Category Archives: Testing

Re-opening, How Many New Cases?, endcorona.org Compares Responses, Viral Spread

I have a variety of resources to share with you today. 

Re-opening: First, after many states have started to re-open, Rt Live is showing that all but 3 states have an Rt value below 1. This means that for most states, each infected person is passing the virus to less than 1 other person, and the virus is slowly disappearing in that state.  The states with an Rt above 1 are Minnesota, Maine, and Nebraska.  After a poor initial response, I’m happy to say that New York State is doing very well now, and daily new cases are low in New York. In California, my home state, the number of new cases is flat, approximately 1700 cases per day since the middle of April.

How many real new cases?  This is going to be a little mathy!  I told you I was going to start tracking the number of tests, and I have been doing that since April 27th.  This will help us know how many of the new cases are just because of more testing, and how many are actual new cases.  I’ve plotted the new cases against the new tests.  For each day, a point comparing the new cases and new tests is shown. If new testing matters, then a day with a high number of tests will also have a high number of new cases. To find out if this pairing exists, we can do a statistical test called the R2 test (pronounced “R squared”, also called the correlation coefficient).  This test creates a best fit line with the data and that creates an R2 value.  This value is a measure of how well the 2 parameters (new tests and new cases) are correlated.  I show a hypothetical graph in which the 2 sets of data are well correlated.  A perfect correlation will have a score of 1.0, while a set of data with no correlation at all will get a score of 0.0.  For scientists (at least the ones in diagnostics, like me) a correlation is considered “true” if the R2 value is above 0.95.  You could also say that the correlation is 95% likely to be true.

Now on to our data. I started plotting on April 27th.  5 days later, the graph for the United States got an R2 value of 0.6559.  This suggests that new cases and new tests are 66% likely to be correlated for this time period.  In real world terms, this probably means that some new cases are because of new testing, but some aren’t.

Interestingly, as of yesterday, a graph like this for the US gets an R2 value of just 0.0117.  This is very low and suggests that there is now no correlation between new testing, and new cases.  This means that new cases we see now are probably “real” new cases, and not just pre-existing ones that are just being found because of new testing.  For California, the correlation between new cases and new testing was never very high.  Right now, the R2 value is only 0.0039 for California, suggesting that most new cases discovered are “real” new cases.  What this means going forward is that we probably have enough testing now to locate new cases.  As we go forward, I expect we will start to see a steeper decline is new cases.

Good news!  This good news comes with a warning, however!  Those living in the West will easily understand a comparison to a brush fire.  Right now, we are in the “containment” stage.  We have the fire surrounded, and were at the beginning of the end, but if we walk away now, the fire will start to spread again.  We need to stay on task and keep fighting the fire!  I am all for re-opening, but we need to remain diligent.  Wear a mask when you go out into public, and continue to keep your distance from others!  If your workplace re-opens, you will probably want to wear a mask, wash your hands frequently, and sterilize your workspace often. I am probably going to start traveling for work again soon, and I’m very glad that everyone will be wearing a mask on the plane!

Endcorona.org compares responses: I discovered a new website the other day, endcorona.org, from the New England Complex Systems Institute.  The group compares the responses and results from different countries.  First, “green” countries responded very well, and were able to get the virus under control quickly.  Aside from the good response, I also notice that most of these countries have relatively small populations.  You may notice that China also appears on this list.  Most experts agree that the data coming from China is not reliable, and they probably have many more cases than they are reporting. After intermediate cases in yellow are countries in red that need more action.  This includes the US.  If you’ve been reading my posts, you’ll recognize the “flat” curve of the US.  Yes, we’ve flattened the curve, but we haven’t been able to knock down our case load yet.  Other countries with similar flat curves include Canada, Finland, Indonesia, Panama, Poland, Sweden, and the UK. Other countries had low cases at first, but are now experiencing explosive growth in new cases, including Brazil, Mexico, and Russia.

After analyzing the responses of these countries, endcorona.org recommendations include the following, many of which you’ll recognize:

  1. Lots of testing to identify new cases.
  2. Isolating infected individuals, even from family members!
  3. Strict lockdowns.  The stricter the lockdown, the shorter it will be.
  4. Travel restrictions, even within the same country.
  5. Adequate health care capacity.
  6. Safe practices for essential services.
  7. Masks in public for everyone.

Viral spread: Erin Bromage, an Associate Professor of Biology at U Mass Dartmouth, has a very nice article on his blog describing how the virus spreads. It is well written for non-scientists and has lots of links to original research.  The take home lesson is that the virus spreads particularly well in-doors.  In addition, cough, sneezing, and to a lesser degree shouting, singing, and even talking are all risk factors in spreading virus.

That’s all for now!

Don’t fear, but be smart!

Erik

COVID Vaccine, Herd Immunity, and California Re-Opening

Today I’m going to wade into the piranha filled waters of the vaccine discussion. I’m also going to talk about the issue of herd immunity, and my advice for re-opening.  I’m not prepared for a discussion of the MRM vaccine that has been raging for the last several years, I’m going to discuss vaccines in general, and the hopes for a COVID vaccine in particular. I will say to start out, that I’m a big fan of vaccination in general, but each vaccine is different, and I may not be in favor of a particular vaccine.

Vaccines: I’m not an immunologist and I haven’t made vaccines myself, I’m just sharing with you what I’ve learned from an informed perspective over the last few months.  When I first started sharing about COVID, I said something wrong, that it would take at least a few months to create a vaccine against COVID, which seemed like a long time to many.  This was based on the time it takes to develop a flu vaccine every year.  In the Spring and Summer, scientists find out that strains are likely to cause flu later that year, and they begin making a vaccine. This process takes several months. As it turns out, it’s only this fast for flu because there is a standard way to make a flu vaccine, they just need to know what strains will be likely to arise in the Winter. And sometimes they are wrong. 

Unfortunately, however, there isn’t just one way to make a vaccine.  There are many different ways, and it can be different for every virus or bacteria.  So for every new infectious disease, a vaccine must be developed from scratch, testing all these different methods.  The process can take from 2 to sometimes as long as 30 years!  Some scientists have said that Dr. Fauci’s prediction of a vaccine by next Summer is actually very optimistic! In my informed, but not expert opinion, we should not count on a vaccine for this current COVID-19 crisis.  However, the vaccine work being done will likely help with future outbreaks.  At least part of Dr. Fauci’s optimism is that a lot of red tape is being cut to speed the process, and that’s good, but less development time will also mean more risk for the final product.

Herd immunity: I have heard many people promoting the idea that herd immunity will help us get out of the crisis. Even some governments have been promoting this idea.  Herd immunity is a useful discussion for diseases for which there is a vaccine, but in my opinion, it is not something we should be striving for now with COVID.  We shouldn’t put a bunch of people in danger to keep fewer different people out of danger. Herd immunity requires a lot of people to be immune, and that number is different for every virus.  I’ve heard the numbers 50 – 70% for COVID thrown around.  That’s a majority of the population!  Why would we risk exposing the majority to the virus to save the minority? To be crass, it’s kind of like saying that once the pool is full of bodies, no one else will drown.

Reopening: More states continue to begin the reopening process. I actually strongly support this, as long as people continue to take care as they interact in public!  Even California has entered Phase 1 (CA calls it Stage 2) today, Friday May 8.  The stages CA will use, as well, as the announcement for the May 8th reopening were announced by Twitter by the Governor.  Not my favorite method of making an official announcement, but there it is.  Re-openings have a much higher chance of being successful if we continue to take care! Continue to wear masks in public, and continue to distance when appropriate (see my May 5th post).  I’m hopeful that we can advance quickly through the stages if people continue to take precautions.  Also, it will be important for us to continue to expand testing, and for businesses to take advantage of expanded testing by screening employees as appropriate.  Some municipalities are starting to have drive through testing, including parts of San Diego (you must still have an appointment to be tested).  Check with your health care provider or public health department to see if and how you can be tested.  Keep watching how other states are doing!  We can learn a lot by observing what methods are working, and what methods are not!  I predict that outbreaks will occur in places that become relaxed too soon.

2nd Wave:  Again, I’m not an epidemiologist, and the following is an informed guess, not an expert assessment.  In my informed opinion, we will have second wave in the Fall or Winter, and history suggests it may be more severe than the first wave.  But I’m still optimistic.  Why?  Because I think that with expanded testing, we will be able to test far more broadly this Fall than we could in March and April.  This will help us identify and quarantine infected people rapidly, and will help us control the spread much better than in the first wave. For the 2nd wave to go well, we will need to stay diligent!

Don’t fear, but be smart!

Erik

San Diego County Will Scale Up Testing and Contact Tracing

Originally posted on April 29th, 2020 on Facebook

Brit Colanter just shared some info from San Diego County Public Health. San Diego will be scaling up contact tracing soon! This is the practice of informing those who have been in contact with sick individuals. This technique has been very helpful in some of the more successful countries, So. Korea, Taiwan, and others. It will help us get back to normal more quickly!

Quest Releases Antibody Test That you Can Order Online

Originally posted April 28th, 2020 on Facebook

Friends,
Karen Parrott just informed me that Quest Diagnostics has released an antibody test for SARS-2 that you can order online without visiting your doctor. You will still need to visit a lab and have your blood drawn and the test will be performed at a Quest facility. It remains to be seen if the general public will be offered the test right away, or if only essential workers will get the test initially. If you order the test, please let me know about your experience!

The test only detects IgG antibodies, and not IgM (see my April 22nd post). Thus, it can tell you if you were exposed to the virus more than 7 days ago, but not necessarily if you are currently infected. The test has not yet received Emergency Use Authorization (EUA) status, but Quest claims it is based on well known technology and will receive EUA status soon. No information on the likelihood of false negatives or false positives have yet been published. A false negative result is more likely than a false positive result for this kind of test.

If you take this test, make sure you read all the material they give you on interpretation! The list cost of the test is $119.

Full disclosure, I worked at Quest for 15 years, but I don’t work for them now, and have no financial connection to them.

Thanks,
Erik

Quest Diagnostics Launches Consumer-Initiated COVID-19 Antibody Test Through QuestDirect™

When should we re-open? Opposite valid interests

Originally posted April 13th, 2020 on Facebook

Friends,
This will be a longer post, so buckle up!

While I certainly have political opinions, I’ve been trying to minimize them for the purposes of these posts, in order that more of you will be willing to read! Today, some of you may be able to figure out where I stand on some things, although I’ll still try to keep the controversy to a minimum. This last weekend, there were protests in many cities of the US asking for the economy to be opened up. Of course, most of these requests took the form of slogans shouted or written on signs, rather than specific policy proposals. I’m very sympathetic to the need of many to get back to work so they can provide for their families, pay the rent, etc. I also share the frustration that much of the information provided by the media and government agencies is untrustworthy or incomplete. This is why I write these posts!

I want to reiterate the differences between the typical flu and the SARS-2 virus:

The R0 value (a measure of infectiousness, see my April 13th post) for the flu is 1.28. For SARS-2, it’s 5.7, 4.5 times higher!

The incubation time for the flu is 2-4 days, for SARS-2, it’s 2-14 days, and asymptomatic people are often contagious!

Yes, the fatality rate for both is impossible to know. And it’s probably over-estimated for both, since we don’t know the number of infected people with mild to moderate symptoms for either disease. But estimates are that the fatality rate for the typical flu is 0.14%. The current rate for COVID-19 in the US is 5.36% (deaths/confirmed cases), 38 times higher.

In short, SARS-2 is not the typical flu.

We have to concede that in an event like this one, there are many valid interests that are in some ways are opposed to each other. People at risk want to stay safe. Doctors and nurses want to treat their patients, but also face constant exposure of themselves and their families to the virus. Those in government do not want to expose their constituents to unnecessary risk. On the other hand, many have lost their jobs and need to get back to work. Mental health workers worry that their patients cannot withstand prolonged isolation and stress. Employers wonder if they have to lay off more people or close their businesses. All of these are real concerns, and they can’t be dismissed.

It will be difficult moving forward to strike a balance between these competing interests, and no solution will be perfect. We need to understand that most are doing their very best to manage a very difficult situation. There is lots of blame to go around, but remember that the nature of the virus has never been completely clear. For myself, I gave a talk at my church on March 13th (Posted here on March 18th). During the previous week, I was trying to determine if the virus was spread by droplet transmission (coughing and sneezing), or by aerosol transmission (shouting, laughing, singing, even talking). At the time, most outlets including the CDC said it was only spread by droplet transmission, but a few scientists were warning that it may be aerosol. Should I really be giving a talk on virus safety to room full of people? It appeared at the time that it would be OK, so I moved forward. Luckily for me, the decision was made to cancel gatherings, and my talk was recorded for the web. As it turned out, the SARS-2 virus is much more infectious that originally thought (see my post from April 13th), so add me to the list of people who were wrong! Thank God I didn’t have a crowd in the room during my talk!

Again, I am not an epidemiologist, I am a molecular biologist specializing in infectious disease. But in my informed opinion, reopening the economy without great care is a mistake. A similar experiment has already been done. On March 11th, California Governor Gavin Newsom banned large gatherings including sporting events, church services, and university classes. On the same day, New York Mayor Bill De Blasio was encouraging people to eat out and enjoy themselves. As of this writing (April 19th), California has 31,000 confirmed cases, and New York City alone has 138,000, more than all but 6 countries (yes, I’m including China, the Chinese Communist Party is almost certainly heavily under-reporting their case load)1. For a time, New York hospitals were overwhelmed, and bodies were being temporarily buried on Hart Island. This is the possible consequence of going back to normal too quickly! If you choose to gather in large groups during this time (for example at protests in downtown San Diego), I would strongly encourage you to take extra care to isolate yourself from those at risk or those who may come in contact with them.

I am less sympathetic to those who want to get back to normal just so they can go to Disneyland or to their favorite restaurant. As we reopen the economy, we have to do so carefully. Theaters, restaurants, and amusement parks are among the last things that should be reopened.

We will need have adequate testing and hospital capacity to handle the additional case load. Each area will be different in this regard, and New York City should not be treated the same as Ennis, Montana. We will also need to have grace for one another, as well-intentioned mistakes will be made along the way. Ideally, we should also have contact tracing, contacting those potentially exposed to an infected person. This practice, along with aggressive testing, was used very effectively in Taiwan, So. Korea, and Singapore, to minimize caseload. Unfortunately, we are not yet able to do contact tracing in the US.

While I am very sympathetic to individual rights, and am in general for small government, we may need to voluntarily lay down certain rights for a time in order to protect each other. Pray for our leaders, regardless of party, and take care of each other!

I’ll have another post soon on the topic of antibody testing.

Don’t fear, but be smart!
Erik

Workers temporarily bury bodies on Hart Island in New York City

1 Editor’s note: As of the date of posting, the statistics here were correct. As of July 7, 2020, however, the situation has reversed. New York State as 398k confirmed cases, California has 284k confirmed cases. New York state daily cases are trending downward, while California daily cases have been trending upward.

Video: Why Testing Was Late

Originally posted March 26th, 2020

This is the best description I’ve seen so far on why the US is so behind on testing. As a person heavily involved in diagnostics, this is pretty on point.

This presenter is kind of a comedian, so some of what he says is not strictly accurate, but I’m guessing you can guess which things those are.

Despite the photo of the president in the thumbnail, there isn’t really any political material in the video that I recall.