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🤮 Coronavirus (Community Thread)

"Nobody tells you about the dread," writes columnist Bill Plaschke on getting COVID-19. "From the moment my doctor phoned me with the test results, to the moment I am writing this column, I have been scared out of my mind."

It hit me in an inspired bit of irony, at the exact moment I filed my column on the NBA restart opening game between the Lakers and Clippers.

After marveling about the return of the intensity of a live sports event, I literally curled up with the chills.

After celebrating how our local teams renewed their rivalry with exhausted passion, I was so fatigued I could barely walk from my office chair to my bed.

It was a night filled with hope that this country’s long-stalled sports machine was finally chugging its way out of the novel coronavirus pandemic.

It was also the night I began showing symptoms that later resulted in a positive test for COVID-19.

Yeah, I’ve got the ‘Rona. Who’d have guessed? After I spent four months writing about how this nasty incurable coronavirus should shut down the sports world, it laughingly shut me down too. It didn’t care that I respected it. It didn’t matter that I used noted scientists to warn sports fans of its perils.

It was as if my ominous words were lifted from the page and injected directly into my veins. In an instant, my fears for others became prayers for myself.

I picked up COVID-19 at the end of July, tested positive a few days later, suffered through it for about a week, and now am quarantining for the rest of this week while waiting for the danger to pass.

I am lucky. I am blessed. According to the latest numbers, I am one of the around 212,000 confirmed cases in Los Angeles County, but I am not among the around 5,000 deaths, and I had the incredibly good fortune to avoid hospitalization.

I basically lived through a really strange and bad flu. You’ve heard the stories, and mine is actually one of the better ones. Many victims would love to be alive to tell such a relatively benign tale. The depth of their nightmare resonates deeply in me now. This column honors their struggle and commemorates their spirit. May we never forget that behind every coronavirus statistic there is unquantifiable human suffering.

I’m the first person I know who has had the coronavirus. I would occasionally hear acquaintances wonder if it was truly that awful. I can now offer indisputable confirmation. Yes, it really sucks.

My temperature hovered in the upper reaches of 102. It felt like my head was on fire. One night I sweated through five shirts. I shook so much from the chills I thought I chipped a tooth. My chest felt like LeBron James was sitting on it. My fatigue made it feel as if I was dressed in the chains of Jacob Marley’s ghost. I coughed so hard it felt like I broke a rib.

I would fall asleep in a chair and wake up terrified from a hallucinatory dream where I was chased through a playground by old women with giant heads. During phone calls I would get confused and just stop talking. I would begin crying for no reason. I lost my sense of taste, smell, and five pounds in the first four days.

None of this is probably news to anyone who has read about these cases. Everyone knows what happens, even if they never believe it will happen to them.

But still, there are things about this insidious illness that nobody tells you. There are things that surprised me, things that stick with you long after the fever has spiked and the headaches have stopped.

Nobody tells you about the dread. From the moment my doctor phoned me with the test results, to the moment I am writing this column, I have been scared out of my mind.

I know the minuscule overall fatality percentages. I know the overwhelming odds of survival for a 61-year-old male in good health with no preexisting conditions. It doesn’t matter. Once you realize you have a virus that could kill you and there’s nothing anybody can do about it, you live in constant fear.

With every trickle of sweat off your forehead, you worry. With every deep cough, you wonder. You check your temperature 53 times every day, and every single time that thermometer is in your mouth, you close your eyes and pray. You stick your finger in the pulse oximeter every hour, and beg for the number to rise.

Then there are the late nights, when your quarantine feels most acute — when you are the most alone. You start coughing into a wet pillow and you can’t stop and your breath becomes ragged and your bed is soaking and you wonder, is now the time? Do you try to drive yourself to the hospital? Do you call an ambulance? Are you just being a baby? You can’t call any friends or family for help because they can’t be exposed. You can’t call your doctor because he’s already told you there’s nothing he can do. You don’t know what to do, so you simmer alone in the darkness doing nothing, paralyzed by fear and chasing your breath and praying that 102.1 does not become 103.1.

The other emotion nobody tells you about is the anger. You followed all the rules, you wore countless masks, you never strayed far from home, you spent four months battling this thing, and still it hits you with a sucker punch.

In my social circles, I was considered among the least likely person to contract the disease because, basically, I abandoned the circles. For four months I avoided all crowded driveway happy hours and cul-de-sac cocktail parties. I didn’t set foot inside my church even during the brief time it was open. I didn’t set foot inside a grocery store as my youngest daughter Mary Clare, who was quarantined with me for most of the summer, did all the shopping.

I wore a mask everywhere. I followed all the rules, but a couple of weeks ago I didn’t follow my instincts. I briefly let my guard down. The coronavirus came out swinging.

The weekend before my symptoms appeared, for the first time in four months, I met friends for two dinners at two socially distanced patio tables. Nobody is required to wear masks at the tables, so I removed my mask when I sat, as did my dining partners, and we left them off during the entire time we were at the table.

I didn’t do anything that was prohibited, right? I was just following the rules, right?

My guess is that I caught it there.

I’m angry not at the coronavirus, but at myself, because I should have known it doesn’t fight fair, because I was stupid enough to relax around it for even a second, and now my mistake could fester in my system forever.

Framed against the sports world of which I write, my illness has further convinced me that organized team sports played outside an NBA or NHL-style bubble don’t have a chance this fall.

This is why all of college football should follow the smart Pac-12 and Big Ten conferences and cancel their seasons. This is why the NFL should shut down training camps before they begin practicing in earnest. This is why baseball needs to get into a postseason bubble if it has any chance of crowning a champion.

I’ve written all this before, and so I write it again with feeling. It didn’t take much for COVID-19 to make my unexciting life hell. Imagine the increased risk for someone who actually hits and hugs and huddles and hangs out with other people?

The novel coronavirus is not a statistic. It’s not an agenda. It’s not a debate. COVID-19 is real enough to rise up and beat me senseless. We need to stop giving it license to do the same to others.

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Thankfully when the respected Doctors - Fauci 'n Co say that it is premature to launch a treatment for Covid-19, that they will listen. These plasma trials are not released willy-nilly to the public. Thankfully we have enough of a true science barrier to prevent all sorts of remedies which the Administration wants to have and message with.

Thank you Dr. Fauci, Dr. Collins and Dr. Lane for intervening.

Last week, just as the Food and Drug Administration was preparing to issue an emergency authorization for blood plasma as a Covid-19 treatment, a group of top federal health officials including Dr. Francis S. Collins and Dr. Anthony S. Fauci intervened, arguing that emerging data on the treatment was too weak, according to two senior administration officials.

The authorization is on hold for now as more data is reviewed, according to H. Clifford Lane, the clinical director at the National Institute of Allergy and Infectious Diseases. An emergency approval could still be issued in the near future, he said.

Donated by people who have survived the disease, antibody-rich plasma is considered safe. President Trump has hailed it as a “beautiful ingredient” in the veins of people who have survived Covid-19.

But clinical trials have not proved whether plasma can help people fighting the coronavirus.

Several top health officials — led by Dr. Collins, the director of the National Institutes of Health; Dr. Fauci, the government’s top infectious disease expert; and Dr. Lane — urged their colleagues last week to hold off, citing recent data from the country’s largest plasma study, run by the Mayo Clinic. They thought the study’s data to date was not strong enough to warrant an emergency approval.

The three of us are pretty aligned on the importance of robust data through randomized control trials, and that a pandemic does not change that,” Dr. Lane said in an interview on Tuesday.

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You know I think it really says something about me that one of my strongest reactions to the sports thing was “okay if you’ve sweated through two shirts why would you keep putting on shirts?”

Not being able to do anything in indoor public spaces is terrible for my kids. It is currently impossible to go to a park because we’ve had an excessive heat wave in effect for nearly a week, and will have it for around another week, and I mean at least we’re not literally on fire I guess?

We’re being asked in this area to curb power usage between 2 and 9pm to try to stave off damage to the power grid here because AC usage has been so heavy. I’m trying not to use my PC during those times among other things. Normally we’d just go to the mall or something, but if the power grid is that big a problem I don’t know what two days is going to do when this is meant to last days more.

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Some great breaking news
A simple cheap and relatively reliable Covid test - multiple simple tests help to bring certainty.

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Very consequential that scientists are finding that children 0- 22 can carry much higher viral loads than adults and therefore are considered greater super spreaders. Does not bode well for in-class educational options it would seem. :boom:

In the most comprehensive study of COVID-19 pediatric patients to date, researchers provide critical data showing that children play a larger role in the community spread of COVID-19 than previously thought.

In a study of 192 children ages 0-22, 49 children tested positive for SARS-CoV-2, and an additional 18 children had late-onset, COVID-19-related illness. The infected children were shown to have a significantly higher level of virus in their airways than hospitalized adults in ICUs for COVID-19 treatment, according to Harvard-affiliated Massachusetts General Hospital (MGH) and Mass General Hospital for Children (MGHfC).

The study, “Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Reponses,” was published today in The Journal of Pediatrics.

“I was surprised by the high levels of virus we found in children of all ages, especially in the first two days of infection,” says Lael Yonker, director of the MGH Cystic Fibrosis Center and lead author of the study. “I was not expecting the viral load to be so high. You think of a hospital, and of all of the precautions taken to treat severely ill adults, but the viral loads of these hospitalized patients are significantly lower than a ‘healthy child’ who is walking around with a high SARS-CoV-2 viral load.”

Transmissibility or risk of contagion is greater with a high viral load. And even when children exhibit symptoms typical of COVID-19, like fever, runny nose and cough, they often overlap with common childhood illnesses, including influenza and the common cold. This confounds an accurate diagnosis of COVID-19, the illness derived from the SARS-CoV-2 coronavirus, says Yonker. Along with viral load, researchers examined expression of the viral receptor and antibody response in healthy children, children with acute SARS-CoV-2 infection and a smaller number of children with Multisystem Inflammatory Syndrome in Children (MIS-C).

https://www.usnews.com/news/health-news/articles/2020-08-20/high-viral-loads-make-kids-silent-spreaders-of-covid-19

The largest study of its kind finds that children can carry exceedingly high amounts of the new coronavirus, even in the absence of symptoms.

Researchers say that could make them ideal “silent spreaders” of COVID-19, throwing the safety of reopening schools into question.

If schools were to reopen fully without necessary precautions, it is likely that children will play a larger role in this pandemic,” said study senior author Dr. Alessio Fasano. He directs the Mucosal Immunology and Biology Research Center at Massachusetts General Hospital in Boston.

The study of 192 children and young adults – newborns to 22-year-olds – found that 49 tested positive for SARS-CoV-2 and another 18 showed symptoms of COVID-19 illness.

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It’s good… I guess… but I narrow my eyes at emergency approval from the FDA based on a pre-print study. It could be a great test, but there could also be another shoe up there somewhere just beginning its descent.

Still traumatized by all those antibody tests.

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I half feel like this should be under humor. It’s devastating.

Anderson Cooper just exposed the coronavirus quackery of one of Donald Trump’s most loyal allies

Mike Lindell (aka the “MyPillow Guy”) has long been one of Donald Trump’s staunchest allies. He’s called Trump the “greatest president” ever and suggested that Trump was chosen by God for the role.

And because Trump likes people who like him, the President has been similarly complimentary of Lindell. “Boy, do you sell those pillows,” Trump told Lindell at an event at the White House in March. (Lindell’s pillow, which is touted for its comfort, has made him a multimillionaire.) Lindell has also claimed that Trump has urged him to run for office.

But Trump has done more than just praise Lindell. He allowed Lindell to take part in a July White House meeting about the potential therapeutic properties of something called oleandrin, an extract from the oleander plant.

“He was enthusiastic, as he is on everything that’s going to help people,” Lindell told CNN of Trump’s reaction to the extract and its possible uses, including as a potential therapeutic for coronavirus. (Important note: Neither Lindell nor Trump are medical doctors or infectious disease experts.)

And in an, uh, interesting coincidence, Lindell was added to the board of (and received a financial stake in) Phoenix Biotechnology, which produced oleadrin, earlier this month.

All of which brings me to Tuesday, when Lindell was interviewed by CNN’s Anderson Cooper. It was, by any objective measure, an absolute and total disaster for Lindell – and oleandrin.

Lindell began the interview by recounting how, shortly after he asked the entire country to pray for a solution to the coronavirus pandemic, he was contacted – on Easter Sunday! – by the maker of oleandrin. He immediately took the notion to Secretary of Housing and Urban Development Ben Carson, who is an actual medical doctor, despite the fact that there had been no peer-reviewed studies of the efficacy (or not) of the extract. Lindell told Cooper he felt that the 1,000 people who had taken oleandrin in 2016 – long before Covid-19 existed – and not had any adverse reactions was proof enough.

That led to this epic exchange (it’s long, but soooo worth your while):

Lindell : Well, the 1,000 people are out there. I don’t know if you can’t find it. But I’m not a medical doctor. I just know that Ben Carson, who’s on the task force, he brought it to the President, going –

Cooper : OK. But, stop, sir. Ben Carson has in the past been paid to promote supplements and got in trouble for it in 2015. So he has a track record on that. You are telling people that this cures Covid. You have no studies to prove it. And you are saying 1,000 people were tested –

Lindell : You know what: I got my own study. When I took the – When I’ve seen the test of 1,000 people that it was safe. That’s all I needed.

Cooper: Sir, OK, if you’ve seen this test, where is this test?

Lindell: I’ve been taking it since April. I’ve been taking it since April. I have 100 friends and family – this thing works. It’s the miracle of all time.

Cooper : You said – Sir, you said you’ve seen this test, where is it?

Lindell : The tests are out there. The thousand people – phase one, phase two.

Cooper : Where is the test? Show it to us.

Lindell: I don’t have the test.

Whoa boy. And it only got worse from there.

Lindell claimed that the “FDA has had it since April” and accused Cooper of misconstruing him “because the media’s trying to take away this amazing cure that works for everybody.”

(Note: The FDA has not approved oleandrin. The agency generally does not approve dietary supplements, but says it’s the company’s responsibility to make sure its products are safe and claims are true. FDA has gone after hundreds of products for making false claims about diagnosing, preventing or treating Covid-19.)

Cooper responded to Lindell with this:

“Sir, just for our viewers, you have no medical background. You’re not a scientist. A guy called you in April, said he had this product. You are now on the board and going to make money from the sale of this product. … And you stand to make money from it. How do you sleep at night?”

Lindell kept at it, noting, “this works and I’m standing by what I believe in. I have no monetary gain here.” (That last part is demonstrably false.)

He suggested Cooper “probably” sleeps on a MyPillow. (Cooper said he doesn’t.)

And he insisted that he had done “my due diligence and studies with the Covid and humans and not published yet.” (Er, OK.)

These are the people who Trump has elevated to positions of power and influence as the country continues to fight the coronavirus pandemic. People who do what he does – push unproven cures (hydroxychloroquine! bleach injections! – without any sense of the damage they are doing to those who follow them most ardently.

Kudos to Anderson for exposing just how thin the “science” on claims like the ones Lindell are making really are. Swallowing Lindell’s junk science isn’t just embarrassing. It could be dangerous.

Not the full interview but a key portion:
https://www.youtube.com/watch?v=spouhfBiQjs

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Trump claimed in a tweet during one of his weekend twitter storms that the ‘deep state’ at the FDA is delaying a coronavirus vaccine until after the election.

But the head of the FDA, Dr Stephen Hahn, was nominated by Trump for the role in 2019.

Donald Trump pushed a baseless conspiracy theory that the “deep state” is delaying a coronavirus vaccine until after the election in an early morning Twitter rant on Saturday.

“The deep state, or whoever, over at the FDA is making it very difficult for drug companies to get people in order to test the vaccines and therapeutics,” he wrote.

“Obviously, they are hoping to delay the answer until after November 3rd. Must focus on speed, and saving lives!”

The head of the Food and Drug Administration, Dr Stephen Hahn, was nominated by Mr Trump for the role in 2019.

Human trials for a Covid-19 vaccine are currently ongoing around the world. But there are still many aspects which scientists don’t fully understand the virus, which has killed some 800,000 people worldwide.

Mr Trump followed up on his tweet with another referencing the FDA’s decision to revoke emergency authorisation of hydroxychloroquine and chloroquine for treating Covid-19, citing evidence that it is “unlikely to be effective” in treating the coronavirus.

“Many doctors and studies disagree with this!” he said, without providing any evidence.

Dr Anthony Fauci, America’s top infectious disease doctor and member of the White House coronavirus taskforce, said he expects a safe vaccine to be ready around the end of 2020 or the beginning of 2021.

Mr Trump claimed earlier in August that a vaccine would possibly be ready by the US presidential election, or “right around that time.”

This week Dr Fauci cautioned against rushing the process, following Russian claims they have already produced a safe vaccine.

“We have to be careful when you hear from Russia or China or anyplace else that they have a vaccine that they know works. They may have a product that they’re willing to take the risk to give it to people without necessarily showing yet that it’s effective or that it’s safe,” Dr Fauci said.

The Trump administration has pre-ordered hundreds of millions of doses from companies developing vaccines, which be distributed for free.

The death toll from the coronavirus in the US passed 173,000 this week, while total cases passed 5.5 million.

While cases have trended downward nationwide in recent weeks, fatalities have not. Most of the deaths are occurring in Arizona, Florida, California and Texas.

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Don’t worry, his bus is equipped with wheels big enough that it won’t get stuck

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Drug makers rebut Trump tweet that FDA ‘deep state’ is delaying Covid-19 vaccines and drugs

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Announcing today at 2:30p PST/5:30p EST

T is getting revved up to announce the ‘breakthrough’ Covid-19 Therapy through arm twisting the FDA…just in time for the RNC convention, and the election. WOW, what timing!!!

If this man could be believed…it would be a better world. He is full of lies and selling snake-oil.

From Politico below - The agency held off on the decision last week over concerns from government scientists that evidence for the treatment’s effectiveness is thin

LINK TO THE TRIALS


The Food and Drug Administration will issue an emergency authorization for blood plasma as a coronavirus treatment, President Donald Trump is set to announce Sunday evening, according to three administration officials.

The agency held off on the decision last week over concerns from government scientists that evidence for the treatment’s effectiveness is thin — prompting Trump to accuse the FDA of slow-walking the therapy to harm his reelection chances without offering any evidence to support his claim. It is not clear whether the FDA has received additional clinical trial data in the last week that would support the therapy’s use.

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A very dense and complicated story about the bypass of the CDC data reporting. I’m too tired to summarize this one.

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I will help:

It’s a recap of pretty much everything in the covid-reporting world since it became a thing in this country - or rather, since the CDC decided to stop letting JHU have all the fun and actually report that there were more cases than some sick people on a cruise ship somewhere - until now.

Once the CDC was on board that this thing is actually happening, they started collecting data and everything was fine

For like four minutes until CARES got through forcing hospitals to also report to TeleTracking if they want access to funding and treatments, and from there everything has only become more of a mess over time because it creates confusion between hospitals, the state and federal governments, and this vendor, who by the way if you’ve been seen for covid has your data now.

So to this point everyone has been trying to distance themselves from each other: hospital administrations from TeleTracking because it’s unreliable and… problematic, TeleTracking from the CDC because there is currently a coordinated effort to de-legitimize the CDC, the CDC from TeleTracking because TeleTracking is doing weird shit and collecting data they shouldn’t have for lots of reasons, Fauci etc. both of them because waves hands wildly at all of this, and the CDC and TeleTracking from Fauci etc. because both are relatively consistently being called out for being shady.

There’s more interplay than that but it’s 2am and I’m not making a flow chart. We need a grown-up so badly right now because everyone is a victim in this in some way or other except the Trump administration and TeleTracking, who is literally getting paid CARES money to make off with private data.

I think that’s it more or less?

Also my kids are getting real weird guys, they need to get out really badly and if the heat here doesn’t let up we’re going to need to figure something out. That’s not in there though, that’s my thing.

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HHS denies report COVID-19 hospital data going back to CDC

The Department of Health and Human Services says a report by the Wall Street Journal about the future reporting of hospital COVID-19 is wrong.

https://www.10tv.com/article/news/health/coronavirus/covid-19-cdc-data-collection/507-0bc1a893-8865-476a-956b-a44b52d66a5c

The Department of Health and Human Services is denying a report by the Wall Street Journal which stated that hospitals would return to the practice of sending critical COVID-19 data to the Centers for Disease Control and Prevention. Data collection was moved to HHS in July.

“HHS made repeated attempts to explain to the Wall Street Journal that the process for COVID-19 data reporting has not and is not changing," said Michael Caputo, HHS Assistant Secretary for Public Affairs in a statement to TEGNA. “This false reporting will sow more confusion and only undermines the public health response.”

The report cited Dr. Deborah Birx, a top White House coronavirus official, who reportedly told hospital executives and government officials this week that reporting to HHS was “solely an interim system.”

“CDC is working with us right now to build a revolutionary new data system so it can be moved back to the CDC, and they can have that regular accountability with hospitals relevant to treatment and PPE,” Dr. Birx said, according to WSJ.

In a statement to TEGNA, an HHS spokesperson said that when Birx mentioned an interim system, she was referring to the “current method of requiring hospitals to manually collect and then manually enter data every day.”

HHS said the CDC is collaborating with the U.S. Digital service in building a “modernized automation process.” The data will still go to the HHS Protect system, where it has been going since last month, “where all users in the response will have access to it.”

The move in July to switch the reports from CDC to HHS was met with controversy.

The Trump administration said it would speed up reporting. But critics said the data was important to guiding the pandemic response and suggested the move was aimed at silencing the CDC, which President Donald Trump has sometimes disagreed with during the coronavirus outbreak.

The information includes bed occupancy, staffing levels, the severity of coronavirus patients, ventilators on-hand, and supplies of masks, gowns and other personal protective equipment.

When the switch to HHS first occurred the CDC took down a web page with national hospitalization data, a decision that received backlash. The page was later restored with a note that the information would not be updated going forward.

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Direct video from the Washington Post of Trump contradicting himself on his COVID-19 response.


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Genetic data show how a single superspreading event sent coronavirus across Massachusetts — and the nation

The emerging field of genomic sequencing provides critical information into how the virus spreads.

https://www.washingtonpost.com/climate-environment/2020/08/25/boston-coronavirus-superspreading-event/

None of the biotech executives at the meeting noticed the uninvited guest. They had flown to Boston from across the globe for the annual leadership meeting of the drug company Biogen, and they were busy catching up with colleagues and hobnobbing with upper management. For two days they shook hands, kissed cheeks, passed each other the salad tongs at the hotel buffet, never realizing that one among their number carried the coronavirus in their lungs.

By the meeting’s end on Feb. 27, the infection had infiltrated many more people: a research director, a photographer, the general manager for the company’s east division. They took the virus home with them to the Boston suburbs, Indiana and North Carolina, to Slovakia, Australia and Singapore.

Over the following two weeks, the virus that circulated among conference attendees was implicated in at least 35 new cases. In April, the same distinctive viral sub-strain swirled through two Boston homeless shelters, where it infected 122 residents.

Scientists know all this thanks to a mistake made during the coronavirus’s replication process — a simple switch of two letters in the virus’s 30,000-character genetic code. This mutation appeared in two elderly patients in France at almost exactly the same time that genetically matching viruses were sickening dozens of people at the Biogen meeting. After the conference, each time the infection spread, the mutation spread with it.

Now, a sweeping study of nearly 800 coronavirus genomes, conducted by no less than 54 researchers at the Broad Institute, Massachusetts General Hospital, the Massachusetts Department of Public Health and several other institutions in the state, has found that viruses carrying the conference’s characteristic mutation infected hundreds of people in the Boston area, as well as victims from Alaska to Senegal to Luxembourg. As of mid-July, the variant had been found in about one-third of the cases sequenced in Massachusetts and 3 percent of all genomes studied thus far in the United States.

The study, which was added Tuesday to the preprint website MedRxiv, is probably the largest genomic analysis of any U.S. outbreak so far and is among the most detailed looks at how coronavirus cases exploded in the pandemic’s first wave.

It documents the cost of the world’s naivete this spring, when people traveling for events like the Biogen conference unwittingly imported the virus into Massachusetts dozens of times. It reveals the connections between seemingly disparate communities, showing how an outbreak at a gathering of wealthy executives was only a few infections removed from sickening some of Boston’s most vulnerable residents. It highlights the outsize role of indoor “superspreading events” in accelerating and sustaining transmission. With genetic data, said co-author Bronwyn MacInnis, “a record of our poor decisions is being captured in a whole new way.”

Although the study must undergo the rigors of peer review before it is published in a scientific journal, both outside experts and the scientists involved say it shows the power and promise of an emerging field of research known as genomic epidemiology. The small mutations that accumulate in a virus’s genome are like genetic bar codes; by tracking them, researchers can trace infections to their sources and develop more effective interventions to stop the disease.

“This is the kind of study that … defines why genomics can be so useful in outbreak reconstruction,” said Vaughn Cooper, a microbiologist at the University of Pittsburgh who was not involved in the Boston research. “It reflects a great deal of coordinating work, and that’s what in part makes this so powerful."

But if the new research shows the powerful potential of genomic surveillance to unveil the path of the virus through communities, it’s also an exception in terms of the large volume of data it contains. In the United States, such sophisticated genetic tracking has been “patchy, typically passive, reactive, uncoordinated, and underfunded,” experts at the National Academies of Sciences, Engineering and Medicine wrote in a lengthy report last month. Advocates for the cutting-edge technique say more coordinated and comprehensive sequencing efforts could dramatically improve contact tracing and infection control.

As the nation flounders ahead of a second wave of infections, the study serves as both a portent and an opportunity, MacInnis said. The virus’s genome may continue to record the consequences of the nation’s failures — the too-large gatherings and too-fast reopenings, the testing shortages and lack of protective equipment, and the silent spread.

Or it may answer lingering questions about how the virus is transmitted. It may provide the insights that finally allow workplaces to reopen and schools to safely resume. The virus’s own genetic instruction manual may be “invaluable” for teaching us to control the pandemic, MacInnis said — but only if we are willing to heed its lessons.

The anatomy of an outbreak

On the day the Biogen meeting was set to begin, 15 cases of covid-19 had been diagnosed within the United States, nearly all of them among travelers or their close contacts. The Centers for Disease Control and Prevention had just acknowledged an instance of possible “community spread” — an infection without an obvious source. Vice President Pence was to lead a coronavirus task force, and President Trump declared that the risk to Americans was “very low.”

Just like organizers of Mardi Gras in New Orleans, the Democratic primary in South Carolina, and the U.S. Mixed Doubles Curling Championship in Bemidji, Minn. — all of which were held the same week — those coordinating the Biogen conference saw no reason to change plans.

In a statement to The Washington Post, a Biogen spokeswoman pointed out that the company was following all U.S. guidelines at the time and notified health officials as soon as it realized attendees had gotten sick.

“February 2020 was nearly a half year ago, and was a period when general knowledge about the coronavirus was limited,” said Anna Robinson, the company’s head of U.S. media relations. “We never would have knowingly put anyone at risk."

Biogen has since announced a collaboration with the Broad Institute and Partners HealthCare to compile biological data that could help battle the disease.

The analysis of virus sequences shows that the coronavirus was introduced into Boston and its surrounding area more than 80 separate times by international and domestic travelers — most of whom were probably unaware of the germs they carried.

“We didn’t know better,” said Jacob Lemieux, a physician and infectious-disease expert at Massachusetts General Hospital and lead author of the study. “The difference now is there is increasing scientific evidence to show what can happen from a single event like that. We do know better. So we need to learn the lesson.”

The Boston event opened with breakfast at the Marriott Long Wharf hotel’s ballroom overlooking the wintry, gray harbor. Roughly 175 people were there, including guests from Italy, where officials had recently locked down more than a dozen towns in an effort to contain the country’s 400 cases.

Everything that felt so normal about the meeting seems sinister in retrospect, said Lara Woolfson, a Boston-based photographer who had been hired to document the conference. In a Facebook live video posted in March, Woolfson reflected on all the doorknobs she’d touched, the strangers she’d sat beside.

In the days that followed, dozens of attendees developed flu-like symptoms, according to the Boston Globe. By March 4, the company was instructing everyone who’d gone to the meeting to self-quarantine. The next day, Biogen confirmed that three out-of-state attendees had been diagnosed with covid-19; genetic data show that at least 12 others were sick by that point.

But Woolfson knew nothing about her potential exposure until a friend texted her a news article about the outbreak. Suddenly the dry cough and mild ache she’d been feeling seemed serious enough to call her doctor, who immediately sent her to the ER for testing. She was positive.

The Massachusetts Department of Public Health ultimately identified 97 coronavirus cases among meeting attendees and people who lived with them. Every individual linked to the conference whose genome was sequenced — 28 people in total — carried the conference’s characteristic mutation. It was dubbed “C2416T” for its location at the 2,416th spot on the genome and the two nucleic acids, cytosine © and uracil (T), that got switched.

Sequencing also revealed how the coronavirus evolved even as the Biogen conference was going on. About a quarter of attendees were sickened by a virus whose genome contained both the C2416T mutation and a second mutation, G26233T. In one case, the scientists found both versions of the virus replicating in a single set of lungs.

This shows that the G26233T variant is a descendant of the germ that originally arrived at the meeting, Lemieux said, an imperfect clone that wound up giving rise to its own distinct lineage.

The conference, the new study finds, amplified both variants, turning what might have been just one more introduction of the virus into a “superspreading event."

About a month later, more than 600 residents and staff members at two of Boston’s biggest homeless shelters were tested as part of a universal screening effort. Officials were shocked to discover that 230 people were already infected with the coronavirus, the large majority of them asymptomatic.

Genetic analysis showed that nearly two-thirds of sequenced infections among shelter residents could be traced back to the conference.

“Our jaws dropped,” said Pardis Sabeti, a computational biologist at the Broad Institute and one of the lead researchers on the study. “It was the realization that these events really affect the most vulnerable among us.”

Scientists can only speculate as to exactly how the infection among biotech executives made its way into Boston’s homeless community. But that’s precisely the point of genomic epidemiology, Sabeti said. Genetic data can reveal connections no one thought to look for, helping health officials seek out and sever chains of transmission.

There’s another lesson in the data, said James O’Connell, a professor of medicine at Harvard Medical School and the founder and president of the Boston Health Care for the Homeless Program: Packed shelters, like the conference, provide ideal conditions for superspreading.

“And by the time we realized how bad it was, so much asymptomatic spread had happened that it was too late,” O’Connell said.

The findings match what has been observed on a smaller scale in other studies, said Dave O’Connor, a virologist at the University of Wisconsin at Madison. Superspreading events, which provide the virus with huge numbers of hosts in a small amount of time, are driving the global outbreak. Delays in returning test results make it much more difficult to mitigate their effects; by the time those infected in such events know they’re sick, they have probably infected many more people.

“Right now, there are almost certainly people sparking new transmission clusters‚” O’Connor said.

If the United States continues to repeat the mistakes of February, he added, the same patterns of transmission will play out over and over again.

‘Just throwing away the crown jewels’

Of the 5.7 million confirmed coronavirus cases in the United States, scientists have sequenced the genomes for about 19,008, according to the Global Initiative on Sharing All Influenza Data (GISAID), the widely used international genome database. That’s roughly 0.33 percent of the nation’s epidemic.

Even though most tests work by detecting viral RNA in swabs from patients’ airways, those samples are rarely studied further once doctors get a diagnosis.

But if it were up to MacInnis, every coronavirus sample collected in the United States would be sent to a genetics lab for sequencing. Each of those sequences would be analyzed and submitted to the GISAID database. The results would be shared with health officials and contact tracers, deepening their understanding of their local outbreaks.

“If you’re spending whatever money large organizations seem to be putting into large-scale testing,” MacInnis said, “throwing away that very same extracted [RNA] that could tell you about how cases are connected within your organization or within communities is just throwing away the crown jewels of what you really want to know.”

Genetic insights could be “invaluable” for communities balancing the need to control the virus with the desire to reopen, MacInnis said. Suppose four students at an elementary school became sick. If genetic analysis showed they shared a common strain, the virus was most likely transmitted at school, suggesting the facility should close or at least conduct a thorough review of infection-control procedures. But if the infections were genetically unrelated, it’s likely they independently contracted the illness elsewhere, in which case the students should stay home but the school could remain open.

“It’s not testing that can answer that question,” MacInnis said. “It’s having genomic data to tell you whether they appear to be connected.”

But individual scientists and the National Academies alike say that the United States currently lacks the resources to carry out surveillance in a comprehensive way. Other countries have devoted millions of dollars to sequencing a representative sample of cases, producing a comprehensive picture of their national outbreaks. In the United States, meanwhile, genetic investigations have been led largely by individual institutions or small regional coalitions like the one in Boston. The resulting genetic portrait is patchy — the global GISAID database of SARS-CoV-2 sequences currently contains 1,807 submissions from Michigan and just 13 from Alabama, for instance — and that makes it less useful, scientists say.

Even the Broad Institute, a leader in this kind of work, has been stymied by a shortage of funds. MacInnis said her team has had to stop sequencing entirely while they apply for new grants. The scientists have not been able to collect any samples from the resurgence of cases in Boston.

The National Academies’ report calls for the Department of Health and Human Services to fund and coordinate widespread genomic surveillance of the coronavirus, as well as build a national infrastructure for recording and analyzing the resulting data.

That such a system has not been implemented already, Lemieux said, “is a failure of the federal government.”

Without fast, widespread and coordinated sequencing, he said, scientists can produce only studies like the one out of Boston — “postmortems” on outbreaks that are already over.

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QFT

The current outbreak here in Auckland has been “ring fenced” by just this sort of genome sequencing analysis. All 100 + cases have been linked to the first identified case through speedy contract tracing, (of the 2000+ close contacts of the positive cases, well over 80% have contacted, tested, and isolated pending results - most returning negative tests). The whanau (family members) of those with Covid are are also encouraged to enter supported quarantine with them in a managed quarantine facility. Obviously, family contacts are the most likely to pick up the infection.
With genome sequencing of all positive tests, occurring within 24 hours, the Govt has been able to say with a high degree of certainty, that the current outbreak is contained, and that Auckland will be able to move to a lower level of restrictions on Monday next week.

The only other out break where the genome sequencing did not link back to the main event involved 2 people - a woman returning from America, and a maintenance worker at the isolation facility where she was in 14 day managed isolation. The woman tested positive on her day 3 test (All returnees spend 14 days in managed isolation and are tested on day 3 and day 12. Should they test positive on either of those tests then they move into a dedicated quarantine facility for their recuperation). Since these people did not have direct contact, the transmission of the virus was a mystery, until cctv revealed that the maintenance worker used the same lift shortly after the woman. The pressing of a button was the instant of transmission.

In short, contact tracing, maintaing high testing rates especially around target populations, and genome sequencing to determine the extent of the particular strains of the virus and its progression, combined with effective social distancing, travel restrictions, and essential service regimes, are all vital tools in dealing with this pandemic. These tools need to be not just district wide, or region wide, or State wide but Nation wide. This is a very tricky virus, and can sneak across borders easily, and no wall, or fence, or ocean wide moat, is going to keep it out.

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HHS Bullies Hospitals; Florida’s Public Health Fail; Who’s Leading Pfizer’s Vaccine Efforts?

— This past week in healthcare investigations

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You know I just want so badly to be able to have faith in any vaccine they fart out in October, and I just don’t, and I feel terrible about that but like… my husband has this weird heart thing and my 4yo catches everything, and I’m having a hard time putting those things aside for “Trump doctors better than doctors” because someone slapped “vaccine” on the bottle and taking the eventual vaccine is important.

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@celena I plan to wait for the vaccine the reputable doctors recommend.

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