This blog is a way of sharing the information and resources that have helped me to recover my son Roo from an Autism Spectrum Disorder. What I have learned is to view our symptoms as the results of underlying biological cause, which can be identified and healed. I say "our symptoms" because I also have a neuro-immune disorder called Myalgic Encephalomyelitis.

And, of course, I am not a doctor (although I have been known to impersonate one while doing imaginative play with my son)- this is just our story and information that has been helpful or interesting to us. I hope it is helpful and interesting to you!


Monday, September 8, 2014

Are Vaccines Necessary, Safe, and Effective?

For studies regarding the variability of vaccine response based on genetic and other factors, see this post:    Studies Show That Individual Responses to Vaccination Vary Widely

This post discusses shedding from live vaccines.

This post discusses contamination of vaccines.

EFFECTIVENESS OF VACCINATION AS A PUBLIC HEALTH POLICY

PEDIATRICS Vol. 106 No. 6 December 1, 2000 pp. 1307 -1317
"Thus vaccination does not account for the impressive declines in mortality seen in the first half of the century"


Pediatrics Published online February 14, 2011 (doi: 10.1542/peds.2010-2008)
"The incidence of pediatric ambulatory CAP (Community Acquired Pneumonia) visits has not changed significantly between 1994 and 2007, despite the introduction of heptavalent pneumococcal conjugate vaccine in 2000."

[Susceptibility to measles and varicella in healthcare workers in a tertiary hospital in Catalonia]
Enferm Infecc Microbiol Clin. 2012 Apr;30(4):184-8
"Healthcare workers born after 1980 were 20 times (95% CI: 11.0 to 37.2) more likely to be susceptible to measles, and 2 times (95% CI: 1.2 to 3.2) more likely to be susceptible to varicella than those those born before 1965...  The susceptibility to measles in healthcare workers in our centre is higher in younger cohorts, with values higher than expected in a community with high vaccination coverage against measles, mumps, rubella vaccine (MMR) in the paediatric population for many years."

Lack of Efficacy of Haemophilus b (HiB) Polysaccharide Vaccine in Minnesota
JAMA 1988;260:1423-1428
"Our results indicate that vaccination with Haemophilus b polysaccharide vaccine had no effect in preventing H influenzaetype b disease in Minnesota children."  

VACCINE SAFETY CONSIDERATIONS

Public should be told that vaccines may have long term adverse effects
BMJ, Jan 16, 1999;318(7177):193
"Research into immunisation has been based on the theory that the benefits of immunisation far outweigh the risks from delayed adverse events and so long term safety studies do not need to be performed. When looking at diabetes—only one potential chronic adverse event—we found that the rise in the prevalence of diabetes may more than offset the expected decline in long term complications of H influenzae meningitis. Thus diabetes induced by vaccine should not be considered a rare potential adverse event. The incidence of many other chronic immunological diseases, including asthma, allergies, and immune mediated cancers, has risen rapidly and may also be linked to immunisation.

We believe that the public should be fully informed that vaccines, though effective in preventing infections, may have long term adverse effects. An educated public will probably increasingly demand proper safety studies before widespread immunisation. We believe that the outcome of this decision will be the development of safer vaccine technology."


Pharmacogenomics in the evaluation of efficacy and adverse events during clinical development of vaccines.
Methods Mol Biol. 2008;448:469-79.
"The understanding of vaccine-induced immune responses in adults and infants is limited. Current vaccination schedules for infants are frequently debated. Especially, the relationship among the timing, the frequency of the dosing, and the generation of an immunological memory are debated. Vaccine antigen-induced cytokine responses to vaccinations given in infancy are of particular interest because little is known about cellular responses in this age, and the information available is based on antibody responses. Pharmacogenomics is ideally suited to study cellular responses related to immune response; in addition, toxicity, inflammation, apoptosis, stress, and oncogenesis can be monitored, since the expression of thousands of genes can be measured in a single experiment."


Pharmacogenomics in the preclinical development of vaccines: evaluation of efficacy and systemic toxicity in the mouse using array technology.
Methods Mol Biol. 2008;448:447-67
"The development of vaccines, conventional protein based as well as nucleic acid based vaccines, and their delivery systems has been largely empirical and ineffective. This is partly due to a lack of methodology, since traditionally only a few markers are studied. By introducing gene expression analysis and bioinformatics into the design of vaccines and their delivery systems, vaccine development can be improved and accelerated considerably. Each vaccine antigen and delivery system combination is characterized by a unique genomic profile, a "fingerprint" that will give information of not only immunological and toxicological responses but also other related cellular responses e.g. cell cycle, apoptosis and carcinogenic effects. The resulting unique genomic fingerprint facilitates the establishment of molecular structure--pharmacological activity relationships and therefore leads to optimization of vaccine development."

Combining Childhood Vaccines at One Visit Is Not Safe
Journal of American Physicians and Surgeons Volume 21 Number 2 Summer 2016
"Although health authorities including the Centers for Disease Control and Prevention (CDC) claim that childhood vaccines are safe and recommend combining multiple vaccines during one visit, a review of data from the Vaccine Adverse Event Reporting System (VAERS) shows a dose-dependent association between the number of vaccines administered simultaneously and the likelihood of hospitalization or death for an adverse reaction. Additionally, younger age at the time of the adverse reaction is associated with a higher risk of hospitalization or death."
You can read more about this study here.


Am. J. Epidemiol. (1992) 136 (2):121-135.
"Several social and medical attributes are associated with both avoidance or delay of vaccination and an increased risk of adverse events such as sudden infant death syndrome or childhood encephalopathy. Studies that fail to control adequately for such confounding factors are likely to underestimate the risks of adverse events attributable to vaccination."

Combination Vaccines: Postlicensure Safety Evaluation
Clin Infect Dis. (2001) 33(Supplement 4): S327-S333.
"The well-known limitations associated with prelicensure trials have led many to hope that postlicensure studies can address safety issues. This article reviews measures that have been or should be taken to meet this expectation...Only by investing in vaccine safety infrastructure at a level commensurate with investments in vaccine development can we hope to retain the public's confidence in immunization."


Adverse events following immunization with vaccines containing adjuvants.
Immunol Res. 2013 Jul;56(2-3):299-303
"A traditional infectious disease vaccine is a preparation of live attenuated, inactivated or killed pathogen that stimulates immunity. Vaccine immunologic adjuvants are compounds incorporated into vaccines to enhance immunogenicity. Adjuvants have recently been implicated in the new syndrome named ASIA autoimmune/inflammatory syndrome induced by adjuvants. The objective describes the frequencies of post-vaccination clinical syndrome induced by adjuvants. We performed a cross-sectional study; adverse event following immunization was defined as any untoward medical occurrence that follows immunization 54 days prior to the event. Data on vaccinations and other risk factors were obtained from daily epidemiologic surveillance. Descriptive statistics were done using means and standard deviation, and odds ratio adjusted for potential confounding variables was calculated with SPSS 17 software. Forty-three out of 120 patients with moderate or severe manifestations following immunization were hospitalized from 2008 to 2011. All patients fulfilled at least 2 major and 1 minor criteria suggested by Shoenfeld and Agmon-Levin for ASIA diagnosis. The most frequent clinical findings were pyrexia 68%, arthralgias 47%, cutaneous disorders 33%, muscle weakness 16% and myalgias 14%. Three patients had diagnosis of Guillain-Barre syndrome, one patient had Adult-Still's disease 3 days after vaccination. A total of 76% of the events occurred in the first 3 days post-vaccination. Two patients with previous autoimmune disease showed severe adverse reactions with the reactivation of their illness. Minor local reactions were present in 49% of patients. Vaccines containing adjuvants may be associated with an increased risk of autoimmune/inflammatory adverse events following immunization."

Relative trends in hospitalizations and mortality among infants by the number of vaccine doses and age, based on the Vaccine Adverse Event Reporting System (VAERS), 1990–2010
Hum Exp Toxicol October 2012 vol. 31 no. 10 1012-1021
"Our findings show a positive correlation between the number of vaccine doses administered and the percentage of hospitalizations and deaths. Since vaccines are given to millions of infants annually, it is imperative that health authorities have scientific data from synergistic toxicity studies on all combinations of vaccines that infants might receive. Finding ways to increase vaccine safety should be the highest priority."

Association between Birth Order and Emergency Room Visits and Acute Hospital Admissions following Pediatric Vaccination: A Self-Controlled Study
PLoS ONE 8(12): e81070
"Birth order is associated with increased incidence of ER visits and hospitalizations following vaccination in infancy. 1st-born children had significantly higher relative incidence of events compared to later-born children."

Adverse Events Following 12 and 18 Month Vaccinations: A Population-Based, Self-Controlled Case Series Analysis
"Live vaccines have distinct safety profiles, potentially causing systemic reactions one to 2 weeks after administration. In the province of Ontario, Canada, live MMR vaccine is currently recommended at age 12 months and 18 months...  The primary reason for increased events was statistically significant elevations in emergency room visits following all vaccinations. There were non-significant increases in hospital admissions. There were an additional 20 febrile seizures for every 100,000 vaccinated at 12 months."

Common variants associated with general and MMR vaccine–related febrile seizures
Nature Genetics 46, 1274–1282 (2014)
"Febrile seizures represent a serious adverse event following measles, mumps and rubella (MMR) vaccination. We conducted a series of genome-wide association scans comparing children with MMR-related febrile seizures, children with febrile seizures unrelated to vaccination and controls with no history of febrile seizures. Two loci were distinctly associated with MMR-related febrile seizures, harboring the interferon-stimulated gene IFI44L (rs273259: P = 5.9 × 10−12 versus controls, P = 1.2 × 10−9 versus MMR-unrelated febrile seizures) and the measles virus receptorCD46 (rs1318653: P = 9.6 × 10−11 versus controls, P = 1.6 × 10−9 versus MMR-unrelated febrile seizures)."


Current Medicinal Chemistry, vol.18: 17 pp 2630-2637
"Experimental research, however, clearly shows that aluminum adjuvants have a potential to induce serious immunological disorders in humans. In particular, aluminum in adjuvant form carries a risk for autoimmunity, long-term brain inflammation and associated neurological complications and may thus have profound and widespread adverse health consequences. In our opinion, the possibility that vaccine benefits may have been overrated and the risk of potential adverse effects underestimated, has not been rigorously evaluated in the medical and scientific community."

Autoimmune hazards of hepatitis B vaccine
Autoimmun Rev. 2005 Feb;4(2):96-100
"According to Hippocratic tradition, the safety level of a preventive medicine must be very high, as it is aimed at protecting people against diseases that they may not contract. This paper points out that information on the safety of hepatitis B vaccine (HBV) is biased as compared to classical requirements of evidence-based medicine (EBM), as exemplified by a documented selectivity in the presentation or even publication of available clinical or epidemiological data. Then, a review is made of data suggesting that HBV is remarkable by the frequency, the severity and the variety of its complications, some of them probably related to a mechanism of molecular mimicry leading to demyelinating diseases, and the others reproducing the spectrum of non-hepatic manifestations of natural hepatitis B. To be explained, this unusual spectrum of toxicity requires additional investigations based upon complete release of available data."

Hepatitis B vaccine induces apoptotic death in Hepa1-6 cells.
Apoptosis. 2012 May;17(5):516-27
"Vaccines can have adverse side-effects, and these are predominantly associated with the inclusion of chemical additives such as aluminum hydroxide adjuvant. The objective of this study was to establish an in vitro model system amenable to mechanistic investigations of cytotoxicity induced by hepatitis B vaccine, and to investigate the mechanisms of vaccine-induced cell death. The mouse liver hepatoma cell line Hepa1-6 was treated with two doses of adjuvanted (aluminium hydroxide) hepatitis B vaccine... Hepatitis B vaccine exposure increased cell apoptosis as detected by flow cytometry and TUNEL assay. Vaccine exposure was accompanied by significant increases in the levels of activated caspase 3, a key effector caspase in the apoptosis cascade. We conclude that exposure of Hepa1-6 cells to a low dose of adjuvanted hepatitis B vaccine leads to loss of mitochondrial integrity, apoptosis induction, and cell death, apoptosis effect was observed also in C2C12 mouse myoblast cell line after treated with low dose of vaccine (0.3, 0.1, 0.05 μg/ml). In addition In vivo apoptotic effect of hepatitis B vaccine was observed in mouse liver."

Genetic Profile of an Oka Varicella Vaccine Virus Variant Isolated from an Infant with Zoster
J Clin Microbiol. 2004 Dec; 42(12): 5604–5608.
"Conceivably, genomic mutations or reversions to wild type, particularly those that confer amino acid substitutions, could affect virulence and restore wild-type pathogenicity. Furthermore, VZV strains with unique pathogenic qualities could emerge. The comparison of DNA sequences between V-Oka and P-Oka revealed 42 base substitutions associated with 20 amino acid changes. Specific amino acid substitutions in ORF 62 have been associated with enhanced virus growth and spread in cell culture, and substrains purified from the vaccine mixture display variable properties in cell culture"

Gardasil Vaccination: Evaluating the Risks Versus Benefits
Lucija Tomljenovic, PhD,Neural Dynamics Research Group, Dept. of Ophthalmology,
University ofBritish Columbia, 828 W. 10th Ave, Vancouver, BC. Jan 2011

"Cervical cancer is a rare disease in developed countries which invalidates the recommendations for universal immunization with any HPV vaccine. The incidence of cervical cancer has dropped substantially since implementation of regular Pap screening procedures. Currently, in the US, the death rate from cervical cancer(2.4/100,000 women)is lower than the rate of reported serious adverse events, including death,from Gardasil (3.34/100,000 doses distributed)"

Arch Dis Child doi:10.1136/archdischild-2011-300646
"Surprisingly, even though the children with the best nutritional status were vaccinated early, early DTP vaccination was associated with increased mortality for girls."

Elderly Subjects Have a Delayed Antibody Response and Prolonged Viraemia following Yellow Fever Vaccination: A Prospective Controlled Cohort Study
PLoS ONE 6(12): e27753
"We found that elderly subjects had a delayed antibody response and higher viraemia levels after yellow fever primovaccination. We postulate that with older age, a weaker immune response to yellow fever vaccine allows the attenuated virus to cause higher viraemia levels which may increase the risk of developing SAEs. This may be one piece in the puzzle of the pathophysiology of YEL-AVD."

VACCINE FAILURE

Chickenpox Outbreak in a Highly Vaccinated School Population
PEDIATRICS Vol. 113 No. 3 March 1, 2004 pp. 455 -459
"211 (97%) had been vaccinated before the outbreak. Twenty-one cases occurred in 9 of 16 classrooms. In these 9 classrooms, 18 of 152 (12%) vaccinated students developed chickenpox, compared with 3 of 7 (43%) unvaccinated students. Vaccine effectiveness was 72% (95% confidence interval: 3%–87%). Students vaccinated >5 years before the outbreak were 6.7 times (95% confidence interval: 2.2–22.9) as likely to develop breakthrough disease as those vaccinated ≤5 years before the outbreak (15 of 65 [23%] vs 3 of 87 [3%])."

The genetic basis for measles vaccine failure.
Acta Paediatr Suppl. 2004 May;93(445):43-6; discussion 46-7.
"The US measles epidemics of 1989-1991 included a series of outbreaks resulting from vaccine failure."

Hum Immunol. 2003 Jan;64(1):103-9.
"Despite the success of the current measles vaccine in controlling disease in industrialized countries, the importance of vaccine failure has become increasingly apparent."

The influence of the HLA-DRB1*13 allele on measles vaccine response.
J Investig Med. 1996 Jun;44(5):261-3."Measles remains a public health threat in the United States with over 50,000 cases being reported from 1989 through 1991 with continued smaller outbreaks. Measles vaccine failure is in part to blame for these large-scale outbreaks. "

Expert Rev Vaccines. 2013 Jan;12(1):57-70.
"The live-attenuated measles vaccine is effective, but measles outbreaks still occur in vaccinated populations."

FRAUD IN VACCINE SAFETY STUDIES

Indian J Med Ethics. 2014 Oct-Dec;11(4):218-22."In 2004, the US Center for Disease Control (CDC) published a paper showing that there is no link between the age at which a child is vaccinated with MMR and the vaccinated children's risk of a subsequent diagnosis of autism. One of the authors, William Thompson, has now revealed that statistically significant information was deliberately omitted from the paper. Thompson first told Dr S Hooker, a researcher on autism, about the manipulation of the data. Hooker analysed the raw data from the CDC study afresh. He confirmed that the risk of autism among African American children vaccinated before the age of 2 years was 340% that of those vaccinated later."

Methodological Issues and Evidence of Malfeasance in Research Purporting to Show Thimerosal in Vaccines Is Safe
BioMed Research International Volume 2014 (2014), Article ID 247218, 8 pages
"There are over 165 studies that have focused on Thimerosal, an organic-mercury (Hg) based compound, used as a preservative in many childhood vaccines, and found it to be harmful. Of these, 16 were conducted to specifically examine the effects of Thimerosal on human infants or children with reported outcomes of death; acrodynia; poisoning; allergic reaction; malformations; auto-immune reaction; Well’s syndrome; developmental delay; and neuro- developmental disorders, including tics, speech delay, language delay, attention deficit disorder, and autism. In contrast, the United States Centers for Disease Control and Prevention states that Thimerosal is safe and there is “no relationship between [T]himerosal[-]containing vaccines and autism rates in children.” This is puzzling because, in a study conducted directly by CDC epidemiologists, a 7.6-fold increased risk of autism from exposure to Thimerosal during infancy was found. The CDC’s current stance that Thimerosal is safe and that there is no relationship between Thimerosal and autism is based on six specific published epidemiological studies coauthored and sponsored by the CDC. The purpose of this review is to examine these six publications and analyze possible reasons why their published outcomes are so different from the results of investigations by multiple independent research groups over the past 75+ years."
For more discussion of this study, see this article.
VACCINE POLICY CAN HAVE UNINTENDED CONSEQUENCES

Indian J Med Ethics. 2012 Apr-Jun;9(2):114-7.
"It was hoped that following polio eradication, immunisation could be stopped. However the synthesis of polio virus in 2002, made eradication impossible. It is argued that getting poor countries to expend their scarce resources on an impossible dream over the last 10 years was unethical. Furthermore, while India has been polio-free for a year, there has been a huge increase in non-polio acute flaccid paralysis (NPAFP). In 2011, there were an extra 47,500 new cases of NPAFP. Clinically indistinguishable from polio paralysis but twice as deadly, the incidence of NPAFP was directly proportional to doses of oral polio received. Though this data was collected within the polio surveillance system, it was not investigated. The principle of primum-non-nocere was violated. The authors suggest that the huge bill of US$ 8 billion spent on the programme, is a small sum to pay if the world learns to be wary of such vertical programmes in the future."

N Engl J Med 2013; 369:1662-1663, correspondence
This is a series of letters to the editor regarding a study published in July of 2013, which presented evidence about the long term effectiveness of the 7-valent pneumococcal conjugate vaccine, in which concerns are raised about potentially dangerous unintended consequences of this vaccine.  "Griffin and colleagues (July 11 issue) report a reduction in the incidence of pneumonia after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). The authors address the concern regarding serotype replacement, whereby a vaccine-mediated reduction in the disease burden of Streptococcus pneumoniae PCV7 serotypes is offset by a proportional increase in nonvaccine serotypes. However, species replacement by other pathogens, particularly Staphylococcus aureus, is equally troubling."  A number of letters discuss this possibility and the evidence that it has occurred. 

Review of the United States universal varicella vaccination program: Herpes zoster incidence rates, cost-effectiveness, and vaccine efficacy based primarily on the Antelope Valley Varicella Active Surveillance Project data.
Vaccine. 2013 Mar 25;31(13):1680-94
"In the prelicensure era, 95% of adults experienced natural chickenpox (usually as children)-these cases were usually benign and resulted in long-term immunity. Varicella vaccination is less effective than the natural immunity that existed in prevaccine communities. Universal varicella vaccination has not proven to be cost-effective as increased HZ morbidity has disproportionately offset cost savings associated with reductions in varicella disease. Universal varicella vaccination has failed to provide long-term protection from VZV disease."

Infection with hepatitis B virus carrying novel pre-S/S gene mutations in female siblings vaccinated at birth: two case reports
Journal of Medical Case Reports 2010, 4:190
"Despite the success of mass vaccination, breakthrough of HBV infection was reported in vaccinees, resulting in acute or chronic hepatitis. The majority of HBV infections developed after immunization were caused by wild type viruses. However, up to 20 to 30 percent of breakthrough infections were proved to be caused by surface gene mutants, especially those with mutations located at the "a" determinant "

High incidence of treatment-induced and vaccine-escape hepatitis B virus mutants among human immunodeficiency virus/hepatitis B-infected patients
Hepatology. 2013 Sep;58(3):912-22
"Vaccine escape mutants selected by NA exposure were frequent and steadily increasing during follow-up. Although the high antiviral potency of TDF can mitigate incident mutations, other antiviral options are limited in this respect. The public health implications of their transmission need to be addressed."

INFLUENZA

Effectiveness of trivalent inactivated influenza vaccine in influenza-related hospitalization in children: a case controlled study
Allergy Asthma Proc 2012 Mar-April;33(2):e23-7
"TIV did not provide any protection against hospitalization in pediatric subjects, especially children with asthma. On the contrary, we found a threefold increased risk of hospitalization in subjects who did get the TIV vaccine. This may be a reflection not only of vaccine effectiveness but also the population of children who are more likely to get the vaccine."

Increased risk of non-influenza respiratory virus infections associated with receipt of inactivated influenza vaccine
Clin Infect Dis. (2012)
"We randomized 115 children to trivalent inactivated influenza vaccine (TIV) or placebo. Over the following 9 months, TIV recipients had increased risk of virologically-confirmed non-influenza infections (relative risk: 4.40; 95% confidence interval: 1.31-14.8). Being protected against influenza, TIV recipients may lack temporary non-specific immunity that protected against other respiratory viruses."  It is worth noting that the study found that "There was no statistically significant difference in the risk of confirmed seasonal influenza infection between recipients of TIV or placebo" and suggests that although there was no difference in influenza illness between the experimental and control groups, the experimental group did form antibodies, so that is considered "serological evidence".  So "success" of a vaccine is not based on whether it prevents the disease itself.


Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice
18 February 2014 mBio vol. 5no. 1 e01040-13
"Community interactions at mucosal surfaces between viruses, like influenza virus, and respiratory bacterial pathogens are important contributors toward pathogenesis of bacterial disease. What has not been considered is the natural extension of these interactions to live attenuated immunizations, and in particular, live attenuated influenza vaccines (LAIVs). Using a mouse-adapted LAIV against influenza A (H3N2) virus carrying the same mutations as the human FluMist vaccine, we find that LAIV vaccination reverses normal bacterial clearance from the nasopharynx and significantly increases bacterial carriage densities of the clinically important bacterial pathogens Streptococcus pneumoniae (serotypes 19F and 7F) and Staphylococcus aureus (strains Newman and Wright) within the upper respiratory tract of mice. Our findings are, to the best of our knowledge, the first to demonstrate that vaccination with a live attenuated viral vaccine can directly modulate colonizing dynamics of important and unrelated human bacterial pathogens, and does so in a manner highly analogous to that seen following wild-type virus infection."


An MIT researcher finds that "pandemic" flu not more deadly than the regular flu.

Influenza: marketing vaccine by marketing disease
BMJ 2013;346:f3037
"Closer examination of influenza vaccine policies shows that although proponents employ the rhetoric of science, the studies underlying the policy are often of low quality, and do not substantiate officials’ claims. The vaccine might be less beneficial and less safe than has been claimed, and the threat of influenza appears overstated."

Annual Childhood Flu Vaccines May Interfere with Development of Crossresistance
Journal of Virology, 2011; 85(22): 11995
"Vaccinating children annually against influenza virus interferes with their development of cross-reactive killer T cells to flu viruses generally, according to a new study. The research points up potentially conflicting policy outcomes. Annual flu vaccines are effective against seasonal flu, but could leave people more vulnerable to novel pandemics."

Effect of influenza vaccine on markers of inflammation and lipid profile.
J Lab Clin Med. 2005 Jun;145(6):323-7.
"Our findings show that the influenza vaccination causes transient changes in select markers of inflammation and lipids. Consequently, clinical and epidemiologic interpretation of the biomarkers affected should take into account the possible effects of influenza vaccination."

PLoS ONE 8(4): e56700
"Our study suggests the immune response to the 7.5 µg MF59-adjuvanted Focetria®H1N1pnd09 vaccine in pregnant women may be diminished compared with non-pregnant women."

Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated with Killed and Live Influenza Vaccines
PLoS ONE 7(11): e49941.
"Vaccine adverse events (VAEs) are adverse bodily changes occurring after vaccination. Understanding the adverse event (AE) profiles is a crucial step to identify serious AEs. Two different types of seasonal influenza vaccines have been used on the market: trivalent (killed) inactivated influenza vaccine (TIV) and trivalent live attenuated influenza vaccine (LAIV)... There were evidences of two severe adverse events (Guillain-Barre Syndrome and paralysis) present in TIV. Although these severe adverse events were at low incidence rate, they were found to be more significantly enriched in TIV-vaccinated patients than LAIV-vaccinated patients. Therefore, our novel combinatorial bioinformatics analysis discovered that LAIV had lower chance of inducing these two severe adverse events than TIV. In addition, our meta-analysis found that all previously reported positive correlation between GBS and influenza vaccine immunization were based on trivalent influenza vaccines instead of monovalent influenza vaccines."

PERTUSSIS

Bordetella pertussis Strains with Increased Toxin Production Associated with Pertussis Resurgence
Emerging Infectious Diseases Volume 15, Number 8—August 2009
"We present evidence that in the Netherlands the dramatic increase in pertussis is temporally associated with the emergence of Bordetella pertussis strains carrying a novel allele for the pertussis toxin promoter, which confers increased pertussis toxin (Ptx) production. Epidemiologic data suggest that these strains are more virulent in humans. We discuss changes in the ecology of B. pertussis that may have driven this adaptation. Our results underline the importance of Ptx in transmission, suggest that vaccination may select for increased virulence, and indicate ways to control pertussis more effectively."

Pertussis Infection in Fully Vaccinated Children In Day-Care Centers, Israel
Emerging Infectious Diseases, vol. 6 no. 5, October 2000
"We tested 46 fully vaccinated children in two day-care centers in Israel who were exposed to a fatal case of pertussis infection. Only two of five children who tested positive for Bordetella pertussis met the World Health Organization's case definition for pertussis. Vaccinated children may be asymptomatic reservoirs for infection."

Vaccination Against Whooping Cough- Efficacy vs Risks
(this is an older study, published in The Lancet in 1977, which showed little if any benefit from Pertussis vaccine and significant risks "The claim by official bodies that the risks of whooping-cough exceed those of vaccination is questionable")

Acellular pertussis vaccines protect against disease but fail to prevent infection and transmission in a nonhuman primate model
Proc Natl Acad Sci USA 2014 Jan 14;111(2):787-92
"The observation that aP, which induces an immune response mismatched to that induced by natural infection, fails to prevent colonization or transmission provides a plausible explanation for the resurgence of pertussis and suggests that optimal control of pertussis will require the development of improved vaccines."

Discussion of this study in Scientific American)
Effectiveness for Pertussis Vaccines For Adolescents and Adults: case control study
BMJ 2013;347:f4249
"Tdap vaccination was moderately effective at preventing PCR confirmed pertussis among adolescents and adults"

Unexpectedly Limited Durability of Immunity Following Acellular Pertussis Vaccination in Pre-Adolescents in a North American Outbreak
Clin Infect Dis. (2012) doi: 10.1093/cid/cis287
"This first detailed analysis of a recent North American pertussis outbreak found widespread disease among fully vaccinated older children. Starting approximately three years after prior vaccine dose, attack rates markedly increased, suggesting inadequate protection or durability from the acellular vaccine."

New Emerging Clones of Bordetella Pertussis Carrying prn2 and ptxP3 Alleles Implicated in Australian Pertussis Epidemic in 2008-2010
J Infect Dis. (2012) 
(This is evidence that vaccines contribute to resistant strains of pathogens the same way that antibiotics do).
"The data suggest increasing selection among the B. pertussis population in Australia in favor of strains carrying prn2 and ptxP3 under the pressure of acellular vaccine–induced immunity."

Decrease of Hospital Admissions for Febrile Seizures and Reports of Hypotonic-Hyporesponsive Episodes Presenting to Hospital Emergency Departments Since Switching to Acellular Pertussis Vaccine in Canada: a report from IMPACT
PEDIATRICS Vol. 112 No. 5 November 1, 2003 pp. e348 
"The risks of febrile seizures and HHEs after pertussis-containing vaccine declined significantly with the introduction of acellular pertussis vaccine in Canada. Active surveillance systems are important for detecting trends in uncommon adverse events after routine immunizations."

Imperfect vaccine-induced immunity and whooping cough transmission to infants
Vacccine 2010 Dec;29(1):11-16
"Whooping cough, caused by B. pertussis and B. parapertussis, has increased in incidence throughout much of the developed world since the 1980s despite high vaccine coverage... In addition, the data indicate that the B. pertussis vaccine is not protective against disease induced by B. parapertussis."

Acellular pertussis vaccination facilitates Bordetella parapertussis infection in a rodent model of Bordetellosis
Prco Biol Sci 2010 Jul 7;277(1690):2017-25
"Despite over 50 years of population-wide vaccination, whooping cough incidence is on the rise. Although Bordetella pertussis is considered the main causative agent of whooping cough in humans, Bordetella parapertussis infections are not uncommon. The widely used acellular whooping cough vaccines (aP) are comprised solely of B. pertussis antigens that hold little or no efficacy against B. parapertussis... We show that aP vaccination helped clear B. pertussis but resulted in an approximately 40-fold increase in B. parapertussis lung colony-forming units (CFUs)... Further, we show that aP vaccination impedes host immunity against B. parapertussis-measured as reduced lung inflammatory and neutrophil responses. Thus, we conclude that aP vaccination interferes with the optimal clearance of B. parapertussis and enhances the performance of this pathogen. Our data raise the possibility that widespread aP vaccination can create hosts more susceptible to B. parapertussis infection."
Discussion of these findings from the Center for Infectious Disease Dynamics

Neurological Complications of Pertussis Immunization
Br Med J. Jul 5, 1958; 2(5087): 24–27

POLIO

Mechanism of injury-provoked poliomyelitis.
J Virol. 1998 Jun;72(6):5056-60.
"Skeletal muscle injury is known to predispose its sufferers to neurological complications of concurrent poliovirus infections. This phenomenon, labeled "provocation poliomyelitis," continues to cause numerous cases of childhood paralysis due to the administration of unnecessary injections to children in areas where poliovirus is endemic. Recently, it has been reported that intramuscular injections may also increase the likelihood of vaccine-associated paralytic poliomyelitis in recipients of live attenuated poliovirus vaccines. We have studied this important risk factor for paralytic polio in an animal system for poliomyelitis and have determined the pathogenic mechanism linking intramuscular injections and provocation poliomyelitis. Skeletal muscle injury induces retrograde axonal transport of poliovirus and thereby facilitates viral invasion of the central nervous system and the progression of spinal cord damage. The pathogenic mechanism of provocation poliomyelitis may differ from that of polio acquired in the absence of predisposing factors."

SMALLPOX

Genetic Basis for Adverse Events Following Smallpox Vaccination
J Infect Dis. 2008 July 1; 198(1): 16–22.
"Genetic polymorphisms in an enzyme previously associated with adverse reactions to a variety of pharmacologic agents (MTHFR) and an immunological transcription factor (IRF1) were associated with AEs after smallpox vaccination in two independent study samples. These findings highlight common genetic variants with promising clinical significance that merit further investigation."

An emergent poxvirus from humans and cattle in Rio de Janeiro State: Cantagalo virus may derive from Brazilian smallpox vaccine
Virology. 2000 Nov 25;277(2):439-49.
"The biological properties of poxvirus isolates from skin lesions on dairy cows and milkers during recent "The biological properties of poxvirus isolates from skin lesions on dairy cows and milkers during recent exanthem episodes in Cantagalo County, Rio de Janeiro State, Brazil, were more like vaccinia virus (VV) than cowpox virus. PCR amplification of the hemagglutinin (HA) gene substantiated the isolate classification as an Old World orthopoxvirus, and alignment of the HA sequences with those of other orthopoxviruses indicated that all the isolates represented a single strain of VV, which we have designated Cantagalo virus (CTGV). HA sequences of the Brazilian smallpox vaccine strain (VV-IOC), used over 20 years ago, and CTGV showed 98.2% identity; phylogeny inference of CTGV, VV-IOC, and 12 VV strains placed VV-IOC and CTGV together in a distinct clade. Viral DNA restriction patterns and protein profiles showed a few differences between VV-IOC and CTGV. Together, the data suggested that CTGV may have derived from VV-IOC by persisting in an indigenous animal(s), accumulating polymorphisms, and now emerging in cattle and milkers as CTGV. CTGV may represent the first case of long-term persistence of vaccinia in the New World."

Smallpox and smallpox vaccination: neurological implications
Neurology. 2003 Apr 22;60(8):1241-5.
"Cutaneous complications of vaccination occur in immunosuppressed subjects and in those with atopic dermatitis. Among the most serious complications is postvaccinal encephalomyelitis (PVEM). A related condition, postvaccinial encephalopathy (PVE), may be seen in children less than two years of age. There are no markers to predict who will develop PVEM. In the past, mortality was high, ranging from 10 to 50%. The neuropathology of PVEM suggested an immune-mediated attack on the CNS, but the target of the immune response is unknown. Comprehensive programs are needed for surveillance and confirming case definitions for neurologic complications. Multi-institutional controlled trials of antiviral and immune modulating therapy of PVEM should be considered. Neurologists should be actively involved in the planning process for vaccination programs and in the treatment of neurologic complications."

Frequency of Adverse Events after Vaccination with Different Vaccinia Strains
PLoS Med 3(10): e429
"Previous analyses of smallpox vaccination policies, which rely on the commonly assumed value of one death per million vaccinations, may give serious underestimates of the number of deaths resulting from vaccination. Moreover, because there are large, strain-dependent differences in the frequency of adverse events due to smallpox vaccination, it is difficult to extrapolate from predictions for the NYCBH-derived vaccines (stockpiled in countries such as the US) to predictions for the Lister-derived vaccines (stockpiled in countries such as Germany). In planning for an effective response to a possible smallpox outbreak, public-health decision makers should reconsider their strategies of when to opt for ring vaccination and when to opt for mass vaccination."