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Some thoughts – written down by Anne S. De Groot but compiled from discussions with Lenny Moise, Tobias Cohen, Liz McClaine, Matt Ardito and Bill Martin at EpiVax.

The outbreak of a novel H1N1 influenza in the spring of 2009 took scientists, epidemiologists, immunologists and vaccinologists by surprise. What followed was a massive worldwide effort to produce millions of vaccine doses to protect against this single influenza strain. Significant delays in production, major disparities in the distribution of vaccine (between rich and poor nations) and the recall of some vaccines due to dosage inconsistencies hampered global response to the pandemic.

We have proposed an approach to vaccine design that would dramatically accelerate the protection of vulnerable populations, by eliciting broad cell-mediated immune responses against epitopes selected directly from the genome using an immunoinformatic approach. This approach could also be considered for other emergent infections or bioterror threats. The approach is based on the hypothesis that highly conserved T cell epitopes present in the secreted and surface antigens of pathogens are the most important proteins to target for protective (but not necessarily prophylactic) immunity. While sterile protection from infection is clearly the preferred effect of vaccination, control of disease following infection and more rapid clearance of the pathogen could be considered equally desirable outcomes, if large numbers of individuals no longer need to seek specialized medical care.

The concept that vaccines driving cell-mediated immunity might be protective, in the absence of sterile (humoral) immunity, is not as far-fetched as it may seem. Cell mediated immune response to protective T cell epitopes may have contributed to the surprising epidemiology of the recent influenza epidemic, which affected young adults more than older adults, who may have been protected due to prior exposure to similar vaccine strains [,].  Very little cross-protective antibody was seen, especially following vaccination with seasonal influenza strains, but nonetheless, individuals who might have been vaccinated or exposed to a prior H1N1, appeared to be less likely to be hospitalized [].

It is important to note that even in the absence of antibody responses, a cellular immune response has been shown to provide effective protective immunity in animal models [Epstein et al. original paper published in 1998 (); follow up study published this year: []. Both cross-reactive CTL and helper T cells have been identified by a number of investigators; cross-reactive T cell responses have already been demonstrated between circulating strains of influenza and epidemic strains (such as H5N1) in the absence of cross-reactive antibodies []. We postulated that cross-reactive T cell responses might also explain why 2009 H1N1 ran an inverted course – sparing older people, who were less ill with H1N1 but also – if the hypothesis is correct – making them the main reservoirs of transmissible infection, rather than children as is usually the case.

We recently tested this hypothesis, by identifying highly conserved HA and NA T cell epitopes that were shared among circulating, seasonal H1N1 strains and the conventional trivalent influenza vaccine (TIV). We (1) identified cross-conserved influenza class II epitopes contained within the peptide array of influenza virus A/California/04/09 (H1N1) hemagglutinin protein (BEI Number NR-15433) using in silico analysis. We then (2) validated candidate epitopes for their ability to bind relevant HLA molecules by examining publication records in IEDB and by performing HLA competition binding assays.

We found greater than 50% conservation of T helper and CTL epitopes between novel H1N1 influenza and conventional influenza vaccine HA for selected HLA. Conservation was lower among NA epitopes. Sixteen promiscuous helper T-cell epitopes were contained in the pandemic H1N1 HA sequence, of which nine (56%) were 100% conserved in the 2008-2009 influenza vaccine strain; 81% were either identical or had one conservative amino acid substitution. Fifty percent of predicted CTL epitopes found in pandemic H1N1 HA were also found in seasonal HA sequences []. The value of the seasonal flu vaccine or live-attenuated influenza vaccine containing the 2008-2009 vaccine strains, as defense against H1N1, is being further tested in our laboratory by evaluating human immune responses to the conserved T-cell epitopes using PBMC from individuals infected with H1N1 and from seasonal flu vaccinees.

As it turns out, this contrarian theory was supported by an important case study from Mexico, which showed that adults who had prior TIV were less likely to fall ill with H1N1. While their T cell response (in the absence of a cross-reactive humoral immune response) may not have provided complete protection against novel H1N1 infection, the severity of the illness appears to have been reduced, leading to a lower hospitalization rate compared to unvaccinated adults in the same older age groups. TIV vaccination effectiveness against laboratory confirmed cases of influenza A/H1N1 was 73% (95% confidence interval 34% to 89%) []. These epitopes may have contributed to protection against symptomatic influenza in older subjects, accounting for the unusual age distribution of pandemic H1N1 influenza.

As we observed for influenza, conserved pathogen sequences, which are important to viral fitness, may also be of value for vaccine development, in that they may contribute to protection from serious disease. Thus – vaccines based on cell mediated immune responses, not humoral immunity, may reduce morbidity while also reducing the impact of pandemics and bioterror threats on hospitals and medical personnel. This approach promises to address the need for prompt preparedness and delivery of a safe and efficacious vaccines while accelerating the timeframe of response to virulent, emergent, or bioterror-induced infectious disease.


Hancock K, Veguilla V, Lu X, et al. Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus. N Engl J Med 2009;361. DOI: 10.1056/NEJMoa0906453.

Centers for Disease Control and Prevention. Serum antibody response to a novel influenza A (H1N1) virus after vaccination with seasonal influenza vaccine. MMWR Morb Mortal Wkly Rep 2009;58(19):521-4.

Jain S, Kamimoto L, Bramley AM, Schmitz AM, Benoit SR, Louie J, Sugerman DE, Druckenmiller JK, Ritger KA, Chugh R, Jasuja S, Deutscher M, Chen S, Walker JD, Duchin JS, Lett S, Soliva S, Wells EV, Swerdlow D, Uyeki TM, Fiore AE, Olsen SJ, Fry AM, Bridges CB, Finelli L; the 2009 Pandemic Influenza A (H1N1) Virus Hospitalizations Investigation Team. Hospitalized Patients with 2009 H1N1 Influenza in the United States, April-June 2009.N Engl J Med. 2009 Oct 8.

Epstein SL, Lo CY, Misplon JA, Bennink JR. Mechanism of protective immunity against influenza virus infection in mice without antibodies. J Immunol. 1998 Jan 1;160(1):322-7.

Price GE, Soboleski MR, Lo CY, Misplon JA, Pappas C, Houser KV, Tumpey TM, Epstein SL. Vaccination focusing immunity on conserved antigens protects mice and ferrets against virulent H1N1 and H5N1 influenza A viruses. Vaccine. 2009 Sep 1.

Lee LY, et al. Memory T cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. J Clin Invest. 2008;118:3478-89

De Groot AS,  Ardito M. McClaine E.  Moise, L. Martinb W. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-09 Conventional Influenza Vaccine. Vaccine. 2009 Sep 25;27(42):5740-7.

Domínguez-Cherit G, Lapinsky SE, Macias AE, Pinto R, Espinosa-Perez L, de la Torre A, Poblano-Morales M, Baltazar-Torres JA, Bautista E, Martinez A, Martinez MA, Rivero E, Valdez R, Ruiz-Palacios G, Hernández M, Stewart TE, Fowler RA.Critically Ill Patients With 2009 Influenza A(H1N1) in Mexico. JAMA. 2009 Oct 12. Published on line ahead of print. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758337/?tool=pubmed