Monday, August 24, 2015

"Vaccine Whistleblower": A Review of the Preface and Foreword

This book is being released today and is surely much anticipated by the anti-vaccine brigade which has desperately sought to get their "whistleblower" William Thompson heard by, well anyone in a position of authority or respected media.  Even the anti-vaxx-funded Rep. Bill Posey, R-FL couldn't raise any interest in the "CDC Whistleblower" manufactroversy when he made allegations against the CDC parroting William Thompson's uncorroborated claims.  Kent Heckenlively, a contributor to the autism-hating, anti-vaccine blog Age of Autism breathlessly proclaims:
"This is a slim, elegant book which can be read in a few hours and has the potential to change the minds of a lot of people."
It will, no doubt change the minds of a lot of people, it certainly changed mine but not in the way that Kent Heckenlively hopes.  It will only reinforce the true believers' minds but certainly illuminates the true colours and motives of those involved as well as show how desperate some are to think that so little is of such import as to have a congressional hearing over it.  This book is so bad that it's good, so good in the sense that it contains such demonstrably false information and a re-hash of previously debunked claims that I have chosen to review it in parts, the first being the Preface (Boyd Haley) and Foreword (Robert F. Kennedy, Jr. (RFK Jr.)), Introduction and then groups of chapters.

Preface by Boyd Haley, PhD

The Preface is written by Boyd Haley, PhD and formerly with the University of Kentucky Department of Chemistry.  Boyd Haley has been a long term steadfast proponent of the "autism is mercury poisoning" failed hypothesis.  He has referred to autism as "Mad Child Disease" and has created OSR #1 as an industrial sludge chelator but saw the financial opportunities and re-branded OSR #1 as a "supplement" for "treating autism". Fortunately the FDA forced Haley to remove OSR #1 from the market as a supplement but that hasn't stopped him from still attempting to take advantage of desperate parents; he's just doing what he should have done to begin with which is properly test and manufacture the product as a drug that needs approval.
I was exposed to the opinions of both autistic parents and the CDC on the involvement of vaccines, or components of vaccines, in the well-recognized epidemic of autism that started in approximately 1990. I came to this issue as a scientist. I am not the parent of a child with autism, nor, to my knowledge, are any of my relatives afflicted with this illness.
Thank you Boyd Haley for that time-saving tip.  Here I thought that autism prevalences were estimated via systematic collection and analyses of data but all we need to do is get the opinions of "autistic parents" [sic] and the CDC.  Haley's contempt of autistics is also noted.
I'm not sure what his significance is as a scientist is; he's a chemist and his only contribution to "autism research" has been some self-serving, dodgy letters and studies with the likes of the Geiers, Sykes and Blaxill.
The material herein, mostly presented by Dr. Thompson, a self-described whistleblower, details his experiences with inappropriate CDC handling of data used in peer reviewed journals to demonstrate vaccine safety. His statements are incredibly damaging to the reputation and credence of any work that the CDC supported that addresses the autism and vaccine safety issue.
There is indeed a disconnect with this claim by Haley as according to him and his confederates, the studies which cannot find any association between particular vaccines and vaccine constituents are never accepted by them but someone like William Thompson can make mere assertions and that's somehow damaging to the CDC and unravels all the vaccine safety studies they have conducted.  Haley like RFKJr. seem to think that the CDC is the sole arbiter of vaccine science everywhere in the world.
The inability of the CDC to identify the causes of Autism Spectrum Disorders, no matter the rate, is apparent. Perhaps the reluctance of its leaders to appropriately consider potential causes that they find unpleasant to accept is the reason.
Haley is erecting an absurd strawman here.  He somehow tasks the CDC with being the only agency responsible for identifying Autism Spectrum Disorders aetiology and when they don't, it must be vaccines and that is an inconvenient truth they don't wish to acknowledge.  It's really a shame that anti-vaxxers can't get better representation.
Vaccine safety goes well beyond autism as well. It is disturbing to think that the comparatively high infant mortality rate that the US has compared to its peer nations, many of which have schedules far less aggressive than the US’s schedule and many of which do not mandate vaccination, may be explained, at least in part, by the possible illness-inducing effects of our vaccine program. Would the lack of safety research be an explanation for the CDC’s claim of one in six children with neurodevelopmental issues in the United States?
Haley makes a very rookie mistake by invoking the vaccines-cause-infant-mortality canard.  There is no association and one of the biggest mistakes that people who believe this and disseminate this make is that the definition of infant mortality from country to country is static.  It is very disingenuous of Haley to perpetuate this myth; he claims he has the acumen to comprehend vaccinology but completely fails to apply any scrutiny to what amounts to be an urban, anti-vaxx myth.
However, with the recent success in the push by the vaccine industry supporters to demand all children be vaccinated, this series is as necessary for parents and pediatricians to read as it is for our congressional members to read and investigate thoroughly.
This is a case of "be careful what you wish for".  I know true believers like Boyd Haley think that this book is going to be the spark that finally gets their congressional hearing or somesuch but I suspect all it will do is fall by the wayside like their previous attempts to garner attention for #cdcwhistleblower.  If this is any indication of what the book contains then a bunch of unsupported statements and a few talking heads telling readers what they ought to believe is going to have a very disappointing outcome indeed.

Foreword by Robert F. Kennedy, Jr.

RFKJr. begins with the obligatory, "I have always been fiercely pro-vaccine." but then predictably degrades into the usual anti-vaccine rhetoric.  RFKJr. bemoans the "continued presence of vaccines..." implying that Thimerosal is still in vaccines; it isn't.  It's only present in some multi-dose influenza vaccines and not paediatric vaccines nor those recommended for pregnant women.  He makes a claim that displays his ignorance and/or dishonesty regarding influenza vaccines:
Thimerosal is still present in four American vaccines, including giant “bolus” doses in fifty million flu vaccines administered each year to American adults, pregnant women, and infants.
What exactly are "giant bolus doses"?  RFKJr. would like us to believe that somehow larger-than-recommended doses of influenza vaccines are administered just because they contain thimerosal.  But let's look at some actual numbers.  Thimerosal-free influenza vaccines comprise the bulk of the supply, 66-68% to be exact or 116-118 million out of a total of 171-179 million manufactured.  The uptake for pregnant women and infants and young children is about 50% which is an order of magnitude below the availability of thimerosal-free influenza vaccines which are what is recommended for pregnant women and children less than three years old.   RFKJr. can't even qualify his statements with any evidence that these populations are receiving thimerosal-containing influenza vaccines.  In my opinion, his statement is intentionally inflammatory rhetoric and is relying upon those reading to just take his word based upon his namesake.

RFKJr. proclaims that because he published a book (my friend's ten year-old son published a book too) that he is some kind of expert in thimerosal.  He goes on to make lofty and completely unsupported claims that thimerosal is responsible for a litany of disorders and diseases.  Amusingly, other self-appointed "vaccine experts" jockeying for notoriety amongst the anti-vaxx brigade all have their own pet claims that aluminium, GMOs and foetal DNA are responsible for the same disorders and diseases that RFKJr. says thimerosal is responsible for.  RFKJr. even goes on to repeat the same hoary old trope that a broken multi-dose vial of influenza vaccine in a physician's office requires evacuation and environmental hazmat clean-up:
Thimerosal is so toxic that when a doctor carelessly shatters a multidose flu vial, state laws require evacuation of the building and clean-up by trained hazmat crews wearing protective boots, gloves, and respirators. Common sense should tell us that it’s not a good idea to inject this poison into infants or expectant mothers.
No, no and no; this is patently false and as an environmental activist or at least know someone at the EPA who could have helped him out with this one, RFKJr. should know better; I suspect he does but the reality doesn't make for whipping up indignation.  Multi-dose influenza vials contain ten doses or 5mL total volume.  There is 25μg ethylmercury per dose or 250 μg total in a full vial of a thimerosal-containing influenza multi-dose vial.  Let's compare this to a compact fluorescent bulb or CFL which contains 4-5 mg of elemental and highly volatilised mercury and what is required for cleanup and disposal.
Ventilate the room, clean it up and dispose of in a proper hazmat container.  But RFKJr. is perpetuating the myth that a full multi-dose vial with about 20 times less mercury (and a less toxic form) than a CFL somehow requires full hazmat cleanup.

RFKJr. introduces the thrust of the book and the players involved, namely Brian S. Hooker and William Thompson by immediately inflating their credentials and work to make them seem more relevant and knowledgeable than they actually are.  To whit:
Barry built his book upon four legally taped conversations between CDC senior vaccine safety scientist Dr. William Thompson and Simpson College professor and epidemiologist, Dr. Brian Hooker.
"Legally taped conversations" is arguable since William Thompson stated he didn't know he was being recorded and Brian Hooker lives in a state which requires knowledge and permission of both parties being recorded.  William Thompson isn't nor ever has been a "senior vaccine safety scientist".  He's a psychologist and worked briefly in the CDC's National Center for Immunizations and Respiratory Diseases, Influenza Division and also the National Immunisation Program.  Thompson also used to work for Merck but I guess that's only cause to discount someone if they are pro-vaccine.  Brian Hooker is a biochemical engineer, he has no epidemiology education nor experience as evidenced by his retracted Translational Neurodegeneration study in which he attempted a "re-analysis" of the 2004 DeStefano et al. MMR study and failed miserably.  Brian Hooker works in a second tier, private Christian liberal arts college with an undergraduate enrolment the same size as my child's elementary school.
He [Thompson] is also coauthor of the CDC’s seminal 2004 study known as DeStefano 2004, which dismissed the link between the MMR vaccine and autism. That study has been cited in ninety-one subsequent published studies and is one of the principal cornerstones for claims by the CDC and the vaccine industry that vaccines do not cause autism.
Another easily falsifiable claim by RFKJr.  DeStefano et al. (2004) is not a "seminal" study about MMR and autism.  Hell, reviews of MMR-Autism studies were being conducted prior to 2004 and DeStefano et al. (2004) is only one in a long list of studies from all over the world which cannot find any association between MMR vaccination or Thimerosal and autism.  RFKJr. goes on ad nauseam about (completely unsupported) statements William Thompson has made about rampant corruption within the CDC's Immunisation Safety Office.  RFKJr. also reiterates Thompson's claims of details about the "CDC's tricks for executing the fraud" but is nothing but hearsay from a person who hasn't even conducted statistical analyses for the studies he claims are fraudulent nor does he even have any expertise.  Thompson via RFKJr. claims:
That’s the gimmick the CDC has perfected, in order to preserve the illusion of Thimerosal safety. In the 2007 study, CDC scientists removed the low IQ individuals and individuals with autism or other neurological diagnosis from the pool before even beginning their study on Thimerosal exposure.
This is about as dishonest as someone can get since "Early Thimerosal Exposure and Neuropsychological Outcomes at 7 to 10 Years" wasn't even inclusive of autism per the own authors' parameters who include William Thompson.
Since the CDC is conducting a separate case–control study of autism in relation to mercury exposure, a measure of autism was not included in the test battery.
That is because a separate study examining Thimerosal exposure and autism was in the works and subsequently published as "Prenatal and Infant Exposure to Thimerosal From Vaccines and Immunoglobulins and Risk of Autism".  This study is remarkably absent from discussion for some very (not really) strange reason i.e. people like RFKJr. are confounded by the results:
In the covariate adjusted models, we found that an increase in ethylmercury exposure in 2 of the 4 exposure time periods evaluated was associated with decreased risk of each of the 3 ASD outcomes.
More on this later.  Going back to the Thompson et al. (2007) study, RFKJr. confidently proclaims that:
Despite those crooked presentations, scientists still found a persistent signal for tics, a family of grave neurological injuries, including Tourette’s syndrome that are associated with autism. Thompson now says that his bosses at the CDC pressured him to also alter the results of that study in order to conceal Thimerosal’s risks. Thompson says that the CDC’s Developmental Disabilities branch chief, Frank DeStefano, and his superiors at the CDC pressured him to manipulate the study’s findings and to bury the truth. In response to this pressure, the published version downplayed data showing that Thimerosal causes “tics.”
These are very serious allegations, allegations that would result in possible criminal penalties.  But glaringly absent is how?  Thompson didn't conduct the statistical analyses but being the lead author, he would have access to them and the raw data so should be able to provide definitive and conclusive evidence as to how the study's findings were manipulated but there is none.  Thompson et al. (2007) assessed 42 neuropsychological outcomes, tics being just one.  Thompson via RFKJr.   claims that "the published version downplayed data showing that Thimerosal causes "tics." yet the study results state:
Among boys, higher exposure to mercury from birth to 7 months was associated with significantly better performance on letter and word identification on the Woodcock–Johnson test, third edition (WJ-III), poorer performance on the parental rating of behavioral regulation on the Behavior Rating Inventory of Executive Function, and a higher likelihood of motor and phonic tics, as reported by the children's evaluators.
That is an accurate reporting of what they found and they can't say that "Thimerosal causes tics" because they also found significant positive associations:
We found no consistent pattern between increasing mercury exposure from birth to 7 months and performance on neuropsychological tests. Among girls, the only significant findings were two associations with better test performance. Among boys, there was a beneficial association between mercury exposure and identification of letters and words on the WJ-III and a detrimental association with behavioral regulation and motor and phonic tics according to the ratings of evaluators. An association with tics was also found in one HMO in the screening analysis of the CDC's Vaccine Safety Datalink4 and an analysis of the General Practice Research Database.21 The replication of the findings regarding tics suggests the potential need for further studies.
Thompson can say anything he likes but without evidence, they are just baseless charges.  Thompson too appears to be very dishonest by claiming causality.  If he is such a good investigator he should know that an epidemiological study cannot establish causality.  RFKJr. then veers the crazy train back to the MMR-causation claim:
The damage isn’t isolated to mercury-triggered neurological injuries. When Thompson discovered that the MMR vaccine was causing dramatic rises in autism in African American boys, his CDC bosses ordered him to keep his mouth shut. Thompson coauthored a seminal 2004 study on the MMR subsequently published in Pediatrics. He now admits that, under pressure from his superiors, his team fraudulently withheld data demonstrating a 340 percent higher risk of autism in African American boys who received that vaccine on time compared to boys who delayed the vaccine.
There is that claim of "seminal 2004 study" again; it's not and makes me wonder if RFKJr. knows what the word means.  DeStefano et al. (2004) did not find a "340 percent higher risk of autism in African American boys...", that was Brian S. Hooker and his incompetent "re-analysis" that apparently William Thompson helped him with.  Again I ask, if there were manipulation of the data in the DeStefano et al. study, how and why didn't Thompson give the missing data to Hooker?
When Thompson sent a letter complaining about the fraud to CDC director Julie Gerberding, her lackey, Robert Chen, chief at the Immunization Safety branch, stalked Thompson into the CDC’s parking lot to menace and threaten him. Thompson would be fired, Chen explained pointedly, if his complaints persisted.
Where is this letter?  In all of the "more than 100,000 documents" that Thompson allegedly gave Rep. Bill Posey and many to Brian Hooker, none are this letter?  Julie Gerberding has not been director of the CDC since 2009, just one of now countless facts RFKJr. can't seem to nail down.  More importantly, Thompson makes another serious allegation which is possibly a criminal activity and that is being menaced and threatened by a very accomplished and respected CDC scientist with more than 30 years of employ with the agency.  How very odd that such a blatant display of harassment could take place but Thompson is the only one to have experienced this.
Because of that study, doctors and public health officials continue to give that vaccine to children, even though its links to autism are proven in this and many other studies. On the basis of all the population data and the CDC’s most recent autism incidence estimates, at least 100,000 African American male children could have been spared debilitating neurological injury if the CDC scientists had told the truth when Thompson and his team first discovered the increased risk in 2001.
It truly boggles the mind that RFKJr. can make this leap; there are no other studies that "prove" MMR is "linked" to autism and again, even removing the DeStefano et al. (2004) study from the literature, there still exists dozens more powerful studies which cannot find any association.  It's pure race-baiting.  RFKJr. goes on to use Thompson's completely unsubstantiated hearsay to "verify" the "well-documented corruption at the CDC's Immunization Safety Office."  This appears to be the only somewhat supported allegation that RFKJr. has been able to make but has nothing to do with Thompson as he wants us to believe.  RFKJr. cites some reports such as Conflicts of Interest in Vaccine Policy Making (2000) which certainly exposes some problematic practices and it's also 15 years old, much has happened since then.  He also cites CDC Off Center (2007) in which then Senator Tom Coburn didn't agree with some spending that the CDC engaged in and even blamed the CDC when they got ripped off by employees and grantees, not much there.  Levinson (2008) found a substantial percentage of Special Government Employees within the CDC were not completing financial and conflicts of interest disclosures.  RFKJr. also invokes David Wright's scathing exit from the Office of Research Integrity but the CDC is not mentioned contrary to what RFKJr. claims.  None of this is any evidence of fraudulent behaviour by CDC scientists which is the crux of this book.
Thompson and his attorney have handed over thousands of damning CDC documents to Congressman Bill Posey of Florida in the hope that Congress will subpoena him to testify under oath.
So where are they?  If anti-vaxxers like RFKJr. and Brian Hooker want action then why is this the best they have to offer?  Rep. Bill Posey read a statement allegedly from William Thompson on the House floor in July:
At the bottom of Table 7 it also shows that for the non-birth certificate sample, the adjusted race effect statistical significance was huge. All the authors and I met and decided sometime between August and September ’02 not to report any race effects for the paper. Sometime soon after the meeting, we decided to exclude reporting any race effects, the co-authors scheduled a meeting to destroy documents related to the study. The remaining four co-authors all met and brought a big garbage can into the meeting room and reviewed and went through all the hard copy documents that we had thought we should discard and put them in a huge garbage can. However, because I assumed it was illegal and would violate both FOIA and DOJ requests, I kept hard copies of all documents in my office and I retained all associated computer files. I believe we intentionally withheld controversial findings from the final draft of the Pediatrics paper. 
If this is from Thompson, he has yet to acknowledge it although I don't doubt the veracity of the statement; it's just curious that this appears to be what Thompson wanted but is silent on the matter.  Thompson states that they decided to exclude reporting race effects but yet the final study does report race effects.  If Thompson can be this confused about such an easily verifiable fact in his own study, what does that say about his actual expertise and integrity?  His allegation that documents were illegally destroyed is very suspect and contrary to standard procedure for document dumps after electronic records are established.  Thompson so much as admits he reviewed the documents and thought they should be discarded but in the same breath accuses his co-authors of illegal document destruction.  Anti-vaxxers are putting their faith in yet again, another very suspicious person.

To be continued...

Monday, June 1, 2015

Once Again No, Vaccines Did Not Harm Children in Mexico

A couple of weeks ago the autism-hating, anti-vaccine blog Age of Autism ran a story of vaccines killing and hospitalising several infants in Chiapas, Mexico during a routine immunisation programme.  As of this writing only one commenter linked to a news story of possible bacterial contamination and the author of the blog post hasn't even bothered to issue a correction.

However, Orac in his usual Respectful Insolence style correctly urged patience for the investigation to conclude and that bacterial contamination was a more likely explanation.  Well that investigation has concluded and it was a bacterial source but not from the vaccines themselves but rather externally during handling and administration:
  • Although no hypothesis is not rejected, the only vaccine given in common to all children affected was that of Hepatitis B, so the research focused on the biological.
  • The batch of the vaccine was properly certified.
  • No adverse events were recorded after 100,000 doses were administered in various parts of the country since Oct. 2014.
  • Results of blood cultures at that time showed the presence of the local external contamination, outside the biological vaccine, in particular bacteria, which was consistent with the clinical pictures of hospitalized children. Microbiology studies conducted on children reported the finding of Staphylococcus hominis, a type of bacterium commonly found in the skin of people. These findings rule out other bacteria, such as those found in the gastrointestinal tract and airways. Molecular studies demonstrated that isolated Staphylococcus hominis in different patients was the same, namely that the bacteria came from a single source of contamination.
  • In conclusion, the Federal Commission for Protection Against Health Risks (COFEPRIS) analysis found that the vaccine was not defective and remained in temperature. Therefore, bacterial contamination occurred during the procedure of handling and application of the vaccine.  
While the conclusion that the vaccines were manufactured and stored properly can help establish confidence in vaccine programmes, two infants are dead and dozens were hospitalised due to improper handling of the vaccines.  This tragic result emphasises the need for more rigorous training of personnel administering any medications.  This was an avoidable error and the focus should be on that, not vaccinesdidit.

Thursday, May 14, 2015

In Remembrance of Lilady

A friend and fellow skeptic known as "Lilady" has passed away leaving a huge hole in our hearts and on the internet.   She was an omnipresent voice on numerous blogs and articles regarding vaccines and autism and will be sorely missed.

Lilady had a severely developmentally and medically disabled son whom she cared for with the deepest love and commitment I have ever known.  She became a fierce opponent of state mental institutions that cruelly warehoused special needs people and fought tirelessly for their closure.  She was the original Mother Warrior.  Through her trials and tribulations along with other parents of special needs children, she "adopted" the son of a friend whom she helped care for until Lilady passed away.

Lilady's advocacy extended to the internet where she was a prolific commenter on vaccine and autism articles.  She fearlessly questioned dubious stories, provided sound evidence to support her claims and was never intimidated by anyone.  Her decades-long expertise as a public health nurse along with her experience with special needs children and adults and fierce passion made her a formidable foe of anti-science purveyors.

Our thoughts are with her and her family and hope they know how appreciated, respected and missed their Lilady will always be.

Monday, February 23, 2015

18 month old, unvaccinated, previously healthy toddler dies of measles in Berlin outbreak

Berlin, Germany's capital, has seen a very large measles outbreak on the past months. Since October 2014, 574 measles cases had been reported.

Today, the Berlin health senator confirmed that on 18 February 2015, an 18 month old toddler, who had not been vaccinated against measles, and did not have any chronic disease, died after having been treated for measles infection in the Charité hospital for 5 days. While the child was vaccinated against some diseases, according to the German media, he had not received the recommended MMR. In Germany, the first MMR is usually given between 11 and 14 months and the second is recommended between 15 and 24 months.

Over the past couple of years, discussions about mandatory vaccination had come up in Germany, some child care centers had begun to only accept vaccinated children, and discussions are unlikely to subside now. The question is whether parents, who are already afraid/suspect of the government could be convinced by a mandate - suggestions are welcome how to reach them better.

Meanwhile, our heartfelt thoughts go to the boy's family and everyone whose lives he touched. Another preventable measles death too many.

Tuesday, February 17, 2015

The Measles Vaccines (MMR and MMRV) Protect Against Measles


A new anti-vaxx myth has surfaced which seems to have been developed as a result of my recent blogpost Disneyland Measles Outbreak is Due to Measles which discussed the measles genotype responsible (hint: it wasn't the vaccine strain).  Some, with no knowledge of virology nor immunology are spreading the myth that since the measles strain in the MMR vaccine is genotype A that it couldn't possibly protect against measles genotype B3 which is the genotype responsible for the latest U.S. outbreak and has spread to Mexico and Canada.  I will discuss how and why MMR vaccines are cross-protective for wild-type measles strains.

First there is some terminology which must be understood to follow along:
Serotype: Microorganisms of the same species can be further divided into serotypes, serovars or sub-groups based upon their surface antigens.

Antigen: A structural protein on the surface of a pathogen that is able to recognise cell receptors on the surface of a host cell.  The antigen is also the part of the pathogen which provokes the host adaptive immune response that generates antibodies.

Epitope: The very specific part of the antigen which antibodies attach to.

Genotype: The nucleotide sequence of certain regions of a viral genome which classifies differences.

The measles virus has only one serotype and causes measles unlike Human Papillomavirus which has dozens of serotypes and can cause different diseases.  This is why we see multiple serotypes included in the HPV vaccine and only one strain in each of the available measles vaccines which are all genotype A.
Many of the attenuated strains in use are derived from the Edmonston strain isolated in 1954, including the Schwartz, the Edmonston-Zagreb, and the Moraten strains. Other strains which are not derived from Edmonston strain include the CAM-70, TD 97, Leningrad-16, and Shanghai 191 (Ji-191) strains.
Measles virus genotypes are based upon their nucleotide sequences at the least conserved regions of the viral genome:
Wild-type measles viruses have been divided into distinct genetic groups, referred to as genotypes, based on the nucleotide sequences of their hemagglutinin (H) and nucleoprotein (N) genes, which are the most variable genes on the viral genome.
The 450 nucleotides encoding the carboxy-terminal 150 amino acids of the nucleoprotein has up to 12% nucleotide variation between genotypes. The 450 nucleotides that encode the carboxy-terminal region of the nucleoprotein (N–450) are required for determination of the genotype. The measles genotyping protocol is available from CDC.


What this means is that whenever a measles case occurs, a sample (throat or nasal swab) is taken from the patient, submitted to RT-PCR (reverse transcription-polymerase chain reaction) and PCR (polymerase chain reaction) which are molecular techniques to essentially isolate amplify the number of DNA copies so that they can be sequenced.  DNA sequencing determines the nucleotide sequences of specific genome regions and then compared to other isolates to see where the measles virus came from and also mutations that may have accumulated.

Recovered measles viruses are constantly monitored, tested and characterised to identify areas of the genome which may antigenically-drift.  Circulating measles viruses have also been tested against vaccine-derived antibodies to ensure vaccines will cross-protect against the numerous genotypes that are imported.  This is achieved through virus neutralisation assays for example.  This is a test that combines measles genotypes with serum samples of people either vaccinated or previously infected with wild-type measles to determine if antibody binding occurs.  A fluorescent tag is added and then the antibody-antigen complex is measured. Results of various assays demonstrate that vaccine-derived antibodies protect against many different measles genotypes:
The serum samples from recently vaccinated persons neutralized both the Moraten and Chicago-I viruses equally well (table 1): There was a less than 2-fold difference in neutralization titers. In contrast, serum samples from persons with a recent wild type infection were able to detect antigenic differences between the viruses. Sera in this set had neutralization titers against Chicago-l that were 4-8 times higher (average, 5.1) than the titers against the vaccine strain.
Very specific antibodies called monoclonal antibodies (MAbs) are also developed and tested against measles viruses including the vaccine strains to monitor vaccine efficacy and antigenic drift of measles genotypes:
Overall, the antigenic data indicated that some epitopes have been conserved between the vaccine strain and the recent wild type viruses, while others are unique to the recent wild type virus. The H and F proteins are responsible for the induction of a neutralizing antibody response to measles virus. Therefore, the antigenic differences were most likely due to variation in these surface glycoproteins. 

Protection against the current circulation measles genotype, B3 has been elucidated.  In other words, studies have been and are conducted to test antibodies derived from vaccination against numerous wild-type measles viruses.  Measles genotype B3 which is the currently circulating strain in the U.S., is neutralised by vaccine-derived antibodies.  That, in turn, means that the virus can't bind to host (human) cell receptors and cause disease.
On the basis of the sequences of their N and H genes, MeVs can be assigned to 1 of 23 genotypes and 1 provisional genotype [11, 12]. All vaccine strains and their wild-type progenitors are assigned to genotype A. Experiments with monoclonal antibodies have defined antigenic differences between the H proteins of genotype A vaccines and the H proteins of wild-type viruses grouped in other genotypes [62, 188, 189]. However, there is only 1 serotype for measles, and serum samples from vaccinees neutralize viruses from a wide range of genotypes, albeit with different neutralization titers [188, 190] More importantly, despite the presence of different endemic genotypes, vaccination programs with standard measles vaccines have been successful in every country where they were performed adequately [191193]. Suboptimal seroconversion after vaccination is likely the result of inadequate coverage; improper administration, transport, or storage of vaccine; or age of the vaccine recipients [194196].
It's a bit of a complex issue to digest but some key points are that measles vaccines induce many different antibodies against measles antigens.  There is some antigenic drift that renders a single antibody insufficient binding to a single antigen from some wild-type measles viruses but over all, vaccines protect us from many different genotypes including the currently circulating B3 genotype. The epidemiology of the measles outbreak also demonstrates the effectiveness of the MMR vaccine.  To date there have been 141 cases confirmed (dozens more reported) by the CDC. Measles is one of the most infectious diseases known and this interactive graphic demonstrates how measles can spread in variable susceptible populations.  If the vaccine did not proffer cross-protection, there would be tens of thousands of cases to date.  Obviously this is not the case as the majority of cases are unvaccinated.

A more easily-digestible version of this has been posted at The Scientific Parent.

Sunday, February 8, 2015

Your freedom of choice - somebody else's baby

I am having discussions with my non-vaccinating friend at the moment, who describes herself as "pro-choice" when it comes to vaccination. What seems absolutely impossible to grasp for vaccine refusers is that their choice makes other parents' children ill, and, potentially, kills them. The parents whose babies contract measles did NOT get a choice, NO say in their children's infection. That is the effect of vaccine refusal:

The below is Mobius - there are 24 hours between those pictures - the photographer, a friend of Mobius' family, Donavan Freberg, describes their feelings (shared from Refutations against Anti-Vaccine Memes page with kind permission of Mobius' mum):

This is Mobius Loop. He is the son of my dear friends Ariel Loop and Christopher Loop. He has measles. It was just confirmed. This is real, this is awful and these two photos are 24 hours apart. The good news? He's getting better. Quarantine ends tonight and the baby seems to be recovering well. The bad news? This was caused by one thing only, total and complete ignorance and selfishness of the anti-vaxxers. Because of people not vaccinating their kids (and when I say "people", I mean much of the upper crust westside of Los Angeles) this little sprout (who was too young to be protected) fell sick to a HIGHLY CONTAGIOUS epidemic that up until recently, had been a thing of the past. This is infuriating, sad and worst of all, needless. The Loops are dear friends, long time photo clients and informed, smart people. Ariel is a nurse. You don't just vaccinate your kids to protect them, you do it to protect other's who are too wee to get the shots. You are doing it as a selfless act. Please send good thoughts and prayers to this little muppet and to his parents, who are truly some of the best people I know.

Side note: I was scheduled to photograph this sweet everlasting gobstopper, but then this happened. I intend to photograph him the moment he has fully recovered and will be donating 100% of my shoot fees to charity to raise awareness of the necessity of vaccines. As a photographer, I must do everything within my power to document this and see that the awareness of this spreads faster than the disease in question. To all people reading this and for those who may be on the fence about vaccinating your kids, please, for Mobius and for all those who are affected by this terrible and PREVENTIBLE disease, DO IT. Vaccinate!!!! Don't even think twice. Just think.

ETA: Mobius' mum, Ariel, also weighs in:

I have a lot of mixed feelings right now, but ultimately I'm relieved that Mobius is doing so well. The horrific cough aside, he's doing way better than anyone expected at this point.
However, I'm furious that we're now part of the problem. While he's up to date with his vaccines, at 4 months he isn't old enough for the one that should have made this whole outbreak almost impossible. During the four days he was contagious before his rash appeared, we went out to eat twice, ran countless errands, and have potentially infected other kids who are too young to have to go through this. That kills me. And might kill one of them.
I understand that vaccines are scary. Having to hold him tight while a stranger hurts him is hard. Having three people hold him still to get the blood to test him for measles, however, was infinitely harder. Even at the time I had this passing thought of, "Am I being paranoid? Am I putting him through more trauma while he's sick for no reason?" I found myself almost hoping it was measles then so at least having to torture him would be "worth it."
It isn't, though. He shouldn't have had to go through any of it. I shouldn't have had to set alarms for myself in the middle of the night to make sure he was still breathing. It's bittersweet--I can't be as comforted by his recovery as it is clouded with guilt and fear that we might put another family through this.
Please, don't put other families through this.

Wednesday, January 28, 2015

Disneyland Measles Outbreak is Due to Measles

The current measles outbreak primarily emanating from Disneyland in California is up to 100 cases but not all are epidemiologically-linked to the Disneyland outbreak.  As is usual with measles outbreaks, most were completely unvaccinated, some were too young to be vaccinated.  There are numerous articles highlighting this well-known fact and that has anti-vaxxers on the defensive.  In fact, this screed by Laura Hayes appeared on the anti-vaxx, autism-hating blog Age of Autism:
1.  Has there been any laboratory confirmation of even one case of the supposed measles related to Disneyland?  If yes, was the confirmed case tested to determine whether it was wild-type measles or vaccine-strain measles?  If not, why not?  These are important questions to ask. Is it measles or not? If yes, what kind, because if it's vaccine-strain measles, then that means it is the vaccinated who are contagious and spreading measles resulting in what the media likes to label "outbreaks" to create panic (strange how they've completely missed the Autism outbreak going on for the past 25 years). It would be what one might call vaccine fallout.  People who receive live-virus vaccines, such as the MMR, can then shed that live virus, for up to many weeks...and can infect others.  Multiply that in your head by all of the people who receive not only the MMR live-virus vaccine, but many others. Other live-virus vaccines include the nasal flu vaccine, shingles vaccine rotavirus vaccine, chicken pox vaccine, and yellow fever vaccine.
That's right, apparently Laura Hayes is really good at asking the really dumb questions but not too adept at finding the answer before postulating what measles strain is circulating amongst those infected.  Hint: it isn't the vaccine strain.  This wasn't hard to find and is very specific about the genotypes:
Measles genotype information was available from 9 measles cases; all were genotype B3 and all sequences linked to this outbreak are identical. The sequences are also identical to the genotype B3 virus that caused a large outbreak in the Philippines in 2014. During the last 6 months, identical genotype B3 viruses were also detected in at least 14 countries and at least 6 U.S. states, not including those linked to the current outbreak.
And even more information regarding the differences in wild-type strains and vaccine-strains can be found here:

Genetic Characterization and Sequencing

Wild-type measles viruses have been divided into distinct genetic groups, referred to as genotypes, based on the nucleotide sequences of their hemagglutinin (H) and nucleoprotein (N) genes, which are the most variable genes on the viral genome.
The 450 nucleotides encoding the carboxy-terminal 150 amino acids of the nucleoprotein has up to 12% nucleotide variation between genotypes. The 450 nucleotides that encode the carboxy-terminal region of the nucleoprotein (N–450) are required for determination of the genotype. The measles genotyping protocol is available from CDC.
For each genotype, a reference strain is designated for use in genetic analysis (phylogenetic analysis), usually the earliest known virus isolation of that group. The means of referring to the genotypes has been standardized using alphabetical designations for the main groupings (clades). Within the main clades, numerals are added to identify the individual genotypes.
The following 19 genotypes have been detected since 1990:
A*, B2, B3, C1, C2, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, G2, G3, H1, H2
*Vaccine strains Moraten, Edmonston, Zagreb are all genotype A.
 There were 2 putative wild-type cases of measles identified as genotype A in 2008.
During 2011, 8 genotypes were identified by global surveillance:
B2, B3, D4, D8, D9, D11, G3, H1
Gosh that was simple.  Laura Hayes asks a lot more dumb questions and fills in the answers with her own fact-free assertions but there is too much stupid and not enough time to take them apart.  The important point here is that measles outbreaks are caused by measles viruses (not vaccine-strain) and a critical mass of anti-vaxxers clustering and causing large gaps in herd immunity.