Friday, March 27, 2020

UMC Can Test for Covid19

UMC issued the following statement.


The University of Mississippi Medical Center began performing in-house testing for COVID-19 Thursday, providing a major boost in the state’s ability to manage the pandemic.

The Medical Center’s pathology laboratory has finished validating its ability to use a commercially available kit to test for the novel coronavirus, said Dr. Timothy Allen, professor and chair of the Department of Pathology, adding that the department has been working extremely hard to get the protocol fully functional at UMMC.

“The pathology laboratory team has done a phenomenal job under great pressure. It typically takes about four months to do what they did in two weeks,” Allen said.

At full capacity, this method can deliver test results for 180 people daily, run in two 90-test batches that take about eight hours each, said Dr. Patrick Kyle, professor of pathology.

“Initially, these tests are being prioritized for patients in our intensive care units, other inpatients at UMMC and UMMC employees,” he said.

Previously, UMMC sent its testing to the Mississippi State Department of Health, which has handled most of the COVID-19 testing in the state so far. Now, MSDH will be able to devote more resources toward testing patients from other locations.

UMMC is also working to bring a second commercial test to its labs as well as creating its own Laboratory Developed Test for COVID-19 based on the Centers for Disease Control and Prevention protocol. If all three options become available, UMMC could process as many as 700 samples per day, Allen said.

“There has been a lot of concern about a national shortage of COVID-19 tests,” said Dr. Richard Summers, associate vice chancellor for research. “We’re looking at using a variety of approaches to testing, including tests that could run on our own platforms or use methods developed by commercial laboratories.”

Summers, Allen, Kyle, Dr. Larry McDaniel, professor and chair of the Department of Microbiology and Immunology; Dr. Sarika Jain, assistant professor of pathology; and Dr. John Bates, assistant professor of microbiology and immunology, are meeting twice daily and in constant contact to develop the in-house test.

Bates says that access to COVID-19 tests is limited primarily because of the strain the pandemic has put on the supply chain.

The hardest supply to acquire has been the one needed to get the test started: nasal swabs to collect samples from those potentially infected with COVID-19. It’s also been difficult to purchase viral transport media, which preserves the sample until it arrives in the laboratory.

“Demand for tests has skyrocketed in the United States, and everyone is trying to order materials at the same time,” Bates said. “Companies have ramped up production of different supplies to help meet the demand.”

In response to the demand for testing, the U.S. Food and Drug Administration has changed some of its standards for Laboratory Developed Tests, or LDT, making it easier for institutions like UMMC to start independent testing.

“For example, we can now use saline solution to store swabs if viral transport media isn’t available,” Bates said.

Putting together enough tests to meet demand requires not only supplies, but labor. To meet that need, UMMC student volunteers are preparing test collection kits. The kits, which include swabs, media, collection tubes and plastic bags, will be used to help expand mobile collection sites.

The commercial test UMMC is now using tests for COVID-19 by taking the nasal swab and separating the RNA on it from the rest of the biological material. RNA, or ribonucleic acid, is found in all organisms and makes up the genetic code of viruses such as coronavirus. They then test for COVID-19-specific RNA using polymerase chain reaction, or PCR. This technique uses temperature cycles, lab-made nucleic acids called primers and other reagents to detect the pathogen.

The UMMC LDT will use similar methods to the commercial test, but because it is an LDT, will require FDA approval before use in patient testing. Summers is hopeful that the UMMC test will be approved within the next week. Scientists and technicians working on the test stress that it must work well before they can implement it.

“It is very important to have an accurate test when developing any new test in the laboratory. We have to go through an extensive validation process to make sure that an individual who tests positive is positive, and the individual who tests negative is really negative,” Jain said. “We test many known positives and known negatives, repeatedly and in many different concentrations, to make sure that the results coming out of the molecular laboratory are accurate. This validation process of our new test may take some days to complete, but is extremely critical for our patients.”

“There have been several changes from CDC and FDA regarding this process,” Bates said, adding that the FDA is working on ways to help labs test more samples per day without sacrificing quality control. Private industry is working on ways to make the testing more efficient as well. Companies that made the needed products for these lab tests are now producing them in much higher volumes, he added.

UMMC also needs to gather the physical infrastructure and human capital needed to conduct larger-scale testing. The Department of Pathology’s molecular lab has borrowed an RNA extraction machine from the Molecular and Genomics Core Facility and a pipetting machine from another group to make testing more efficient once it is available.

“This is truly an interdisciplinary effort, and people are eager to help. When we put up a request for help on the research list-serv, we receive responses almost instantly from people all over campus offering their supplies or expertise,” Bates said.

Even as more hospitals start their own testing, not everyone who is screened may be able to receive a test. COVID-19 symptoms, which include fever, cough, sore throat and shortness of breath, are common among viral respiratory infections.

“The demand for COVID-19 testing in the United States is not close to peaking yet,” Bates said. “Just as infectious disease doctors practice antibiotic stewardship, we will need to worry about diagnostic test stewardship.”



33 comments:

Anonymous said...

This is why we shouldn't panic. We have the best healthcare system in the world and they will show us that. This will show that socialized medicine was inferior to the US system.

Better Than Ever said...

@2:09 We have the benefit of seeing other countries get this before us. And now we're in the lead for infections, the new epicenter. That's a BIG leap to call our healthcare system better.

We have shorter lifespans than many other developed nations. We have higher incidences of serious illnesses. Our infant mortality rate is poor, and abysmal here in MS.

Anonymous said...

@2:09
The USA isn't even ranked in the top 19 healthcare systems in the world. We have a few individual hospitals ranked in the top. Overall, we are below the rest of the developed world.
https://www.businessinsider.com/the-healthiest-countries-in-the-world-according-to-legatum-2018-2?op=1

Anonymous said...

Not sure if this will help much. If we do end up with a 1% death rate, about 1500 Jacksonians will die. Having the testing may help with patient triage and for when to tell a healthcare worker to go home for 14 days. But not much else.

Anonymous said...

Uh, 2:09, isn't UMMC a state-owned hospital. You know, where the state owns the hospital, the labs, and pays the employees. Just like the socialism you say it isn't?

Calm Down said...

Our country has a long history of adapting, innovating, and overcoming. With God's help, we'll make that point again.

Anonymous said...

Where's my check? I want my free stuff. I be entitled!

Anonymous said...

@325, not true. Treating sick patients presumed to have COVID 19 wastes drugs (that are in short supply) and PPE (which is in short supply) for 3-4 days currently, if they come back negative. Now you will have an answer in 12-18 hours and will result in much less waste.

Anonymous said...

3:33, the short and easy answer to your idiotic analysis is -- No.

The fact that UMMC is a state facility is not 'socialized medicine' - but I and probably most others that read this blog realize that your lack of thinking ability fits well with your political persuasion.

Anonymous said...

MEA (now owned by SD) is St D's test site here. Had a family member tested yesterday/Thursday and they said results would be in a week.

If UMMC can do results in 24 hours, I say nothing but good!

Anonymous said...

A week ago, Kingfish claimed UMMC had set up a drive through testing protocol at the fairgrounds which turned out to be a bullshit claim.

Show up, get screened, drive on a little further to be tested. Right.

Anonymous said...

Hope you guys are on the 6 month plan, it's going to take that long or longer.
If a Vaccine isn't discovered soon. Let's pray the summer kills it, and that it doesn't come right back in the Fall.

Anonymous said...

5:47, its interesting to watch how quick you are with perjoratives. Without regards to whatever tribal beliefs you may profess, I’m glad you feel safe cocooned in the projection of being with “most others.” But I try not to be scared of my ignorance, so please help me some more with your sure knowledge. Since the state owns the hospital, and pays the employees, and the state decides who can and can’t get the test, and the state (Fed-level) pays for all of the Covid testing and mandates that every private insurer pay for the testing without co-pay, deductible, or having charged premiums, what part is not the socialized medicine about which you claim I am ignorant?

Anonymous said...

Azar nodded at one point as the president noted that "they're making millions more [tests] as we speak."

AZAR tries to explain that more tests are coming, but Trump waves him off to jump in.

TRUMP: “Anybody that needs a test gets a test…. the tests are all perfect like the letter was perfect. The transcription was perfect. Right? This was not as perfect as that but pretty good.”





pic.twitter.com/A3hgYOJLUt
— Dan Diamond (@ddiamond) March 6, 2020

Anonymous said...

Ole Miss can move monuments faster than deal with a new Chinese Flu.

Anonymous said...

What if we don't even know what it is?



"You can call it a germ. You can call it a flu. You can call it a virus. You can call it many different names. I'm not sure anybody even knows what it is."

Anonymous said...

If we thought past today and just our personal situation, what would the true costs be of this shutdown and bringing life to a grinding halt? While every life is important, what are the long term costs to the current approach and are they worth it for the few lives of the most vulnerable we may save? If we as a society want to prevent every death that may be preventable, when will we change the speed limits on all roads to 5 or 10mph? This is analogous to what we have done to society during this pandemic. In addition, we do not truly know how effective the measures we are taking have been. We can hypothesize and speculate based on modeling, but is there another model that is as effective that doesn't adversely impact our entire country? This has been "group think" at its finest because any voice with an idea other than complete shutdown is either not published or is quickly labeled as insensitive or worse.

We all see the economic costs in terms of jobs, but what about the extra debt we are strapping on the school age kids today (2 to 6 trillion in extra government spending not counting the lost tax collections due to the economic downturn)? How will this negatively impact their futures and their kids' futures? What about the consequences of not doing routine check ups and diagnostic screenings (mammograms, colonoscopies, blood work, etc) that may lead to a diagnosis at a stage with a much better prognosis versus a more advanced stage which could be the difference in living and dying. This is for kids with pediatric cancers, etc., and younger, productive adults in the prime of their life. How many of these preventable deaths will the current approach to the pandemic cost? What about the elementary kid who is struggling with math or reading that will now miss out on a fourth of their academic year, which may be the most important part of the year? Will these kids get promoted when they are not ready and forevermore be behind in school, which will negatively impact their future? The list goes on and on, but we need to be thinking beyond the hysteria and look at the big picture.

Hospitals in Jackson have very low censuses, and are cutting hours of healthcare personnel (nurses, pharmacists, etc). The media is not talking about this, but bed space is not a problem for someone who needs one in Jackson. These hospitals are hemorrhaging financially, and so are many physician practices who are seeing a 1/5 of the normal patient load because people are told to stay away. Telemedicine is great, but it cannot do bloodwork or diagnostic tests. Again, what are the costs to a delayed diagnosis or treatment for a serious illness other than Covid-19? All the other afflictions and diseases do not stop because Covid-19 is here.

We need to stop staring only at the one tree called Covid-19 and start looking at the forest. I shudder to think what would have happened had The Greatest Generation put their individual interest ahead of my generation or the country as a whole. We can do what is best for the entire country and her future while helping the most vulnerable isolate themselves.

Anonymous said...

8:14 - You don't need a validated procedure to move a statue. There is very little harm done if you don't move it perfectly. Trust me (or don't - I couldn't care less), it is a lot harder to test for a Chinese virus than it is to move a statue.

Anonymous said...

@9:13 - Finally a voice of reason, and no one, repeat no one, making these "decisions" has the balls to even address your questions. We, as a state and country, simply cannot shut the country down.

Anonymous said...

To 2:40. While the US is not ranked in the top 19 in the poll you referenced, I see many of their residents coming to the good ole USA for their medical attention. And you are not comparing apples to apples when you take into consideration the population and the population make up of these countries.

Better Than Ever said...

@9:13 & @10:36 There has already been more than one analysis of the costs of a semi-shutdown versus wide open and let the chips fall approach. The semi-shutdown wins. If you want the real benefit from all this... maybe it will be to move toward a single payer healthcare system in the US.

Wow... even the poor and jobless would be able to get checkups & screening, receive care, and stay healthy and productive. Imagine the economic impact (this is where I use my feelings and imagination to justify something). Wait, I don't have to imagine and hope. There have been hard studies and the overall effect is positive and cheaper than what we currently have (this is where I use data to justify something).

Anonymous said...

@10:41
Your anecdotes don't equal evidence. It is also the 21st century. So your recollection of dictators like the Shah Pahlavi or Ferdinand Marcos dont count anymore. Who do you see coming here and where from? Guaranteed not going to be one of the nations listed higher than us in global ranking.

Anonymous said...

9:13pm You are completely ignoring the economic data from the 1918 pandemic in THIS country as well as ignoring the economics of the countries who have been dealing with the current pandemic.
The facts are that countries who shut down early , bounce back economically faster as did cities in the 1918 pandemic.
Economists have studied pandemics in great detail. You can get specifics city by city as to what was done and not done.
Please do more research before opining. Your inadequate knowledge is dangerous .

Anonymous said...

I'm a physician. We have a for profit healthcare system that is, frankly, more about profit than patient care. Our healthcare system is abysmal compared to other first world countries. Our president is an ignorant narcissist and we've fallen behind the rest of the world in the fight to contain this virus. Worse, governors like Tate Reeves who pander to the president are risking not only lives in Mississippi but lives of others across the country. It's a disgrace and history will tell the tale.

Anonymous said...

@12:00 Can you please tell us what specialty you are in? Also, if our system is so bad, why do people from Europe and other countries come to the US seeking care for life threatening conditions rather than stay in their higher ranked system if our healthcare is abysmal?

Anonymous said...

...and history will tell the tale.

Yes, but since you are anonymous we'll never know whether you were accurate, or not, or actually a physician despite your appeal to authority as one.

Better Than Ever said...

@12:51 It's completely possible to have bright spots in healthcare even as the whole thing is overall worse than other countries. Look at the stats: we spend more than other nations, we have worse outcomes than other nations, infant mortality is higher, and on and on...

Anonymous said...

Let 12:00 PM answer the question.

Anonymous said...

@12:51 I am also a physician and I agree with the previous physician's sentiments. I practice lab medicine and have board-certification. My company has been working diligently to produce test kits (and lab analyses) for COVID-19. Our President (and Vice President) are stupid assholes. Remember what they said: "Tests are free." Do you know what that means? It means that at least 40,000 of the tests we have done (at huge expense) will be billed to patients who answer our bill with, "Tough shit. We are not paying this. The President said it was free."

Our medical system is a disgrace. Do you know how many people declare medical bankruptcy? Do you know how many people have no access to the system because they will declare bankruptcy when they seek medical attention? It is a horrible disgrace. We need to have a safety net like they have in Europe.

Anonymous said...

LOL Sure you are.

Anonymous said...

@4:05. How much will you wager on that? Put your wallet on the line.

Allow Me To Share An Observation said...

It's shameful when physicians who happen to be liberal socialists can't restrain themselves and are compelled to belch out their hatred for their president instead of providing sound medical guidance. They can't eat, speak or fart without telling the world how much they hate Trump. Wonder why? Think about it.

Anonymous said...

@5:31 I assume you are referring to my 2:50 pm response. Let me ask you this: You own a grocery store. The President and the Vice President announce that groceries are "free." People run into your store and take all your groceries. At this point, your comment would be, "Wow! President Trump is great! He is the Easter Bunny!" Or, at this point you would say, "President Trump is an asshole." Which would it be?

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