests. The caviat however, is that we are also supposed to rule out influenza first before testing for Corona. Those with positive influenza are currently considered "low risk" for Corona at this time. But we can't even do that, I am having a difficult time wrapping my head around the way things are unfolding, and they are nowhere near their peak.
This is interesting and unfortunately not all that surprising to me. I did wonder if a lack of adequate supply of viral transport media might also be contributing to the bottleneck in testing. We often found it difficult to come by at times for our relatively small scale research projects. I know that hospitals usually run molecular tests that require this media for influenza testing, but given the shortage I wonder if they can allow antigen based immuno diagnostics like they use in primary care settings? Those type of tests can use samples collected in VTM, but it's not required since the patient swab can be put directly into the extraction media included in the rapid test kit.
My wife is an NP in a pediatrician's office and they have 75 tests available to them, no more. So far this week they have been down over 50% in the number of patients that they typically see. A few have requested covid19 testing but they did not meet the symptom criteria for testing. Shes even had to do a couple curb side visits of patients that ended up as ear infections.
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1 hour ago, darksabre said:
This is my company right now. Apparently half my office has had it ?
There are potential tests on the horizon that will detect if you have generated an immune response to covid19 which will tell you if you were exposed. The tests detect IgM (early response) and IgG (later response). I consulted for this company awhile ago on developing a similar test for a different application. There are also other small companies out there developing rapid diagnostic tests for antibody response.
https://www.ncbiotech.org/news/biomedomics-seeks-fda-ok-covid-19-rapid-diagnostic
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39 minutes ago, LGR4GM said:
There's so much misinformation and stupid in this thread is it mind-boggling. At least I haven't read another debate about what Peer- Review means so that's a plus. Just remember kids, even though Governments around the world are involved in this topic we can't talk about or mention the Federal Government shortfalls of the US. That's is ...
Sure you can. I've mentioned numerous times how the CDC, a government agency, dropped the ball right here in this thread.
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7 hours ago, Huckleberry said:
not really true, both SARS and MERS are both in the Corona family and test kits based on those are being used in Asia.
Also the reason why they believe Chloroquine that was used against malaria in the day will help against Covid-19. Was already found to be useful against SARS in a lab here in Belgium in 2004. The Chinese got informed about that and started using it though was never tested outside of a lab.
From a diagnostic perspective it is absolutely true that the world never saw this before. A new assay specific to this virus had to be built from the ground up. Those kits are similar in that they are based on the same PCR platform, but the test itself has to pick up covid19 and not other coronavirus. That's a brand new test with a brand new set of challenges and hurdles.
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10 hours ago, Huckleberry said:
It most likely been going around much longer, thing is that countries like South-Korea that had to deal with SARS have a good supply of test kits. Something the West is severely lacking in.
The CDC had plenty of test kits originally but they had a contaminated negative control which rendered them useless. Strike one to a manufacturing failure.
The WHO offered test kits, but as regulations stood at the time the CDC test kits were the only ones authorized for use. Strike two to red tape regulations.
It was only after lifting these regulations that more public lab homebrewed tests and those from the private sector were allowed. Hopefully this wont be strike 3.
Edit..its also important to emphasize again that the world had never seen this virus before very late in 2019. To develop any reliable molecular diagnostic in that short of a time frame is moving at light speed in the laboratory diagnostics world.
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30 minutes ago, kas23 said:
There’s no reason to believe this virus will not lead to immunity, at least temporarily. In fact, Eli Lily is teaming up with a small biotech company (these evil drug companies!!) to reverse engineer naturally produced anti-Covid antibodies.
The way they are doing it is extremely cool. They received a vial of blood from one of the first patients in the US to recover. They then sequenced the immunoglobulin regions of each B cell to see what antibodies they were making. They have about 500 candidates to test for in vitro viral neutralization. This antibody(ies) will then be mass produced. This will be a form of “passive” immunity.
Just like some of the vaccines that are in trials this sounds promising, but will likely have no effect on this current outbreak. Identifying the best neutralizing IgG's, testing them for efficacy and then scaling up even if done at light speed on a pharmaceutical development scale with lifting of normal regulations will take months.
I think a more likely current intervention that I first read about weeks ago, but have heard more of the TV MD's mentioning recently is to recover plasma (and the antibodies therein) from recovered covid19 patients and giving it to the sick and most vulnerable as a form of passive immunization.
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4 hours ago, MODO Hockey said:
Yea but that is not really the point, it is whats going on in the world with this hysteria, its like were all getting Ebola.
Between 250.000 and 650.000 people die each year in flue, 6501 people have died from covid19 for now since december 31th, ye that sucks but it is what it is, people also die in cancer and we cant do ***** about it, yet.
Same with covid, since there is no vaccine.
We should have focused on containing old people and people with bad immunesystem, not containing the whole fkn world cuz imo that just gonna prolong this issue.
There are so many sensitive people in this world, a sneeze and they demand to see a doctor, the doctor that also has to handle all other illness and ***** that happends.
I f-king hate media for what they are doing now, only talking about death and destruction, instead of trying to TEACH people and calm the ***** down.
There is alot that matters with this issue and world wide spread, i get that, but how we handle this now is just wrong imo.Traditional media and social media are contributing to the hysteria, no doubt about it. But....these measures that are being put in place are very much prudent and necessary. Unfortunately, when these types of unprecedented measures are put into action in a world drenched in 24/7 media coverage and rampant social media misinformation you end up getting what we are now witnessing with the hoarding and general hysteria.
As a population this is a very big problem. I'm not scared for myself or my family because I know the risk is low if any of us were to become infected, but the right thing to do and the altruistic thing to do for society as a whole is to follow these guidelines as best as we can on a population scale, preferably without the run on grocery stores and pharmacies. If we end up seeing what is happening in Italy here in this country, rationing of patient care because there isn't enough healthcare infrastructure to properly treat all those who truly need it, then we ain't seen nothing yet in terms of mass panic. That could still happen..or it might not. Nobody knows, but erring on the side of caution with the current measures is unquestionably the right thing to do at this point.
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12 minutes ago, PASabreFan said:
Someone help me with this. The social isolation measures make sense and probably will have to be ramped up (shut down air travel, restrict travel in some areas, make certain businesses close, like restaurants, bars, non essential retail stores, movie theaters and the like). But that can't last forever. When things get back to normal, what's going to stop the virus from starting to spread again?
We are past the point of no return in terms of widespread infection nationwide, as you've heard these measures are in place to hopefully flatten the curve and prevent the healthcare system from being stretched to its limits and beyond. Hopefully it will work to flatten the curve overall, but we are going to see reported cases rise dramatically this week. I have little hope that the overreaction and hysteria has any hope of subsiding with the coming spike.
There are two factors that immediately come to mind that should help limit mass spread of the virus once measures are relaxed.
1.) We are approaching the end of the peak time period when traditional respiratory viruses spread (influenza, rsv etc.) Respiratory viruses do not spread as readily when the weather turns warmer and theres no reason to think this novel coranovirus will behave differently in that regard.
2.) As more of the population becomes exposed and infected with the vast majority having mild symptoms that dont require medical treatment (or testing) they will have mounted an immune response to the infection and will therefore be far, far less likely to become infected if challenged with another covid19 virus exposure. Naturally immunized by live virus challenge.
This is again not meant to minimize the threat. This is a big deal and should be concerning on a population scale, even though it should not pose much of threat to many people individually.
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29 minutes ago, PASabreFan said:
Getting into the jingleweeds here, but what if I touch my cheek? Is the virus going to make its way into my eye, nose or mouth? They're saying don't touch your face. Also, should people be washing their faces?
The closer you touch your contaminated hands on your face to one of the points of entry the greater the probability of infection.
In recent weeks I've been more cognizant of how often I touch my face, and I often touch it without realizing I'm doing it. The more we properly wash our hands, the lower the probability we transfer anything to the skin on our faces. Vigilant hand washing and washing your face more than you normally do cant hurt.
Maybe some of the docs can chime in, but I'd think you're more likely to receive an infectious dose of virus by being near an infected person who is coughing or sneezing and releasing aerosolized virus into the air, than you are by touching contaminated surfaces.
Social distancing and hand washing. Hand washing and social distancing.
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11 hours ago, Hank said:
Someone help me out. Can the virus be passed through the exchange of paper, like a cashier making change or a server giving you your bill?
Yes, but this is where the hand washing comes in. The virus isnt going to infect you through your skin, youd need to touch a surface contaminated with virus and then subsequently touch your eyes, nose or mouth before you had a chance to properly wash/sanitize your hands.
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2 minutes ago, PASabreFan said:
I bought extra toilet paper, not a shitload or anything, but more than I usually do. Social isolation — I don't want to be in the store if the virus is spreading. Pretty basic and definitely not dumb. Hoarding? Sure.
The best thing about this post is knowing that shitload isn't caught by the filter. Interesting. In fairness, knowing my wife she would have bought more than one pack but Wegman's had a limit of one per shopper.
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Covid19 is going to keep my streak intact. Since 2002 I have attended every regular season Sabres game here in Raleigh, but I had no intention of going to the one next week because it fell on St. Patrick's day.
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4 minutes ago, shrader said:
A neighbor shared a picture from that Costco yesterday. Did I see an entire wall of bottled water in the back of that store? That portion of this craze makes even less sense to me than the TP run. Do they think all of their faucets suddenly stop working?
And speaking of Wegman's, they can't build that one here soon enough. That one will be walkable for me.
Yep, not only did they have that wall of water in the back but they had stacks of it sprinkled around the store too. Nuts. When we have a hurricane bearing down on us I always fill a few of my homebrew kegs with tap water as there is a real risk of not having water for a period of time, but not with this.
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2 minutes ago, shrader said:
Until you have to go to the store to pick up a random item. Then you'll care if people aren't calm. The run on stores is truly a sight to behold. Yesterday I stopped to pick up a box of spaghetti for dinner at a store that would have maybe 3 customers at that time. Each of their 5 or 6 registers had lines of 3+ people each with full shopping carts. And of course it's those highly necessary items like bottled water since all of our faucets are now broken. Just my luck, I wound up next to the super chatty old guy who wanted to know my life story. You try staying calm when an old guy is rambling on and on about how back during the war they used to wear onions on their belt because it was the style at the time.
One lady did get things right though. Her full shopping cart? Nothing but alcohol... they kind you actually get to drink, not the homemade hand sanitizer variety.
I had heard that our local Costco was a mad house late last week and over the weekend with the TP and water runs so I avoided it until Wednesday. I got there when they opened and the parking lot was already jammed packed. Apparently they got in a new shipment of toilet paper and wipes so the back of the store was a war zone. Even though we were down to less than 12 rolls of TP in our house I refused to take part in that insanity, although I did walk as close as I could get to observe the madness. After I picked up a my few items I walked passed the long checkout lines to the fantastic new self checkout kiosks they put in not too long ago and zipped right out of there.
So yesterday when I get home I notice that there is a new pack of 24 rolls of TP on our storage shelf in the garage. My wife went on her weekly Raleigh Wegmans run on her day off and the shelves were completely stocked, no insanity.
Joke I heard on Stern the other day:
New IQ equation....
IQ = 150 - # rolls of TP currently in your house.
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For those concerned about reliable information sources I suggest not listening to the TV news, social media, random blogs, sports radio hosts or what you heard from a friend. The doctors you hear pontificating on TV and the internet are largely getting their information from the published literature. Here is a good resource that I found from the National University of Singapore that is compiling the latest information and research in a weekly digest format. You can either scan the summaries or dive deeper into the provided citations so that you can look up and read the papers for yourself. No middle man/woman required.
https://sph.nus.edu.sg/covid-19/
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6 minutes ago, Huckleberry said:
What is proven ? really nothing is proven with this new virus. They are just starting to figure it out and most scientists make contradicting claims. Last week it was nothing to worry about, only a small flu, now those same guys say we need to go on lockdown.
The reason you hear contradicting claims from doctors and scientists is because individually they dont know where this is going. It could end up being a worst case scenario or it could up up largely fizzling out. Nobody knows. However, you hear no contradictory information from these people on what we can actually control like personal hygiene and social distancing.
Everyone should be concerned, this is serious. Everyone should be concerned about flu as well as that is serious too. The concern should be commensurate with the risk, which for most people remains pretty low.
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Just heard on the news that Roche got approved for covid19 testing yesterday that has a faster time to result of about 3 hours. I'm guessing that they developed reagents for a diagnostic test using their isothermal PCR technology.
Edit: sounds like this is it. Traditional PCR depends on thermocycling, rapidly raising and lowering the temp of the reaction to amplify the target sequence. This test is done at a constant temperature
We describe here a rapid, highly sensitive, point-of-care, molecular test amenable for use at home, in the clinic, and at points of entry by minimally trained individuals and with minimal instrumentation. Our test is based on loop mediated isothermal amplification (COVID-19 LAMP) and for higher sensitivity on nested nucleic acid, two stage isothermal amplification (COVID-19 Penn-RAMP). Both tests can be carried out in closed tubes with either fluorescence or colorimetric (e.g., leuco crystal violet LCV) detection.
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19 minutes ago, Sakman said:
Based on some of the comments on this board I'm surprised the stores are not also out of aluminum foil as well as toilet paper. You know, for hats.
I'll make a prediction. When this is all said and done, this event will provide a gold mine of data for researchers studying human psychology and panic in the age of the 24/7 news cycle and pervasive social media as compared to what it provides for infectious disease epidemiologists studying pandemics.
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COVID-19
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Thanks for keeping all of us updated with your evidence from the trenches.