A Computational Framework for Influenza Antigenic Cartography

Influenza viruses have been responsible for large losses of lives around the world and continue to present a great public health challenge. Antigenic characterization based on hemagglutination inhibition (HI) assay is one of the routine procedures for influenza vaccine strain selection. However, HI assay is only a crude experiment reflecting the antigenic correlations among testing antigens (viruses) and reference antisera (antibodies). Moreover, antigenic characterization is usually based on more than one HI dataset. The combination of multiple datasets results in an incomplete HI matrix with many unobserved entries. This paper proposes a new computational framework for constructing an influenza antigenic cartography from this incomplete matrix, which we refer to as Matrix Completion-Multidimensional Scaling (MC-MDS). In this approach, we first reconstruct the HI matrices with viruses and antibodies using low-rank matrix completion, and then generate the two-dimensional antigenic cartography using multidimensional scaling. Moreover, for influenza HI tables with herd immunity effect (such as those from Human influenza viruses), we propose a temporal model to reduce the inherent temporal bias of HI tables caused by herd immunity. By applying our method in HI datasets containing H3N2 influenza A viruses isolated from 1968 to 2003, we identified eleven clusters of antigenic variants, representing all major antigenic drift events in these 36 years. Our results showed that both the completed HI matrix and the antigenic cartography obtained via MC-MDS are useful in identifying influenza antigenic variants and thus can be used to facilitate influenza vaccine strain selection. The webserver is available at http://sysbio.cvm.msstate.edu/AntigenMap

Antigenic Characterization of H3 Subtypes of Avian Influenza A Viruses from North America

Besides humans, H3 subtypes of influenza A viruses (IAVs) can infect various animal hosts, including avian, swine, equine, canine, and sea mammal species. These H3 viruses are both antigenically and genetically diverse. Here, we characterized the antigenic diversity of contemporary H3 avian IAVs recovered from migratory birds in North America. Hemagglutination inhibition (HI) assays were performed on 37 H3 isolates of avian IAVs recovered from 2007 to 2011 using generated reference chicken sera. These isolates were recovered from samples taken in the Atlantic, Mississippi, Central, and Pacific waterfowl migration flyways. Antisera to all the tested H3 isolates cross-reacted with each other and, to a lesser extent, with those to H3 canine and H3 equine IAVs. Antigenic cartography showed that the largest antigenic distance among the 37 avian IAVs is about four units, and each unit corresponds to a 2 log 2 difference in the HI titer. However, none of the tested H3 IAVs cross-reacted with ferret sera derived from contemporary swine and human IAVs. Our results showed that the H3 avian IAVs we tested lacked significant antigenic diversity, and these viruses were antigenically different from those circulating in swine and human populations. This suggests that H3 avian IAVs in North American waterfowl are antigenically relatively stable. Además de infectar a los seres humanos, los subtipos H3 del virus de la influenza A (IAVs) pueden infectar a varios huéspedes animales, incluyendo aves, porcinos, equinos, caninos, y especies de mamíferos marinos. Estos virus H3 son tanto antigénica y genéticamente diversos. En este estudio, se caracterizó la diversidad antigénica de virus H3 contemporáneos recuperados de aves migratorias en América del Norte. Se realizaron pruebas de inhibición de la hemaglutinación (HI) en 37 H3 aislamientos de origen aviar recuperados de 2007 a 2011 usando sueros de pollo de referencia. Estos aislamientos fueron recuperados de las muestras tomadas de las rutas migratorias de aves acuáticas del Atlántico, Mississippi, Centro y del Pacífico. Los antisueros de todos los aislamientos H3 analizados mostraron reacciones cruzadas entre sí y en menor medida, con aquellos virus H3 de origen canino y equino. La cartografía antigénica demostró que la mayor distancia antigénica entre los 37 virus de este tipo de aves es de aproximadamente cuatro unidades, y cada unidad corresponde a una diferencia de dos logaritmos en el título de inhibición de la hemaglutinación. Sin embargo, ninguno de los virus H3 de este tipo mostró reacción cruzada con sueros de hurón específicos para virus de cerdos y humanos contemporáneos. Estos resultados mostraron que los virus H3 de origen aviar que se analizaron carecían de diversidad antigénica significativa y estos virus fueron antigénicamente diferentes de las que circulan en poblaciones de cerdos y de humanos. Esto sugiere que los virus H3 de aves acuáticas de América del Norte son relativamente estables antigénicamente

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

Distinguishing mutations that determine an organism's phenotype from (near-) neutral ‘hitchhikers’ is a fundamental challenge in genome research, and is relevant for numerous medical and biotechnological applications. For human influenza viruses, recognizing changes in the antigenic phenotype and a strains' capability to evade pre-existing host immunity is important for the production of efficient vaccines. We have developed a method for inferring ‘antigenic trees’ for the major viral surface protein hemagglutinin. In the antigenic tree, antigenic weights are assigned to all tree branches, which allows us to resolve the antigenic impact of the associated amino acid changes. Our technique predicted antigenic distances with comparable accuracy to antigenic cartography. Additionally, it identified both known and novel sites, and amino acid changes with antigenic impact in the evolution of influenza A (H3N2) viruses from 1968 to 2003. The technique can also be applied for inference of ‘phenotype trees’ and genotype–phenotype relationships from other types of pairwise phenotype distances

Integrating influenza antigenic dynamics with molecular evolution.

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001

Predicting Influenza Antigenicity by Matrix Completion With Antigen and Antiserum Similarity

The rapid mutation of influenza viruses especially on the two surface proteins hemagglutinin (HA) and neuraminidase (NA) has made them capable to escape from population immunity, which has become a key challenge for influenza vaccine design. Thus, it is crucial to predict influenza antigenic evolution and identify new antigenic variants in a timely manner. However, traditional experimental methods like hemagglutination inhibition (HI) assay to select vaccine strains are time and labor-intensive, while popular computational methods are less sensitive, which presents the need for more accurate algorithms. In this study, we have proposed a novel low-rank matrix completion model MCAAS to infer antigenic distances between antigens and antisera based on partially revealed antigenic distances, virus similarity based on HA protein sequences, and vaccine similarity based on vaccine strains. The model exploits the correlations of viruses and vaccines in serological tests as well as the ability of HAs from viruses and vaccine strains in inferring influenza antigenicity. We also compared the effects of comprehensive 65 amino acids substitution matrices in predicting influenza antigenicity. As a result, we applied MCAAS into H3N2 seasonal influenza virus data. Our model achieved a 10-fold cross validation root-mean-squared error (RMSE) of 0.5982, significantly outperformed existing computational methods like antigenic cartography, AntigenMap and BMCSI. We also constructed the antigenic map and studied the association between genetic and antigenic evolution of H3N2 influenza viruses. Finally, our analyses showed that homologous structure derived amino acid substitution matrix (HSDM) is most powerful in predicting influenza antigenicity, which is consistent with previous studies

Analyzing the Human Serum Antibody Responses to a Live Attenuated Tetravalent Dengue Vaccine Candidate

BACKGROUND: Dengue virus serotypes 1-4 (DENV-1-4) are the most common vector-borne viral pathogens of humans and the etiological agents of dengue fever and dengue hemorrhagic syndrome. A live-attenuated tetravalent dengue vaccine (TDV) developed by Takeda Vaccines has recently progressed to phase 3 safety and efficacy evaluation. METHODS: We analyzed the qualitative features of the neutralizing antibody (nAb) response induced in naive and DENV-immune individuals after TDV administration. Using DENV-specific human monoclonal antibodies (mAbs) and recombinant DENV displaying different serotype-specific Ab epitopes, we mapped the specificity of TDV-induced nAbs against DENV-1-3. RESULTS: Nearly all subjects had high levels of DENV-2-specific nAbs directed to epitopes centered on domain III of the envelope protein. In some individuals, the vaccine induced nAbs that tracked with a DENV-1-specific neutralizing epitope centered on domain I of the envelope protein. The vaccine induced binding Abs directed to a DENV-3 type-specific neutralizing epitope, but findings of mapping of DENV-3 type-specific nAbs were inconclusive. CONCLUSION: Here we provide qualitative measures of the magnitude and epitope specificity of the nAb responses to TDV. This information will be useful for understanding the performance of TDV in clinical trials and for identifying correlates of protective immunity

Limited Antigenic Diversity in Contemporary H7 Avian-Origin Influenza A Viruses from North America

Subtype H7 avian–origin influenza A viruses (AIVs) have caused at least 500 confirmed human infections since 2003 and culling of \u3e75 million birds in recent years. Here we antigenically and genetically characterized 93 AIV isolates from North America (85 from migratory waterfowl [1976–2010], 7 from domestic poultry [1971–2012], and 1 from a seal [1980]). The hemagglutinin gene of these H7 viruses are separated from those from Eurasia. Gradual accumulation of nucleotide and amino acid substitutions was observed in the hemagglutinin of H7 AIVs from waterfowl and domestic poultry. Genotype characterization suggested that H7 AIVs in wild birds form diverse and transient internal gene constellations. Serologic analyses showed that the 93 isolates cross-reacted with each other to different extents. Antigenic cartography showed that the average antigenic distance among them was 1.14 units (standard deviation [SD], 0.57 unit) and that antigenic diversity among the H7 isolates we tested was limited. Our results suggest that the continuous genetic evolution has not led to significant antigenic diversity for H7 AIVs from North America. These findings add to our understanding of the natural history of IAVs and will inform public health decision-making regarding the threat these viruses pose to humans and poultry

The contrasting phylodynamics of human influenza B viruses

A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.Dhanasekaran Vijaykrishna, Edward C Holmes, Udayan Joseph, Mathieu Fourment, Yvonne CF Su, Rebecca Halpin, Raphael TC Lee, Yi-Mo Deng, Vithiagaran Gunalan, Xudong Lin, Timothy B Stockwell, Nadia B Fedorova, Bin Zhou, Natalie Spirason, Denise Kühnert, Veronika Bošková, Tanja Stadler, Anna-Maria Costa, Dominic E Dwyer, Q Sue Huang, Lance C Jennings, William Rawlinson, Sheena G Sullivan, Aeron C Hurt, Sebastian Maurer-Stroh, David E Wentworth, Gavin JD Smith, Ian G Bar

The Impact of Receptor Binding Avidity and Immune History on the Antigenic Determination of Influenza A Viruses

Most humans are repeatedly infected with new strains of influenza throughout their lifetime even though protective neutralizing antibodies against the viral hemagglutinin (HA) are generated after both natural infection and vaccination. This observed lack of protection against variant strains is largely attributed to a process termed `antigenic drift\u27, where accumulating mutations in HA quickly abrogate recognition by antibodies elicited by earlier strains. Consequently, current influenza vaccines must be updated frequently in an attempt to match the antigenic profiles of vaccine strains to those of circulating strains. However, the existing process of antigenic determination is imperfect: it fails to consider the effects of receptor binding avidity in the interpretation of hemagglutination inhibition (HAI) assays or the effects of pre-exposure history on how a novel virus is viewed antigenically by an altered immune system. Here, we designed a series of experiments to address these issues. First, we computationally modeled how variation in receptor binding avidity could affect the antigenic characterization of historic H3N2 strains and experimentally demonstrated that single point mutations in HA can skew HAI titers without actually affecting antibody binding. Additionally, using the same H3N2 system, we showed that a single amino acid mutation can significantly alter the immunodominance of the anti-HA antibody response. We then completed a series of studies to determine how immune history influences the specificity of antibody repertoires. In examining patient serology, we found that the specificity of the human antibody response against the 2009 pandemic H1N1 virus (pH1N1) was highly correlated with pre-exposure history to different seasonal H1N1 (sH1N1) strains during childhood. Using a ferret model, we demonstrate that the anti-pH1N1 antibody response can be shifted to highly conserved epitopes on HA when the animals were primed with sH1N1s that are otherwise antigenically distinct. Collectively, our studies demonstrate that accounting for receptor binding avidity and factors that alter antibody repertoires will improve influenza vaccination strategies in the future