Wear a Mask, Everybody

Like many of you, I was told not to wear a mask at the beginning of the outbreak, so I did not purchase N95’s prophylactically. I’ve been kicking myself for this. But it turns out that if everyone wears even a homemade mask whenever they go outside, the rate of spread seems to be a lot lower. Correlation is not causation, but…it sure does seem correlated.

I was going to write a whole essay on why we need to be wearing masks, but this person did a great twitter thread on it instead, so here you go. Click on the “March 25” link for the whole thing.


The Next Stage: Hiding Bad Data

A few weeks ago, when we didn’t yet have adequate testing, I started going to individual state public health pages. States are required to make weekly reports about flu activity, and most states also collect “syndromic surveillance” meaning flu symptoms even without a positive flu test. The lingo for this is “ILI” or “influenza-like illness.”

It was a lagging indicator to be sure, as it takes time to compile the data and write the report, but by last week it started to be clear that even without proper testing, things were looking bad in terms of Covid-19 cases in a large number of states. So then I knew.

I knew that as time went on, they were going to have to start hiding the data.

And that’s what appears to be going on. Here’s what happened when I attempted to access the syndrome data for Louisiana’s latest report:

LA lies week 10

Well, that’s ok, because even though they’re hiding the data now on the state website, it’s still visible on the federal fluview website. So here’s what they don’t want you to see — the spike in recent cases:

ILI Louisiana week 11

Bear in mind this is data for “week 11,” which ended March 14th. It’s now March 26th so the data is waaay out of date.

What about Florida?

Well, their reports are still visible, and at first glance they appear to be the same. The charts look similar, and they have the same number of pages. So they’re not hiding anything….or are they?

Here’s Figure 1 from Week 9:

FL week 9 figure 1

And here’s the “same” chart from Week 12:

FL figure 1 week 12

If you just look at the chart, it appears that the numbers of ill people are going down. But if you look at the fine print, they’ve changed the report. The reports for weeks 9, 10, and 11 were for “influenza-like illness,” but for week 12 it changed to “diagnosis of influenza or flu.” Hiding the Covid.

But wait there’s more! Let’s look at this series of graphs. Looks like things are improving since week 9, right?

Week 9:

FL figure 16 week 9

Week 12:

FL figure 16 week 12

Again, they changed the criteria of the report. If they’d kept it about “influenza-like illness,” then floridians could see what is probably a massive uptick in cases. But no, they just quietly decided to change the report instead.

The only place you can get a hint of what’s happening is here:

FL fig 12 week 12

See how “flu” is going down in elder care facilities, while “ILI outbreaks” are increasing? That’s (most likely) Covid.

How hard is Florida trying to hide? Well, I can’t say for sure, but when you go to the National FLU VIEW page, the only state with no ILI data is Florida.

So, to review — Louisiana is putting its latest syndromic surveillance data behind a firewall, while Florida is completely changing its reports to keep the information off the radar. Not good.

Just thought y’all should know. Maybe your state is hiding the data, too.


This post is getting a lot of traffic, so I wanted to add some links for those who want to do their own research:

Florida Flu Review Week 9, includes lots of ILI data

Florida Flu Review Week 10, same format

Florida Flu Review Week 11, same format

Florida Flu Review Week 12, most ILI data now missing

Note: I have downloaded all of these reports, so if anything changes later, please let me know.


As someone who has suffered on and off with disability and isolation for 10 years, I’m getting an awful lot of feelings right now about how easily the world is moving to accommodate disability and isolation when it happens to, you know, them. 

More on that to come. Just wanted to say: disabled folks are seeing this, and noting it, and being very angry, and very tired, about this.

The Next Wave

My next question is, can folks who have been infected and then recovered still be carriers?

Or do they *not* carry the disease?

There could be a whole job category for them. They could work in the factories making masks and so forth, or delivering food to vulnerable populations.

It’s Not Neglect, It’s Murder

One of the hardest things about being murdered is wrapping your head around the concept that someone is trying to kill you.

For example, let’s say your boyfriend, whom you love, currently has his hands around your throat. He squeezes, tighter and tighter. You’re in the kitchen, you could stab him with a knife but . . . that would be lethal force!

Is he really trying to murder you?

Like, murder-murder?

Or is he just . . . murdering you ever so slightly? Maybe you shouldn’t fight back yet? Maybe you’ll stab him to death and the cops will say accusingly, “You killed a man because you couldn’t tell when he was just kidding?

Right now, in America, facing this virus with no help from our federal government . . . we’re all that woman, in the kitchen, trying to figure out if it’s “just sorta murder” or if it’s really “murder-murder.”

Spoiler: It’s murder-murder.

Everything right now is just inchoate agony and questions. Why did our administration refuse tests from WHO? Why did they discourage testing for so long? Why didn’t they do sampling months ago? Contact tracing? Why did they allow flights from epidemic countries without quarantine? Where are our masks? Why did they tell us not to wear them? Where is our medical stockpile? Where are our respirators? Why was our pandemic response team disbanded? Where is FEMA? Where are our field hospitals? Where is the Army Corps of Engineers? Where is the National Guard?

For those of us still lost in the fog of war, thinking, “Well, we shouldn’t worry that it’s malicious, because Trump is perfectly capable of killing us through sheer incompetence” . . . well yes, that may be true, but it’s not what’s happening.

Let me remind you who this man is. Here’s something Trump has actually said, using his outside voice, on the record:

“You know what solves it?” Trump said of America’s alleged troubles during a 2014 interview. “When the economy crashes, when the country goes to total hell and everything is a disaster. Then you’ll have a [chuckles], you know, you’ll have riots to go back to where we used to be when we were great.”

And, lest we forget, here’s what his comrade-in-arms Steve Bannon said,

Lenin wanted to destroy the state and that’s my goal too. I want to bring everything crashing down and destroy all of today’s establishment.”

Trump is a serial rapist. He is a pedophile. He is a mafioso. He is a criminal. He put a hit out on his own ambassador to Ukraine. He is a Russian Asset. And he is currently, this very morning, committing genocide by putting people in concentration camps. It’s not neglect, it’s murder.

He is trying to murder us.

We need to work together, respond quickly and decisively, the way you would respond with a surgical team to cut out a Stage 4 Cancer. We need to put enormous amounts of pressure on our state and local government officials to mobilize. We need to put enormous amounts of pressure on Congress. And in the meantime, until we can get the resources of the government mobilized, we need to become our own rescue team. Share supplies, share information, share resources, evade the social media blackouts, help our fellow citizens.

Let’s get to work.

Any wisdom I have about this comes from reading and listening to Sarah Kendzior and Andrea Chalupa. You can listen to their terrifying podcast at Gaslit Nation.


Well, it looks like the stress of looking at stories about how many thousands of people are going to die has made my intermittent recurring shingles…recur. So I guess I need to take a few days off from the maelstrom.

Stay safe, folks. Don’t forget to:

  • Refill your meds (!!)
  • Buy toilet paper
  • Assume the Trump regime is lying and act accordingly:
    • Be more cautious than they’re telling you to be
    • Remember that they love the stock market more than people
    • Maybe avoid unnecessary gatherings for now

COVID-19: China Numbers Seem Accurate; Ideas for Getting More Accurate Public Health Numbers in Your Locality

When COVID-19 hit China, it took off like a wildfire, with thousands dead. It looked like the Case Fatality Rate (CFR) was about 2%, which was alarming. But there were a lot of reasons to think this situation might not reproduce exactly in other countries:

  • China was caught by surprise; we’re prepared (sort of?)
  • China might have been underreporting their total cases — if so, the real CFR would end up being a lot lower
  • China has one of the highest rates of smoking in the world, which might make the population more vulnerable
  • China was being so weird and secretive about some of their data that the world really didn’t know what to think

Well, now that the virus is well-entrenched in Italy, S. Korea, and Iran, I’ve got good news and I’ve got bad news: the China numbers mostly hold up. The disease spread, the CFR, they all seem to mostly match China. The good part of it is that this gives us more data that we can use to prepare. The bad part is that that data is…double plus ungood.

I’ve been crunching the numbers on the Johns Hopkins Coronavirus Map . Here’s the Case Fatality Rate by Country, as of today:

Feb 29, ’20 Case Fatality Rate by Country Total # Cases
Singapore 0 102
Germany 0 79
Korea 0.005 3150
USA 0.015 68
Japan 0.02 241
Hong Kong 0.021 94
Italy 0.026 1128
France 0.027 73
Iran 0.072 593

As you can see, there’s quite a wide range, but a lot of CFR’s are hovering around 1-2.5%. The average CFR for all countries is 2%; if you remove Iran and its very high numbers, the average is 1.4%. However, bear in mind that any CFR will be preliminary and low for the time being. You cannot know the true CFR until the disease has run its course and you divide the TOTAL deaths by the TOTAL number of people who got the disease, including those fully recovered; in the meantime, the numbers are always changing.

Some thoughts on this:

  • The higher the sample size, the more useful the numbers are. So Korea and Italy are more useful than Germany.
  • However, once you get too high, it becomes clear that no government can keep up with testing, and the numbers will likely get distorted again.
  • Singapore’s government is a high functioning government; they have had zero deaths so far, and by all accounts their rate of infection increase has slowed.
  • Iran’s government is a low functioning government; they have the highest death rate so far, and by all accounts their infections are totally out of control.
  • I repeat; I’m very worried about Iran. If China’s numbers are a model, Iran at this rate will have at least 1,500 deaths by the end of March.

What begins as an epidemiological problem is rapidly becoming a dysfunctional government problem, as anyone with experience in epidemiology or governments — or anyone who’s ever watched a disaster movie — could have foreseen.

Which brings us to the US. We are about to see in real time whether we’re a mostly-first-world country that’s fallen on hard times, or whether we’re more like a second or third world country that’s still talking about its past glories. We have a lot of policies in place that were supposed to only screw the poor — no sick leave! Expensive healthcare! Deductibles that reset Right About Now! — but it turns out that a broken healthcare system affects rich people too, because infectious disease control IS healthcare.

On top of the clusterfuck of the usual American healthcare issues, we have a truth-averse malignant narcissist in charge who would rather fudge the truth than see the stock market go down (more).

What we’re seeing the last 48 hours or so has been the push-pull between the Trump administration and government officials on the ground. Trump has a news conference to say everything’s fine? Gavin Newsom immediately has a news conference to announce community transmission in California. More “everything’s fine” from the administration? More news conferences, more community transmission, this time from Oregon, Washington…

So, while normal folks are out there looking for answers, they’re finding out that they’ve accidentally walked out into the demilitarized zone with the truth on one side, and crazy Twitter trolls typing “the FLU is WORSE,” and everyone is shooting at each other, and those ‘answers’ you were looking for are becoming ever more elusive.

If you are looking for answers the next few days, the closest you’re going to get are public health briefings from big blue states like NY, CA and WA. Another thing to do is see if your local government keeps a public health website on the number of flu and pneumonia cases / deaths. A lot of COVID-19 cases are going to be mis-reported as flu and pneumonia to start out. Moreover, some public health rank-and-file folks are going to be afraid of retaliation from the Trump administration, so they’re not going to publicize these numbers, but they will put them there, hoping the public can find them.

For example, here’s the State of Idaho’s chart keeping track of “Influenza-like illness.”

As you can see, the rate is ticking up slightly for our current week (“week 8”), while not at all going into alarming territory yet. BUT, if you look at the chart for your state / city, and it starts going up into “weird” territory while the government says everything’s “fine,” then you’ll know it’s not necessarily “fine.” (That said, compare to the year 2017-2018 for an example of a really bad flu season for reference.)

Good luck figuring out what the hell is going on in your personal corner of the woods.

In the meantime, stock up on toilet paper.

Covid-19 Update: Poop Gets Real

All right, y’all, the time for this to be contained — always a longshot — is officially over. Wherever it is you live, sooner or later, you may be impacted by this, and it’s time to get ready.

What does “get ready” mean?

Here’s a great post that will calmly and rationally guide you through some preparedness ideas by Virology Down Under.

Additional Thoughts:

Food and Supplies — Italy went from “no problem” to “OMG LOCKDOWN!!!” in a matter of days. There was a run on the shops. So, over the next few days and weeks, start stockpiling so you have enough food, etc. to survive a few weeks stuck in your home. Basically, prepare as if a hurricane / blizzard were coming, plus a few more days at least.

Medications — A lot of meds are manufactured in China. Supply chains are already starting to be impacted. So if you take regular medications — and especially if you have a severe medical condition — try to get an extra 2-3 month supply now. Today.

Financial — Have some extra cash on hand in your home if possible. On 9/11 I withdrew my rent money just in case. When the crisis passed I re-deposited it in time for my October rent.

Mental / Emotional — Poop’s gonna get real. The problem with this disease is that there’s up to a 30 day incubation period. So one way this is playing out in countries is that everything’s fine…fine…fine…HOLY SHIT! So, just, be aware. It’s going to be disorienting. I read recently that there is an “OMG” stage for these kinds of things, and you have to go through the OMG stage. One thing that can help make it easier is doing your preparedness shopping / organizing.

Mental, Part II — You’re about to find out just how shittily our government is functioning right now. Remember Katrina? Remember Maria? Well, we’re all about to face that level of gross neglect and incompetence. Trump has already stated — with his outside voice — that he doesn’t want folks to know about Covid19 cases because it might tank the stock market / his re-election plans. He already fired most of the people in pandemic prevention positions, like 2 years ago. This means you can expect the following:

  • Lack of transparency about new cases / locations of cases
  • “Everything is Just Fine” levels of denial to save his One True Love — the Stock Market
  • Underprepared, underfunded, understaffed and undersupplied disaster response
  • We will have to save ourselves. Look to your family, your community, your town. The feds are not equipped to deal with this. If they ever were, they sure as hell aren’t now.

Look, it’s not all doom and gloom. We have Netflix these days, and there have been no reports of water / power outages in China, so that’s hopeful for a long period of self isolation.

But, like, Get some extra toilet paper this week and stock up on supplies and get your meds refilled.

Love to all.



Covid-19: China’s Cooking the Books; Smoking May Contribute to Mortality; All Eyes on Singapore

Today’s installment of Sofi’s Armchair Epidemiology is all about ignorance. Specifically, our ignorance about China’s real numbers.

A few days ago, China made an announcement that they were changing how they counted COVID-19 cases. Previously, they were counting only the cases that were confirmed with a positive test. Since the tests they use have a lot of false negatives, and since hospitals were clearly too overwhelmed to test everybody, it was already clear that cases were being undercounted.

The new criteria they announced was that they would start counting both positive tests and positive symptoms — “ground glass” pneumonia showing up on scans, etc. And so, suddenly the number of positive cases jumped.

They made another announcement at the same time, though not as well-publicized. They have started dropping some patients from the count, specifically, patients who test positive but are asymptomatic. This is, of course, bullshit. We now know that asymptomatic carriers can still infect lots of people around them, so thinking that they “don’t count” is completely bonkers (that’s the scientific term for it). No doubt by dropping asymptomatic carriers from the rolls, the new total case number will look less alarming. There is no other reason to drop potentially infectious patients from the rolls.

Similarly confusing, the number of deaths doubled from what was expected in one day — theoretically due to these new inclusion criteria — but then the next day, 100 people vanished from the tally (“we realized we had double counted 100 people”). Considering how chaotic things are in Wuhan, the likelihood that they have an overcount is almost zero. Also, are deaths now being counted according to the old criteria (positive test) or the new criteria (positive test OR positive symptoms)? And what about people who die at home before they can be tested? Are they being counted towards the official tally?

Clearly China is massaging the numbers to to avoid a panic and financial meltdown. That is…not great. It also means that, without accurate numbers, the rest of the world can’t make informed decisions.

This leaves Singapore, because unfortunately, there is now an outbreak in Singapore as well.

Unlike China, Singapore has been doing an excellent job at transparently releasing information about their COVID-19 patients:

spore virus

Moreover, experts say Singapore’s been doing a good job at proper public health measures. So my take on things is that the next 2-4 weeks will give us real, actionable data, and also our best shot at seeing a country nip this in the bud. Singapore is highly regarded as one of the most technologically sophisticated countries in the world, which gives us the sense that if anybody can get this under control, it’s Singapore.

Here’s what the next 2-4 weeks should let us know in terms of data:

  • What is the actual Case Fatality Rate in a best-case scenario, i.e. a country with excellent health care that is not totally overwhelmed?
  • What is the reproducibility rate of the disease with proper containment protocols in place? (Note: the reproducibility rate is called the R0, pronounced “R-nought.”)
  • What’s the breakdown between mild/moderate/critical cases that test positive? (There will probably also be mild cases that don’t ever get tested, but it will be a start)
  • Will COVID-19 be less dangerous / will the male death rate be less skewed in a country with a lower smoking rate?

Which brings us to Item #3: Smoking. In China, the number of serious cases skews slightly male, but the male death rate is much higher than the female death rate. Some folks have theorized that this could be due to innate immune differences between men and women, but others are saying it’s due to smoking:

  • COVID-19 targets the ACE2 receptor
  • Tobacco use appears to affect ACE2 gene expression. From a new study: “We observed significantly higher ACE2 gene expression in smoker samples compared to non-smoker samples. This indicates the smokers may be more susceptible to 2019-nCov and thus smoking history should be considered in identifying susceptible population and standardizing treatment regimen.”
  • The male population of China has about a 49% smoking rate; the female population in China has about a 2% smoking rate.
  • By contrast, in Singapore the rate is about 18% men / 6.3% women.

Hopefully, Singapore’s advanced health system and lower rate of smoking will keep infections, critical cases, and deaths to a minimum. That is the best case scenario.

If Singapore can’t stop it, though, then…that’s not a good sign for the rest of the world. So let’s hope for the best case scenario and keep our fingers crossed.