Antigenic Drift Of Influenza Research Articles

Antigenic Drift of Influenza A(H7N9) Virus Hemagglutinin

Since the emergence of influenza A(H7N9) virus in 2013, there have been 5 waves of influenza A(H7N9) epidemics in China. However, evolution of the hemagglutinin (HA) protein antigenicity has not been systematically investigated. To better understand how antigenic drift in HA proteins of influenza (A)H7N9 virus occurs, 902 influenza A(H7N9) virus HA protein sequences from a public database were retrieved and analyzed. Fifty-three mutants with single amino acid substitutions in HA protein were introduced into pseudoviruses, and their antigenic characteristics were analyzed using pseudovirus-based assays. The frequencies of 9 mutations incrementally increased over the past 5 years, with mutations identified at multiple sites. While mean neutralization titers of most variants remained unchanged, 3 mutations, A143V, A143T, and R148K, displayed a median 4-fold lower susceptibility to neutralization by antisera against influenza A/Anhui/1/2013(H7N9) virus. Notably, A143V and A143T were located outside the previously reported antigenic sites. The most dominant variant (A143V/R148K) in the most recent season constituted 74.11% of all mutations and demonstrated a 10-fold reduction in its reactivity to influenza A/Anhui/1/2013(H7N9) virus antisera. Importantly, compared with the DNA construct without the corresponding HA protein mutation, DNA vaccine encoding the A143V/R148K mutant induced a 5-fold increase in the neutralizing activity against this circulating virus. An appropriate vaccine strain should be considered in response to increasing antigenic drift in influenza A(H7N9) virus HA protein.

Heterogeneity in antibody range and the antigenic drift of influenza A viruses

In this paper we explore the consequences of a heterogeneous immune response in individuals on the evolution of a rapidly mutating virus. We show that several features of the incidence and phylogenetic patterns typical of influenza A may be understood in this framework. In our model, limited diversity and rapid drift of the circulating viral strains result from the interplay of two interacting subpopulations with different types of immune response, narrow or broad, upon infection. The subpopulation with the narrow immune response acts as a reservoir where consecutive mutations escape immunity and can persist. Strains with a number of accumulated mutations escape immunity in the other subpopulation as well, causing larger epidemic peaks in the whole population, and reducing strain diversity. Overall, our model produces a modulation of epidemic peak heights and patterns of antigenic drift consistent with reported observations, suggesting an underlying mechanism for the evolutionary epidemiology of influenza, in particular, and other infectious diseases, more generally.

Patterns of Predicted T-Cell Epitopes Associated with Antigenic Drift in Influenza H3N2 Hemagglutinin

Antigenic drift allowing escape from neutralizing antibodies is an important feature of transmission and survival of influenza viruses in host populations. Antigenic drift has been studied in particular detail for influenza A H3N2 and well defined antigenic clusters of this virus documented. We examine how host immunogenetics contributes to determination of the antibody spectrum, and hence the immune pressure bringing about antigenic drift. Using uTOPE™ bioinformatics analysis of predicted MHC binding, based on amino acid physical property principal components, we examined the binding affinity of all 9-mer and 15-mer peptides within the hemagglutinin 1 (HA1) of 447 H3N2 virus isolates to 35 MHC-I and 14 MHC-II alleles. We provide a comprehensive map of predicted MHC-I and MHC-II binding affinity for a broad array of HLA alleles for the H3N2 influenza HA1 protein. Each HLA allele exhibited a characteristic predicted binding pattern. Cluster analysis for each HLA allele shows that patterns based on predicted MHC binding mirror those described based on antibody binding. A single amino acid mutation or position displacement can result in a marked difference in MHC binding and hence potential T-helper function. We assessed the impact of individual amino acid changes in HA1 sequences between 10 virus isolates from 1968–2002, representative of antigenic clusters, to understand the changes in MHC binding over time. Gain and loss of predicted high affinity MHC-II binding sites with cluster transitions were documented. Predicted high affinity MHC-II binding sites were adjacent to antibody binding sites. We conclude that host MHC diversity may have a major determinant role in the antigenic drift of influenza A H3N2.

Molecular basis of antigenic drift in Influenza A/H3N2 strains (1968-2007) in the light of antigenantibody interactions.

The emergence of new strains of Influenza virus have caused several pandemics over the last hundred years with the latest being the H1N1 Swine flu pandemic of 2009. The Hemagglutinin (HA) protein of the Influenza virus is the primary target of human immune system and is responsible for generation of protective antibodies in humans. Mutations in this protein results in change in antigenic regions (antigenic drift) which consequently leads to loss of immunity in hosts even in vaccinated population (herd immunity). This necessitates periodic changes in the Influenza vaccine composition. In this paper, we investigate the molecular basis of the reported loss of herd immunity in vaccinated population (vaccine component: Influenza A/X-31/1968 (H3N2)) which resulted in the outbreak due to strain Influenza A/Port Chalmers/1/1973 (H3N2). Also, the effects of antigenic drift in HA protein (H3N2 vaccine strains 1968-2007) on the 3D structures as well as interactions with BH151, a 1968 antibody, has been studied. Rigid body molecular docking protocol has been used to study the antigen-antibody interactions. We believe that the present study will help in better understanding of host-pathogen interactions at the molecular level.

Coexistence conditions for strains of influenza with immune cross-reaction

The accumulation of cross-immunity in the host population is an important factor driving the antigenic evolution of viruses such as influenza A. Mathematical models have shown that the strength of temporary non-specific cross-immunity and the basic reproductive number are both key determinants for evolutionary branching of the antigenic phenotype. Here we develop deterministic and stochastic versions of one such model. We examine how the time of emergence or introduction of a novel strain affects co-existence with existing strains and hence the initial establishment of a new evolutionary branch. We also clarify the roles of cross-immunity and the basic reproductive number in this process. We show that the basic reproductive number is important because it affects the frequency of infection, which influences the long term immune profile of the host population. The time at which a new strain appears relative to the epidemic peak of an existing strain is important because it determines the environment the emergent mutant experiences in terms of the short term immune profile of the host population. Strains are more likely to coexist, and hence to establish a new clade in the viral phylogeny, when there is a significant time overlap between their epidemics. It follows that the majority of antigenic drift in influenza is expected to occur in the earlier part of each transmission season and this is likely to be a key surveillance period for detecting emerging antigenic novelty.

William Graeme Laver PhD, FRS (1929–2008)

William Graeme Laver PhD, FRS (1929–2008)

Vaccination and antigenic drift in influenza

The relationship between influenza antigenic drift and vaccination lies at the intersection of evolutionary biology and public health, and it must be viewed and analyzed in both contexts simultaneously. In this paper, I review what is known about the effects of antigenic drift on vaccination and the effects of vaccination on antigenic drift, and I suggest some simple ways to detect the presence of antigenic drift in seasonal influenza data. If antigenic drift occurs on the time scale of a single influenza season, it may be associated with the presence of herd immunity at the beginning of the season and may indicate a need to monitor for vaccine updates at the end of the season. The relationship between antigenic drift and vaccination must also be viewed in the context of the global circulation of influenza strains and the seeding of local and regional epidemics. In the data sets I consider – from New Zealand, New York, and France – antigenic drift can be statistically detected during some seasons, and seeding of epidemics appears to be endogenous sometimes and exogenous at other times. Improved detection of short-term antigenic drift and epidemic seeding would significantly benefit influenza monitoring efforts and vaccine selection.

On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A

Many pathogens exist in phenotypically distinct strains that interact with each other through competition for hosts. General models that describe such multi-strain systems are extremely difficult to analyze because their state spaces are enormously large. Reduced models have been proposed, but so far all of them necessarily allow for coinfections and require that immunity be mediated solely by reduced infectivity, a potentially problematic assumption. Here, we suggest a new state-space reduction approach that allows immunity to be mediated by either reduced infectivity or reduced susceptibility and that can naturally be used for models with or without coinfections. Our approach utilizes the general framework of status-based models. The cornerstone of our method is the introduction of immunity variables, which describe multi-strain systems more naturally than the traditional tracking of susceptible and infected hosts. Models expressed in this way can be approximated in a natural way by a truncation method that is akin to moment closure, allowing us to sharply reduce the size of the state space, and thus to consider models with many strains in a tractable manner. Applying our method to the phenomenon of antigenic drift in influenza A, we propose a potentially general mechanism that could constrain viral evolution to a one-dimensional manifold in a two-dimensional trait space. Our framework broadens the class of multi-strain systems that can be adequately described by reduced models. It permits computational, and even analytical, investigation and thus serves as a useful tool for understanding the evolution and ecology of multi-strain pathogens.

Surveillance for influenza A virus infections in infants and young children in Beijing, China, 2001-2005

To characterize the prevalence and antigenic drift of influenza A viruses isolated during the period from 2001 to 2005 in infants and young children in Beijing. MDCK cell culture, indirect immunofluorescence assay (IFA) and hemagglutination inhibition (HI) assay were used to isolate and identify type A influenza viruses (H1N1 and H3N2) from clinical samples collected from outpatients and inpatients who visited the Affiliated Children's Hospital because of acute respiratory infections from Oct. 2001 to Aug. 2005. The HA1 regions of hemagglutinin gene of H3N2 isolates were amplified by using RT-PCR followed by sequencing. Out of 7338 clinical samples collected during this surveillance period, 347 (4.7%) were positive for influenza A viruses, including 48 (13.8%) of H1N1, 273 (78.7%) of H3N2 and 26 (7.5%) of subtype-unidentified influenza A viruses. Although there was a prevalence season of influenza A from October each year to April of next year during the 2001-2004 period, it was worth noting that a consecutive influenza A activity was detected from Aug. 2004 to Aug. 2005, when some influenza A viruses were detected even in summer. The positive rate of H3N2 was 14.2% in August, 2005, which was equal to that of the peak season of 2003-2004. H3N2 were predominant in most of the influenza seasons during the surveillance period, and H1N1 was detected only in the influenza seasons of the 2001-2002 and 2004-2005 along with H3N2. The positive rates for both H3N2 and H1N1 were higher in specimens from outpatients than those from inpatients. A total of 46.6% (110/236) of the H3N2 were detected from children younger than 2 years of age, and 14.0% (33/236) were from children older than 5 years, whereas, more H1N1 was found in children older than 5 years (48.0%, 12/31) than in those younger than 2 years (6.5%, 2/31) during a period from Nov. 2003 to Aug. 2005. Sequence analysis of the HA1 regions of hemagglutinin of H3N2 isolated in a series of years revealed amino acid changes in the HA1 domain of H3N2 isolates in the antigenic sites (A-E) each year. H3N2 and H1N1 prevailed in each influenza season during the surveillance period in Beijing, and H3N2 strains were predominant. The data from all-year around surveillance of influenza in Beijing indicate that continuous surveillance throughout a year and use of both antigenic and molecular analysis will be more helpful for early identification of any antigenic variants as well as prevention and control of influenza by promoting development of vaccines.

Cross-reactivity of influenza A (H3N2) hemagglutination-inhibition antibodies induced by an inactivated influenza vaccine

The antigenic drift of influenza A (H3N2) virus in 2003–2004 necessitated a change in the vaccine from the A/Panama to the A/Wyoming strain for the 2004–2005 season. Using hemagglutination inhibition, we therefore tested antibodies in sera of 39 individuals (mean age 64.6 years) at the end of the 2003–2004 season for cross-reactivity to vaccine strains and H3N2 antigens subject to antigenic drift. Antibodies against both A (H3N2) Panama and Wyoming developed in 5/13 (38.5%) unvaccinated individuals, whereas, 22/26 (84.6%) vaccinees developed antibodies to Panama and 21/26 (80.8%) to Wyoming. None of these individuals suffered an influenza episode that season. The results suggest that the elderly might develop protective levels of cross-reactive A (H3N2) Wyoming HI antibodies following vaccination with the Panama strain. Such strains, like the ones included in the 2003–2004 influenza vaccine, might be expected to provide a broad-spectrum antibody response that could be effective even in the face of single season antigenic drift.

On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A

Many pathogens exist in phenotypically distinct strains that interact with each other through competition for hosts. General models that describe such multi-strain systems are extremely difficult to analyze because their state spaces are enormously large. Reduced models have been proposed, but so far all of them necessarily allow for coinfections and require that immunity be mediated solely by reduced infectivity, a potentially problematic assumption. Here, we suggest a new state-space reduction approach that allows immunity to be mediated by either reduced infectivity or reduced susceptibility and that can naturally be used for models with or without coinfections. Our approach utilizes the general framework of status-based models. The cornerstone of our method is the introduction of immunity variables, which describe multi-strain systems more naturally than the traditional tracking of susceptible and infected hosts. Models expressed in this way can be approximated in a natural way by a truncation method that is akin to moment closure, allowing us to sharply reduce the size of the state space, and thus to consider models with many strains in a tractable manner. Applying our method to the phenomenon of antigenic drift in influenza A, we propose a potentially general mechanism that could constrain viral evolution to a one-dimensional manifold in a two-dimensional trait space. Our framework broadens the class of multi-strain systems that can be adequately described by reduced models. It permits computational, and even analytical, investigation and thus serves as a useful tool for understanding the evolution and ecology of multi-strain pathogens.

Antigenic structure of the hemagglutinin of influenza virus B/Hong Kong/8/73 as determined from gene sequence analysis of variants selected with monoclonal antibodies

Antigenic variation among influenza B viruses is different from that of influenza A in several ways. Antigenic shift has not been observed, distinct antigenic variants of influenza B cocirculate, and antigenically similar viruses have been isolated many years apart. To study the mechanism of antigenic drift in influenza B viruses, monoclonal antibodies were used to select antigenic variants of B/Hong Kong/8/73 virus hemagglutinin (HA). Analyses of the nucleotide sequences of the HA gene of B/Hong Kong/8/73 and the eight variants identified specific regions of the influenza B HA molecule involved in antigenicity, and enabled antigenic mapping data to be correlated with the structure of the protein. The altered amino acids in the variants, when compared to the HA of A/Aichi/2/68, A/Aichi/2/68, were found in two of the four antigenic regions previously identified for type A viruses. In addition, four of the eight variants showed multiple nucleotide changes some of which gave rise to double amino acid changes. In addition, in the present study monoclonal antibodies which belong to the same antigenic group recognize amino acid changes in regions corresponding to antigenic sites A and B of the H3 HA. These results are in contrast to those obtained with HA variants of A/Memphis/1/71 virus. In the influenza A studies only single amino acid changes were found and these correlated well with the three-dimensional structure as determined by D. C. Wiley, I. A. Wilson, and J. J. Skehel, (1981, Nature (London) 289, 366–373); monoclonal antibodies which recognized one region did not recognize any of the other antigenic sites. Our results suggest that although the basic three-dimensional structure of the influenza B HA may be similar to that of A viruses, the B HA molecule may be folded in a more compact manner so that antigenic sites A and B are in closer proximity to each other than in the H3 structure.

Sequential mutations in hemagglutinins of influenza B virus isolates: definition of antigenic domains.

Comparative analysis of the amino acid sequences of hemagglutinins (HAs) of influenza B/Lee/40, B/Md/59, and B/HK/73 viruses has allowed examination of the molecular basis of antigenic variation in type B viruses. As seen with influenza type A viruses, antigenic drift in influenza B viruses proceeds mostly through the accumulation of amino acid substitutions within the HA1 portion of the HA molecule. However, the rate of variation observed among the influenza B virus HAs appears to be significantly lower than the observed rate of variation among influenza A virus HAs. The overall rate of amino acid change in the HA1s of the influenza B viruses studied is 2% per 10 years, whereas the HA1s of H3 influenza A viruses vary by 9.2% per 10 years. The sequences of the influenza B HAs were also examined in relation to the three-dimensional model for the A/Aichi/2/68 HA. When the primary amino acid sequences are compared, it appears that most of the important structural features of the type A HAs--such as the sialic acid binding site, the disulfide linkages, and the stem structure of the trimer--are conserved in the influenza B virus HAs. Regions are also identified where extensive amino acid substitutions have occurred among the three antigenically distinct influenza B virus HAs. The locations of these areas in the B HA structure correspond to antigenic regions proposed for the A virus HAs. In addition, modulation of antigenic regions in B virus HAs may also occur through amino acid deletions and variation in glycosylation sites.

Antigenic drift in influenza A/USSR/90/77(H1N1) variants selected in Vitro with monoclonal antibodies

Variants of A/USSR/90/77(H1N1) virus were selected in vitro by breakthrough neutralization with monoclonal antibodies, at a frequency consistent with them arising by single-step point mutations. When examined by hemagglutination-inhibition tests with postinfection ferret sera, all those variants with a change in the epitope recognized by antibody 264 exhibited significant antigenic drift away from A/USSR/90/77, whereas no variants lacking a change in the epitope recognized by this antibody differed from A/USSR/90/77 when tested with the heterogeneous sera. One of the in vitro variants had acquired a distinctive specificity with ferret sera similar to that of a previously described sporadically detected, natural variant, A/Lackland/3/78, that exhibits reciprocal antigenic drift from A/USSR/90/77. Another variant was quite similar to the epidemic strain A/Brazil/11/78 in its ferret serum reaction pattern, exhibiting modest asymmetric antigenic drift from A/USSR/90/77. The in vitro variants were not, however, identical to natural variants in reaction patterns with both monoclonal antibodies and ferret sera. Nevertheless, the findings support the possibility for significant antigenic variation of A/USSR/90/77 influenza virus to occur by means of a point mutation at a critical locus in the determinant recognized by monoclonal antibody 264, and suggest that some natural variants may have arisen by point mutations in this determinant.

Effect of test system on the ability of monoclonal antibodies to detect antigenic drift in influenza A(H1N1) virus haemagglutinins.

Results of analysing antigenic variation in the haemagglutinin (HA) molecule of naturally occurring influenza A (H1N1) viruses from 1977 to 1979 with monoclonal antibodies were found to be dependent in some instances on the test system used. In several instances A/USSR/90/77 HA-specific monoclonal antibodies had sharply reduced haemagglutination-inhibition (HI) titres with variant virus although they bound to the variant and A/USSR/90/77 HAs with similar efficiencies as judged by titration in a sensitive and accurate solid-phase immunofluorimetric assay. In another instance, the converse situation was observed: monoclonal antibodies having a reduced efficiency of binding to the HA of a variant virus nevertheless had comparable HI titres with the variant and with A/USSR/90/77. The chemical basis and epidemiological significance of these observations remain to be elucidated. Nevertheless, the finding that the reaction of monoclonal antibodies can, in some cases, be markedly dependent on the test system employed is of significance for the efficient design and correct interpretation of immunochemical studies which employ monoclonal antibodies to investigate the basis for variation in influenza strains.

Antigenic drift in influenza A viruses. I. Selection and characterization of antigenic variants of A/PR/8/34 [HON1] influenza virus with monoclonal antibodies

Antigenic variants of A/PR/8/34 [HON1] influenza virus were selected after a single passage of the parent virus in embryonated chicken eggs in the presence of monoclonal antibodies to this virus. The monoclonal antibodies were produced by a hybridoma and were specific for an antigenic determinant on the HA molecule of the parent virus. Seven antigenic variants were analyzed with 95 monoclonal anti-HA antibodies prepared in vitro in the splenic fragment culture system. Three subgroups of antigenic variants were distinguished. The antigenic changes were primarily recognized by monoclonal antibodies to the strain- specific determinants of the parental hemagglutinin (HA) molecule. Monoclonal antibodies to HA determinants shared (in an identical or cross-reactive form) by parental virus and more than three heterologous viruses of the HON1 and H1N1 subtypes were unable to recognize the antigenic change on the variants. Similarly, heterogeneous antibody preparations could not differentiate between parental and variant viruses. The results are compatible with the idea that the HA of PR8 has available a large repertoire of antigenic modifications that may result from single amino acid substitutions, and that antigenic changes can occur in the strain- specific determinants on the HA molecule in the absence of concomitant changes in the cross-reactive HA determinants. The findings suggest that antigenic drift, in order to be epidemiologically significant, probably requires a series of amino acid substitutions in, or close to, the antigenic area on the HA molecule.