Blood antibody testing is telling some uncomfortable Origin Stories.
Antonio wanted to know if the guy was a nut case.
Antonio Regalado, of MIT Technology Journal, had emailed me an informal five-page document entitled “Community Serum Antibody Testing For Past COVID-19 Infection.” He said he had been making the rounds on the internet. Was it for real? Or was it a hoax?
Hoaxes were on the brain at the time. On Tuesday, April 7, 2020, KSBW in Monterey, California, had aired a story about California’s potential “herd immunity” to SARS-CoV-2. The station cited the theory of frequent Fox News guest and military historian Victor Davis Hanson, who claimed Covid-19 had been spreading silently throughout California all throughout the fall of 2019.
I read the 5-page screed. It looked real enough to me. “If this guy’s making this all up,” I reported back to Antonio, “It’s a waste of talent.”
Antonio was casting about for an quasi-expert to take the fall…just in case this thing did turn out to be a hoax. “So it’s a study you would write up in your blog?” he asked.
“The blog has low standards, Antonio,” I cautioned. “My own.”
Antonio went silent. I decided to encourage him. “Run it, Antonio. It’s news. Did you see the date on Patient 32?”
In fact, he had already called Patient 32 on the telephone. Whose story checked out. But still.
I told Antonio about the autopsies in Santa Clara. Those made him feel better.
On 21 April, the County of Santa Clara Medical Examiner-Coroner reported that two individuals who had died on 6 February and 17 February left tissue samples that tested positive for the virus.
That was the first thread to unravel from the dominant West Coast Patient Zero narrative. The hypothesis had been very persuasively argued by Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle.
West Coast Patient Zero, indeed the first known case of Covid-19 in the United States, was a 35-year-old man who had visited his family in Wuhan, China and returned home to Snohomish County on 15 January.
Bedford is a well-known genetic sleuth, a practitioner of genetic epidemiology. And he had been the first to prove, rather than just assume, community spread.
Hutchinson, where Bedford works, is part of a the Seattle Flu Study, which collects swab samples from flu tests given in local doctors’ offices.
A swab from a teen-age boy’s test got forwarded to Seattle Flu. It happened to get the then-new CDC PCR test for SARS-CoV-2. It was positive.
That was bad enough. Trevor Bedford took cause for alarm another level. He sequenced the RNA of the virus in both samples. The boy and the man didn’t know each other, but they live only 15 miles apart.
Except for three minor mutations, the sequences were identical. Bedford concluded the virus the boy got was a descent of Patient Zero’s. It was the first very hard evidence of community spread.
In the months since, Bedford had sequenced hundreds, maybe thousands, of viruses collected in West Coast swab tests.
And all trace their family tree back to the virus of Patient Zero in Seattle.
And now we had an amateur citizen-scientist reporting a case in Portland, Oregon, in December 2019.
It was hard to get tested in Portland in March. The PCR tests were rationed. You had to come in with obvious symptoms, have a referral from your doctor, and so on.
For someone like Charles “Derris” Hurley, a former pharmacist, March was too late. He had his symptoms in December.
But not for a blood antibody test. But you couldn’t get one of those, either.
Ian Hilgart-Martiszus, a friend of Hurley and his wife, Jan Spitsbergen, a PhD microbiologist who tends zebrafish at Oregon State University, had an idea.
He could whip up a blood antibody test — DIY. Do-it-yourself.
Hilgart-Martiszus used to work in a lab at Oregon State. He had run hundreds of ELISAs.
He also, apparently, forgot to turn in his key to the lab.
Hilgart-Martiszus went online and bought the SARS-CoV-2 Spike S1-RBD IgG & IgM ELISA Detection Kit, Cat. No. L00831, from a company called GenScript.
GenScript warns that this is Version 1.0 of the kit.
This is what Hilgart-Martiszu got:
On the ELISA plate Ian planned to use, there was room for 40 samples. He contacted friends, and friends of friends, and drew blood on the kitchen table. He had 6 wells left over so, as his document states, the last blood samples were “collected from homeless individuals living on the streets of Portland, OR.”
There’s a glorious tradition of amateur scientist.
We have to look no farther back than Gregor Mendel, father of heredity. His day job as an Augustinian monk did not interfere with his famous experiments on the peas.
And then there’s Michael Faraday, without whose work the electric grid, television, radio, and the modern world as we know it would not exist.
At the beginning of the pandemic, in the grips of the testing crisis, there was a serious proposal to mobilize if not amateur, at least semi-pro scientists.
Dr. Jack Lipton, chair and professor of Translational Neuroscience at Michigan State University, pointed out that academic labs around the U.S. have approximately 10,000 ELISA machines, which gives them the potential, he calculated, to process 1 million tests a day.
There was also, Lipton asserted, a reservoir of highly skilled students and faculty eager to help out. Lipton talked about a volunteer National Guard of scientists. The bureaucratic obstacles — CLIA accreditation, board certification for lab directors — could surely be relaxed for emergency.
Like all good ideas, this one went disappeared with the next news cycle.
Ian Hilgart-Martiszus makes it no secret that he enjoys hunting and owns guns.
Antonio asked me what sort of objections the academics might have to the methods of his study.
“Aside from being queasy about the blood draws taken on the kitchen table?”
“Aside from that.”
“Lots of things,” I ventured. “Maybe he put the samples in his freezer next to the venison steaks…”
Antonio went silent again. “It wasn’t venison,” he said.
I didn’t want to know.
After all the set-up, the ELISA run itself was an anti-climax.
Patient 32 tested off the chart:
Patients 13, 35, and 6 were positive, depending on where you draw the line. Patients 32 and 35 are reported in the document as friends. (Personally, I think they’re more than friends, but I’ll be circumspect here.)
Patient 32 was sick as a dog in late December 2019. Patient 35 less so, in January.
Antonio wanted to know if the date surprised me.
Not after compiling the Kate File, I answered.
He wanted, and deserved, an explanation. What was that?
While writing about the blood draw for Dr. Jay Bhattacharya’s Santa Clara County serosurvey, [Here] I started reading the Stanford Daily, the student newspaper.
The articles by Kate Kim Selig, in particular, had lots of good detail, of the sort this inquiring mind wants to know. Like, how long did you have to wait sitting in your car, anyway? And did people turn off their engines, or idle?
I started reading the Comments to Kate’s stories. When I did, I immediately emailed and asked if she had looked at them.
“I don’t read the Comments,” she said.
They have some very smart student journalists at Stanford. No one should read the Comments.
“What about those stories?” I asked, telling her what I was taking about.
“Oh, those,” Kate said. “We get hundreds of those.’
I started copying selected Comments to a file. I had no idea what to name it. I called it “Kate.”
These were the sort of anecdotes no self-respecting mainstream journalist would touch with a barge pole.
Fortunately, we don’t have to worry about that around here.
I hadn’t looked at the Kate File in some time. I found it and opened it while talking to Antonio on the phone.
An entry by Sylvia L was typical:
Myself, I feel I may have as well Dec 27 — all the symptoms and it was the most horrible experience I have ever felt.
But the very top entry, by Anne Paskett, read:
I flew to San Diego on November 9th from PDX, did all of the touristy things and flew from San Diego to PDX on November 12th. The afternoon of the 12th I developed a cough, flew home and the next day I had all the COVID symptoms, before COVID was a thing. I work in healthcare so I had already received the flu shot for the season. The entire time I thought to my self how different the symptoms felt then any other sickness I’ve experienced. I know exactly the times and places I visited while I was there if you would like further information, feel free to reach out.
I had to look up airport code PDX.
It takes a certain mindset to want to read other people’s accounts of wretched symptoms and frustration with a mystified healthcare system.
A London woman, who describes herself as a retired respiratory research nurse, recounted a long list of symptoms from November-December 2019 including:
Painful throat so bad i could hardly drink water, it was like razor blades in throat.
Developed Night sweats woke up cold and shivering night clothes bedding wet through
She carefully logged her body temperature, blood pressure, and heart rate. At one point, afraid she was developing a bacterial chest infection, she visited NHS A&E, to be tested and “Told was virus so no antibiotics just sent home.”
The dead sometimes speak louder than the living. Or perhaps we pay more attention to them.
It took the two dead in Santa Clara to open the gate. One of them worked for a company that had an office in Wuhan. After the Santa Clara discovery, California Gov. Gavin Newsom directed local medical examiners to investigate, going as far back as December. No additional cases have yet been found. But, contrary to television, relatively few deaths result in autopsies.
In the time since, there has been a steady drip, if not a flood, of other reports.
A patient near Paris diagnosed with pneumonia on 27 December appears now to have actually had coronavirus. He recovered, and his case earned a write-up in the International Journal of Antimicrobial Agents. Its conclusion was simple:
SARS-COV-2 was already spreading in France in late December 2019
On 10 May, the Ohio Department of Health said that six people who had tested antibody positive reported they were ill in January, one as early as 7 January.
In April, Miami-Dade County in Florida, together with the University of Miami Miller School of Medicine, decided it wanted to start doing weekly serosurveys of its population to ascertain the true prevalence of SARS-CoV-2 infections in the county.
In so doing, Miami-Dade joined San Miguel in Colorado, and Santa Clara and Los Angeles in California.
The result, 6% seropositive in each of the first two surveys, are in line with others in the United States. Miami-Dade has a large Latino population that has been hard hit.
One aside in the Miami-Dade Health Department press release was:
of the individuals who tested positive for the antibodies each week, more than half had NO symptoms in the seven to fourteen days prior to screening.
The all-caps NO is in the original.
Among those who tested positive for antibodies were 11 people in a small Delray Beach neighborhood.
But they did report having had symptoms. In November and December 2019.
Donna and John Van Horn are convinced they had the coronavirus in December. “It drained every ounce of energy from my body,” Donna said. They still feel weak from the illnesses.
Van Horn’s neighbors, Fred and Sharon O’Connor, got severely sick in December. They had just returned from a seven-day cruise in the western Caribbean. “I was coughing in my sleep,” Fred O’Connor said.
Another neighbor, Uf Tukel, was first among them to feel sick, in late November. For weeks, he had body aches, a severe cough and night sweats. He’s not sure what to call it. “I had all the symptoms, though.”
The Tropic Isle neighborhood was a mini-hotspot:
At least 11 people living within two blocks of one another in the city’s Tropic Isle neighborhood all told The Palm Beach Post the same thing: They had been sick with COVID-19-like symptoms and when they got better they took the antibody test and got results indicating they had successfully fought off the coronavirus.
Today, even Raul Pino, health officer for the Florida Department of Health in Orange County, believes he went through Covid in the first week of January.
Back in Snohomish County, Washington, there were new inroads, right on West Coast Patient Zero’s home turf.
On 14 May, the Seattle Times reported that two residents who tested positive for antibodies were convinced they went through Covid-19 in December and January.
The district’s health officer, Dr. Chris Spitters, felt compelled to argue against this hypothesis in a press briefing 15 May.
In Spitters’s view, it was more likely the two suffered a bad flu in December, then contracted a mild or asymptomatic case of Covid-19 this year.
Which sounds plausible. Although it also sounds like this classic:
Q: Which of the two following has a higher probability?
- Susan like taking walks on the beach.
- Susan owns a dog and likes taking it for walks on the beach.
Humans like little stories so much, they will commit the conjunction fallacy to build them. (The answer is 1.) Conjoining two events reduces their joint probability. It’s two opportunities to be wrong. Much as you might want Susan to get a dog.
There’s no prize being given out for being first case in the U.S.
The winner might be looking at becoming footnote in Wikipedia, not even an entry in the Guinness Book of Records.
To many, the little origin stories don’t much matter. The virus was coming anyway.
In this official history the epidemic, one tsunami came from China and hit the West Coast while another wave rolled in from Europe, funneled through New York City, and poured onto the East Coast.
We’ve all seen those epistemological star diagrams with the little red dots connected by the R-naught lines. Once the epidemic gets going, it goes.
I think the origin anecdotes do tell us something we need to keep in mind as we try to deal with the epidemic going forward.
Each little cluster of 3, or 11, or was like an glowing ember wafting over in the wind. Most landed, burned through a few people, then burned out.
A few made the big time. It has to do with scale. I’ve been reading a Twitter thread by Dr. Muge Cevik, a physician and scientist at the School of Medicine, University of St. Andrews, who examined a series of contact tracing studies. I skimmed through those, too.
One line from a study published in the Lancet stuck in my head:
80% of infections by 9% of cases
I’ve seen that kind of distribution before. The last time, in Santa Fe playing with the Fire Model, which has a Pareto distribution.
In California, everyone is always worrying about The Big One.
Earthquakes, I’m talking about now.
The thing about The Big One is that, the way earthquake magnitudes are distributed, you have a lot of Little Ones for every Big One.
In the case of earthquakes, it’s a special Pareto distribution, described by the Gutenberg–Richter law, that being the Charles Francis Richter of the Richter Scale.
We’ve actually talked a lot about the Pareto distribution since the 2008 Financial Crisis. That’s because it’s also known as the winner-take-all distribution. It’s the crazy logic that makes what the pundits say true when they talk about the 1%, then the top 1/10th of the 1%, and then the top 1/10 of the top 1/10 of the 1%.
People interested in transmission, like Dr. Muge Cervik, talk about ‘seeding’ and ‘case importation’ events.
For each such event, trace the chain of infection and tally the total cases it produces.
Our graph would look like this, a few Big Ones and a lot of Little Ones. I’ll use a log normal distribution, rather than the Pareto, because it shows up better on the page:
Winner-take-all. Or in this case, loser.
Does this probability distribution describe anything — besides earthquakes — in the real world?
Actually, it does. Accident claims, for one thing. Most are minor fender-benders.
Mardi Gras and meat-packing plants are big accidents waiting to happen.
In the Fire Model, the fire usually spreads a bit, then burns out. The magic number for trees on a regular grid is between 57% and 62%. Less than 57%, there is almost zero probability the forest will burn completely. Above 67% density, the fire undergoes a phase transition, and always burns the whole forest.
In fires, the wind blows embers forward. Most of these land were there is little or no fuel, and fizzle out.
A very few — given by a Pareto distribution — don’t. They start a new hot spot.
In fighting fires, it’s a given that you can’t eradicate it. You have to prioritize were you put your resources. Some things are worth protecting at high cost. Other areas you let burn and hope for the best. These are difficult decisions, can be wrong, and sometimes have tragic consequences, say when someone loses a home.
(Thinking about epidemics as fire leads to curious analogies. Masks are spark arresters. Washing your hands is playing water on the roof to put out sparks. Controlled burning is variolation, intentional infection. Firebreaks are surrounding the vulnerable with the recovered immune, so-called shield immunity.)
The legions of contact tracers may enjoy an image upgrade if we think of them as the fire brigade, or smoke jumpers. Their job is prevent large outbreaks, which numerically have so many more cases, rather than act like the Gestapo and roust random individuals into quarantine for a cough or sneeze.
The Portland story had a simple ending. Patient 32 and Patient 35 had a Chinese exchange student in their home in December. Think of them as a cluster of three. It went no farther.
Every human culture has its origin stories, its myths. We listen to them not because we think they are literally true, but because we find lessons in them. Let’s do that with these stories.
You can follow the COVID aB Tracking blog on Twitter @Will_Bates_sci