Category Archives: Contact Tracing

The Next Pandemic

In yesterday’s post, I outlined some of the factors that resulted in the very high COVID case rate in the US. Today I will discuss how we can prepare for the next pandemic.

I have a PhD in molecular biology, and I specialize in infectious disease testing. I am not a physician or epidemiologist. I have an informed but not expert opinion.

Identifying the threat:

First, most new infectious diseases do not pose a global threat.  SARS-2 was so dangerous because of its high infectivity, long incubation time, and asymptomatic spread. Most diseases do not have these parameters.  Whenever a new disease comes around, and they will, we should soberly and cautiously assess the real threat.  Coming to the wrong conclusions about the threat will lead to the wrong conclusions about combating it.

There have been several important new infectious disease outbreaks in the last few years, including Hantavirus (1993), SARS (2003), Avian Influenza (2004), H1N1 Swine Flu (2009), Ebola (2013), Zika (2015), and of course HIV in the 80s.  They all have different disease parameters which make them behave very differently.  Most of these diseases did not have global impact.  The first SARS for example was much less infectious than SARS-2, but much deadlier, so it was contained quickly and didn’t spread much beyond Asia.  HIV can be spread by asymptomatic victims for a full 8-10 years, avoids the immune system, and evades vaccination efforts, so it has become endemic in much of the world.

The following parameters determine how a new disease will behave:

  • Mechanism of spread
  • Infectivity
  • Asymptomatic/ambulatory spread – can the victim walk around and spread disease?
  • Incubation period
  • Fatality rate
  • Vector – what carries the virus to a new host
  • Non-human reservoir – diseases that come from non-humans are harder to control and cannot be eradicated.

Obviously, we cannot respond to different diseases in the same way. Part of the reason we failed to contain the virus was that we used measures that were designed for viruses that spread by droplet transmission against a virus that spreads through aerosol transmission.  Using the wrong measures was less effective.

Much of my concern with the SARS-2 virus was the Antibody Dependent Enhancement issue, which is very uncommon among viruses, so is not usually a concern.

Be cautious.
Whenever a new threat arises, it is wise to be extra cautious until information can be gathered.  Although many of our precautions turned out to be unnecessary, I still support taking extra precautions early on.  Remember that early estimates were that the fatality rate for COVID was 3.68%.  With the 82 million confirmed cases in the US, this would have been over 3 million deaths if the fatality rate had really been this high.  As it stands, we have had almost 1 million COVID related deaths, a death rate of approximately 1.2%.  Yes, I know we can debate how many of these are deaths really resulted from COVID and how many infections there really were.  But we cannot discount that COVID had an enormous impact.

What if COVID were deadlier? Or what if it had selectively killed children, or caused more long-term symptoms like polio did? Things would have been much different.

All this to say, I think caution was warranted in the beginning of COVID, and we should continue to be cautious in future pandemics. On the other hand, we should also learn to abandon precautions that are not effective.  Maintaining ineffective precautions wastes resources, causes extra economic and social suffering, and causes people to lose confidence in government agencies.  It started to become clear to me by May of 2020 that lockdowns were ineffective, and that transmission was happening mostly indoors, but I still see people wearing masks outside to this very day.

Persuasion, not coercion:
From the beginning of the pandemic, public communication was terrible.  Official guidelines were confusing and often contradictory.  Far worse, explanation or evidence was rarely given for policies.  Instead, disagreement was met with accusations of being anti-science, rather than persuasion.  This approach contributed to the loss in confidence in official channels. 

Going forward, officials need far better communication skills when dealing with emergencies.  Give evidence rather name-calling, and respect the population enough to tell the whole truth.

Then came the vaccine mandates.  Many people I know were coerced into getting vaccinated against their will, and many others were fired.  All at a time when information about the vaccines was being hidden from the public.  This is unacceptable, and no way to run an emergency.

Here is a link to my post on science communication:

Restoring Trust:
Both the CDC and FDA hid information from the public.  In order to restore confidence, senior leadership needs to be replaced and new leadership should explain how things will be better in the future.  Is likely to happen?  No, it is not.

Government agencies need to be far more transparent.  Lack of transparency forces people to wonder what is going on, and create their own theories.  Government agencies often decry conspiracy theories, but they had a big role in creating them.

Freedom of speech, censorship, and misinformation had a major role in the public discussion over the pandemic.  Doctors and scientists were frequently censored, shunned, or fired for sharing ideas that went against WHO or CDC guidelines. This includes ideas like the lab leak hypothesis that later turned out to be likely.

Freedom of speech is a foundational principle of American life.  It’s in our DNA, as some would say.  We are not America without it.  Some will say that too much freedom of speech leads to misinformation and conspiracy theories.  While it’s true that this freedom allows the spread of falsehoods, it also allows all ideas to be debated, true ideas to be raised up, and false ideas to be discredited. Freedom of speech is the solution to misinformation, not the cause.  Most of the leaders in world history that wanted to control freedom of speech had something to hide. It is essential that we maintain this basic right.

State emergency powers:
As discussed in yesterday’s post, the US federal government has surprisingly little power to deal with a public health crisis.  The CDC can develop guidelines, but most of the real work is done at the state and local level.  State officials need to step up and realize it’s their responsibility to respond well.  Citizens need to hold state and local officials accountable.

The US needs to maintain manufacturing capacity for certain essential items like personal protective equipment, testing kits and equipment, and medications.  Tax incentives need to exist to encourage companies not to send these functions overseas.

In addition, we should have national and state stockpiles of certain equipment.  I know many hospitals and labs are now creating stockpiles of their own.

Most countries that did well produced lots of COVID testing early.  In the US, the CDC tried to manage all the testing themselves, and quickly became overwhelmed.  By the time private labs were allowed to develop their own tests, it was way too late.  Testing capacity didn’t become nearly adequate until at least July of 2020. Next time, the CDC needs to allow testing by private labs right away.  Ideally, anyone who wants a test and anyone potentially exposed to an agent should be tested.

Quarantine, not Lockdown:
Countries that did well did not quarantine healthy individuals, although some of these countries had more restrictions during the big Winter waves.  Instead, only COVID positive people should be quarantined.  This is only effective when tests are readily available.

Later in the pandemic, some outlets acknowledged that most infections were happening in private settings.  Basically, people would get infected outside, then bring COVID home to infect everyone in the household.

Here is a very interesting video using computer models to show why our model of lockdown was not effective.  Computer models are only as good as they are programmed to be, so this is only for demonstration purposes, and is not data.

Contact tracing:
Contact tracing was very successful in some countries, but the long incubation time of COVID made this difficult.  Successful programs involved tracking of individuals by cell phone and credit card data, practices that would probably not be tolerated in the US. Such programs would need to be voluntary to not trigger the creepiness factor and violate constitutional rights.

I was a big proponent of wearing a medical grade respirator (N95, KN95, or KN94) indoors during the pandemic.  Because COVID spread as an aerosol as well as droplet form, cloth and blue surgical masks were ineffective.  Simpler masks can be effective against colds and flu, however.  So the choice of mask depends on the agent in question.  CDC guidelines need to reflect the method of spread of the agent in question. 

So what should Dr. Fauci have said early on?  Something like this:

N95 masks offer the best protection against infection by the SARS-2 virus. However, our current supply is very low, and we desperately need to save these masks for our medical professionals.  Please do not purchase N95 masks at this time.  In the mean time, there are some options that will help reduce the risk…

In actuality, of course, I didn’t see an N95 in a store from March 2020 until at least February of 2021, so I couldn’t have bought one if I’d wanted to!

Most medical facilities in the US didn’t treat COVID until a patient was experiencing respiratory distress.  By then, treatment options were limited.  To their credit, intubation was largely abandoned by the medical community when it was learned that this treatment was largely ineffective.

However, controversy swirled over potential treatments that became disfavored by the medical community.  Doctors are usually granted the right to prescribe “off label” medications, meaning they can use medications for treatments outside the guidelines of the manufacturer.  But drugs like Hydroxychloroquine, Ivermectin, and others quickly become forbidden, and some doctors even got fired for prescribing them.  Research on these drugs were minimal.

I am not arguing here that these drugs are effective against COVID.  I’m simply saying that forbidding doctors from working with or publishing papers about these drugs was a big mistake.  While it is of course wise for a doctor to consider guidelines, treating a novel virus may require some “outside the box” thinking.

Let me know in the comments if I missed something important!

Don’t fear, but be smart!

What Went Wrong?

Today I’ll discuss the approach to the pandemic in the United States, and all the factors which contributed to our very high case load during the pandemic.  This article ended up being longer than I thought, so I’ll have a separate post later in the week about how we can prepare for the next pandemic. I have a PhD in molecular biology, and I specialize in infectious disease testing. I am not a physician or epidemiologist. I have an informed but not expert opinion.

The COVID-19 pandemic finally seems to be drawing to a close.  For most of the pandemic, the US had the highest number of daily cases, and has had the most cases over all.  As I write this on May 17th, 2022, the US has 82,629,736 total confirmed cases, approximately 25% of the population, and an unknown but likely very large number of unconfirmed infections.

Meanwhile, the US has the most technologically advanced and well funded medical system in the world.  So what happened? This is a very important question because answering it correctly will help us respond to the next pandemic.

First, we can ask what policies the US had in place, and contrast them with policies that were successful.

Countries that initially did well were Taiwan, Japan, Singapore, and South Korea.  These countries are right next to China, which is the natural source for the seasonal flu.  This is because flu viruses exist natively in aquatic birds from southern China, and there is no practical way to eradicate the flu. We can expect dangerous respiratory viruses to arise from China from time to time.  Neighboring countries know this and are naturally vigilant.  The citizens of Asian countries are used to wearing a mask whenever they have the sniffles, and they are prepared for local epidemics. 

South Korea had the following strategy:

  • Early free testing for anyone who wanted a test.
  • Contact tracing of people exposed to infected individuals. Cell phone and credit card data was used to track residents and produce contact information for infected people.
  • Quarantine COVID positive patients at home, fines imposed for breaking quarantine.
  • Nearly all citizens wore masks in public.
  • Treatment of patients with moderate symptoms.
  • No “Lockdowns”, that is quarantining COVID negative individuals, but schools, cinemas, and gyms were closed. Most stores were open.  Vaccine passports allowed access to high risk areas during the Fall and Winter of 2021/22.

By contrast, the US, and most of the Western world, had the following policies:

  • Testing only for symptomatic people.
  • Treatment only for severe cases.
  • Early “Lockdowns” of all but essential workers.
  • Contact tracing applied too late to be effective.
  • Early communication on masks was incorrect and even deceptive to avoid a run on N95s which happened anyway.  Mask wearing remained controversial and unevenly applied, medical grade respirators unavailable or rarely used for most of the pandemic.

I will point out that most countries, even Japan, South Korea, and Taiwan, had major outbreaks during the Omicron wave.  These countries did have some COVID related restrictions during the Winter of 2020/21 and during the Omicron wave.  I leave China out of the analysis because I don’t trust their data.

Most respiratory viruses like cold and flu are spread by droplet or contact transmission.  However, SARS-2 is spread by aerosol transmission.  Droplets and aerosols are similar, but an aerosolized droplet is much smaller and can linger in the air for much longer than a droplet, more like a cloud than a spray.

Several precautions than became common and even required are designed to prevent droplet transmission rather than aerosol transmission.  These precautions include 6 foot distancing, cloth and blue surgical masks, and those plastic shields at the store.  These measures are mostly ineffective at preventing the spread of aerosols because they do not prevent the movement of small particles.  As you know, I was a strong advocate of masks indoors during the pandemic, but only the medical grade respirators like N95s, KN95s and KF94s.

Peculiarities of the US:
In addition to prevention policies, the US has several cultural and demographic factors which contribute to our high infection numbers. 

Population: Americans know that the 2 most populace countries in the world are China and India, with about 1 billion people each.  These populations appear to dwarf our own estimated population of 330 million.  But we forget that the US is the 3rd most populace country in the world, with number 4 being Indonesia at 272 million. Japan has 125 million, and the most populace European country, aside from Russia is Germany at only 82 million.

Mobility: The US is an enormous country, and Americans are used to traveling much more than other peoples.  We may not fly to other continents as much as the Germans do, but we don’t hesitate to drive several hours for the weekend, or fly across the continent. I was having lunch with an Englishman once who said they might plan for weeks to take a trip that would involve a 3 hour drive.  Many Americans may only plan for a few hours for such a trip. Our high mobility certainly contributed to our high COVID numbers.

Independence:  Our independent nature has been an enormously useful quality, contributing to our high innovation, personal freedom, and economic prosperity.  So I’m certainly not arguing against American individualism.  But I have to acknowledge that our fierce sense of independence did contribute to non-compliance with government recommendations.  And yes, I totally understand that many official recommendations were ineffective or unlawful. But this factor is part of the equation that we will need to consider in order to deal with future pandemics.

Federalism: The US Government has a lot less power than most people think.  The 10th amendment states:

The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.

This means that the only powers the federal government has are those expressly given to it in the Constitution. Much of what the US government does now goes beyond the powers given by the Constitution, and is only done because no one has stopped them.  New federal powers are often popular, so they go forward unchecked. 

The pandemic has caused many to lose trust in several previously trusted federal agencies, and States have started to pull back power from the US.  Many were surprised to discover how limited the President’s power was during the pandemic, limited to suggesting guidelines and creating regulation for federal property and interstate travel.  The vaccine mandate attempted to use private companies to enforce vaccination, but even this was struck down by the Supreme Court. 

Emergency powers outlined in the Constitution only apply in the case of an insurrection or invasion. Unless a Constitutional amendment is passed, the Federal Government can only impose martial law if an emergency forces the courts to close (Duncan v. Kahanamoku, 1946).

States have much broader powers.  In California, the Emergency Services Act allows the Governor to declare a state of emergency at any time, a state which grants him broad powers, including the power to suspend certain laws.  Some have said that this state can only last 90 days without approval from the Assembly, but the ESA allows the Governor to end the state of emergency whenever he deems it necessary, “at the earliest possible date that conditions warrant.” (§8629).

All this to say, the states have much more power to address a pandemic than does the federal government.  Whether you find this good or bad news depends on your own political leanings, and the state you live in!

The national shortage of N95 masks early on in the pandemic painfully revealed that our domestic capacity for manufacturing certain necessary items fell woefully short. Other items in short supply were hospital gowns, gloves, disinfectant, certain medications, and yes, even toilet paper. 

This shortage meant that almost no-one had effective masks early on.  In addition, confused messaging from Dr. Fauci and the CDC later produced a condition in which ineffective masks were common in public areas.  This certainly had a big negative impact on our case load.

Misinformation and freedom of speech:
I have written on this before, so I won’t repeat this now.  Suffice it to say that many Americans lost confidence in government agencies, including the CDC and FDA during the pandemic.  Lost trust is hard to regain and it can take a long time to get back.  I’ll discuss this more in my next post.

Political polarization:
Similar to the erosion of trust in government agencies, the response to the pandemic quickly became a “team sport” with some responses being typical of the “blue team” and others typical of the “red team”.  Unfortunately, both sides often opposed reasonable ideas simply because they came from the other side.  Also, some terrible ideas had a longer life span than they should have because they were favored by certain political groups.  As I’ve said many times before, science and politics are a terrible combination.  When politics gets involved in science, the results are usually terrible. 

Frankly, things have become so polarized that I am pessimistic about the future.  Republicans and Democrats seem to disagree strongly about nearly everything these days, having fundamental worldview differences, not just differences in approach. I know lots of people who lost contact with friends and even family during the pandemic, as have I myself.

Let me know in the comments what factors you think contributed to our response. Later this week, I’ll post on the next pandemic, and how we can prepare.

Don’t fear, but be smart,

Case Update: September 9th, 2020

This is a case update from the last week. For the US and California, confirmed case numbers continue to improve. In San Diego, we seem to be having a small bump in cases right now, after a consistent fall since late July. My friend Brit Colanter who works at San Diego County Public Health tells me that there was an outbreak at SDSU in the last few weeks. 444 cases so far and 1 hospitalization.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County. Some data points of “Active Confirmed Cases” are from SD County, others are calculated.
From Rt Live.

I just got back from a trip to a hospital lab in Rochester, New York, helping them expand their COVID testing. As much as we can grumble about conditions here in California, they are even more strict in New York. New York has a quarantine program going for residents of some states, including California! I was required to check in with Contact Tracing every day, and stay in my hotel room when I wasn’t at the lab. So I was kind of under house arrest!

I have a new appreciation for Door Dash and other delivery people working out there today. So thanks to all of you who are working hard to bring needed items to those who can’t leave their house! You have important work right now!

Don’t fear, but be smart!

PS. I’ve heard a rumor that many African nations are having official events to pray for the US. Many thanks to my African readers for your prayers. We certainly need them!

San Diego County Residents Encouraged to Get Tested for COVID-19

My friend who works for San Diego County Health, Brit Colanter, just posted that all San Diego County residents are encouraged to get tested for COVID-19. Check with your health care provider first to see if they will give you a free test. If not, check the below website, or call 2-1-1 for an appointment at a County Site. State run testing sites are located in Escondido, El Cajon, Chula Vista, San Ysidro and Southeastern San Diego. Check the website for a phone number or link to get an appointment at a state site.

These are likely the Abbott, ID Now rapid COVID test.

Getting a test gives you peace of mind, but also helps scientists understand the real rate of infection in the County!

Happy Testing!

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!