In a tragic vote yesterday, the City Council in Montgomery, Alabama failed to pass an ordinance that would have required the use of face masks in public. This vote came after an impassioned plea from local doctors:

Jackson Hospital pulmonologist William Saliski cleared his throat as he started describing the dire situation created by the coronavirus pandemic in Montgomery to its City Council before they voted on a mandatory mask ordinance. “It’s been a long day, I apologize,” he said.

“The units are full with critically-ill COVID patients,” Saliski said. About 90% of them are Black. He said hospitals are able to manage for now, but it’s not sustainable. “This mask slows that down, 95% protection from something as easy as cloth. … If this continues the way it’s going, we will be overrun.”

More doctors followed him to the microphone, describing the dead being carried out within 30 minutes of each other, and doctors being disturbed when people on the street ask them if the media is lying about the pandemic as part of a political ploy.

There’s a lot to unpack here. Note that Salisky said that units at the hospital are full with critically ill patients. But also note especially that the newspaper adds that he said 90% of the patients are black. Finally, he said that without intervention, the hospital certainly will be overrun.

The intervention measure proposed is simple and direct. Salisky claimed 95% reduction in transmission with a mask. I’m not so sure on that number, but it is becoming increasingly clear that masks, especially when coupled with social distancing, make a huge difference in reducing transmission.

We need to set the stage properly before getting to the details of the council’s vote in order to fully appreciate it.

Montgomery has a truly sordid past. As the Equal Justice Initiative has noted, Montgomery was Alabama’s center for the slave trade. EJI erected this plaque on Commerce Street in downtown Montgomery:

That’s right. Humans were literally warehoused between auction dates in Montgomery. In a bit of rare social justice, that building, 122 Commerce Street, is now one of several Equal Justice Initiative facilities in Montgomery:

I have these photos because, as I mentioned previously, I had the opportunity in February to travel to Montgomery with a busload of people from here in the Gainesville area. We visited two EJI facilities, the National Memorial for Peace and Justice (seen in the featured image for this post) and the Legacy Museum. We also made the approximately one hour bus trip to Selma, where we experienced the Footprints to Freedom Tour which included stops at the National Voting Rights Museum and Institute, the Slavery and Civil Rights Museum and a walk across the Edmund Pettis Bridge.

It turns out we were far from alone in making this trip. In November of 2018, the Montgomery Advertiser noted a significant uptick in visits to Montgomery and traced them directly to the opening of the National Memorial and Legacy Museum that April:

Over 250,000 people have visited the Equal Justice Initiative’s downtown museum and memorial to lynching victims since the sites opened in April. More than that, the burst of international attention that came with those sites has turned the city into a destination, instead of a stop on the way to something else. That’s led more people to discover the city’s other historic sites and attractions, from Martin Luther King Jr.’s church, to the site where Rosa Parks boarded the bus.

/snip/

“EJI has put Montgomery on the world’s radar,” he said. “I think Montgomery is in the best position for tourism appeal than it has ever been.”

Now, they’re voting with dollars.

Hotel room stays in Montgomery inched up by about 5,500 in 2017, according to state figures. This year they’re up 97,579 through October, according to the Montgomery Area Chamber of Commerce’s Convention and Visitors Bureau.

Note the mention of Rosa Parks as another part of Montgomery’s role in civil rights history.  The Montgomery Bus Boycott, from December, 1955 to December, 1956 marked Rev. Dr. Martin Luther King, Jr.’s rise to national attention. This adds significantly to the historic legacy of Montgomery and civil rights.

It should also be noted that Montgomery’s demographics are 61% black and only 33% white.

So with this rich history of civil rights activism, burgeoning civil rights tourism and a population 61% black, surely Montgomery’s City Council would vote for an ordinance that would slow down a disease where one doctor characterized those hospitalized as 90% black, wouldn’t they?

Not so fast. This is, after all, still Alabama. Here’s a link to the current Montgomery City Council. In a city that has 61% black citizens and only 33% white, the City Council has five white men, three black men and one black woman. Hardly representative.

Returning to the Advertiser story on last night’s vote:

After they spoke, and before the council voted on a proposal by Councilman C.C. Calhoun to mandate mask-wearing in public in Montgomery, Councilman Brantley Lyons questioned whether masks and six-foot distancing really helps. They do, the doctors replied. Lyons was unmoved. “At the end of the day, if an illness or a pandemic comes through we do not throw our constitutional rights out the window,” Lyons said.

From the crowd, doctors called for him to visit the hospital sometime.

Instead, the council killed the ordinance after it failed to pass in a 4-4 tie, mostly along racial lines, with Councilman Tracy Larkin absent. Councilman Clay McInnis voted with three Black council members — Calhoun, Oronde Mitchell and Audrey Graham — in favor of the ordinance. Lyons, Charles Jinright, Richard Bollinger and Glen Pruitt voted against it.

Only one white man voted for the ordinance. Sadly, one of the black men on the council was absent. I haven’t seen anywhere whether there might be an attempt at a new vote with all members present, since if no members change their vote, it would have a good chance at passage.

But note especially the behavior of Brantley Lyons. He asked the doctors whether it is true the masks and distancing would help prevent spread of the disease. Even though the doctors assured him it was true, Lyons trotted out the trope that the frothy right has been spewing all through the pandemic. Trying to claim that an ordinance mandating masks somehow would “throw our constitutional rights out the window” is the same sort of stupid rhetoric that racist conservative white people have spewed for generations whenever blacks sought equal protection under the law. And that circles back perfectly on the first quote from this article, where the doctors described being upset when the public approaches them to ask if the media is lying about the pandemic as part of a political ploy.

We know exactly where the real political ploy is coming from. Donald Trump is saying the quiet part out loud to fan the flames of racism in our country and he is directly responsible for these ideas spreading rapidly through people who listen to OAN and Fox News creating the narrative that the pandemic is fake. There also is no doubt that there is a huge component of racism in this entire process. Trump doesn’t hide his, but two-bit worthless politicans like Brantley Lyons happily spew this bunk without regard to the real and ongoing danger to the black citizens of Montgomery. You can rest assured that if this disease primarily attacked old white men, those not wearing masks would risk being shot on sight.

My home county, Alachua County in Florida, has been rocked by news that came out just after noon yesterday, that, as of that time, 76 agricultural workers in the county had tested positive for COVID-19. Today, that number appears to have grown even more, as the Florida COVID-19 dashboard shows 91 new cases of the disease being added on June 10 and 11, bringing the total to only 506. That means that this outbreak in only two days has grown the total for the county by about 20%.

Here is the report from one of the local television stations:

Although the particular farm where the outbreak occurred is not identified, this report appears to confirm my first suspicion, which is that due to the time of year, this outbreak almost certainly had to be among migrant workers harvesting watermelons, which are at the height of their season now locally.

The problem of migrant agricultural workers living and working under conditions conducive to an outbreak of the virus is not localized to Alachua County, of course, as we have been aware for some time of a severe outbreak in Immokalee. As AP reported today:

Immokalee is among several immigrant communities in Florida — and numerous rural areas across the U.S. — that have recently experienced outbreaks of the coronavirus. Once thought likely to be spared because of their remote locations and small populations, such communities have seen spikes in infections while having fewer resources to deal with them.

/snip/

The secluded town of 25,000 north of the Everglades has reported more than 1,000 cases, outpacing in recent weeks the rate of infection in Orlando, which has a population 10 times bigger and is home to a busy international airport. The number of total cases in Immokalee has surpassed those in Miami Beach, with more than 900, and St. Petersburg, which has more than 800, according to state health department statistics.

Meanwhile, the percentage of tests that have come back positive in Collier County, home to Immokalee, is the highest in the state among counties that have tested more than 5,000 people.

Because they initially couldn’t get the attention of state officials in Florida, the Coalition of Immokalee Workers enlisted Doctors Without Borders to help them with testing and treatment. But that is not enough.  See their website for their very simple demands and how you can lend your name to their call for help. Here is Greg Asbed of the Coalition in a New York Times Op-Ed published back in April:

Picture yourself waking up in a decrepit, single-wide trailer packed with a dozen strangers, four of you to every room, all using the same cramped bathroom and kitchen before heading to work. You ride to and from the fields in the back of a hot, repurposed school bus, shoulder-to-shoulder with 40 more strangers, and when the workday is done, you wait for your turn to shower and cook before you can lay your head down to sleep. That is life for far too many farmworkers in our country today.

Those conditions, the result of generations of grinding poverty and neglect, will act like a superconductor for the transmission of the coronavirus. And if something isn’t done — now — to address their unique vulnerability, the men and women who plant, cultivate and harvest our food will face a decimating wave of contagion and misery in a matter of weeks, if not days.

Yes, Greg told us so. The conditions under which migrant agricultural workers are forced to work in the US are horrific and incredibly conducive to disease outbreaks.

Returning to the story here in Alachua County, I want to share information I received today from the farmer who runs the CSA from which our family gets its produce for much of the year (today was coincidentally our final pickup for a while, as production pauses during the hottest part of the summer). It turns out that some of the footage (but not the watermelon harvest footage) in the TV story above was shot, without permission, at his farm, presumably because his farm is very close to town and media outlets tend to contact him about any agricultural story. He shared with us his response to the media organizations that contacted him regarding the outbreak:

Our produce has always been safe. We have always practiced good hygiene and field work is by nature socially distanced work.

The problem is when people work and live and travel in groups. The American system of farming depends on mobile low wage workers who are are powerless to poor conditions. I’ve seen 15 people living in a single wide mobile home that another local farm pays for. The workers don’t make enough to live elsewhere and their work is transient because our American model of production is based on the efficiency of monoculture.

People will get sick when they live in crappy conditions. You should do a story that brings modern day slavery to light in Alachua county. Don’t put our farm in with all the rest. We have a safe normal job with benefits for our workers. We pay a living wage and retain employees for years. That is not the norm for agriculture in the United States. People demand cheap produce and people in the shadows pay the price. That should be the theme of your story.

And don’t call it a community. A community is when people live stably together. These people travel up and down the east coast. Their children miss school or they are separated from their parents. They have no home and their families are split up for economic reasons. Calling it community is just more ignorance for the general public who have no idea where food comes from.

Wow. That is just so damning in how our country goes about producing food. These migrant workers really are trapped in a modern version of slavery with virtually no chance of escape. They are forced into cramped living and working conditions that put them much more at risk than those affluent citizens whom they feed. And our media mostly misses the true impact of those conditions and the fact that it doesn’t have to be that way. My CSA costs are a bit higher than buying the same items at the local grocery store, but the difference is very small. When you factor in the cruelty of the modern slavery system and the cost to society when outbreaks like this hit workers, our current system can be characterized as nothing less than heartless evil.

Oh, and one last note in parting. The Gainesville Sun article on the outbreak opened with this gem:

One farm worker who traveled to Alachua County from Miami-Dade County unknowingly infected at least 76 additional workers with COVID-19.

A total of 98 people traced back to the worker were tested for the virus Saturday evening, said Paul Myers, administrator for the Department of Health in Alachua County. Eight tested negative, and 14 tests are still pending.

Hmmm.  So one person coming here from South Florida managed to infect over 70 (and likely now around 90) people with COVID-19. And yet, our esteemed governor is hell-bent on “opening” the University of Florida this fall. Yes, there are plans to “screen” students before they’re allowed on campus. And students don’t live with 15 or so people in a single wide trailer. But student living groups like fraternities, sororities and dorms do wind up with many students in close quarters. And does anyone really think that student parties or even student bars downtown will follow social distancing guidelines?

This will not end well.

Earlier today, I saw this tweet that suggests a huge excess of pneumonia deaths in Florida this year compared to previous years. The data in the tweet suggested that Florida has around 4000 more pneumonia deaths this year than the average for the previous five years. That sounded a little high to me, as I have spent a lot of time over the past few months poring through the data at this CDC site on weekly numbers for pneumonia and influenza deaths. Looking deeper into the tweet, it appeared to depend on a reddit post and it had a low number for Florida reported COVID-19 deaths, so it was necessary to go back to original sources.

A couple of weeks ago, I spent several hours downloading data from the CDC national database you can access at the link above and picking out just the Florida data to paste into another spreadsheet. I chose a poor strategy that day, as I only looked at the total pneumonia and influenza deaths even though the data are broken down into both categories. I few days later, I realized that I needed to go back into the data and look only at pneumonia deaths, as it seems likely that there could be quite a few deaths attributed to pneumonia in patients who were never tested for COVID-19. Also, flu deaths vary widely from year to year depending on the severity of the outbreaks and the effectiveness of that year’s vaccine, so that total number has a lot of noise year to year. Seeing the tweet today prompted me to go back and download the data again so that the 2019-2020 data would be more up to date.

As downloaded today, there are data in the spreadsheet through week number 20 for each state. For Florida, the week 20 numbers appear to be only partial totals, so for this analysis, I only went through week 19 of 2020. Each season in the data begins with week 40 of the year (so this year’s data starts at week 40 of 2019). However, since the COVID-19 outbreak is generally considered to have started in earnest in mid- to late November of 2019, I included only the last four weeks of 2019 with the first 19 weeks of 2020. I then found the totals for the same time period in each of the five previous seasons.

The totals for pneumonia deaths are:

2014-2015                 5510

2015-2016                 5214

2016-2017                 5540

2017-2018                 5792

2018-2019                 5374

2019-2020                 6772

One of these things is not like the others. The average total for the previous five years is 5486 pneumonia deaths for weeks 49 through week 19 of each season. That means that 2019-2020 has 1286 more deaths from pneumonia than the average for that period in the previous five seasons. The Florida COVID-19 dashboard right now is showing 2319 deaths from the virus. I would suggest that number is more like 3605 when the excess pneumonia deaths are included. Note also that there may well be other deaths due to the virus in patients who were not tested but died due to the other types of pathology seen by the virus that don’t manifest directly as pneumonia.

Last week, I asked how many COVID-19 deaths Ron DeSantis is hiding. We can now account for about 1300 and it seems likely there may well be more.

I had been told a couple of days ago, either here in comments or on Twitter, that Ron DeSantis had put his cronies in charge of the Florida database for COVID-19 cases and deaths. I hadn’t followed up on that, but then on Twitter last night i learned that the scientist who had been in charge of the site was fired back on May 1.  She spoke last night with a West Palm Beach TV station which broke the blockbuster story of why she was fired:

Rebekah Jones said in an email to CBS12 News that her removal was “not voluntary” and that she was removed from her position because she was ordered to censor some data, but refused to “manually change data to drum up support for the plan to reopen.”

Jones made the announcement May 5 in a farewell email to researchers and other members of the public who had signed up to receive updates on the data portal, according to Florida Today. She said that for “reasons beyond my division’s control,” her office is no longer managing the dashboard, involved in its publication, fixing errors or answering any questions.

Wow. Note that DeSantis “reopened” Florida on May 4. So the timing here, coupled with Jones saying she was ordered to change or censor data, shows a clear intent by DeSantis to game the numbers and create the false impression that the reopening would be a success. Just how stupid can a governor be?

Well, in his case, pretty stupid. He can’t even figure out how to wear a mask:

So who would trust this clown, compared to the scientist he fired? Here she is in a photo she supplied to Florida Today:

Near the end of the story filed last night, Jones notes that the Florida database still hasn’t been repaired. Here’s what I got when I checked at 1:40 this afternoon (refreshing 15 minutes later gave a plot for cases but not deaths, so there may be some “repair” work underway as I write this; and both plots were visible at 2:50):

There are big holes where the plots of new cases by day and deaths by date of death for the last 30 days would show up. Back on May 5, when Jones talked to Florida Today about her firing (but without mentioning the orders to censor data), Jones noted that near the end of her time in the job, the database suddenly started to malfunction:

Late last Friday, the architect and manager of Florida’s COVID-19 dashboard — praised by White House officials for its accessibility — announced that she had been removed from her post, causing outcry from independent researchers now worried about government censorship.

The dashboard has been a one-stop shop for researchers, the media and the public to access and download tables of COVID-19 cases, testing and death data to analyze freely. It had been widely hailed as a shining example of transparency and accessibility.

But over the last few weeks it had “crashed” and gone offline; data has gone missing without explanation and access to the underlying data sheets has become increasingly difficult.

The site was created by a team of Florida Department of Health data scientists and public health officers headed by Rebekah Jones. She announced last week her removal as of May 5 in a heartfelt farewell note emailed to researchers and other members of the public who had signed up to receive updates on the data portal.

Citing “reasons beyond my division’s control,” Jones said her office is no longer managing the dashboard, is no longer involved in publication, fixing errors or answering questions “in any shape or form.”

Note that the story from the West Palm Beach TV station says Jones announced her firing on May 5, but this Florida Today story makes it clear she informed people on May 1 that she was being removed May 5. Since she speaks of the database malfunctioning at the time of her firing, for the purposes of discussion here I consider May 1 the firing date and the time when fuckstickery of the database began.  With today being May 19, it’s clear that the database has been malfunctioning for nearly three weeks at a minimum.

The big problem, though, is that the plot for deaths magically starts dropping right after Jones was fired. I captured this version of the death plot around 9 this morning and noted the date Jones was fired (did she insert a parting shot of a bit more reality on her last day of May 4?):

There should be one partial note of caution here even though it’s really hard not to get the impression death numbers are being artificially reduced. There is a note on the death graph that I’m pretty sure popped up fairly recently and may well have been added around the time of Jones’ departure. The note says that deaths are now counted on the day of death rather than on the day the report is entered into the database. Since it can take a while for deaths to be reported depending on the county involved, the last few days in the plot can be expected to show increases as more death reports get entered into the system. But it has been long enough now since Jones was removed for it to be clear that there is a discontinuity in the plot that coincides precisely with her removal.

I haven’t included a plot of cases by day, but I also find the current data there (site is here) not believable. With the partial reopening of the state on May 4, it’s simply incomprehensible that the number of new cases per day is holding steady rather than increasing.

Will DeSantis ever face consequences for this egregious breach of public trust? Odds aren’t good. The Republican Party in Florida has a long tradition of doing whatever it pleases, rules and laws be damned. Just look at how they over-ruled the will of the people on the initiative overwhelmingly passed in 2018 to restore voting rights to felons who have served their sentences. It would seem that firing a scientist because she refused to censor data and mislead the public on a life or death matter would be the end of a normal political career. But in Florida, there is no limit to how criminal Republican officeholders can be.

Recall that back on April 30, I wrote about how the Trump Administration had been orchestrating a propaganda push to claim that SARS CoV-2 was accidentally released from the Wuhan Institute of Virology. Of special importance is that the New York Times article I cited on the topic specifically mentioned Mike Pompeo as one of the primary forces behind pushing the story. Recall also that a part of this propaganda effort came from “leaked” State Department cables.

Apparently, getting called out by the New York Times was not enough to deter Pompeo from this effort. He returned to the airwaves on May 3, telling ABC that there is “enormous evidence” that the virus came from the lab. And then “magically”, but in reality following the aluminum tubes playbook straight out of Cheney’s Iraq WMD playbook, a “report” came into the hands of NBC, who published it May 8. The report purportedly relied on “open source” data to make the case that some sort of accident occurred at the lab in late October, prompting officials to shut down the lab and block roads surrounding it. NBC debunked one aspect of the report in their story, noting that a conference at the lab that the report claims was cancelled in this timeframe actually took place as planned.

Yesterday, Erin Banco and colleagues at Daily Beast published what can only be described as one of the most epic slap-downs of fake intelligence I’ve ever seen. Please go read the piece in full, because summarizing cannot properly capture its full glory.

The dissection of the false intelligence in the report begins with work done by Jeffrey Lewis (one of the best follows on Twitter at @ArmsControlWonk), who utterly destroyed the report’s claims regarding satellite data:

What’s more, imagery collected by DigitalGlobe’s Maxar Technologies satellites and provided to The Daily Beast reveals a simpler, less exotic reason for why analysts believed “roadblocks” went into place around the lab after the supposed accident: road construction. The Maxar images also show typical workdays, with normal traffic patterns around the lab, after the supposedly cataclysmic event.

“This is an illustrated guide on how not to do open source analysis,” said Jeffrey Lewis, director of the East Asia Nonproliferation Program at the Center for Nonproliferation Studies, who analyzed the MACE report for The Daily Beast. “It is filled with apples-to-oranges comparisons, motivated reasoning, and a complete refusal to consider mundane explanations or place the data in any sort of context.”

That’s right. The report took images showing roads blocked for ordinary road construction and claimed they showed that a catastrophic accident in the lab meant that traffic had to be kept away to prevent exposure to the leaked virus.

But the fun doesn’t stop there. I’ll get to who MACE, who prepared the report, is a bit later. The story continues:

MACE’s analysts tried to establish a “pattern of life” at the Wuhan lab in order to reveal what they claim is an anomaly, one purportedly caused by a leak. The MACE document charts the movement of apparent Wuhan lab personnel into and out of the facility leading up to October, when the alleged leak took place. In one slide, analysts wrote that there is an “18 day gap” in which “there were no observable events” from devices at the lab between Oct. 6 and 24, supposedly suggesting an accidental leak.

In doing so, they appear to have been unaware of a key cultural factor complicating the normal course of events: a holiday. “The first week of October is a golden week in China, which is going to disrupt that pattern,” Lewis said.

Yep. The “anomaly” MACE ascribes to leak was in fact an ordinary holiday when activity would be diminished around the lab for a perfectly ordinary reason.

And the Daily Beast investigators spread the fun around, getting the folks at Bellingcat involved in investigating the claims made in the report:

The Daily Beast asked analysts at the award-winning open source investigative news outlet Bellingcat to review the MACE dossier and evaluate the quality of its conclusions. Within minutes of receiving the dossier, Bellingcat senior investigator Nick Waters disproved one of the MACE document’s claims: that a conference on biosafety lab management at the Wuhan lab scheduled for the first week of November was canceled.

But the conference did take place, as NBC first reported. Waters found a Facebook post from a Pakistani scientist who had attended the event and taken selfies there, including at the BSL-3 laboratory.

Wow. And Waters doesn’t stop there:

He also took a dig at one of the many amateurish elements in the MACE presentation. “Perhaps the authors should have spent more time testing their analysis rather than working out how to crop the eye of Sauron into a logo copy-pasted from the internet,” Waters said.

Okay, I got a huge laugh at the eye of Sauron bit. That’s because I’ve run into the folks behind MACE before. As Daily Beast points out, MACE stands for Multi Agency Collaboration Environment. And according to this link they provide, MACE is hosted at a company in Las Vegas by the name of Sierra Nevada Corporation. Way back in 2011, I wrote about a technology called Gorgon Stare, developed by Sierra Nevada Corporation, that claimed to enable real time remote viewing analysis of entire villages in Iraq or Afghanistan from imaging equipment carried by high-flying drones. Of course, this technology turned out to be a very expensive boondoggle that did nothing to help intelligence-gathering. I can’t help wondering if the eye of Sauron bit was an insider joke at Sierra Nevada that Waters understood and shot right back at them to ridicule this report and the old Gorgon Stare technology.

So, while the MACE report clearly originated in the US, what I haven’t seen yet is a clear indication of just when it surfaced, especially when it surfaced for senior Trump Administration officials and the intelligence community. It would not surprise me if it goes all the way back to the propaganda campaign in mid-April I described in my previous post. The version of the report that NBC published has the last several pages redacted with the description that this was done to protect names from being disclosed. That really makes me wonder if the specific question from John Roberts of Fox News to Trump on April 14 about an intern at the lab being infected and then spreading it to her boyfriend and the wet market was based on the redacted portion of the MACE report. All we know about timing is that the report had made its way to Congressional committees by May 8 when NBC published it.

There is another weak intelligence document, though, that this time is traced directly to the State Department. On May 7, the Sydney Morning Herald debunked a “dossier” that had been leaked from the US embassy in Canberra that the Daily Telegraph (a Rupert Murdoch paper in Australia) wrote about on May 2. The Herald says this about Australian officials  looking for the basis of the dossier:

Senior members of the Morrison government and Australian intelligence agencies at first had trouble finding the document. Eventually they found a research report, based on publicly available information including news reports, which appeared to fit the description. The research paper contained no information that was generated from intelligence gathering, according to people who have read it.

Labor MP Anthony Byrne, the deputy chair of the influential intelligence and security committee, was “incensed” by the report of the dossier. Mr Byrne, one of Parliament’s biggest supporters of the US alliance, directly raised his concerns with senior members of the Morrison government and intelligence agencies, saying Australia shouldn’t accept intelligence that doesn’t exist and fall for a “tricked-up document”.

There are now widespread suspicions within senior ranks of the Australian government and the intelligence community that the document was leaked to The Daily Telegraph by a staff member in the US embassy in Canberra. This suspicion, whether true or not, underlines how the positions between sections of Canberra and Washington national security circles have diverged over the claim. Some senior officials clearly believe the US embassy is pushing a narrative in the Australian media that could be counter to the beliefs and interests of its hosts.

The story continues:

The episode highlights the danger of mischaracterising the work of intelligence agencies. Some of the footnotes in the document contained references to US media reports that were based on unsubstantiated assertions from the US government – the same kind of circular intelligence which resulted in the “children overboard” affair in 2001.

Wow. The Herald also goes there, comparing this propaganda ploy to an Australian false information scandal of similar magnitude to the Iraq WMD operation in the US.

But again, Pompeo and those under him seem to be central to this whole operation. The Daily Telegraph story appeared just a day before Pompeo claimed “huge evidence” and likely was based on a document leaked by a US embassy. And then NBC published the MACE document a few days later. I haven’t seen anyone suggest that the document in Australia is the MACE document, but the Herald’s description and debunking of it sure would fit with them being the same or at least having the same source.

Given Pompeo’s central role in spreading propaganda that has been so easily refuted, I can’t help wondering if we will have another shoe drop on the firing of Steve Linick. Note that in his letter to Congress on the firing (which will be complete at the end of a 30 day clock starting Friday night), Trump said it was based on Pompeo’s suggestion that Linick be fired. Also note that we were first told it was because Linick was investigating Pompeo using State Department personnel to run personal errands. Today, that’s been expanded to cover the fast-tracking of arms sales to Saudi Arabia. But in their article on that, CNN notes:

But at this time, House Democrats say they do not yet know which investigation was the biggest factor behind the decision to dismiss Linick.

“I wouldn’t assign percentages,” a Democratic committee aide said.

Democrats on both the House Foreign Affairs and Senate Foreign Relations committees are interested in learning more about Linick’s investigations into Pompeo, and Engel emphasized the importance of cooperation from the administration in his statement Monday.

“The administration should comply with the probe I launched with Senator Menendez and turn over all the records requested from the Department by Friday,” he said, a reference to Sen. Bob Menendez of New Jersey, the ranking Democrat on the Senate Foreign Relations Committee.

I find it hard to believe that Pompeo would have felt truly threatened by either the investigation into using aides for personal errands or expediting the Saudi arms sales. Those just seem like garden variety Trump corruption that gets shrugged off as the next daily outrage appears. However, if Linick had started nosing around the leak of the State Department’s own Wuhan cables and/or the allegation of the leak of the report from the Canberra embassy, I think Pompeo would see a bigger danger. That would represent an investigation into an ongoing propaganda operation in which Pompeo disseminated easily disproved disinformation.

The final beautiful irony here is that if Linick had started such an investigation, it likely was based on open source information. Unlike the MACE information though, this open source information would consist of Pompeo’s own recorded media appearances and the subsequent public debunking of the propaganda. That propaganda getting debunked would be both Pompeo’s direct statements and the debunking of the “supporting” material that appears to have been released either by him or those doing his bidding.

Marcy has touched on, and revisited today, the awful toll that COVID-19 is exacting on Albany, Georgia. An early in-depth look by the Atlanta Journal Constitution into how the outbreak started there showed us a very closely-knit community that has a deep history in the civil rights movement. Another very touching peek inside the community came yesterday from USA Today and really got to me, as it hit on what I saw as an echo of the complicated history of the Albany Movement.

The USA Today article goes into detail on how the Albany community refuses to “reopen” as Brian Kemp would have them do. Leaders of the community are coming together on their own to declare that they will only reopen when local health officials pronounce it safe to do so, and that point is still off in the future:

With so much loss, the idea of resuming normal life in Albany and risking a deadly second spike in cases is unthinkable. Town officials, business owners and church pastors are collectively rejecting Gov. Brian Kemp’s decision to allow certain businesses to reopen and lift a shelter-in-place order.

The people here say they will decide when their community can go out to dinner again, get a haircut at a local barbershop and worship together at church on Sunday.

And they are not ready yet.

“We are not going to listen to the federal and state people,” said Glenn Singfield Sr., who owns two restaurants in Albany. “We are going to listen to our local health community, because that’s where our trust is.”

To make the losses in Albany personal, the article opens with a focus on Elaine Williams, who lost her 38 year old son to the virus in early April. Near the end of the article, we return to Elaine Williams and her son, Kenya. They reproduced this photo she provided:

Here’s their description of how the loss has affected Ms. Williams:

Williams, meanwhile, is urging her neighbors to stay home so others are spared the pain she has endured losing her son.

Williams still doesn’t know how Kenya, who was born with Down syndrome, contracted the coronavirus. The only public place they visited in Albany was Sam’s Club on March 12.

She misses his forehead kisses, his gentle voice calling her “my dear” and the sound of him singing in his bedroom while blaring Frankie Beverly & Maze songs.

You see, singing and Albany have a deep history. You might recall that I had the opportunity back in February to join a group of people from here in Gainesville on a bus trip to important civil rights sites and museums in Montgomery and Selma, Alabama. As preparation for the trip, I started reading Hands on the Freedom Plow, which is a wonderful compilation of over 60 essays written by women who were part of the Student Non-violent Coordinating Committee (SNCC) on the roles they played as the civil rights movement unfolded in the South in the early 60’s. The essays are grouped into sections covering different aspects of the overall movement. The stories from the women on the front lines of the Albany Movement are among the most gut-wrenching in the book (which I’m still reading–it’s very long and takes time to process).

I will confess that I had not been aware of the Albany Movement and how it was one of the earliest sustained programs of mass demonstrations in the South and brought SNCC and Rev. Dr. Martin Luther King, Jr,’s Southern Christian Leadership Conference  (SCLC) together for the first time. Most “official” histories of the Albany Movement refer to it as a failure (see for example, here) since the demonstrations were halted without the local police and others instituting the reforms the demonstrators wanted. The “failure” was ascribed fairly often to infighting over power and funding between SNCC and SCLC, but my impression after reading the essays gave me more of a feeling that the people of Albany realized that the extreme physical and sexual brutality inflicted by those in power were not likely to end without structural change on a more national than local level. The Stanford history linked here does admit that the lessons learned in Albany were put to good use in the next movement in Birmingham and eventually in Selma, so the “failure” characterization isn’t really justified.

But there’s more. Although most of those who provided essays to the book only have one appear, one of the early organizers in Albany has two separate essays. Bernice Johnson Reagon played a dual role in Albany. She was a student at Albany State when demonstrations began breaking out on campuses in 1960 and she played a major role in getting demonstrations started in Albany in December of 1961. As the movement progressed, she found herself leading a key aspect of the gatherings: group songs. Her essay that focuses on the musical side of her work opens with the lyrics to “Since I Laid My Burden Down”, which she sings here in a 1986 recording:

Here is what she had to say about the song:

The Albany Movement conquered my fear of going to jail, and the songs helped to do that. They allowed us to name the people who were using jail against us, like Mayor Asa Kelley and Chief of Police Laurie Pritchett.  Not only could we call their names and say what we wanted to say, but also they could not stop our sound. Sometimes the police would say, “Stop the singing.” And we would know we were being heard, and we would just sing louder and longer. “I feel better, so much better since I laid my burden down” expressed what I felt like inside the Albany jail cell. There was a clarity about everything. I knew where I was; I knew what I was doing.  I did not like being locked up, and it was not easy. It was where I was supposed to be. My life was being used for a purpose–fighting racism–and it lifted me up to find that I could take a stand and make clear what I thought about the way we were treated in this country and in my hometown. My body was locked in jail, but I was free and centered.

The parallels between 1961 and 2020 in Albany are striking. The citizens of Albany took a stand for what is right in 1961 and were locked up for it. They realized that this suffering while locked up would help everyone in the struggle for civil rights. Today, the citizens of Albany are once again organizing and this time they’re locking themselves up. Just like before though, this round of being locked up is being undertaken with the knowledge that it is for the good of their community and their country.

But the music didn’t stop. Bernice Johnson Reagon was one of the four founders in Albany of the Freedom Singers. Even after the Albany Movement was over, the Freedom Singers went on tour raising money for SNCC. Here’s a 1963 recording that uses as a backdrop a photo of founders Bob Zellner, Bernice Johnson Reagon, Cordell Reagon, Dottie Miller (Zellner), and Avon Rollins:

And here they are singing at the March on Washington in August of 1963:

Oh, and Bernice didn’t stop there. She later founded “Sweet Honey in the Rock” and she is the performer of “Keep Your Eyes on the Prize” in the theme music for the PBS civil rights documentary series “Eyes on the Prize“.

Keyna Williams’ voice is now missing from the choir of Albany, but its rich tradition carries on and has made a lasting contribution to civil rights in our country. Now, the citizens of Albany are stepping up once again to lift their voices and dedicate their lives to making a more healthy world for us all. They are still being subjected to brutal racism from their governor and president, but they are far from new to this battle and know how to proceed.

In my last two posts, I went into detail on what is known on the scientific front about the origin of SARS CoV-2, the virus responsible for the COVID-19 outbreak and then into what evidence Shi Zhengli of the Wuhan Institute of Virology (WIV) has offered to refute the rumors of the virus escaping from her lab. This post will set aside discussion of the science (other than to eventually provide a few quotes that have been provided by scientists addressing these issues) and will instead focus on what has been increasing evidence that there has been a concerted effort akin to an information operation to create acceptance of the idea that the virus escaped from WIV. Today, the New York Times confirmed these suspicions and indicated clearly who is behind the operation. Here’s a partial screen capture of the story by a team that includes Mark Mazzetti and Adam Goldman:

Although I was becoming convinced of an information operation, I wasn’t sure who was orchestrating it. This Times article leaves no doubts:

On Saturday, I took a deep dive into the origin of SARS CoV-2, the virus that is the cause of the deadly COVID-19 pandemic. That post was the result of several long days of deep reading and thinking. Somehow, I missed that Scientific American had put out an update on Friday of their profile of Dr. Shi Zhengli, the scientist responsible for much of what the world knows about bat coronaviruses, including isolating the bat coronavirus from Yunnan Province that is the closest relative to SARS CoV-2 that has been seen in a laboratory. Even worse, commenter Zinsky linked to the Scientific American article in one of the earliest comments on my post.

I finally got around to reading the article today. As you might imagine, this editor’s note at the top really got my attention:

Editor’s Note (4/24/20): This article was originally published online on March 11. It has been updated for inclusion in the June 2020 issue of Scientific American and to address rumors that SARS-CoV-2 emerged from Shi Zhengli’s lab in China.

I strongly urge you to read the entire article. It provides an effective look into work that Shi had been doing prior to the outbreak and then takes us along with her as she gets the news on December 30 that a novel coronavirus had been detected in two patients in Wuhan with atypical pneumonia. On instruction from the lab director, Shi left the conference she was attending in Shanghai and rushed back to Wuhan to concentrate all of her attention on the new virus.

It is important to keep in mind that Shi’s career up to the SARS CoV-2 outbreak was aimed at just such an event. In fact, she and her team had warned us. From the Scientific American article:

With growing human populations increasingly encroaching on wildlife habitats, with unprecedented changes in land use, with wildlife and livestock transported across countries and their products around the world, and with sharp increases in both domestic and international travel, pandemics of new diseases are a mathematical near certainty. This had been keeping Shi and many other researchers awake at night long before the mysterious samples landed at the Wuhan Institute of Virology on that ominous evening last December.

More than a year ago Shi’s team published two comprehensive reviews about coronaviruses in Viruses and Nature Reviews Microbiology. Drawing evidence from her own studies—many of which were published in top academic journals—and from others, Shi and her co-authors warned of the risk of future outbreaks of bat-borne coronaviruses.

With that as background, her actions in digging into the new virus make perfect sense for how a respected scientist engaged in work with dangerous viruses would seek the source of the outbreak.

She and her team jumped into work on the train trip back to Wuhan from the conference in Shanghai:

On the train back to Wuhan on December 30 last year, Shi and her colleagues discussed ways to immediately start testing the patients’ samples. In the following weeks—the most intense and the most stressful time of her life—China’s bat woman felt she was fighting a battle in her worst nightmare, even though it was one she had been preparing for over the past 16 years. Using a technique called polymerase chain reaction, which can detect a virus by amplifying its genetic material, the team found that samples from five of seven patients had genetic sequences present in all coronaviruses.

But here’s where the character of a person who has been dedicated to science her entire career comes out:

Shi instructed her group to repeat the tests and, at the same time, sent the samples to another facility to sequence the full viral genomes. Meanwhile she frantically went through her own lab’s records from the past few years to check for any mishandling of experimental materials, especially during disposal. Shi breathed a sigh of relief when the results came back: none of the sequences matched those of the viruses her team had sampled from bat caves. “That really took a load off my mind,” she says. “I had not slept a wink for days.”

Yes, months before the rumors of an accidental release from her lab started circulating, one of Shi’s very first steps was to make sure that the sequence of the virus found in patients from the wet market did not align with the sequences of any of the viruses isolated from bats that she had in her lab. She had already warned the world of the danger posed by some coronaviruses jumping from bats to humans. [Note: even though we talk about SARS CoV-2 and the bat virus RaTG13 being “closely related”, they still differ by enough that it is clear that SARS CoV-2 came from a different source than either the virus circulating in that bat population at the time it was isolated or the virus as it exists now in the lab.]

Even more importantly, she checked lab safety records and did not sleep until she could eliminate the nightmare of her lab being responsible for the outbreak.

The article goes on to detail the steps taken to confirm SARS CoV-2 as the agent for the outbreak and the use of sequencing of multiple isolates from different patients over time to indicate that it’s very likely that there was only a single introduction of the virus into humans.

Clearly, the rumors of a leak from her lab have bothered Shi, but she will not allow them to stop her:

Despite the disturbance, Shi is determined to continue her work. “The mission must go on,” she says. “What we have uncovered is just the tip of an iceberg.” She is planning to lead a national project to systematically sample viruses in bat caves, with much wider scope and intensity than previous attempts.

/snip/

“Bat-borne coronaviruses will cause more outbreaks,” Shi says with a tone of brooding certainty. “We must find them before they find us.”

Epilogue

In my post on Saturday, I posited that if we are to believe that the outbreak was the product of an accidental release from Wuhan Institute of Virology, we would have to claim that China has removed from the record any evidence of workers from the lab, or the family or other close contacts, being infected or dying.

Now, after the details that Shi has provided, we would have to believe that a scientist with a long history of top-notch peer reviewed research would be involved in such a lie and would further fabricate the story that none of the previous isolates in her lab match the outbreak.

A scientist of this caliber would know that such a lie would eventually be uncovered. That Shi intends to continue her work unabated is very strong evidence that she is being truthful and can rightfully proceed with a clear conscience.

Those considerations prompted me to return to the “evidence” that was presented to suggest an accidental release. Recall that in my post Saturday, I was perplexed by what looked like the outlines of an information operation. First, the specificity, out of the blue, of the question from John Roberts of Fox about an intern at the lab being infected. I still haven’t heard any others make this same suggestion, so that still stands out as suspicious.

But then I went back and looked at the Josh Rogin column from the same day, where Rogin concentrated on two State Department cables from 2018 about Wuhan Institute of Virology. Here’s the setting Rogin provided for the cables:

In January 2018, the U.S. Embassy in Beijing took the unusual step of repeatedly sending U.S. science diplomats to the Wuhan Institute of Virology (WIV), which had in 2015 become China’s first laboratory to achieve the highest level of international bioresearch safety (known as BSL-4). WIV issued a news release in English about the last of these visits, which occurred on March 27, 2018. The U.S. delegation was led by Jamison Fouss, the consul general in Wuhan, and Rick Switzer, the embassy’s counselor of environment, science, technology and health. Last week, WIV erased that statement from its website, though it remains archived on the Internet.

What the U.S. officials learned during their visits concerned them so much that they dispatched two diplomatic cables categorized as Sensitive But Unclassified back to Washington. The cables warned about safety and management weaknesses at the WIV lab and proposed more attention and help. The first cable, which I obtained, also warns that the lab’s work on bat coronaviruses and their potential human transmission represented a risk of a new SARS-like pandemic.

And yet, even though Rogin says he got a copy of the first cable, this is the only money quote he chose to put into his column:

“During interactions with scientists at the WIV laboratory, they noted the new lab has a serious shortage of appropriately trained technicians and investigators needed to safely operate this high-containment laboratory,” states the Jan. 19, 2018, cable, which was drafted by two officials from the embassy’s environment, science and health sections who met with the WIV scientists. (The State Department declined to comment on this and other details of the story.)

Rogin then adds what I think is the most important part:

The Chinese researchers at WIV were receiving assistance from the Galveston National Laboratory at the University of Texas Medical Branch and other U.S. organizations, but the Chinese requested additional help. The cables argued that the United States should give the Wuhan lab further support, mainly because its research on bat coronaviruses was important but also dangerous.

Really? The scariest language that Rogin could lift from the cable warned of a “shortage of appropriately trained technicians and investigators needed to safely operate”, but then he grudgingly had to note that this was in fact tied to a request from the lab for more outside assistance in getting that training. When we couple that thought with the failure, so far, of Rogin or anyone else to have actually published the full cables, I am more convinced than ever that the whole cable story is part of a coordinated information operation where Roberts asked the specific question and then Rogin took information that had been twisted inside-out from a cable asking for help with training at the lab to try to turn it into a potential whistle-blowing event.

One more bit. I did some digging. Rick Switzer, the “embassy’s counselor of environment, science, technology and health” is not a scientist:

Rogin says the cable he saw was written by “two officials  from the embassy’s environment, science and health sections who met with the WIV scientists”. One would hope that there was at least one actual scientist among those two officials.

Update: In a new post we find that Shi Zhingli of Wuhan Institute of Virology has provided convincing evidence to Scientific American that SARS CoV-2 is the result of a natural jump to humans from an animal host and was not accidentally released from her lab, which had no isolates of any viruses that match closely enough to be the outbreak virus.

Although it seems that all of this has been going on forever at this point, it’s important to realize that the COVID-19 pandemic outbreak probably began less than six months ago. In the context of how we develop an understanding of a disease like this one, and the virus that causes it, SARS CoV-2, that means that we really have only just begun our analysis. Nevertheless, because of the ongoing disastrous impact on global public health as well as the global economy, it is imperative that we learn as much as we can as fast as we can.

In this post, I want to take a deep dive into what virologists and epidemiologists have pieced together on the emergence of SARS CoV-2. The problem is that what might initially appear to be straightforward scientific and public health questions eventually get muddled by accusations of disinformation, accusations of hiding data and offerings of potential leaks of intelligence that also have a chance to be disinformation. These noisy battles relate to basic facts that have a direct bearing on our understanding of the virus’ origin.

As a result, it needs to be stated from the outset that because some of the needed basic information may be hidden or some of what we think we know might be wrong. Therefore, this analysis will be unable to come to a definite conclusion. With any luck, the discussion will help us to have a framework within which we can proceed as more facts become verified.

Overview Derived From SARS CoV-2 Genetic Sequence

I want to start with the science.  The very helpful graphic below is lifted from this paper in Current Biology. It is in three sections. The section on the left illustrates what we know from the genetic sequence of the virus when that is compared to other known viruses. What it shows is that the closest overall relative to SARS CoV-2, with a sequence identity of 96%, is RaTG13, another coronovirus isolated from a bat:

Let’s move to this Nature Medicine article from March 17 and this Cell article from April 16 for the narrative on diving into the distinguishing features of SARS CoV-2 from its genetic sequence.

From the Nature Medicine article, we get a description of the features of SARS CoV-2 that distinguish it from other known viruses (these features are what the center and right panels of the graphic address):

Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies and biochemical experiments, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides, which additionally led to the predicted acquisition of three O-linked glycans around the site.

To translate some of the terms and clarify a bit, there are four genera of coronaviruses, with alpha and beta infecting mammals and delta and gamma infecting birds. The genome is the genetic sequence of the virus. I would usually say the DNA sequence, but coronaviruses are RNA viruses. There has been much discussion of ACE2 on this blog in the comments, so for now let’s just say ACE stands for angiotensin converting enzyme and ACE2 is present on the surface of many cell types found in many different tissues within the body. So what stands out here is that the structure of the virus spike protein, as determined from its genetic sequence and tests in the lab, allows it to bind exceptionally well to ACE2 when compared to other coronaviruses.

The middle panel of the graphic shows us that although the overall sequence of SARS CoV-2 is very closely aligned to the bat virus, when we narrow it down to only compare the region where the spike protein binds to ACE2, it is a perfect match of that part of a pangolin virus, while it is very different from the bat virus. For the important stretch of the spike protein (these amino acids are not next to each other when the gene sequence is read from start to finish, but once the protein is assembled from amino acids, the amino acids are close to each other from the way the protein assumes its three dimensional structure), the gene encodes a string of five amino acids in the protein that matches exactly with the pangolin virus sequence but in only the first of the five positions on the bat virus sequence.

But that final panel and the second half of the Nature Medicine snippet goes further in what is different about this virus. The gene for the spike protein encodes two subunits, S1 and S2. Remarkably, SARS CoV-2 has acquired a site where the two subunits can be separated using a enzyme called furin that is found in mammalian cells. The right panel shows us that neither the bat sequence nor the pangolin sequence has a furin cleavage site.

The Cell paper tells us that a furin cleavage site has not been seen in the betacoronaviruses closely related to SARS CoV-2. It has been seen in other human coronaviruses, though. Of further significance is that a furin cleavage site also appears in the more pathogenic bird flu viruses.

Not A Lab Construct

From the Nature Medicine article, we get one of the most convincing arguments I’ve seen against the virus being created in a lab:

While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.

So, in other words, if someone in the lab wanted to set out to make a virus with the best possible ACE2 binding site, this is not the sequence the computer or the literature would have given them. That suggests that this very good binding sequence is a product of natural evolution instead. The Nature Medicine article also further noted that the genetic sequence of SARS CoV-2 differs too much from that of any other known coronavirus sequence for one of the known viruses to have been used as a starting point in engineering this stronger pathogen.

The Species Jump

Perhaps the most important step in the emergence of SARS CoV-2 is the jump from its initial host species to humans. This could have happened directly, or as in the case of MERS CoV, which went from bats to camels to humans, with an intermediate host. Note that MERS still has not adapted to efficient human to human transmission, and so when we see it, it’s usually from multiple camel to human events.

The problem here is that we don’t have proof of the host from which humans were first infected with SARS CoV-2. In other words, no virus isolated from an animal so far is related closely enough at the sequence level to SARS CoV-2 that we can say this is where humans were first infected, as we can tell from the MERS jumps from camels to humans. As we will discuss below, and as you are well aware, early suspicion on the origin of human infection centered on the wet market in Wuhan. Remarkably, authors of the Cell paper visited the market and took these pictures in October 2014 because they were concerned that wet markets in general, and this one in particular, represent a particularly large risk for bringing humans into contact with less commonly encountered hosts of potentially deadly viruses:

The caption properly notes that many early cases are linked to the market, but we don’t yet have proof of where and how the first human infection(s) took place. In discussing the jump and subsequent outbreak, the Cell authors continue:

The emergence and rapid spread of COVID-19 signifies a perfect epidemiological storm. A respiratory pathogen of relatively high virulence from a virus family that has an unusual knack of jumping species boundaries, that emerged in a major population center and travel hub shortly before the biggest travel period of the year: the Chinese Spring Festival.

/snip/

While our past experience with coronaviruses suggests that evolution in animal hosts, both reservoirs and intermediates, is needed to explain the emergence of SARS-CoV-2 in humans, it cannot be excluded that the virus acquired some of its key mutations during a period of “cryptic” spread in humans prior to its first detection in December 2019. Specifically, it is possible that the virus emerged earlier in human populations than envisaged (perhaps not even in Wuhan) but was not detected because asymptomatic infections, those with mild respiratory symptoms, and even sporadic cases of pneumonia were not visible to the standard systems used for surveillance and pathogen identification. During this period of cryptic transmission, the virus could have gradually acquired the key mutations, perhaps including the RBD and furin cleavage site insertions, that enabled it to adapt fully to humans. It wasn’t until a cluster of pneumonia cases occurred that we were able to detect COVID-19 via the routine surveillance system. Obviously, retrospective serological or metagenomic studies of respiratory infection will go a long way to determining whether this scenario is correct, although such early cases may never be detected.

So, the sequence information comes to a dead end here until the details of the epidemiology are reconstructed. As the authors note, it likely will prove impossible to sample many of the most important animals and humans that would clarify the route and timing. It is further worth noting that the bat from which the RaTG13 sequence is derived was found in Yunnan province, a very long way from Wuhan.

Epidemiology

It appears that as of this writing, the earliest known infection may have been a shrimp seller in the wet market who first developed symptoms on November 17. Also, this Lancet article provides further details on some of the early studies showing a high concentration of cases affiliated with the market in December. The Lancet graphic suggests a case on December 1 not affiliated with the market and the start of the market cluster on the tenth, with 27 of the 41 early patients considered here being associated with the wet market. If that were indeed the earliest case, we might think we’ve seen the index case. But if the South China Post article is to be believed, the shrimp seller fell ill on November 17 and, according to the article, one to five people a day from that day forward had the disease. If we believe that information, then the virus appears to have already been circulating before the middle of November.

It is when we start getting into this information that accusations of hiding information are thrown about. Were there earlier cases that China suppressed or that simply went undetected? We have no way of knowing at this point.

A further point that comes from the Cell paper is that SARS CoV-2 has been circulating long enough that minor variations in the gene sequence are arising that don’t affect pathogenicity but allow for tracing of various lineages of the virus in its spread around the globe. They also note that the lineages allow them to go back in time over the evolution of those sequences and the diversity diminishes a lot as they get back to the early isolates from Wuhan. This is further confirmation for Wuhan being essential in the earliest part of the outbreak.

Accidental Release

It is here that the noise gets really loud. If we accept the really strong evidence that SARS CoV-2 was not deliberately made in a laboratory, there remains the possibility that the virus could have escaped from a laboratory that studies potential pandemic agents.

As long ago as 2004, Rutgers scientist Richard Ebright spoke out against the massive amount of funding that was funneled into research on bioweapons after the 2001 anthrax attacks. From the New York Times:

Jim here.

Long time readers of the blog know that whenever I hear something about Battelle, my spidey senses go on full alert. Suffice it to say that the Battelle facility in West Jefferson, Ohio  is one of only a few facilities on the planet that has both the expertise and the equipment to produce something like, say, a fully weaponized anthrax powder. So I’ve been going on alert the last few days as word has come out on Battelle’s process for sterilizing used N95 masks for re-use. West Jefferson is just outside Columbus, so I had a false alarm on Marcy’s post earlier today about the Washington Post needing to go to Columbus, but she wasn’t discussing Battelle.

Don’t get me wrong. I am fully in favor of anything that can be done to provide safe PPE to those on the front lines of the COVID-19 pandemic response. Finding safe ways to re-use these masks has to be one of the many approaches we must rely on while the masks are in such short supply. But when I finally started digging deeper into what is going on with the contract that the Defense Logistics Agency awarded to Battelle for this process, I was staggered by the total cost compared to what looks, on the surface, to be a straightforward, inexpensive already proven approach.

On April 13, the Department of Defense announced a $415 million contract to Battelle for N95 mask sterilization:

The Department of Defense’s Defense Logistics Agency, on behalf of the Department of Health & Human Services (HHS), has awarded a $415 million contract for 60 Battelle Memorial Institute Critical Care Decontamination Systems (CCDS), that can decontaminate up to 80,000 used N95 respirators per system per day, enabling mask reuse up to 20 times.

Spearheaded by the Department’s Joint Acquisition Task Force, six units have already been delivered to locations including two to New York, and one each to Columbus, Ohio, Boston, Chicago and Tacoma, providing the ability to sterilize 3.4 million masks a week, reducing the need for new masks by the same number.

All 60 systems will be available by early May for prioritization and distribution by FEMA and HHS. Once all are delivered, these 60 units will allow 4.8 million masks to be sterilized per day, almost 34 million per week.

‘I remain extremely proud of the selfless efforts of Department of Defense personnel who continue to do everything they can to help provide medical masks, test kits, medicine and meals to support America’s military, medical, emergency services and law enforcement professionals who are on the front lines and need them most,’ said Under Secretary of Defense Ellen Lord.

This procurement includes a service contract to cover operations and maintenance.

A couple of days earlier, on April 11, the New York Times visited Battelle and provided a photoessay on the Battelle process for sterilization. Here is a Times photo of masks hanging in one of the decontamination units. This photo is also the featured image for the post:

One thing that jumps out immediately is to notice that standard food/medical grade shelving is used in the unit. So at least that part isn’t very expensive. I am disturbed, though, by the “extra” rods between shelves that have masks hanging in a way that we can see multiple pairs of them closely nested, raising concern about circulation of the vapor used in the sterilization process. Just below the photo, the Times notes that workers take “care to avoid overlapping”. Okay, then, but I’m still nervous about those that look nested.

The sterilization process itself is carried out by hydrogen peroxide vapor (HPV). Of course, safety dictates that the chamber in which the masks are exposed to the vapor is perfectly sealed as vapors escaping would be toxic to the staff working around the chamber. Technology to inactivate the peroxide in the exhaust stream from the chamber is known, off the shelf technology and would be a part of the air handling for the chamber. Hydrogen peroxide itself is very inexpensive and is produced in bulk by the chemical industry.

Battelle already validated the process under a contract from FDA, with the final report issued in July of 2016 (thanks, Obama!). Here’s a partial screengrab from the report with a photo of the simple machine used to generate the HPV (gratuitous anthrax mention included for grins):

Sure enough, the Times found a very similar machine when they were at Battelle:

This is not a very complicated piece of machinery. I’m not sure of the full retail price, but I found a used “as is” listing for $4500. I’d be surprised if these are costing Battelle more than $20,000 per unit.

And the “chambers”? They’re shipping containers. Again, from the Times photos:

Also visible in this photo is very standard-looking air handling equipment.

So, making 60 units out of shipping containers, outfitting them with an HPV generator and air handling equipment doesn’t look very expensive to me at all when compared to the total value of the contract. It’s very hard to estimate more than $10-15 million in materials costs for 60 units.

The Times article provides an accessible description of the sterilization process. Here’s what happens in the chamber:

A contraption known as a vapor phase hydrogen peroxide generator, which looks like a washing machine with two hoses, is then used to circulate the colorless gas into and out of the room. During the first four hours, workers increase the humidity inside the chamber, causing the hydrogen peroxide to collect as condensation on the masks, neutralizing the coronavirus and other contaminants.

Over the next four hours, the gas is flushed out of the room. The teams then re-enter the chamber to inspect the masks and conduct spot tests for harmful levels of residual hydrogen peroxide. They then confirm that chemical indicator cards placed throughout the chamber have changed color — the sign of a successful decontamination.

The process itself is very labor intensive, although the masks are inside the chamber for what looks like 8 hours in between bouts of activity. The masks have to be handled and inspected both before and after the sterilization procedure.

Is the labor the reason the contract costs so much? A key missing piece of information is just how long the contract lasts. Recall that the DOD press release indicates that Battelle is providing the labor for the process along with maintenance of the chambers.

After a bit of digging, I found a few more details. Here is information from a Defense News post that is dated April 13 in its URL:

Battelle has already set up two machines in the New York City area, as well as one each in Chicago, Illinois; Tacoma, Washington; Columbus, Ohio; and in the suburbs of Boston, Massachusetts. A solicitation on the organization’s website, found by the Boston Globe, says the group anticipates a need of at least 2,300 workers for 100 sites — or 23 staff per site, which is expected to run 24 hours a day. The $20 per hour job is expected to last at least four weeks.

“We are anticipating a surge over the next two months,” the solicitation read.

Let’s be generous here and extend that two month surge to a full year. If there are 2300 workers each making $20 an hour for a year, I calculate a little under $96 million in direct costs. Being generous again, travel expenses (Battelle in their solicitation mentioned the employees may need to move among sites), benefits, and overtime may bring total personnel costs close to $200 million.

My gut feeling here is that Battelle stands to make quite a bit of money off this contract, even if they run full-out with these chambers for a full year.

But rest easy, citizens.  Battelle plans to provide the sterilization service free of charge for those submitting masks and other equipment for processing.