Zika Alert

The CDC has gone to its highest alert level due to concerns about the Zika virus.

From US News & World Report, February 8, 2016:

The Centers for Disease Control and Prevention said Monday that the agency’s command center is going to its highest level of alert, a measure reflecting growing concern about the prospect of Zika virus gaining a foothold in the mainland U.S


This represents the fourth time that CDC’s command center has declared a Level 1 alert. The other emergencies were Hurricane Katrina, the H1N1 flu threat in 2009 and the Ebola epidemic in West Africa.


So far, 50 cases been identified in the U.S., with several in Texas, Illinois, California and Washington, D.C. Five days ago, Florida Gov. Rick Scott declared a state of emergency in four counties, where health officials have diagnosed nine cases of Zika virus in travelers returning from Zika-affected areas.


“Once Zika got a foothold in Brazil, it spread like wildfire through Latin America, the Caribbean and Central America. Now it’s on our doorstep,” Vasilakis says. “There’s a lot of traffic between the U.S. and many countries in Latin America. If an infected individual ends up on our shores, it’s quite possible they could infect local mosquitoes and start a transmission cycle in the U.S., especially the southern U.S.”

“We already had three dozen infected individuals in the U.S. Starting in late March and April, when the weather becomes hotter and more rainy, the mosquito population will greatly increase in the Gulf states, increasing the risk,” he says.


Since it was first identified in Brazil last May, the virus has spread to more than 25 countries and territories in the Americas and Caribbean. It has been linked with a neurological ailment, called Guillain-Barre syndrome, which can cause paralysis, and at least 4,000 cases of a devastating birth defect, microcephaly. Babies born with microcephaly have malformed craniums and smaller brains, which often leads to lifelong cognitive impairment and disability.


Flu Vaccines – Special Guest Post By Pixie

It is the anti-vaccine pseudo-science websites and blogs which convince the moms that there is more danger in their child getting a vaccine than not.

The solution may not be to provide “correct information” on *safety* — often dismissed by the reader out of hand — but to provide “correct information” on the dangers of *not* getting vaccinated. That’s the missing piece. And that information can’t be presented once or twice. It can’t just be ponied out at the beginning of flu season. CDC has to go toe-to-toe with the 24/7/365 information cycle of the anti-vaccine websites and bloggers. They are relentless. The contrary message would have to be just as round-the-clock and relentless to have a hope of success.

The solution would, then, be to provide the public with outcome information, rather than statements about dry counter-studies filled with data, data which readers often suspect has been manipulated to serve someone else’s ends.

In the world of new media, whats lacking are the *stories* of adverse outcomes. Most moms, most pregnant women, have absolutely no idea *why* they should be vaccinated on a personal level. And I do mean not from a public health standpoint (which is often the stance that CDC takes) but from an individual perspective. The anti-vaccine websites and bloggers focus on the individual, not on some dry construct like “public health.” They talk about that mom’s kid, specifically. They seem to care.

When reading CDC statements, many moms find them to be self-serving of the interests of the CDC and other monolithic (and often, to them, suspect) entities. When CDC lists negative possible outcomes for their unvaccinated children, it’s often stated in dry, succinct, language. These statements are all too easy to disregard.

In contrast, the anti-vaccine propagandists use the new media very well indeed. They spell out, in technicolor language, all the horrors of vaccination as they see them. They provide a complex and convincing argument for vaccinations benefitting not some mom’s child, but “big pharma” and other powerful shadowy entities.

This “information” is repeated endlessly in various flavors. There is always something new to come back and “learn” on these websites.

In the mind of the mom, soon there’s no contest.

If CDC wants to promote the benefits of vaccination, they will need to promote the reality of some very negative outcomes that can happen to the unvaccinated. But they need to be serious about it, and do it in the style of the best new media practitioners. If they do that, then there’s a counter-artument, and the mom or the pregnant woman will have to take some time to actually weigh the vision of one negative outcome against another. At least, in that light, vaccination might stand a chance.

Will popping up in September with a photo and story of one unvaccinated kid on an ECMO machine work if CDC tries such a halfway measure? Of course not. They’ll be throwing rocks at a mountain, and their timing and motives will seem highly suspicious.

Now, CDC will say that privacy laws prevent the telling of these stories. Balderdash. Every day we see stories in local media in which the relatives of unvaccinated and critically ill or dead flu patients say that they’ll do anything it takes to let others know that they need to get vaccinated. And they often state that they’re sorry that they believed the anti-vaccine propaganda.

Each and every time a family is faced with their child barely surviving weeks on a heart/lung machine (and damaged for life) or worse, the death of their child from something “ordinary” like influenza, they say: “We just didn’t know what could happen. We never imagined it. We never knew. We had no idea.”

So if CDC wants to fight an information war, they have to fight it with the kind of information that their opponent has been using to win it. NONE of my co-op class students apart from my own was vaccinated against flu this year. ALL of their families “believe in” the dangers of vaccines. NONE of them know anything at all about the kinds of adverse and tragic outcomes that can come from remaining unvaccinated. NONE of the modern moms I know have any idea at all what it was like for families, for kids, before the era of childhood vaccines.

That’s an abject failure of communications on the part of the CDC. CDC doesn’t need a multi-million dollar communications center and budget. It needs a few good bloggers and a website or two that can tell a STORY.

As long as CDC acts like the bureaucracy it is, as long as it does not step up and provide a counter-story, the other, more dramatic, stories and claims (no matter how bogus) will win, vaccination rates will continue to remain low, and more kids and pregnant women will die. The tragedy is that they will die not ever knowing anything about the real danger they were entertaining by making the choice to remain unvaccinated.

If they had been able to compare the true dangers, they may have made another choice.

Moms don’t want to hear about “societal costs” or economics. They don’t want to hear about “pubic health.” They want to protect their kids from danger. Until you appeal to that hard-wired sentiment, forgetaboutit.

False Security

From NPR, March 30, 2012

The Obama administration has announced a new policy to handle the risks posed by legitimate biological research that could, in the wrong hands, threaten the public.

The move comes in response to a huge debate over recent experiments on bird flu virus that got funding from the National Institutes of Health. Critics say the work created mutant viruses that could potentially be dangerous for people, or give terrorists a road map for making a bioweapon.

A committee that advises the government called the National Science Advisory Board for Biosecurity (NSABB) is again meeting Friday to discuss those flu studies. Late last year, it recommended keeping some details secret. But a panel of experts, including flu virologists assembled by the World Health Organization, called for full publication.

The new policy is aimed at preventing this kind of controversy from happening in the future. It covers federally-funded research — both ongoing work and future proposals. And it calls for special reviews of work that involves a list of 15 particularly nasty pathogens and toxins, including highly pathogenic bird flu virus, anthrax, and Ebola.

Funding agencies will have to evaluate certain kinds of experiments to see if they pose special risks. The idea is “to really upfront ask the questions: Should they be done? And if so, under what conditions should they be done,” explains Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases at the NIH.

If an agency wants to fund an experiment that might yield potentially dangerous information, Fauci says, scientists could be asked to hold back on publishing details in order to receive funding.

Or, in some cases, the work might need to be classified. Fauci notes that the NIH does not do classified studies. “We would have to refer it to an agency that does classified research because we don’t,” he says.

This sets a very dangerous precedent. There are lots of types of biological research “that could, in the wrong hands, threaten the public”. Although the intent now may be to restrict this measure to certain types of research, once the precedent is set, there is no guarantee that it will not be extended to others. Who will decide what knowledge could or could not “threaten the public”? If it is politicians (or scientists who depend on the patronage of politicians), then almost by definition, this measure will be politicised. One can get whatever type of research one wants banned by picking the right members of the committee that will do the banning. There are recent of examples of this, for those whose memories go back a few years.

It is also disturbing that there is still no discussion of State sponsored bioweapons research, especially in China. There are many countries with the capacity to do this research without any help from the US. If this research in the US is classified, the general public in the US will have no idea what is or is not possible, what is or is not a threat.

I have a great deal of respect for the US military’s ability to fight conventional wars. However, in my opinion, their work on biological weapons defense is extremely poor. The DoD has demonstrated no grasp of the strategic threat involved nor any particular expertise in developing countermeasures. To be fair, their ability to detect emerging pandemic flu threats is apparently better than the CDC’s as they were the ones who first reported pH1N1. But this is not nearly enough.

The CDC conducted the same types of experiments as Fouchier and Kawaoka but failed to reveal the threat of a high CFR H5N1 pandemic. It would be a mistake to rely on the CDC for this research.

The DoD has USAMRIID, but it is not clear that they have the breadth or depth of personnel to cover all potential agents. Further, scientists there will be hampered if they cannot discuss their work with their colleagues at other institutions (as would happen if the work is classified). Given that the anthrax attacks apparently originated from a scientist at USAMRIID, it is not obvious why entrusting this group with work on dangerous pathogens is safer than to let this work be done by NIH scientists.

In my opinion, this ruling is tantamount to hearing the noise of breaking glass in your house and then pulling the covers over your head. Hiding from the threat will not save you. As scary as it is, your best option is to develop a strategy to defeat it, which may involve confronting the threat head on.

We could have delayed the threat of biological weapons by controlling the sale of gene synthesis machines to foreign countries. But no-one in the US government, including apparently the entire leadership at DoD, seems to have understood the risk of proliferating this technology. Given that the ability to create a high CFR pandemic virus already exists and has been actively pursued by countries like China, the question now is: what is likely to provide our best defense? Part of the answer will involve politically unpalatable decentralisation and the incorporation of citizen resilience in national defense policy. But part of the answer will come from a free exchange of information among the best scientists. We cannot develop countermeasures to a threat if we do not know what it is.

Novel H3N2 flu virus infects child in Maine

A 8 year old boy in Cumberland County Maine has been infected with the same H3N2 influenza virus that has previously infected three people in Pennsylvania and one in Indiana. This virus is apparently circulating in pigs in the US.

The people in Indiana and Pennsylvania were infected in late July and August 2011. The 8 year old boy in Maine became ill in early October 2011. He is reported to have been in close proximity to pigs at an agricultural fair. There is disagreement regarding the severity of her symptoms. Although most reports suggest that she was not hospitalised, one media source says that she was.

From Kennebec Journal, October 21, 2011

The Maine Center for Disease Control and Prevention is investigating a new type of swine flu that sickened a child in Cumberland County.

The agency has not provided any more details about who was affected or where, but said it is an isolated event in Maine and has not been detected in people who had contact with the child. The child was hospitalized and is recovering, it said.

The Maine CDC is recommending the following precautions for health care providers:

  • Maintain a heightened awareness for influenza-like illness (ILI) defined as fever greater than 100° with cough or sore throat, in the absence of another known cause.
  • Consider influenza testing by PCR for:
    1. patients with ILI with recent exposure to pigs.
    2. patients with ILI who are hospitalized,
    3. patients with ILI who have died,
    4. patients where a diagnosis of influenza would affect clinical care, infection control, or management of contacts.
  • Consider use of antivirals to quickly limit potential human transmission
  • Vaccinate patients and healthcare workers as a primary strategy to prevent influenza

The virus that infected the boy in Maine, the three people in Pennsylvania and the child in Indiana has a complex ancestry. The HA and NA genomic segments are originally derived from humans, but are different from those currently circulating in H3N2 human flu viruses. The PB1 genomic segment originated in humans. The PB2 and PA genomic segments originated in birds. The NP and NS genomic segments originated in pigs. The Matrix or M segment, came from the human 2009 pandemic H1N1 virus, apparently as a result of reassortment between a virus that has been circultating in pigs and the pandemic 2009 H1N1 virus.

Five individuals have now been reported to be infected with this virus within a relatively short time. Pig to human transmission is likely, although it is not know if this was due to direct contact or respiratory spread. Although sustained human to human spread of the new virus has not been reported, this could happen at any time. The virus could change further as result of reassortment, recombination or mutation.

Swine-Origin Influenza A (H3N2) Virus Infection in Two Children — Indiana and Pennsylvania, July–August 2011
Morbidity and Mortality Weekly Report (MMWR), September 9, 2011/60(35);1213-1215

[corrected age and gender of child based on new information, October 24, 2011. Hat-tip, Dr. Niman]

Hypocrisy Grips the Huffington Post – Anti-Vaccine Site Reviews “Contagion” … and Flublogia

Flublogia receives little attention from the MSM. However, in a recent review of “Contagion” a blogger at the Huffington Post, Peter Christian Hall, discusses Flublogia. Well, part of it anyways.

In “Contagion” an anti-vaccine, magic-bean selling flu blogger is portrayed with calculated nastiness by Jude Law. It is ironic that a blogger at the Huffington Post would review this movie, and discuss its relationship to Flublogia, given that the Huffington Post has been the source of virulent anti-vaccine blogs. Bloggers at the Huffington Post like Jim Carrey, Joseph Mercola and Bill Maher are strongly anti-vaccine, and, frankly, anti-science. At a critical time in the pandemic when vaccine was just becoming available (September 2009) Dr. Frank Lipman wrote the following at the Huffington Post:

Summer is over and the question I am being asked most frequently in my practice is, “what do I do about Swine flu?” My patients are wondering whether or not they should get vaccinated and the simple answer I give most of the time is ..NO!

From what you may have read, you might think that the swine flu vaccine is the answer to swine flu. Unfortunately this is not true and until we know that the vaccine is safe, I cannot in good conscience recommend it to most of my patients.

All of the available evidence suggests that the pH1N1 vaccine given in the US was both safe and effective. However, due to belief in the anti-vaccine message, some parents did not vaccinate their children. Some of these children subsequently died of pH1N1. How many of these deaths is the Huffington Post responsible for? It is impossible to know. No-one collects statistics on death caused by misinformation.

In his article, Mr. Hall lists many members of Flublogia, but leaves out me and one of the most popular flu forums (which I moderate): Pandemic Flu Information (PFI) . Why? Well, one possibility is that I and many members of PFI_Forum were frequent critics of the Huffington Post and its team of anti-vaccine bloggers, any one of which would have been a good model for the anti-vaccine blogger in “Contagion”. We also criticised the CDC, not for promoting vaccine, but for not promoting vaccine effectively enough. We also criticised the CDC for its lousy testing throughput and incompetence in articulating the need for rapid treatment with Tamiflu. Although some would like to lump PFI in with the anti-science magic bean sellers, the fact is that this is the role the Huffington Post played during the pandemic. We were on the other side.

The continued blacklist of PFI bothers me. But not due to personal pique. I write anonymously and have no magic beans to sell. What bothers me is that the Director of the CDC is so insecure that he cannot countenance any criticism, even when its constructive and accurate. Although the CDC risk communicators claim that they want to “engage” the public, this is a lie. They wish to be praised lavishly and will reward only those who do so.

The Huffington Post also appears to be unable to handle the truth. Goju from PFI tried to post some links demonstrating HuffPo’s role as an anti-vaccine propaganda agent during the 2009 pandemic. His comments were censored. So much for the Huffington Post’s committment to free speech.

I don’t expect the people I criticise to like me. I’m OK with being called names or just being ignored. But censoring valid criticisms and only listening to people who tell you what you want to hear will lead to disaster. The many people who died unnecessarily during the 2009 pandemic are proof of that.

Contagion Review

[Warning, this review contains spoilers]

I recently saw the new movie “Contagion”, directed by Steven Soderbergh. Although I’ve enjoyed many of his films for their artistic merit, this review will focus on the movie from the standpoint of the accuracy of its science, as well as how it depicts the CDC, the World Health Organisation (WHO), the Department of Homeland Security and the blogosphere.

Briefly, the movie is about how ordinary people, scientists and public health officials respond to a new virus. It was apparently spread both by respiratory droplets dispersed by coughing and by touch (fomites). In addition to coughing, symptoms included bad headaches and seizures indicating that the virus could spread to the brain. The virus starts out with an R0 of 2 but this increases with time. The case fatality rate (CFR) is 20-25%. It’s not a flu virus, but the exact nature of the virus is not described. It apparently originated in bats, was transferred to pigs via a piece of fruit and then to humans at restaurant. It is said to have been based on Nipah virus.

The movie is relatively believable for this genre, partly because of the quality of the script and the acting. The cast includes Gwyneth Paltrow, Jude Law, Matt Damon, Laurence Fishburne, Kate Winslett and Eliot Gould. These are far superior actors to the B-list hacks found in other pandemic movies from recent years. The only false note was provided by Marion Cotillard as a WHO representative.

The quality of the science in the movie was mixed. A highly infectious virus with a CFR of 20-25% is certainly possible, especially if the carriers are asymptomatic but infectious in the early stages of the disease. They appeared to use real equipment in real labs for many of the scenes. One minor flaw was that it was stated that an attenuated virus would be used but one of the scientists was shown injecting herself. Killed viruses are usually injected. Attenuated viruses are usually given orally or nasally. Indeed, some people later in the movie were shown being given nasal sprays similar to Flumist. The most egregious science errors related to the rapidity with which the CDC was depicted sequencing the genome of the virus and characterising the proteins. Last year during the pH1N1 pandemic, it was revealed that the CDC was conducting PCRs one tube at time, by hand, even though they had bought expensive robots which could have greatly increased their throughput. Although the CDC has the budget to perform cutting edge science, they do not have the personnel for even basic tasks like high throughput PCR. De novo assembly of the genome of a novel virus requires a much higher level of expertise currently not available at the CDC. The recent outbreak of the new E coli strain demonstrated this. German and Chinese labs rapidly sequenced the bacteria and made the sequences public. A number of groups then rapidly assembled the genome. The CDC was not among these groups. Further, the depiction of rapid progress in determining the three dimensional structure and function of novel proteins is not realistic. Nucleotide sequencing can go fast, protein work takes much more time.

The depiction of the role of public health officials during this pandemic was mostly laudatory, but not very accurate. A CDC official played by Laurence Fishburne warns his fiancé to leave a city with a high level of infected people but not to tell anyone else of their danger. This is realistic as these sorts of private warnings have occurred before (see Nights of the Weak-Kneed – Past and Future for more). As mentioned above, the CDC scientists are depicted in the movie as performing miracles of discovery while the truth is that they struggle with basic methods. Mr. Soderbergh was likely snookered by convincing PowerPoints and a VIP tour of very elaborate equipment at the CDC. Some epidemic intelligence officers likely are brave and determined as portrayed by Kate Winslett. However, the extensive role of “Risk Communicators”, otherwise known as PR spin “doctors” at the CDC is not given much attention, although it is hinted at in one scene.

The least realistic, and frankly bizzare, subplot of the movie involved the WHO. We don’t see much going on at the WHO itself. Instead, we follow the strangely robotic Marion Cotillard to China to investigate the source of the virus. One of the Chinese scientists suggests that the WHO is in bed with the American drug companies. A strange line given that the WHO is currently run by Margaret Chan, an unqualified incompetent who owes her position to the Chinese Communist Party and billions of dollars in bribes to African countries. In any case, the WHO representative is kidnapped by Chinese scientists and held in a small village in an attempt to acquire vaccine from the WHO. Mr. Soderbergh obviously knows nothing of contemporary China if he thinks this is a serious possibility. Security forces would be blasting away at everyone in that village within hours of such a crazy scheme. The idea that the location of a kidnapped WHO representative could be kept secret from the central government for weeks to months is beyond silly. In any case, if there was such a virus on the loose now, the Chinese governement would get whatever it wanted from Margaret Chan whenever it wanted it. This was demonstrated during the pH1N1 pandemic when China got early access to the virus and was allowed to prepare a vaccine more quickly than other countries.

The depiction of the Department of Homeland Security (DHS) was brief. A DHS representative raises the possibility of a weaponised bird flu virus which was immediately shot down by the CDC official. This is realistic, imo. DHS is far more aware of the negative consequences of a pandemic than the CDC, imo, and much more willing to warn people to prepare. However, the CDC has apparently overruled them on this. In the movie, the DHS representatives are depicted as scary, unappealing guys. A pity, given their message in support of individual preparedness could save a lot of lives. I wish Mr. Soderbergh had taken their concerns more seriously and perhaps assigned one of his A list actors to portray a DHS official.

There was no mention of Flublogia or the preparedness community in general in the movie. Instead, the only blogger mentioned was a quack selling a fake cure to the disease caused by the virus. This character, portrayed by Jude Law, was obviously patterned on Mike Adams of NaturalNews, an anti-vaccine activist who pushes supplements of dubious effectiveness. Although I agree with the charterisation of the blogger in the movie as irresponsible and immoral, I am disappointed that Mr. Soderbergh decided to ignore the rest of the online community which follows and contributes to identifying outbreaks. The SARS cover-up in China was first reported on BOXUN, an anti-Communist ex-patriot website. I am aware of several instances where the online community of flu watchers made positive contributions to science and public health. Too bad that, once again, the mainstream media implies that the online community consists entirely of “those crazy internet people”. Maybe we need to make our own movie.

Commentators at PFI_Forum have characterised the portrayal of everyday events as a mild version of what the real thing would be like. I agree. Although overcrowded ERs, empty grocery shelves, home invasions, and movement restrictions are shown briefly, the full impact of a high CFR pandemic is not depicted. However, for all its faults, this movie might convince some that prepping is not a bad idea. Although I hate to say it, I think the the early scene where Gwyneth Paltrow dies was one that will affect many people the most. If Gwyneth can die from a virus, then surely no-one is safe!

Whatever works.

The Return of H3

Flu viruses can be characterised in many different ways. One system uses types and subtypes. There are three “types”, A, B and C. Subtyping is based on two of the eight influenza genomic segments, hemagglutinin (H) and neuraminidase (N). Different versions of these two genes are designated with a number. For example: H5N1, H1N1 and H3N2 are three different subtypes of type A influenza. There are some important limitations to this system. Most importantly, two very different viruses may have the same subtype. For example, there is a “seasonal” H1N1 flu virus which is very different from the currently circulating “2009 pandemic” H1N1 virus. Further, the flu virus that caused devastating flu pandemic in 1918 was also subtyped H1N1, although it is significantly different from both “seasonal” H1N1 and “2009 pandemic” H1N1. This confusing situation arises because the subtyping system only reflects two of the eight flu genomic segments. Reassortment events can mix and match different genomic segments resulting in viruses that share some, but not all genomic segments in common. The only way to know whether or not a reassortment event has occurred is to sequence all eight genomic segments, not just the hemagglutinin and neuraminidase genes.

During the major outbreaks of 2009 pandemic H1N1 in the United States, “seasonal” H3N2 and H1N1 were almost entirely absent. There was some speculation that 2009 pandemic H1N1 would drive the “seasonal” flu viruses to extinction. This idea appears to be premature.

In Taiwan (Focus Taiwan, July 27, 2010), Singapore (asiaone, July 23, 2010) and Hong Kong (Center for Health Protection, July 17, 2010), 20%, 45% and 27% of all recently reported flu viruses were found to be H3, respectively.

There have been recent reports of H3 viruses in Iowa, Minnesota, Arkansas, Wisconsin, Pennsylvania, and Hawaii (Iowa Department of Public Health, July 30, 2010) [hat-tip, Pixie]. This has apparently led to the mass emailing of an Health Alert by the CDC advising doctors to be on the look out for H3N2 infections (CDC, August 4, 2010) [hat-tip, Goju]. The reason for this Advisory is unclear.

It is not clear whether all eight genomic segments in the viruses causing these outbreaks in Asia and the United States have been sequenced. Thus, we cannot know for sure that they are truly the “seasonal” H3N2. Dangerous reassortments between H3N2 and H5N1 have recently been reported in pigs in China (Bi et al. 2010). It is important to characterise flu viruses causing new outbreaks by sequencing all eight genomic segments. This is neither expensive nor technically difficult. However, it is not clear that the CDC has the necessary expertise to process samples rapidly. It is also not clear how rapidly a detection of a change in circulating flu viruses would be reported.


Bi Y,  et al. (2010) Novel swine influenza virus reassortants in pigs, China. Emerg Infect Dis.