Serology and energetics of cross-reactions among the H3 antigens of influenza viruses

A human coronavirus evolves antigenically to escape antibody immunity

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these "future" viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.

Cross-reactivity of antibody responses to Borrelia afzelii OspC: Asymmetry and host heterogeneity

The tick-transmitted bacterium Borrelia afzelii consists of a number of antigenically different strains - often defined by outer surface protein C (OspC) genotype - that coexist at stable frequencies in host populations. To investigate how host antibody responses affect strain coexistence, we measured antibody cross-reactivity to three different OspC types (OspC 2, 3 and 9) in three different strains of laboratory mice (BALB/c, C3H and C57BL/6). The extent of cross-reactivity differed between mouse strains, being higher in C3H than BALB/c and C57BL/6. In one of three pairwise comparisons of OspC types (OspC2 vs OspC9), there was evidence for asymmetry of cross-reactivity, with antibodies to OspC2 cross-reacting more strongly with OspC9 than vice versa. These results indicate that the extent of antibody-mediated competition between OspC types may depend on the composition of the host population, and that such competition may be asymmetric. We discuss the implications of these results for understanding the coexistence of OspC types.

Antibodies of influenza A(H1N1)pdm09 virus in pigs' sera cross-react with other influenza A virus subtypes. A retrospective epidemiological interpretation of Norway's serosurveillance data from 2009-2017

Since the incursion of influenza A(H1N1)pdm09 virus in 2009, serosurveillance every year of the Norwegian pig population revealed the herd prevalence for influenza A(H1N1)pdm09 (HIN1pdm09) has stabilised between 40% and 50%. Between 30 September 2009 and 14 September 2017, the Norwegian Veterinary Institute and Norwegian Food Safety Authority screened 35,551 pigs for antibodies to influenza A viruses (IAVs) from 8,636 herds and found 26% or 8,819 pigs' sera ELISA positive (titre ≥40). Subtyping these IAV antibodies from 8,214 pigs in 3,629 herds, by a routine haemagglutination inhibition test (HAIT) against four standard antigens produced 13,771 positive results (HAIT titre ≥40) of binding antibodies. The four antigen subtypes eliciting positive HAIT titre in descending frequencies were immunogen H1N1pdm09 (n = 8,200 or 99.8%), swine influenza A virus (SIVs) subtypes swH1N1 (n = 5,164 or 62%), swH1N2 (n = 395 or 5%) and swH3N2 (n = 12 or 0.1%). Of these 8,214 pig pigs sera, 3,039 produced homologous HAIT subtyping, almost exclusively immunogen H1N1pdm09 (n = 3,026 or 99.6%). Using HAIT titre of pig and herd geometric mean titre (GMT) as two continuous outcome variables, and with the data already structured hierarchically, we used mixed effects linear regression analysis to investigate the impact of predictors of interests had on the outcomes. For the full data, the predictors in the regression model include categorical predictors antigen subtype (H1N1pdm09, swH1N1, swH1N2 & swH3N2), and production type (sow herd or fattening herd), ordinal predictors year (longitudinally from 2009 to 2017) and number of antigens in heterologous reactions (1, 2, 3, 4) in the same pig serum. The last predictor, the proportion of HAIT positive (antigen specific) in tested pigs within the herd, was a continuous predictor, which served as a proxy for days post-infection (dpi) or humoral response time in the pig or herd. Regression analysis on individual pig HAIT titres showed that antigen as a predictor, the coefficient for immunogen H1N1pdm09 was at least fourfold higher (P < 0.001) than the three SIVs antigen subtypes, whose much lower coefficients were statistically no different between the three SIVs antigen subtypes. Correspondingly, for herd GMT, immunogen H1N1pdm09 was 28–40-fold higher than the three SIVs antigen subtypes. Excluding the HAIT data of the three SIVs antigen subtypes, regression analysis focusing only on immunogen H1N1pdm09 increased greatly the coefficients of the predictors in the models. Homologous reactions (99.6% H1N1pdm09) have lower HAIT titres while the likelihood of the number of antigens involved in HAIT heterologous reactions in a single pig serum increased with higher HAIT titres of immunogen H1N1pdm09. For predictor ‘production’, sows and sow herds had higher HAIT titres and GMT compared to fattening pigs and fattening herds respectively. Herds with ‘higher proportion of pigs tested positive’ also had higher HAIT titre in the pig and herd GMT.

Pathogen evolution and the immunological niche

Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible-infected-recovered (SIR) model. However, there is growing evidence that the complexity of many host-pathogen interactions is dynamically important. This revised perspective requires broadening the definition of a pathogen's immunological phenotype, or what can be thought of as its immunological niche. After reviewing evidence that interactions between pathogens and host immunity drive much of pathogen evolution, I introduce the concept of a pathogen's immunological phenotype. Models that depart from the SIR paradigm demonstrate the utility of this perspective and show that it is particularly useful in understanding vaccine-induced evolution. This paper highlights questions in immunology, evolution, and ecology that must be answered to advance theories of pathogen diversity.

Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering

The hemagglutination inhibition (HAI) assay is the primary measurement used for identifying antigenically novel influenza virus strains. HAI assays measure the amount of reference sera required to prevent virus binding to red blood cells. Receptor binding avidities of viral strains are not usually taken into account when interpreting these assays. Here, we created antigenic maps of human H3N2 viruses that computationally account for variation in viral receptor binding avidities. These new antigenic maps differ qualitatively from conventional antigenic maps based on HAI measurements alone. We experimentally focused on an antigenic cluster associated with a single N145K hemagglutinin (HA) substitution that occurred between 1992 and 1995. Reverse-genetics experiments demonstrated that the N145K HA mutation increases viral receptor binding avidity. Enzyme-linked immunosorbent assays (ELISA) revealed that the N145K HA mutation does not prevent antibody binding; rather, viruses possessing this mutation escape antisera in HAI assays simply by attaching to cells more efficiently. Unexpectedly, we found an asymmetric antigenic effect of the N145K HA mutation. Once H3N2 viruses acquired K145, an epitope involving amino acid 145 became antigenically dominant. Antisera raised against an H3N2 strain possessing K145 had reduced reactivity to H3N2 strains possessing N145. Thus, individual mutations in HA can influence antigenic groupings of strains by altering receptor binding avidity and by changing the dominance of antibody responses. Our results indicate that it will be important to account for variation in viral receptor binding avidity when performing antigenic analyses in order to identify genuine antigenic differences among influenza virus variants.

Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition

Consumer-resource dynamics of hosts with their pathogens are modulated by complex interactions between various branches of hosts' immune systems and the imperfectly perceived pathogen. Multistrain SIR models tend to sweep competitive interaction terms between different pathogen strains into a single parameter representing cross-immunity. After reviewing several hypotheses about the generation of immune responses, we look into the consequences of assuming that hosts with identical immune repertoires respond to new pathogens identically. In particular, we vary the breadth of the typical immune response, or the average number of pathogen epitopes a host perceives, and the probability of perceiving a particular epitope. The latter quantity in our model is equivalent both to the degree of diversity in host responses at the population level and the relative immunodominance of different epitopes. We find that a sharp transition to strain coexistence occurs as host responses become narrow or skewed toward one epitope. Increasing the breadth of the immune response and the immunogenicity of different epitopes typically increases the range of cross-immunity values in which chaotic strain dynamics and competitive exclusion occur. Models attempting to predict the outcomes of strain competition should thus consider the potential diversity and specificity of hosts' responses to infection.

On the use of hemagglutination-inhibition for influenza surveillance: surveillance data are predictive of influenza vaccine effectiveness

The hemagglutination-inhibition (HI) assay is the main tool used by epidemiologists to quantify antigenic differences between circulating influenza virus strains, with the goal of selecting suitable vaccine strains. However, such quantitative measures of antigenic difference were recently shown to have poor predictive accuracy with respect to influenza vaccine effectiveness (VE) in healthy adults. Here, we re-examine those results using a more rigorous criterion for predictive accuracy -- considering only cases when the vaccine (V) and dominant (D) circulating strains are antigenically different -- and greater numbers of HI titers. We find that the Archetti -- Horsfall measure of antigenic difference, which is based on both the normalized HI titer (NHI) of D relative to antisera raised against V and the NHI of V relative to D, predicts VE very well (R(2)=0.62, p=4.1x10(-3)). In contrast, the predictive accuracies of the NHI of D relative to V alone (R(2)=0.01), and two other measures of antigenic difference based on the amino acid sequence of influenza virus hemagglutinin (R(2)=0.03 for both measures) are relatively poor. Furthermore, while VE in the elderly is generally high in cases when D and V are antigenically identical (VE=35%, S.E.=5%), in other cases VE appears to increase with the antigenic difference between D and V (R(2)=0.90, p=2.5x10(-5)). This paradoxical observation could reflect the confounding effects of prior immunity on estimates of VE in the elderly. Together, our results underscore the need for consistently accurate selection of suitable vaccine strains. We suggest directions for further studies aimed at improving vaccine-strain selection and present a large collection of HI titers that will be useful to such studies.

HI antibody kinetics in adult volunteers immunized repeatedly with inactivated trivalent influenza vaccine in 1990-1992

Volunteers were immunized once, twice or three times in 1990-1992 with commercial trivalent inactivated influenza vaccine and monitored for haemagglutination inhibition (HI) antibodies. The antibodies that already existed when the subjects entered the study derived from natural infections. Immunizations in the second and third years were necessary to maintain the geometric mean titres of antibody and protection rates at the level recorded after the first vaccination. Negative correlations between prevaccination antibody titres and mean fold antibody increases were noted in most instances analysed. Moreover, at each individual prevaccination titre level the mean fold antibody increases and even postvaccination mean titres were higher after the first than after subsequent vaccinations, suggesting that the HI antibody responses might be affected by vaccine-induced pre-existing antibody more than by the same titres of antibody derived from natural infections. This was most obvious for antibody to the H1N1 subtype virus, A/Finland/164/91. In immunization with B/Yamagata/16/88, anamnestic response of antibody to B/Finland/150/90, which belongs to the antigenically distinct lineage of B/Victoria/2/87-like viruses, was more frequent in the first than in subsequent years. This is in contrast to homologous antibodies, which increased significantly after the second vaccination.

Killer T cell responses to influenza A during a drift period: studies in mice

After intravenous immunization of mice with any influenza A H3N2 drift strain attempts to restimulation of cytotoxic T cell (CTL) activities with the same virus or other drift period variants were unsuccessful for up to 6 weeks. Cross-stimulation 4-5 months after primary sensitization yielded, in most situations, positive but lower--as compared to primary--secondary cytotoxic T cell responses. Homotypic challenge was also effective after priming with some influenza A subtypes (A/E/72, A/PC/73, A/T/77) at this time.

Conservation and variation in the hemagglutinins of Hong Kong subtype influenza viruses during antigenic drift

The nucleotide sequence was determined for the hemagglutinin gene of the Hong Kong subtype influenza strain A/Bangkok/1/79. The amino acid sequence predicted from these data shows a total of 36 amino acid changes as compared with hemagglutinin for a 1968 Hong Kong strain, 11 more than had occurred in a 1975 strain. The distribution of these changes confirmed that there are conserved and highly variable regions in hemagglutinin as the viral gene evolves during antigenic drift in the Hong Kong subtype. Of the four variable regions found in this study, only two have been seen previously. Correlation of highly variable areas in the hemagglutinins of Hong Kong subtype field strains with sites of amino acid changes in antigenically distinct influenza variants enabled us to predict likely antigenic regions of the protein. The results support and extend similar predictions made recently, based on the three-dimensional arrangement of hemagglutinin from a 1968 influenza strain.

A mechanism for influenza subtype disappearance

We propose that changes in the antigenic region/s of influenza haemagglutinin can also cause changes in the binding site for host cells. If these changes have an overall deleterious effect on virus binding and hence on viral infectivity and reproduction one has a simple mechanism to explain the limited time span of influenza subtypes. Evidence is presented from the published results of other workers to support this hypothesis.