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10 Years of emptywheel: Jim’s Dimestore

As you saw in Marcy’s posts yesterday, emptywheel is celebrating the ten year anniversary of the move from The Next Hurrah to Firedoglake.   You will notice that the current version of the blog comes to you without ads. If you want this wonderful state of affairs to continue, contributions are a must. A new subscription option helps to make sure the hamsters keep turning the wheels on the magic blog-hosting machines and the ever more sophisticated mole-whacking machinery stays up to date.

Marcy’s outstanding work over the years has received great acclaim. A huge part of the success of the blog, though, has been its ongoing tradition of the best commenting community on the internet. Over the years, the conversations that have taken place on each seminal post have helped to decipher the meaning of cryptic government documents, bring in alternate views and point out new information as it breaks. In the end,  emptywheel isn’t just a blog, it’s a community. For all of your support and participation during these trying times, we thank you.

In keeping with the “10” theme, Marcy has a post highlighting her favorite surveillance posts over each of the last ten years. She has graciously allowed a few of us hangers-on to participate with posts of our own.  I haven’t been an official emptywheeler for all of those ten years.  I did spend a year as an evening editor at Firedoglake around the time of the migration from TNH, so I got to start my friendship with this group of writers and commenters around that time.  I’m going to list my favorite ten posts from the time I started posting here, shortly after the blog moved from Firedoglake to the independent site. Several of these posts link back to earlier work at MyFDL. Sadly, the archives of that work were imperfectly migrated to the Shadowproof successor to Firedoglake, and so searching for those is imperfect and many of the graphics are lost.

So here is Jim’s Dimestore listing my 10 favorite posts on Emptywheel.net, in chronological order:

DETAILS OF SILICON-TIN CHEMISTRY OF ANTHRAX ATTACK SPORES PUBLISHED; WILLMAN TUT-TUTS

Sandia National Laboratories image of attack spore. In the upper frame, silicon, in green, is found exclusively on the spore coat and not on the exosporium (outer pink border).

Perhaps my favorite topic over the years has been a technical analysis of the evidence presented by the FBI in its Amerithrax investigation. It is absolutely clear from this analysis of the anthrax attacks of 2001 that the FBI failed to demonstrate how Bruce Ivins could have carried out the attacks on his own. This post goes deep into the technical weeds of how the spores in the attack material were treated so that they would disperse easily and seem to float on air. The bottom line is that high amounts of silicon are found inside these spores. The silicon could not have gotten there naturally, and it took very sophisticated chemistry to get it there and treat it to make sure it stayed. Ivins had neither the expertise nor the equipment to achieve this highly advanced bioweaponization. Earlier work I did in this series showed that Ivins also could not have grown the anthrax used in the attacks.  My favorite candidate for where it was produced is an isolated lab built by the Defense Threat Reduction Agency on what is now called the Nevada National Security Site (formerly the Nevada Test Site) that Judy Miller described on September 4, 2001.  That article by Miller has always stood out to me as the ultimate limited hangout presented by DoD before the fact, where we see a facility of the perfect size for producing the amount of material used in the anthrax attacks. Those attacks occurred just a short time after the article was published. Miller’s assurance in the article that the site only was used for production of harmless bacteria sharing some characteristics with anthrax just never smelled right to me.

INTELLIGENCE AIDE FLYNN RE MCCHRYSTAL: “EVERYONE HAS A DARK SIDE”

When Michael Hastings’ article in Rolling Stone led to Stanley McChrystal’s firing, little did we know that this would be the beginning of the fall from grace for David Petraeus and his all-star band of torture enablers. These “operators”, as Hastings termed the team, relied on night raids and illegal detentions as the core of their counterterrorism initiatives in Iraq and Afghanistan. These foolishly evil practices fueled massive growth in the insurgencies in response. In this post, Flynn reveals to us that he felt McChrystal, and everyone else, has a “dark side”. As we now await fallout from Flynn’s guilty plea for his lies to the FBI about conversations with Russian Ambassador Kislyak (mainly, his testimony against the rest of Trump’s team), it appears that Flynn himself found the dark side to be quite compelling.

DESPITE METAPHYSICAL IMPOSSIBILITY, US GOVERNMENT REPEATEDLY ATTEMPTS RETROACTIVE CLASSIFICATION

Another favorite topic of mine over the years has been the utter futility of the military’s efforts to “train” troops in both Iraq and Afghanistan. It has been an endless sequence of the military getting countless “do-overs”, with Congress rolling over and believing every single utterance of “This time it will work for sure!”. Part of the military’s strategy in hiding their training failures was to keep changing how Afghan troops were counted and evaluated for combat readiness. A corollary to the futility of the training effort is the horrific death toll of “green on blue” attacks, where the Afghan or Iraqi trainees attacked and often killed those who were training them. When this problem got especially bad in Afghanistan in 2011, DoD commissioned a sociological analysis that returned a result the military did not like. The report indicated that the military was utterly failing to address vast cultural differences between Afghan and coalition troops.  The military, in its infinite wisdom, decided to classify the report, but did so after it already had been released in unclassified form.  Oops.

PERSIANS PUNK PHOTO PRETENDERS: PARCHIN PRETTY IN PINK

Detail from the photo carried in CNN’s story showing the pink tarp over the building said to contain the blast chamber.

Neocons have long lusted after violent regime change in Iran. Cooked up allegations on Iran’s nuclear capabilities have played a central role over the years in how they wished to achieve that war. Despite the neocons’ best efforts to sabotage negotiations, Iran agreed to a comprehensive set of severe restrictions on its nuclear capabilities in return for “dropping” (quotes because the US has claimed other grounds for maintaining other sanctions) the worst of the US sanctions that crippled Iran’s economy. Along the way, I had a ton of fun picking at two of the worst offenders in spreading anti-Iran propaganda: David Albright of the Institute for Science and International Security and George Jahn of AP. Reports that Iran had constructed a high explosives blast chamber at the Parchin military site became quite a point of argument. Albright spent countless hours scouring satellite images of the site and claimed the photographs showed that Iran was attempting to clean radioactivity from the site. Iran seemed to have a lot of fun with this process. I’m sure the pink tarps in the post here were added just to punk Albright. I maintained that the real evidence of what had taken place at the site couldn’t be scrubbed, because the accused activity would have resulted in the steel chamber itself being made radioactive throughout its entire thickness. Perhaps Iran made the same assessment, because once the IAEA gained access to the site, there was no steel chamber to be found. Was there ever a blast chamber there? Who knows? In the end, whether Iran carried out that work is immaterial, as the Joint Comprehensive Plan of Action has the most aggressive inspection regime ever agreed to by a country that hasn’t just lost a war.  We can rest assured that Iran has no capability at the current time of assembling a nuclear weapon, and the neocons are left to pout about diplomacy working better than their war ever could have. If you want to know why Donald Trump put Rex Tillerson in charge of dismantling the Department of State, look no further than the success diplomacy played in achieving the JCPOA.

JOHN GALT KILLS TEXANS IN MASSIVE FERTILIZER PLANT EXPLOSION

When a massive explosion in West, Texas killed 15 people, injured over 250 and destroyed 500 homes, it was clear to me who had killed these Texans: Ayn Rand’s mythical libertarian hero John Galt. How else do  you explain a site being allowed to store hundreds of thousands of pounds of ammonium nitrate with inadequate fire protection and fatally close to inhabited structures than the misguided libertarian belief that free enterprise should rule?  In the post, I pointed to the dangers inherent in the lack of zoning laws that allowed this fatal mixture of structures. As we later learned from the Washington Post,  John Galt’s influence on the destruction was decades in the making:

The plant was a mom-and-pop operation, a distribution center where farmers picked up custom mixes of fertilizer to boost crop yields. It was built in 1962 a half-mile outside West. As the harvests grew, so did the town. In 1967, the rest home opened 629 feet from the plant. In the early ’70s, a two-story apartment complex was built even closer. Then a playground and basketball court, a mere 249 feet away.

We learned last year that ATF has determined that the fire that preceded the blast was intentional.  So while we don’t know who started the fire itself, we know for a fact that, ultimately, it was John Galt who killed these 15 Texans.

US DRONE STRIKE IN PAKISTAN REEKS OF POLITICAL RETALIATION YET AGAIN

The current concern that Donald Trump will lash out in fury with a nuclear strike, somewhere, anywhere, just to vent his anger over Mueller’s noose tightening over his entire administration is not the first time that it was appropriate to be concerned about an  enraged high-ranking government official killing innocent people. In the case of John Brennan, poorly targeted rage attacks carried out as retaliation for a perceived wrong happened repeatedly. In the post linked here, a drone strike in Pakistan’s tribal area seemed timed as retaliation for Pakistan refusing to reopen supply routes that had been closed six months earlier when the US killed 24 Pakistani troops in an erroneous attack. The post goes on to detail other rage drone strikes that Brennan ordered, with the worst probably being the killing of over 40 people who were simply gathered to discuss mineral rights. That strike was carried out the day after the CIA’s Raymond Davis was finally released and was clearly carried out without proper evaluation of targeting criteria, as it seems few if any actual terrorists were killed.

NO, WE AREN’T ALL GOING TO DIE BECAUSE EBOLA PATIENTS ARE COMING TO US FOR TREATMENT

image.ppat.v04.i11.g001

Scary, color-enhanced electron micrograph of Ebola virus particles. Creative Commons license courtesy of Thomas W. Geisbert, Boston University School of Medicine.

The Ebola outbreak in 2014 led to widespread fear in the US, especially when it was announced that medical personnel who had been treating Ebola patients in Africa and became infected would be transported to Atlanta for treatment. There was no appreciation for how the disease actually is spread, what the conditions were where the medical workers became infected in Africa and how such spread would be much less likely in a properly run US hospital. A poorly run hospital in Texas, however, did manage to have personnel treating Ebola acquire infections. Of course, the treatment at CDC in Atlanta was carried out without incident, and the virus did not spread in the US, even after the Texas hospital had its initial failure. In fact, as the virus wound down, those who study and understand the virus were shown to have been completely correct in their analysis when they modeled how large the outbreak would get before receding once proper intervention was carried out. But the fears of Ebola wiping out the US weren’t the only bit of bad science that had to be knocked down during the outbreak. Conspiracy theories started spreading that the Ebola virus in the 2014 outbreak had been genetically engineered in a bioweapons lab and was accidentally released from a lab in Africa. DNA sequence analysis quickly debunked that one.

WASHINGTON POST FAILS TO DISCLOSE HEINONEN’S UANI CONNECTION IN ANTI-IRAN OP/ED

Yes, the Iran nuclear agreement is so important that it is the only topic repeated in my ten favorite posts. In this post, we are in the time just a few months before the agreement is finalized, and the neocon opponents of the deal are reaching a fever pitch. The post outlines a horrible failure of full disclosure by the Washington Post. This occurred after Bezos purchased the paper, but clearly was a failure of beating back the darkness in which democracy dies. In this case, the Post carried an op-ed opposing the Iran deal. Besides allowing an incendiary headline (The Iran Time Bomb) and giving voice to Michael Hayden and neocon nightmare Ray Takeyh, the Post made its biggest failure regarding the middle author, Olli Heinonen. The Post allowed Heinonen to identify himself only by his current Harvard affiliation and his former role in IAEA. What is left out of that description is that Heinonen was also playing a prominent role on the Advisory Board of United Against Nuclear Iran, shadowy group with even more shadowy funding sources. Somehow, in the course of its “advocacy” work against Iran, UANI had come into possession of US state secrets that suddenly allowed it to avoid a civil case for defamation of a businessman they accused of breaking sanctions against Iran. Why, yes, of course the New York Times also allowed Heinonen to deceptively carry out his work on their pages, too. This time it was in a “news” story that came out shortly after the UANI civil court case was dismissed when the judge stated the case could not proceed because of the state secrets involved. Of course, even after more than two and a half years, neither the Washington Post nor New York Times have admitted their omissions in describing Heinonen’s affiliations in the cited articles. It is really remarkable that diplomacy defeated this full court press by the neocons who were working with the full cooperation of the media.

WAVING THE CONSTITUTION AT THOSE WHO IGNORE IT

I waved my pocket copy of the Constitution at Nancy Pelosi on July 19,2008. Khizr Khan waved his at Donald Trump on July 28,2016.

I waved my pocket copy of the Constitution at Nancy Pelosi on July 19,2008. Khizr Khan waved his at Donald Trump on July 28,2016.

I haven’t written much in the last couple of years, but I just couldn’t avoid writing this one only ten days after surgery to replace my aorta. When I saw Khizr Khan’s appearance at the Democratic National Convention, I was really moved when he waved his pocket copy of the Constiution at Donald Trump. I had done the same thing in July of 2008 when Nancy Pelosi appeared at Netroots Nation in Austin. I was waving my Constitution at Pelosi to remind her of her failure to impeach George W. Bush and Dick Cheney for their roles in torture and illegal wars. Khan was calling out Trump for his campaign promises that so clearly violate the Constiution. Sadly, Trump has followed through in enforcing many of those policies Khan warned us about and we are left without much more recourse than continuing to wave our Constitutions at those who violate it on a daily basis.

ON JULY 2016 PANEL, GEORGE PAPADOPOULOS USED SAME COVER ORGANIZATION AS JOSEPH MIFSUD 

My one minor contribution so far to the unfolding saga of Russian influence on the 2016 election was prompted by noticing a photo in my Twitter stream shortly after the George Papadopoulos plea agreement was made public. What initially caught my eye was that my Congressman, Ted Yoho, was in the photo with Papadopoulos while both appeared in a panel discussion in Cleveland in July of 2016. However, once I started digging into the circumstances of the photo, I discovered that when he appeared for the panel, Papadopoulos claimed an affiliation with an entity that was also an affiliation for the shadowy Joseph Mifsud. We still don’t have a satisfactory explanation of how these two came to have a shared cover organization where it seems both Papadopoulos and Mifsud had positions that were grossly inflated with respect to their previous career accomplishments. I still think that if we ever discover who was behind these two getting such inflated positions, we will learn much about who might have been orchestrating later events in which these two played roles.

Ebola Outbreak Finally Receding in Sierra Leone; CDC Modeling Was Incredibly Accurate

Back in late September, just a week before Ebola panic hit a peak in the US when a patient in Dallas was diagnosed with the disease, the CDC produced a remarkable study in which they modeled the expected number of Ebola cases both with and without intervention. That study received a huge amount of press coverage, primarily because the model predicted that without intervention by public health authorities, as many as 1.4 million people could be infected. By contrast, with a program of isolating infected patients and educating survivors on proper burial techniques, the model showed that the outbreak would be much less widespread. The modeling projected cases through yesterday’s date, January 20.

Less reported in the media at the time was the projected number of cases under the scenario of intervention. The model predicted an actual number of cases between 25,000 and 30,000 by this week and a reported number of cases of nearly 10,000. Here are the two projections placed alongside one another:

CDC modeling of projected number of Ebola cases without (left) and with (right) improved patient isolation and safe burial practices.

CDC modeling of projected number of Ebola cases without (left) and with (right) improved patient isolation and safe burial practices.

The latest data from WHO indicate just over 21,000 cases as of January 11. That is a remarkable achievement by the team that developed the model. The observed actual number of reported cases fell squarely within the range predicted by the model. With the influx of health professionals to the region to provide care for infected patients, it seems likely to me that the correction factor applied in the CDC model to correct from the reported number of cases to the actual number would be very different now, so that the reported number and actual number would be much closer to one another, making the prediction even more accurate.

Last time I posted on progress in stopping the spread of the virus, we saw that the rate of appearance of new cases was dropping rapidly in Liberia but was still accelerating in Sierra Leone. The good news is that the improved practices have finally been implemented sufficiently in Sierra Leone that the rate is now dropping there. Here are the plots of weekly new cases in the two countries from the latest WHO Situation Report:

Weekly number of new cases of Ebola in Liberia (left) and Sierra Leone (right). Control of the virus was achieved about two months later in Sierra Leone than in Liberia.

Weekly number of new cases of Ebola in Liberia (left) and Sierra Leone (right). Control of the virus was achieved about two months later in Sierra Leone than in Liberia.

Although the battle is not yet over, all indications are that the outbreak is well past the worst phase and should end soon. Considering how closely the CDC model predicted the eventual size of the outbreak with the control measures that were implemented, it seems safe to say that the world would have witnessed a truly horrific level of spread of the virus had improved safety measures not been implemented. As of the January 14 WHO Situation Report, a total of 825 health care workers have been infected, with 493 of them dying. Without their sacrifices, many more would have been lost.

Ebola Outbreak Receding in Liberia, Still Strong in Sierra Leone

Back in late September, the press had a field day with a mathematical model developed by CDC that estimated that if left unchecked, the Ebola outbreak in West Africa could wind up infecting over 1.4 million people. Almost missed in the hysteria over that high number was the fact that this same model predicted that even with key public health measures (patient isolation, monitoring of at-risk population who had contact with infected people and safe burial practices) falling short of 100% implementation, the outbreak could be brought under control around January of next year.

Word has been leaking out for a while now that the rate of new Ebola infections in Liberia is falling. Reports in the Washington Post on October 29 and November 3 told us as much. A chart in the WHO Situation Report for November 5 drives home just how dramatic the decline in new cases has become:

WHO Ebola Situation Report November 5, 2014

WHO Ebola Situation Report November 5, 2014

As can be seen in the chart, the rate of new infections for the two most recent weeks is less than one fourth the rate at the peak of the outbreak. Unfortunately, the news for Sierra Leone is not as good. While the rate of new infections may be leveling off, it is not yet falling appreciably:

WHO Ebola Situation Report November 5, 2014

WHO Ebola Situation Report November 5, 2014

Digging into the WHO report a bit further, we can find some evidence for how this dramatic drop in new cases has been brought about. We see that 52% of cases are now isolated. The WHO target for December 1 has been set at 70%, with a target of 100% by January 1. When it comes to management of dead bodies, though, the December 1 target has already been surpassed. WHO reports that 87% of the dead are being “managed in a safe and dignified manner” while the targets were set at 70% for December 1 and 100% for January 1. Also, although no benchmarks are reported, WHO states that 95% of registered contacts were reached daily (although in the text of the report, there are suggestions this number may be somewhat overstated).

It should come as no surprise that progress in implementing these basic measures has had a huge impact on bringing down the rate of new infections. It fits perfectly with the CDC mathematical model and it also addresses the known biology of Ebola infections. Patients are most infectious at or near death, so establishing safe burial practices is vitally important. Conversely, identifying infected individuals through daily monitoring of the at-risk population and then isolating infected individuals once symptoms begin means that far fewer people are exposed to people producing large amounts of virus.

Sadly, those who remain exposed are the health care workers who are providing care to those who are infected. Despite shortages of equipment and supplies, WHO and other organizations are doing their best to overcome those shortages and to beef up training to reduce risk to these brave people on the front lines in the work to control the virus. As of this November 5 report, 546 health care workers have been infected, with 310 of them dying. Only four new infections were reported for the week ending November 2, so it is hoped that this rate is also dropping.

Had the alarmists who insisted that this was a new super-strain of Ebola capable of airborne transmission (or even a strain developed in a bioweapons laboratory), it is doubtful that these basic public health measures would have had such a dramatic impact on the rate of new infections. Perhaps those folks can go back to railing about chemtrails or the evils of vaccines, because basic boring science appears to be on the road to controlling the current outbreak before all of mankind succumbs.

In the meantime, we are at about two weeks into the three week incubation period both for anyone “exposed” by Craig Spencer or for Kaci Hickox (or anyone she “exposed”) to show symptoms. No reports of transmission so far, and the odds of any cases showing up are dropping very rapidly from the already very low levels where they started.

Christie’s Quarantine Over-Reaction Ignores How Ebola is Transmitted

While Chris Chrisite toasted fellow quarantine advocate Rick Scott at a fundraiser in Florida on Sunday, Kaci Hickox met with her attorney to prepare a legal challenge to her quarantine.

While Chris Chrisite toasted fellow quarantine advocate Rick Scott at a fundraiser in Florida, Kaci Hickox met with her attorney to prepare a legal challenge to her quarantine.

It’s really difficult to say which poor response to Ebola has done more damage to the public health system in the United States. First, we had the series of unforgivable errors at Texas Health Presbyterian Dallas that resulted in Thomas Duncan being sent home with Tylenol and antibiotics when he first presented with Ebola symptoms. This was followed up after he was admitted by Nina Pham and Amber Vinson coming down with the disease after they treated him. Now, we have Kaci Hickox, who treated Ebola patients in West Africa, confined to an unheated tent in a New Jersey hospital for 21 days even though she is asymptomatic and has tested negative for Ebola. Twice.

The hysteria over retracing the steps of Craig Spencer in New York City just before he developed his fever illustrates the way the US press has misled the public about when and where Ebola risk exists. Abundant evidence from this and previous Ebola outbreaks demonstrates clearly that there simply is no risk of transmission from asymptomatic patients and that transmission risk grows through the course of the infection.

We see that principle demonstrated very clearly in Duncan’s case history. See this terrific ABC timeline for relevant dates quoted below. Duncan arrived in Dallas September 20. No passengers on any of the flights he took have developed Ebola. The incubation period has elapsed, so we know that no transmission of the virus occurred during any of his flights. Duncan had symptoms on his first hospital visit on September 26 but was sent home. He was later admitted on September 28. No patients or personnel from the hospital became infected from his visit September 26. The incubation period has expired, so we know for certain that transmission did not occur for anyone near Duncan that day. Similarly, even though they were in the apartment with him for days after he developed symptoms, none of the residents of or visitors to the apartment where Duncan was staying in Dallas became infected. The incubation period for that exposure also has expired. From this timeline developed by the New York Times, it appears that Pham and Vinson treated Duncan on the day before he died, which would be at the time when the amount of virus being produced by his body was nearing its maximum.

The load of virus in a patient’s blood over the course of Ebola infection has been studied. In this CDC review, we have a graph showing the amount of virus over time: Read more

DNA Sequence Analysis Shows Ebola Outbreak Naturally Ocurring, Not Engineered Virus

In an electron microscope image that has been colorized, Ebola virus particles in blue are being extruded from an African Green Monkey kidney cell in yellow. Photo produced by  National Institute of Allergy and Infectious Diseases, NIH.

In an electron microscope image that has been colorized, Ebola virus particles in blue are being extruded from an African Green Monkey kidney cell in yellow, grown in a laboratory cell culture system. Photo produced by National Institute of Allergy and Infectious Diseases, NIH.

I had really hoped I wasn’t going to have to write this post. Yesterday, Marcy emailed me a link to a Washington’sBlog post that breathlessly asks us “Was Ebola Accidentally Released from a Bioweapons Lab In West Africa?” Sadly, that post relies on an interview with Francis Boyle, whom I admire greatly for his work as a legal scholar on bioweapons. My copy of his book is very well-thumbed. But Boyle and WashingtonsBlog are just wrong here, and it takes only seconds to prove them wrong.

Shortly after getting the email and reading the blog post, I sent out tweets to this summary and this original scientific report which describe work on DNA analysis of Ebola isolated from multiple patients during the current outbreak. That work conclusively shows that the virus in the current outbreak is intimately related to isolates from previous outbreaks with changes only on the order of the naturally occurring mutation rate known for the virus. Further, these random mutations are spread evenly throughout the short run of the virus’s genes and there are clearly no new bits spliced in by a laboratory. Since I wasn’t seeing a lot of traction from the Washington’sBlog post, I was going to let it just sit there.

I should have alerted last night when I heard my wife chuckling over the line “It is difficult to describe working with a horse infected with Ebola”, but I merely laughed along with her and didn’t ask where she read it.

This morning, while perusing the Washington Post, I saw that Joby Warrick has returned to his beat as the new Judy Miller. Along with the line about the Ebola-infected horse, Warrick’s return to beating the drums over bioweapons fear boasts a headline that could have been penned by WashingtonsBlog: “Ebola crisis rekindles concerns about secret research in Russian military labs“.

Warrick opens with a re-telling of a tragic accident in 1996 in a Soviet lab where a technician accidentally infected herself with Ebola. He uses that to fan flames around Soviet work in that era:

The fatal lab accident and a similar one in 2004 offer a rare glimpse into a 35-year history of Soviet and Russian interest in the Ebola virus. The research began amid intense secrecy with an ambitious effort to assess Ebola’s potential as a biological weapon, and it later included attempts to manipulate the virus’s genetic coding, U.S. officials and researchers say. Those efforts ultimately failed as Soviet scientists stumbled against natural barriers that make Ebola poorly suited for bio­warfare.

The bioweapons program officially ended in 1991, but Ebola research continued in Defense Ministry laboratories, where it remains largely invisible despite years of appeals by U.S. officials to allow greater transparency. Now, at a time when the world is grappling with an unprecedented Ebola crisis, the wall of secrecy surrounding the labs looms still larger, arms-control experts say, feeding conspiracy theories and raising suspicions.

/snip/

Enhancing the threat is the facilities’ collection of deadly germs, which presumably includes the strains Soviet scientists tried to manipulate to make them hardier, deadlier and more difficult to detect, said Smithson, now a senior fellow with the James Martin Center for Nonproliferation Studies, a research institute based in Monterey, Calif.

“We have ample accounts from defectors that these are not just strains from nature, but strains that have been deliberately enhanced,” she said.

Only when we get three paragraphs from the end of the article do we get the most important bit of information to be gleaned from the Soviet work on Ebola:

Ultimately, the effort to concoct a more dangerous form of Ebola appears to have failed. Mutated strains died quickly, and Soviet researchers eventually reached a conclusion shared by many U.S. bio­defense experts today: Ebola is a poor candidate for either biological warfare or terrorism, compared with viruses such as smallpox, which is highly infectious, or the hardy, easily dispersible bacteria that causes anthrax.

Note also that, in order to make Ebola more scary, Warrick completely fails to mention the escape of weaponized anthrax from a Soviet facility in 1979, infecting 94 and killing 64, dwarfing the toll from the two Ebola accidents.

And lest we calm down about Ebola and the other bioweapons the Soviets worked on, Warrick leaves us this charming tidbit to end the article: Read more

New CDC Hospital Ebola Guidelines Fall Short of WHO Guidance on Personnel Flow

I’m either a lone voice in the wilderness or just another angry old man shouting at clouds on this, but, to me, the issue of personnel flow inside a facility treating a patient for Ebola is critical. Texas Health Presbyterian Dallas got that issue terribly wrong in the case of Thomas Duncan, and now, although they provide very good guidance on the issue of personal protective equipment and its use, new guidelines just released by CDC sadly fall short of correcting the problem I have highlighted.

The issue is simple and can even be explained on a semantic level. If a patient is being treated in an isolation ward, that isolation should apply not only to the patient but also to the staff caring for the patient. As I explained previously, National Nurses United complained that health care workers at Texas Health Presbyterian Dallas treated Duncan and then continued “taking care of other patients”.

Allowing care providers to go back to treating the general patient population after caring for an isolated patient is in direct contradiction to one of the basic recommendations by WHO in a document (pdf) providing guidance for treatment of  hemorrhagic fever (HF, includes Ebola):

Exclusively assign clinical and non-clinical personnel to HF patient care areas.

By exclusively assigning personnel to care of the isolated patient, then the isolation is more complete.

The new CDC guidelines, released on Monday, offer updated recommendations on the types of personal protective equipment (PPE) to be used and how it is to be used. The guidelines also stress the importance of training on effective PPE use prior to beginning treatment of an Ebola patient. Unfortunately, though, the guidelines still leave open the possibility of health care workers moving between the isolation area and the general patient population.

In the preparations before treatment of an Ebola patient commences, the guidelines state:

Identify critical patient care functions and essential healthcare workers for care of Ebola patients, for collection of laboratory specimens, and for management of the environment and waste ahead of time.

And then once treatment begins, we have this:

Identify and isolate the Ebola patient in a single patient room with a closed door and a private bathroom as soon as possible.

Limit the number of healthcare workers who come into contact with the Ebola patient (e.g., avoid short shifts), and restrict non-essential personnel and visitors from the patient care area.

So the facility is advised to identify the “essential” workers who will provide care to an Ebola patient and to limit the number of personnel coming into contact with the patient. And even though the patient is to be in an isolated room, the guidelines still fall short of the WHO measure of calling for the Ebola treatment staff to be exclusively assigned. Precautions for safely removing the PPE are described, but once removed, the workers presumably are free to go back to mixing with the general patient population. Hospitals are cautioned against allowing large numbers of care providers into the room and to avoid “short shifts”, but there still is no recommendation for workers to be exclusively assigned to the isolation area.

The first thing that comes to mind in this regard is to question whether the CDC recommendations fall short of the WHO call for exclusive assignment in order to allow US hospitals avoid the perceived expense of dedicating a handful of personnel to treatment of a single patient. Is the ever-constant push to reduce personnel costs responsible for this difference between CDC and WHO guidelines? In the US healthcare system, it appears once again that MBA’s can carry more weight than MD’s on critical issues.

Texas Hospital Violated Basic Precaution in WHO Ebola Patient Treatment Guidelines

The incompetence of Texas Health Presbyterian Hospital Dallas is staggering. In following today’s rapidly developing story of a second nurse at the hospital now testing positive for Ebola, this passage in the New York Times stands out, where the content of a statement released by National Nurses United is being discussed (emphasis added):

The statement asserted that when Mr. Duncan arrived by ambulance with Ebola symptoms at the hospital’s emergency room on Sept. 28, he “was left for several hours, not in isolation, in an area where other patients were present.” At some point, it said, a nurse supervisor demanded that Mr. Duncan be moved to an isolation unit “but faced resistance from other hospital authorities.”

The nurses who first interacted with Mr. Duncan wore ordinary gowns, three pairs of gloves with no taping around the wrists, and surgical masks with the option of a shield, the statement said.

“The gowns they were given still exposed their necks, the part closest to their face and mouth,” the nurses said. “They also left exposed the majority of their heads and their scrubs from the knees down. Initially they were not even given surgical bootees nor were they advised the number of pairs of gloves to wear.”

The statement said hospital officials allowed nurses who interacted with Mr. Duncan at a time when he was vomiting and had diarrhea to continue their normal duties, “taking care of other patients even though they had not had the proper personal protective equipment while providing care for Mr. Duncan that was later recommended by the C.D.C.”

From the context of both the New York Times article and the nurses’ statement, it seems most likely that this movement of nurses from treating Duncan to treating other patients took place during the period after Duncan was admitted to the hospital and before the positive test result for Ebola was known. However, from the nurses’ statement showing that at least some of the personnel on duty realized Duncan almost certainly had Ebola, proper isolation technique should have been initiated immediately.

And that movement of nurses from a patient who should have been in isolation back into the general patient population is a huge, and obvious, error. Consider this publication (pdf) put out in August by the World Health Organization, summarizing precautions to be taken in care of Ebola patients. The very first page of actual content, even before the section labeled “Introduction”, is a page with the heading “Key messages for infection prevention and control to be applied in health-care settings”. The page lists nine bullet points about dealing with ” hemorrhagic fever (HF) cases” (hemorrhagic fever diseases include Ebola). Here is the third entry on that list:

Exclusively assign clinical and non-clinical personnel to HF patient care areas.

There really is no point in saying a patient is isolated if staff are freely moving back and forth between the isolation area and the general patient population. I’m wondering how long it will be until there is a whole new management team at Texas Health Resources, the parent firm for the hospital.

Ebola Transmission: Health Care Worker Practice Most Important Consideration

Not long after we learned that a health care worker treating Thomas Duncan has tested positive for Ebola, I ran across this terse tweet from Mackey Dunn, the pen name of Don Weiss, who is “a medical epidemiologist with the New York City Department of Health and Mental Hygiene”. The tweet linked to this short but incredibly important blog post. In the post, Weiss notes the baffling development that a health care worker, who wore full personal protective equipment (PPE), contracted Ebola from Duncan even though at this point, none of his family or other close contacts, who did not have full PPE, have developed symptoms of the disease.

That set of facts prompts Weiss to pose the question “So, what does this tell us about Ebola and how we can attain control?” His answer begins:

One, that Ebola patients become more infectious as the illness progresses. The newly reported case in a healthcare worker had onset on October 10th. If we take 9 days as the mean incubation period for Ebola this means the healthcare worker’s exposure was sometime around October 1, which was day 8 of Mr. Duncan’s illness. This is similar to what was seen with SARS, that patients become more infectious (and dangerous) with time.

In setting up the circumstances for his question, Weiss had noted that Duncan was hospitalized, ending exposure to family members, on day 5 of his disease.

Although he doesn’t mention it, this aspect of Ebola, where patients produce more virus and become more infectious during the course of a fatal infection, also accounts for why burial practices are so important to containing the spread of Ebola. Patients produce the most virus and are thus at their most infectious at death.

The converse also appears to be true. Duncan was symptom-free when he flew from Liberia to Dallas on September 19 to 20. At 24 days since the end of that trip, we have now passed the incubation period, commonly given as 2-21 days, for Ebola to develop in anyone who could have been exposed during the flights. No infections among those airline passengers have been reported. I have yet to see a major media outlet mention this point, though.

We are now at 16 days since Duncan was hospitalized, ending his family’s direct exposure, so we have passed the two-thirds point of the incubation period for them (and well past the 9 days that Weiss gives as the average incubation period for Ebola).

The second part of Weiss’ musings on the infection of the nurse is extremely important:

Second, that only hospitals that are well prepared to care for highly infectious patients should be allowed to do so. Standard practice is to have a staff person dedicated to observing the donning (putting on) and doffing (taking off) of PPE. This observation should continue throughout the period of clinical care (from an ante-room with a window). Perhaps gentle reminders during the doffing can avoid the presumed situation in Spain where the nurse may have touched her face with a gloved hand.

When a patient presents to a hospital early in the illness there is time to transfer to such a facility. That’s the plan here in NYC. Bellevue hospital has a specially equipped ward to care for Ebola patients. Their staff are well trained. The number of healthcare workers entering the room should be kept to a minimum, especially after day 7 of the illness.

Weiss was prescient in his push for an observer for workers putting on and taking off PPE. In today’s New York Times, we have this on the CDC’s thoughts regarding improving practices for health care workers treating Ebola patients: Read more

Bigger Problem in US Than Ebola: Enterovirus D68 Spreading Respiratory, Paralytic Diseases in Children

Electron micrograph of enterovirus particles. Photo by Linda M. Stannard, University of Cape Town as reproduced in Wong's Virology online.

Electron micrograph of enterovirus particles. Photo by Linda M. Stannard, University of Cape Town as reproduced in Wong’s Virology online.

It has now been five days since we learned that Thomas Duncan, who came to Dallas from Liberia, tested positive for Ebola. His condition has been downgraded to critical, but so far none of his contacts have come down with Ebola symptoms. Because those most likely to have been infected by him are now under close observation and have limited contact with others, it seems quite likely the disease will not spread in the US beyond the small handful of people under close monitoring.

By contrast, the US is in the midst of an ongoing outbreak of a virus that has put many children into intensive care units with severe respiratory illnesses. A handful of children in Colorado initially having respiratory illness have progressed to paralysis of some limbs and have tested positive for the virus. Four children who died from severe respiratory illness have tested positive for the virus but the CDC states that the role of the virus in these deaths is not yet known. Late yesterday, a medical examiner in New Jersey stated that the virus was the cause of death for a four year old boy.

The virus involved in this outbreak is Enterovirus D68. Background on the virology of enteroviruses in general can be found here, courtesy of Wong’s Virology online. There are five groups within the enterovirus genus. By far, the most well-known group is the one that comprises the polioviruses. Enterovirus D68 falls within the newest group of enteroviruses that are designated with numbers.

These are some of the smallest and simplest viruses known. The viral particle contains only a single piece of RNA. Inside the host cell, this RNA is turned into a single protein that then is capable of chopping itself into the four smaller proteins found on the viral coat. There is no membrane around the virus and the particles are stable at acid pH, so inactivation is best achieved with bleach or other disinfectants whose label say they are active against non-enveloped viruses.

The CDC released information on the outbreak on September 12, noting that hospitals in Kansas City and Chicago first alerted CDC to unusual numbers of children presenting with severe respiratory symptoms. The latest CDC information on the outbreak includes:

From mid-August to October 3, 2014, CDC or state public health laboratories have confirmed a total of 538 people in 43 states and the District of Columbia with respiratory illness caused by EV-D68.

The report continues:

EV-D68 has been detected in specimens from four* patients who died and had samples submitted for testing. The role that EV-D68 infection played in these deaths is unclear at this time; state and local health departments are continuing to investigate.

The difficulty for healthcare providers with this virus is that symptoms for those infected can range from very mild to severe. As also seen with poliovirus, only a small fraction of those infected get the most severe form of the disease. In the current outbreak, a very high proportion of the children with the worst respiratory symptoms already suffered from asthma:

Of the 19 patients from Kansas City in whom EV-D68 was confirmed, 10 (53%) were male, and ages ranged from 6 weeks to 16 years (median = 4 years). Thirteen patients (68%) had a previous history of asthma or wheezing, and six patients (32%) had no underlying respiratory illness.

/snip/

Of the 11 patients from Chicago in whom EV-D68 was confirmed, nine patients were female, and ages ranged from 20 months to 15 years (median = 5 years). Eight patients (73%) had a previous history of asthma or wheezing.

Parents and school administrators are being encouraged to monitor children with asthma more closely during this outbreak and to be especially vigilant about measures to prevent spread.

Transmission of the virus, according to CDC: Read more

CDC Director: “Zero Risk” to Passengers on Flights With Dallas Ebola Patient

Although not yet widespread, panic and disinformation are emerging surrounding the case of the first patient to have been diagnosed with Ebola while in the United States. The worst of the hysteria surrounds the fact that Thomas E. Duncan flew from Liberia to the United States on a trip that required 28 hours, ending at the Dallas-Fort Worth airport on September 20. It is known that Duncan was screened in Liberia and found not to have a fever when he boarded the first flight. Persons infected with Ebola but not yet exhibiting symptoms are incapable of spreading the disease, primarily because the disease spreads through direct contact of mucous membranes or open wounds with bodily fluids and symptom-free patients are not yet vomiting or having diarrhea, so no virus-carrying fluids are being produced or at risk of being spread in ways that other people will come into contact with them.

On Tuesday, the Director of the CDC, Dr. Tom Frieden, stated outright that there is zero risk to passengers who were on a flight with Duncan:

A national public health official today said there was “zero risk of transmission” of Ebola on a commercial airline flight that a Dallas patient who has tested positive for the disease flew on from Liberia earlier this month.

Centers for Disease Control and Prevention Director Tom Frieden said today in a live briefing from Atlanta that the person — a male who remained unnamed — showed no symptoms before boarding the plane and was not contagious. The CDC doesn’t “believe there is any risk to anyone who was on the flight at that time,” he said.

Despite Frieden’s clear statement that other passengers face no risk, the press continued to hound CDC and the airlines until Duncan’s itinerary was released. While CBS was moderately responsible in their coverage of the flight information, the Daily Mail asked breathlessly in their headline whether YOU were on a flight with Duncan. Even more incredibly, stocks in US airlines were dumped yesterday in response to the news of Duncan’s flights:

Investors were also selling stocks following news that the first case of Ebola had been diagnosed in the U.S. Investors dumped airline stocks and bought a handful of drug companies working on experimental Ebola treatments.

The story of just how Duncan became infected is a sad one. On September 15 (recall that he left Liberia on the 19th and arrived in Dallas the 20th), Duncan helped neighbors take their 19-year-old daughter to the hospital. Sadly, the hospital was already overwhelmed with patients and she was turned away, only to die early the next morning after returning:

In a pattern often seen here in Monrovia, the Liberian capital, the family of the woman, Marthalene Williams, 19, took her by taxi to a hospital with Mr. Duncan’s help on Sept. 15 after failing to get an ambulance, said her parents, Emmanuel and Amie Williams. She was convulsing and seven months pregnant, they said.

Turned away from a hospital for lack of space in its Ebola treatment ward, the family said it took Ms. Williams back home in the evening, and that she died hours later, around 3 a.m.

Mr. Duncan, who was a family friend and also a tenant in a house owned by the Williams family, rode in the taxi in the front passenger seat while Ms. Williams, her father and her brother, Sonny Boy, shared the back seat, her parents said. Mr. Duncan then helped carry Ms. Williams, who was no longer able to walk, back to the family home that evening, neighbors said.

The hospital in Dallas where Duncan is being treated has received a lot of criticism because he first went there on September 26 but was sent home when only exhibiting a low grade fever:

When Mr. Duncan first arrived at the hospital last Friday, six days after he had arrived in America, he told a nurse that he had come from West Africa. Public health officials have been urging doctors and nurses to be on the alert for Ebola in anyone who has been in Guinea, Liberia or Sierra Leone. But information about Mr. Duncan’s travel was not “fully communicated” to the full medical team, said Dr. Mark Lester, executive vice president of Texas Health Resources, the parent organization that oversees Texas Health Presbyterian Hospital.

As a result, that information was not used in the clinical diagnosis and Mr. Duncan was sent home, with the diagnostic team believing he simply had a low-grade fever from a viral infection, Dr. Lester said.

Those with whom Duncan had contact from the time of the onset of his symptoms until he returned the hospital on September 30 28 (corrected; September 30 was when tests confirmed Ebola after he returned to the hospital on September 28) in much worse condition and was then isolated are being monitored for signs that they may be infected:

Officials said Wednesday that they believed Mr. Duncan came into contact with 12 to 18 people when he was experiencing active symptoms and when the disease was contagious, and that the daily monitoring of those people had not yet shown them to be infected.

The incubation period (the time between exposure to the disease and the onset of symptoms in an infected person) for Ebola varies from 2 to 21 days. Recall that Duncan was exposed on September 15 and visited the hospital for the first time on September 26, so his incubation period was around eleven days. We are now around six days into the time since Duncan first visited the hospital, so those with whom he came into contact will need to be monitored for for another two weeks or so until at least 21 days have passed since their last contact with Duncan.

While there is some chance that one or more of those with whom Duncan had contact while he was contagious will become infected, as long as everyone who was in contact with him during that critical period is under observation now, there is virtually no chance of the disease spreading outside that small group of people. And you can rest assured that nobody from any of the flights Duncan was on will come down with disease from exposure to him.