Thursday, February 19, 2015

Genotypes, Serotypes and the MMR: Cognitive Dissonance in Action

Many of those who have bought into the anti-vaccine message seem to hold very tightly to their chosen belief. The more emotionally invested they are, the more likely they will go to great lengths to justify or rationalize their position. True, this is not unique to anti-vaccine activists or those closely associated with them, but it quite commonly dictates their reaction to evidence that challenges their beliefs. Evidence that contradicts their worldview, causing cognitive dissonance, leads to different mechanisms to cope with the psychological discomfort that results. The less entrenched individuals may look at the evidence, accept it as valid, and change their prior beliefs to fit with the new evidence. Some may simply ignore the evidence and pretend it doesn't even exist (e.g., "vaccine have never been studied for safety" despite numerous studies doing exactly that). But more commonly, they will invent rationalizations to explain away the contradicting.

The most recent example of this is the current outbreak of measles that started at Disneyland in California, and to a lesser extent last year's historic case count (644 cases) that hasn't been seen in the past 20 years and surpassed the number of measles cases from the previous five years combined. The Disney outbreak has resulted in 125 cases (through February 8) in just over one month (141 cases in two outbreaks as of February 13) resulting in 17 known hospitalizations. The majority (88%) of cases were either unvaccinated (45% of the total) or had unknown or undocumented vaccination status (43% of the total). The unvaccinated have been a significant contributor to the size of this outbreak and the speed with which it has spread. And the media has taken notice, with the majority of outlets putting the blame right where it belongs: on the anti-vaccine movement.

So how have anti-vaccine types responded?

Early reactions largely consisted of denials that the unvaccinated were spreading the virus. Instead, anti-vaccine activists pointed to the small number of individuals who had received at least one measles vaccine as if it were evidence that the vaccine doesn't work at all. However, they aren't considering the mathematics involved. If the vaccine really did not work at all, as they argue, then we would be seeing significantly more cases than we have, considering that measles will infect and cause disease in about 90% of those who are exposed and who have never been infected or immunized previously. The math just doesn't work out to support this anti-vaccine trope.

Rather than accept the evidence, their argument next shifts to blaming the vaccinated for spreading the disease. This is based on the fact that the MMR is a live attenuated viral vaccine. That means that the viruses contained in the vaccine are weakened so that they cannot cause a full-blown infection but still provide immunity if exposed to the wild virus. As a "live" vaccine, it is hypothetically possible that a person receiving it could develop measles (e.g., if they had a compromised immune system) and pass it along to someone else. However, in the decades of measles vaccination, with billions of doses given, there have been no cases of a vaccinated individual shedding the vaccine virus and causing illness in others. Again, the math does not hold up. Even if 1 out of every 100,000 MMR recipients spread measles to others, we would not only see far more cases of the disease than we currently do, but they would be the same genotype as the vaccine (more on this in a moment), rather than a wild-type genotype.

Despite this, anti-vaccine activists have argued that we don't know whether the virus causing the current outbreak is the vaccine strain or not. Therefore, they conclude, we can't rule out the possibility that it's not the vaccine that's causing the problems. Unfortunately for any anti-vaccine activists who use this argument, they're wrong. Genetic sequencing of viral samples from cases in the Disneyland measles outbreak reveals that the strain that is circulating belongs to the B3 genotype, while the vaccine strain is the A genotype (h/t to Science Mom at Just the Vax).

Denying that the unvaccinated are significantly contributing to this outbreak is refuted by the evidence. Claiming that the vaccine doesn't work fails based simply on the mathematics involved. The evidence does not support the claim that the vaccinated are spreading the disease via viral shedding. Likewise, the claim that we do not know whether the outbreak is a vaccine strain or wild type crumbles under known facts. What else could an anti-vaccine activist do to try to justify their belief that vaccines are bad?

Invent a new explanation, of course. Rather than accept that their belief is wrong, anti-vaccine activists and those who have fallen for their misinformation now accept that the outbreak is caused by a wild-type strain of measles, but use this fact to support their belief that, in fact, the vaccine doesn't work because the vaccine only contains measles genotype A (see, for example, comments at Age of Autism). If their argument were correct, we would be seeing many more cases of measles than just the 125 so far this year (not to mention significantly more cases in all of the other outbreaks in the post-vaccine era). There would be hundreds by now, with the prospect of tens of thousands of cases by the end of the year. Not only that, but this new argument weakens another anti-vaccine trope: that natural immunity is better. If exposure to one genotype of measles only protects against that genotype, but leaves the patient susceptible to different genotypes, the natural infection would not grant lifelong immunity to measles, since you could always be infected with a different strain.

But let's get back to the whole issue of genotypes and why the difference between the vaccine A genotype and the wild B3 genotype from the California outbreak doesn't mean that the vaccine is ineffective. This is going to involve getting into some of the science behind viruses and the immune system, which is pretty complex stuff. I welcome any virologists or immunologists to correct any errors I make or to clarify any points that I don't explain quite thoroughly.

It may help to start by getting some terminology out of the way. First off, what exactly is a genotype? A genotype is essentially the genetic makeup of a virus/bacterium, cell, or organism. For measles, there are 24 different genotypes (PDF): A, B1, B2, B3, C1, C2, D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, E, F, G1, G2, G3, H1, and H2. Of those, six (B1, C1, D1, E, F, and G1) have not been detected anywhere in the world within the last 15 years and are considered inactive. Five others (D2, D3, D10, G2, and H2) have not been detected since 2006, suggesting that they, too may be inactive. Which genotype a particular samples falls into is determined by the genetic makeup of the H and N genes. Yet despite all these different genotypes, there is only a single serotype of measles.

What's a serotype? The serotype of a virus describes the collection of surface antigens or proteins that are targeted by the immune system. If a virus has multiple serotypes, the antigens on one serotype are different than the antigens on another serotype, meaning that immunity to one most likely will not provide immunity to the others. For example, there are four serotypes of dengue virus. If you're infected with one and recover, you'll be immune to that serotype, but immunity to the other three serotypes will be, at best, partial and temporary. Some viruses, like rhinoviruses (one cause of the common cold), have over a hundred different serotypes. This is one reason why even though you might catch a cold in October, you could still catch another one in November. Other viruses, like measles, have only one serotype.

Finally, we should define epitopes. Epitopes are the parts of the surface antigens that are recognized by immune cells. You can think of them as bolt heads, where the size and shape determines whether or not an antibody can grab onto it. The amount of genetic similarity between epitopes of two viral samples determines whether they are part of the same serotype or not. If the epitopes of two viral samples are very different from each other, then the samples may be from different serotypes, and immunity to one would not guarantee immunity to the other.

How does all of this factor into measles immunity, vaccines and wild-type infection? We know that the measles virus uses two main proteins to infect host cells: hemagglutinin protein (H) allows the virus to bind to host cells, while the fusion protein (F) allows it to fuse into the host cell, after which it can start inserting viral RNA. Antibodies to these two proteins neutralize infection, with ~90% targeting the H protein and the remainder targeting the F protein.

We also know from genetic analyses that the epitopes of the H protein are highly conserved across the genotypes, and that the F protein is more conserved than the H protein. [Edited to Add 6/8/15: This Week in Virology (great podcast about viruses) recently discussed a new paper that hints at why these proteins are so stable. Mutations to the genes coding for the H and F proteins render the virus non-viable.] This means that when you are exposed to one genotype, the antibodies you produce are able to recognize all of the genotypes pretty much equally. So whether you get vaccinated with genotype A or are infected by genotype B3, your body is able to recognize and mount a robust defense against not only strains of the same genotype, but all of the other genotypes, as well. This is also confirmed by experiments using serum samples from vaccinated individuals to see if they neutralize wild-type genotypes. The serum from the individuals contains antibodies that they generated in response to the vaccine. When wild-type genotypes are exposed to these antibodies, they are neutralized, showing that the vaccine works, even though the vaccine strain is from a different genotype.

Of course, mutation does occur, but it seems to happen rather slowly for measles. For example, in a 6-month-long outbreak of measles in Spain, samples were taken from the index case and others throughout the duration of the outbreak. The F gene from all of the samples matched the index case, and the H protein ranged from 0% divergence at the beginning of the outbreak to a maximum of 0.38% at the end of the outbreak. However, the longer an outbreak goes on, the more times the virus undergoes replication and the greater the chance that the virus will mutate to escape immunity (either vaccine- or infection-induced). Stopping outbreaks quickly (or preventing them altogether), then, lowers the risk of viral mutation.

In the end, all of the available evidence shows that the antibodies produced against one genotype of measles protect against all of the other genotypes, as well. Even though the vaccine only contains genotype A, the antibodies you produce as a result of being immunized will protect you from infection by, for example, the B3 genotype in the California measles outbreak. Although anti-vaccine activists are now claiming that the vaccine doesn't work because the genotype in the vaccine is different than the wild virus in the outbreak, the evidence shows that they are wrong. Rather than accepting their errors and admitting their mistake, they invent new explanation to defend their ideology. Their claim is simply another in a long line of failed rationalizations to support their belief that vaccines are bad. It's nothing more than cognitive dissonance on display.

For another perspective on this, see Just the Vax (The Measles Vaccines (MMR and MMRV) Protect Against Measles) and The Scientific Parent (How I Accidentally Startedan Anti-Vax Myth in the Name of Science). 
Selected References and Additional Reading:
  • Bankamp B, Takeda M, Zhang Y, Xu W, & Rota PA. (2011) Genetic characterization of measles vaccine strains. The Journal of Infectious Diseases, 204 Suppl 1, S533-S548. PMID: 21666210. Accessed online February 16, 2015 at 
  • Bellini WJ, Rota JS, & Rota PA. (1994) Virology of measles virus. The Journal of Infectious Diseases, 170 Suppl 1, S15-S23. PMID: 7930749. Accessed online February 15, 2015 at 
  • Bellini WJ & Rota PA. (2011) Biological feasibility of measles eradication. Virus Research, 162(1-2), 72-79. PMID: 21963661. Accessed online February 15, 2015 at 
  • Chang A & Dutch RE. (2012) Paramyxovirus fusion and entry: multiple paths to a common end. Viruses, 4(4), 613-636. PMID: 22590688. Accessed online February 16, 2015 at 
  • de Swart RL, Yüksel S, & Osterhaus AD. (2005) Relative contributions of measles virus hemagglutinin- and fusion protein-specific serum antibodies to virus neutralization. Journal of Virology, 79(17), 11547-11551. PMID: 16103210. Accessed online February 16, 2015 at 
  • Haddad-Boubaker S, Rezq M, Smeo MN, Ben Yahia A, Abudher A, Slim A, Ben Ghorbel M, Ahmed H, Rota P, & Triki H. (2010) Genetic characterization of clade B measles viruses isolated in Tunisia and Libya 2002–2009 and a proposed new subtype within the B3 genotype. Virus Research, 153(2), 258-264. PMID: 20728482. Accessed online February 15, 2015 at 
  • Hoang V, Tripp RA, Rota P, & Dluhy RA. (2010) Identification of individual genotypes of measles virus using surface enhanced Raman spectroscopy. The Analyst, 135(12), 3103-3109. PMID: 20838669. Accessed online February 15, 2015 at 
  • Kühne M, Brown DW, & Jin L. (2006) Genetic variability of measles virus in acute and persistent infections. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 6(4), 269-276. PMID: 16172023. Accessed online February 15, 2015 at 
  • Lech PJ, Tobin GJ, Bushnell R, Gutschenritter E, Pham LD, Nace R, Verhoeven E, Cosset FL, Muller CP, Russell SJ, & Nara PL. (2013) Epitope dampening monotypic measles virus hemagglutinin glycoprotein results in resistance to cocktail of monoclonal antibodies. PLoS One, 8(1). PMID: 23300970. Accessed online February 15, 2015 at 
  • Ledford RM, Patel NR, Demenczuk TM, Watanyar A, Herbertz T, Collett MS, & Pevear DC. (2004) VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. Journal of Virology, 78(7), 3663-3674. PMID: 15016887. Accessed online February 18, 2015 at 
  • Liffick SL, Thi Thoung N, Xu W, Li Y, Phoung Lien H, Bellini WJ, Rota PA. (2001) Genetic characterization of contemporary wild-type measles viruses from Vietnam and the People's Republic of China: identification of two genotypes within clade H. Virus Research, 77(1), 81-87. PMID: 11451490. Accessed online February 15, 2015 at 
  • Morita Y, Suzuki T, Shiono M, Shiobara M, Saitoh M, Tsukagoshi H, Yoshizumi M, Ishioka T, Kato M, Kozawa K, Ttanaka-Taya K, Yasui Y, Noda M, Okabe N, & Kimura H. (2007) Sequence and phylogenetic analysis of the nucleoprotein (N) gene in measles viruses prevalent in Gunma, Japan, in 2007. Japanese Journal of Infectious Diseases, 60(6), 402-404. PMID: 18032846. Accessed online February 15, 2015 at 
  • Muller CP, Handtmann D, Brons NH, Weinmann M, Wiesmüller KH, Spahn G, Wiesneth M, Schneider F, & Jung G. (1993) Analysis of antibody response to the measles virus using synthetic peptides of the fusion protein. Evidence of non-random pairing of T and B cell epitopes. Virus Research, 30(3), 271-280. PMID: 8109160. Accessed online February 16, 2015 at 
  • Muñoz-Alía MÁ, Fernández-Muñoz R, Casasnovas JM, Porras-Mansilla R, Serrano-Pardo Á, Pagán I, Ordobás M, Ramírez R, & Celma ML. (2015) Measles virus genetic evolution throughout an imported epidemic outbreak in a highly vaccinated population. Virus Research, 196, 122-127. PMID: 25445338. Accessed online February 15, 2015 at 
  • Muwonge A, Nanyunja M, Rota PA, Bwogi J, Lowe L, Liffick SL, Bellini WJ, & Sylvester S. (2005) New measles genotype, Uganda. Emerging Infectious Diseases, 11(10), 1522-1526. PMID: 16318690. Accessed online February 15, 2015 at 
  • Navaratnarajah CK, Miest TS, Carfi A, & Cattaneo R. (2012) Targeted entry of enveloped viruses: measles and herpes simplex virus I. Current Opinion in Virology, 2(1), 43-49. PMID: 22440965. Accessed online February 16, 2015 at 
  • Rota PA, Brown K, Mankertz A, Santibanez S, Shulga S, Muller CP, Hübschen JM, Siqueira M, Beirnes J, Ahmed H, Triki H, Al-Busaidy S, Dosseh A, Byabamazima C, Smit S, Akoua-Koffi C, Bwogi J, Bukenya H, Wairagkar N, Ramamurty N, Incomserb P, Pattamadilok S, Jee Y, Lim W, Xu W, Komase K, Takeda M, Tran T, Castillo-Solorzano C, Chenoweth P, Brown D, Mulders MN, Bellini WJ, & Featherstone D. (2011) Global distribution of measles genotypes and measles molecular epidemiology. The Journal of Infectious Diseases, 204 Suppl 1, S514-S523. PMID: 21666208. Accessed online February 15, 2015 at 
  • Santak M, Baricevic M, Mazuran R, & Forcic D. (2007) Intra- and intergenotype characterization of D6 measles virus genotype. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 7(5), 645-650. PMID: 17499028. Accessed online February 16, 2015 at 
  • Shakya AK, Shukla V, Maan HS, & Dhole TN. (2012) Identification of different lineages of measles virus strains circulating in Uttar Pradesh, North India. Virology Journal, 9, 237. PMID: 23072489. Accessed online February 15, 2015 at 
  • Shi J, Zheng J, Huang H, Hu Y, Bian J, Xu D, & Li F. (2011) Measles incidence rate and a phylogenetic study of contemporary genotype H1 measles strains in China: is an improved measles vaccine needed?. Virus Genes, 43(3), 319-326. PMID: 21701857. Accessed online February 15, 2015 at 
  • Tahara M, Ito Y, Brindley MA, Ma X, He J, Xu S, Fukuhara H, Sakai K, Komase K, Rota PA, Plemper RK, Maenaka K, & Takeda M. (2013) Functional and structural characterization of neutralizing epitopes of measles virus hemagglutinin protein. Journal of Virology, 87(1), 666-675. PMID: 23115278. Accessed online February 15, 2015 at 
  • World Health Organization. (2012) Measles virus nomenclature update: 2012. Weekly epidemiological record, 87(9), 73-80. Accessed online February 17, 2015 at (PDF)

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