COVID COVID-19 Coronavirus Containment Efforts

[Ygggdrasil]

Three hours suggests some kind of on-site testing without shipments to a central laboratory.

What is nucleic acid testing?
Are there other types of testing with wide spread use?

Nucleic acid testing refers to a technique called RT-qPCR (reverse-transcription + quantitative polymerase chain reaction) that detects specific RNA sequences that occur in the Coronavirus genome. I have performed RT-qPCR for research purposes, and three hours would be enough time to process a specimen from a patient, setup the RT-qPCR reaction, run the reaction in the qPCR machine, and get the results. A three hour turnaround would require having a laboratory and qPCR machine at the testing site.

Most tests for the virus (including those used by the WHO and CDC) are based on RT-qPCR. I have heard that an antibody test is available for the virus (https://www.npr.org/sections/health...-solve-some-medical-mysteries?t=1583003302766), which detects whether a person has antibodies against the virus in their bloodstream. However, this would not be a useful clinical diagnostic test because it could not distinguish between people with an active infection and people who have recovered from the virus.

 

[Ygggdrasil]

I have trouble finding out how long one needs to self-quarantine if they have the virus. For a patient known to have it, they would stay until the test came up negative on consecutive days. I found one source:
https://www.journalofhospitalinfection.com/article/S0195-6701(20)30102-X/pdf

STAT news has a piece covering an unpublished pre-print study that studies how infections people are over the course of recovery:

the study suggests that while people with mild infections can still test positive by throat swabs for days and even weeks after their illness, those who are only mildly sick are likely not still infectious by about 10 days after they start to experience symptoms. [...]

The researchers monitored the viral shedding of nine people infected with the virus. In addition to tests looking for fragments of the virus’s RNA, they also tried to grow viruses from sputum, blood, urine, and stool samples taken from the patients. The latter type of testing — trying to grow viruses — is critical in the quest to determine how people infect one another and how long an infected person poses a risk to others.

Importantly, the scientists could not grow viruses from throat swabs or sputum specimens after day 8 of illness from people who had mild infections.

“Based on the present findings, early discharge with ensuing home isolation could be chosen for patients who are beyond day 10 of symptoms with less than 100,000 viral RNA copies per ml of sputum,” the authors said, suggesting that at that point “there is little residual risk of infectivity, based on cell culture.”

https://www.statnews.com/2020/03/09...-likely-not-infectious-after-recovery-begins/

The results still need to be reviewed and replicated, but these could help provide guidelines for the amount of time needed for quarantine of patients.

 

[bhobba]

and estimated 8% of global population has some autoimmune disease

I thought I was told about 10% so checked it - you are right its about 8%. And I didn't know about the female thing - probably because I am repeating what doctors told me and its of not much value knowing females get it a lot more frequently when you are a male - in fact it may make you feel worse, but I have had it for so long now - since I was 42 and am 65 this year - it doesn't really phase me anymore.

Now diabetes ... The open question for your doctor of course is whether the biologic dosing should come down during this.

I will check with the doctor about that. I have diabetes as well. Interestingly it too is quite possibly an autoimmune disease as has been discovered in recent years:
https://www.healthline.com/health/t...s-an-autoimmune-diease#what-the-research-says.

Now 10% of people have diabetes - so maybe the 8% figure may need revising. It is one of a few not usually treated by a Rheumatologist, but by an endocrinologist - others treated by other specialists are Chrohn's Disease (again controversy if it is an autoimmune disease or not) and MS. Psoriasis is a team effort between a Rheumatologist and Dermatologist, the split depending on which predominates - the arthritic component or the skin component. In my case the Arthritic component predominates and I only rarely see a dermatologist. The percentage of people that get psoriasis and psoriatic arthritis is interesting:
http://blog.arthritis.org/psoriatic-arthritis/psoriatic-arthritis-psoriasis/

That's right it's between 18% and 42% - exact science at its best .

Also at 2.2% of the population it says Psoriasis is the most prevalent auto immune disease. Even though the above is from recent studies they obviously did not take into account Diabetes (probably because its only suspected to be one) - which is also a recent finding. We sometimes think physics moves pretty fast in its knowledge but it may be a Tortoise compared to medical science.

Thanks
Bill

 

[atyy]

Nucleic acid testing refers to a technique called RT-qPCR (reverse-transcription + quantitative polymerase chain reaction) that detects specific RNA sequences that occur in the Coronavirus genome. I have performed RT-qPCR for research purposes, and three hours would be enough time to process a specimen from a patient, setup the RT-qPCR reaction, run the reaction in the qPCR machine, and get the results. A three hour turnaround would require having a laboratory and qPCR machine at the testing site.

In most countries it would require a machine at the testing site, but Singapore is tiny (about 25 km in length), so it may be that the PCR machine is not what Singaporeans would consider on site. This news article seems to indicate the PCR machine is not where the samples are collected: https://www.channelnewsasia.com/news/singapore/covid19-new-test-kits-swab-three-hours-12505658.

 

[Tom.G]

Right now I'm eyeing the leaves that blew over into my lawn from next door...

Take a tip from either:

• Before toilet paper was widely available
  or
• Before you were old enough to use it.

It's called a diaper.

A neighbor, when her grandkids panicked about the no-toilet-paper possibility responded:
"Take some newspaper and crumple it up real good until it gets soft. Then use it. As an extra, you get the comics printed on your behind." The kids loved it!

 

[chemisttree]

Too late to install a https://www.lowes.com/pd/Brondell-White-Bidet-Attachment/1000331497?cm_mmc=shp-_-c-_-prd-_-kab-_-google-_-lia-_--_-toiletseats-_-1000331497-_-0&store_code=2480&placeholder=null&gclid=EAIaIQobChMIxcqFmL-e6AIVSNyGCh19TgW0EAQYAiABEgIph_D_BwE&gclsrc=aw.ds A lot cheaper than scalped t-paper.

 

[Tom.G]

Too late to install a bidet?

At the risk of being risque...

A neighbor installed one recently. After installing it, a test was in order. She aimed it up, stood beside it, and flushed. To her surprise, it shot clear across the room. When the laughter died down I asked, "Well, what did you expect if you got it up and turned it on?"

 

[Borg]

My wife has friends who work for the government that are forwarding her an email that has all of the hallmarks of the typical "forward this to everyone you know" spam. I won't repeat that BS here but that has my wife terrified even more than she was before. I keep sending friends to this thread so that they can get some real information but so far, not one has told me that they even visited it. The only thing that comes is more stupid rumors... End of rant.

 

[bhobba]

but so far, not one has told me that they even visited it.

Welcome to the club. I am watching a talk show at the moment. One panelist, Bill Bowtell, Professor Kirby Institute for Infection and Immunity, was asking simple questions of politicians such as where are the testing kits. No answer. And its not the only issue. Its a real worry.

Thanks
Bill

 

[hagopbul]

how much time is needed to research then deploy a new Covid-19 testing methods based on your expertise ,starting from the paper work before you even start the research ending with mass production and deployment

best
hagop

 

[anorlunda]

how much time is needed to research then deploy a new Covid-19 testing methods based on your expertise ,starting from the paper work before you even start the research ending with mass production and deployment

A year or so after this crisis is over would be a good time to rationally rethink policies. Safety and quality considerations protect the public from many hazards. But in the case of a fast spreading virus, speed in deployment might outweigh the normal safety and quality rules.

Abandoning rules should never be done in haste, but rules should also have predetermined exceptions to cover emergency needs. I'll wager that 3 years from now, the rules will have been modified.

 

[bhobba]

how much time is needed to research then deploy a new Covid-19 testing methods based on your expertise ,starting from the paper work before you even start the research ending with mass production and deployment

I am no expert on the logistics of this, but here is the state of play in Aus:
https://www.theguardian.com/world/2...tralia-can-deliver-results-within-three-hours

The issue Bill Bowtell was concerned about is the politicians should have known the state of play, and probably more importantly started it a lot sooner. The point he was making was they do not seem to understand exponential growth and you must take measures as early as possible or the growth outstrips your ability to handle it.

I am watching an interview with someone in the epicenter of the Italian outbreak and they say the same thing - if you do not act to the point the public says its a way over the top reaction then its not fast enough.

Thanks
Bill

 

[Mondayman]

They all bought mountains of toilet paper. I bought a bidet .

Seriously though, I see no point in me or other healthy people leaving their house to go get tested and possibly get infected by other people.

 

[bhobba]

Seriously though, I see no point in me or other healthy people leaving their house to go get tested and possibly get infected by other people.

You are unlikely to get infected in your car by yourself. You go to drive through testing stations and people in protective gear test you in the car. It's safe and painless. Doctors also are using their car parks for the same thing except a nurse or one of the doctors comes out and does it. Should you be tested? That's easy - simply ring or skype your doctor who will advise. I don't know about other countries but here in Aus the government pays for it.

Thanks
Bill

 

[Mondayman]

I didn't realize that's how they were doing it. I imagined myself waiting in line at a walk-in clinic to get tested.

 

[bhobba]

I didn't realize that's how they were doing it. I imagined myself waiting in line at a walk-in clinic to get tested.

All sorts of innovate solutions are emerging to handle this. And while I am critical of a lack of understanding of basic math eg exponential growth and its consequences, people in power seem to be learning. Our PM is quickly realizing he must go harder and faster, increasing restrictions quickly. You know he is on the right track when people are now saying why is he imposing these highly restrictive rules so fast? That is positive.

Thanks
Bill

 

[nsaspook]

The local CV apocalypse: Day 1

IHOP

We are the only customers. Breakfast was great, the $5.99 2+2+2 is a deal.

 

[bhobba]

We are the only customers. Breakfast was great, the $5.99 2+2+2 is a deal.

Seriously though I go to Sizzlers most days for lunch/dinner. They completely reorganized the restaurant by not allowing customers to sit in certain places to ensure good social distancing. Our main retailers, Woolworth's etc, have now set aside time periods pensioners only are allowed to ensure they get a fair go. We are all trying to do the right thing with innovative solutions.

Thanks
Bill

 

[phinds]

I have it from a so-far accurate source (he told me the NY restaurants would be closed then day before Cuomo closed them) that Cuomo is going to shut down the NY borders to all but essential travel (mail, food, gas, etc deliveries) in and out. I can't decide whether I hope that's just a rumor or think it's a good idea. I'm leaning to good idea if it doesn't go on for too long. What do you all think?

 

[Ygggdrasil]

how much time is needed to research then deploy a new Covid-19 testing methods based on your expertise ,starting from the paper work before you even start the research ending with mass production and deployment

best
hagop

For RT-qPCR testing, the timeline is quite short. The WHO developed a RT-qPCR test fairly quickly after the viral RNA sequence became available (the sequence was released on Jan 10, and the WHO released its RT-qPCR test on Jan 13). Various other organizations and companies have subsequently released tests.

For a completely new method based on new technology, the timeline would probably be on the longer side to get FDA approval. Two companies are developing CRISPR-based tests (https://www.biocentury.com/article/...chnologies-wont-lead-designer-babies/']crispr-diagnostics-their-first-proof-of-principle[/URL]) that could potentialy be faster and easier than RT-qPCR testing, though the companies did not give a timeline as to when approval could be expected.

 

[bhobba]

What do you all think?

I think restaurants that do proper social distancing in seating, and proper hygiene in cooking, plus plenty of hand sanitizing stations can remain open without any issues.

Not knowing New York I can't speak to the other issues eg it may be that its just not possible and/or realistic to maintain proper social distancing in the city unless roads are closed.

Thanks
Bill

 

[Evo]

I have it from a so-far accurate source (he told me the NY restaurants would be closed then day before Cuomo closed them) that Cuomo is going to shut down the NY borders to all but essential travel (mail, food, gas, etc deliveries) in and out. I can't decide whether I hope that's just a rumor or think it's a good idea. I'm leaning to good idea if it doesn't go on for too long. What do you all think?

Won't closing the roads to travelers cause huge amounts of backed up traffic?

 

[hagopbul]

get FDA approval

that means about 3 years starting from theoretical studies to paper work to lab setup , to data analyses , until fda and mass production

best
hagop

hope you are all safe and fine in this troubling times
this is my second day of quarantine and i start reading we should put a thread for members activities and what they are doing during the quarantinejust don't panic

 

[hagopbul]

by the way it is covering 150 countries ?

 

[bhobba]

I just saw an interview with Professor Paterson, UQ Center for Clinical Research director. He is very excited and starting clinical trials of a potential cure in 50 Australian hospitals:
https://www.thechronicle.com.au/news/cure-found-for-coronavirus-in-australia/3973564/

Thanks
Bill

 

[gmax137]

Won't closing the roads to travelers cause huge amounts of backed up traffic?

Yeah, but I'm guessing only for the first week or two...

 

[phinds]

Won't closing the roads to travelers cause huge amounts of backed up traffic?

That's one of a number of good questions. I suspect I haven't even thought of all the ramifications but now that our tri-state area has jointly shut down restaurants, etc. it likely isn't necessary anyway. Probably it WAS just a rumor.

 

[anorlunda]

In NYC, a bigger issue than roads is public transportation. They frequently have >50 people in railroad and subway cars, and sometimes on buses, and often waiting on the train platforms and bus stops. But if they stopped all transportation, then nobody could get to work including police and hospital employees.

 

[Ygggdrasil]

that means about 3 years starting from theoretical studies to paper work to lab setup , to data analyses , until fda and mass production

best
hagop

For the CRISPR-based methods, both companies already have working prototypes of the test (https://www.broadinstitute.org/files/publications/special/COVID-19 detection (updated).pdf https://mammoth.bio/wp-content/uplo...ing-CRISPR-diagnostics-SARS-CoV-2-DETECTR.pdf), so they are well past the theoretical studies and lab setup. They are seeking emergency use authorization from the FDA which is likely to be quicker than the standard timeline for FDA approval. Not sure what the capacity of these companies is for mass production and distribution, however.

 

[kyphysics]

In NYC, a bigger issue than roads is public transportation. They frequently have >50 people in railroad and subway cars, and sometimes on buses, and often waiting on the train platforms and bus stops. But if they stopped all transportation, then nobody could get to work including police and hospital employees.

IIRC, in Wuhan (also a big, modern metro), pretty much EVERYONE was locked in, except for government workers and essential workers (hospitals, obviously). They delivered food and essentials to people.

Could that work for NYC? Could everyone be forced to stay in - enforced by police. And, then, you have a group of volunteers and government workers deliver things to people (non-essential workers) for a month or two?

It'd be miserable, but a way to prevent a health system overcrowding disaster if COVID19 ramped up. High crime neighborhoods would also need extra policing. This sort of idle time, lockdown, and lack of money from commission of crime could cause criminals to "act up."