Antigenic heterogeneity within influenza A (H3N2) virus strains

On the basis of their antigenic properties, influenza virus strains are classified into types and subtypes, which are further subdivided into variants that differ to various degrees in haemagglutination-inhibition assays. Evidence is presented that during infection with an influenza A(H3N2) virus the respiratory tract of a human patient often harbours more than one antigenic virus variant. These variants are frequently propagated by embryonated fowl eggs and monkey cells with different efficiencies, and this may lead to the selection of different variants by either of these host systems. Also, passage of virus by a given host is sometimes attended by changes in reactivity in haemagglutination-inhibition tests. In some cases the heterogeneity described also affects the specific immunogenicity of the virus in ferrets. Virus strains cloned in monkey kidney cell cultures gave variants that were stable upon further passage. These results may have implications for antigenic and biochemical investigations of epidemiologically relevant virus variants. It is argued that the antigenic drift of influenza A(H3N2) viruses is best characterized by analyses, both with post-infection ferret antisera and with panels of monoclonal antibodies, of virus strains isolated and passaged in monkey kidney cell cultures only.     

Antigenic variation and immunity to Plasmodium knowlesi: antibodies which induce antigenic variation and antibodies which destroy parasites

2 types of antibody response specific for intrastrain antigenic variants of P. knowlesi can be detected in the serum of M. mulatta. One induces a change in the parasite serotype, the other is parasiticidal. The rate of synthesis of both types of antibodies to new variants increases as the host develops protective immunity and their rate of synthesis relative to one another also changes. Both these effects are possibly important in determining the level of parasitaemia.     

Antigenic diversity of bovine viral diarrhoea viral isolates contradicts the concept of herd specific strain.

In the epidemiology of bovine viral diarrhoea (BVD), immunotolerant - persistently infected animals (IPI) appear to be major sources of contamination. These animals produce large quantities of replicating virus and have therefore been proposed as being responsible for generating antigenic variability. However, limited studies have failed to detect antigenic or genetic changes in viruses isolated at different times from IPI. An hypothesis is that the immunotolerance of IPI against their homologous strain is accompanied by immune elimination of antigenic variants. The presence of an IPI in a herd could therefore limit antigenic variation, eventually leading to the existence of herd specific strains. To verify this hypothesis we characterized, against a panel of monoclonal antibodies, 37 BVD virus strains isolated from IPI of 12 herds in Eastern Belgium. Intra-herd antigenic variation was compared to inter-herd variation. Antigenic variation within herds was found to be surprisingly high but, nevertheless, significantly lower than variation between herds.     

Poly I:C adjuvanted inactivated swine influenza vaccine induces heterologous protective immunity in pigs

Swine influenza is widely prevalent in swine herds in North America and Europe causing enormous economic losses and a public health threat. Pigs can be infected by both avian and mammalian influenza viruses and are sources of generation of reassortant influenza viruses capable of causing pandemics in humans. Current commercial vaccines provide satisfactory immunity against homologous viruses; however, protection against heterologous viruses is not adequate. In this study, we evaluated the protective efficacy of an intranasal Poly I:C adjuvanted UV inactivated bivalent swine influenza vaccine consisting of Swine/OH/24366/07 H1N1 and Swine/CO/99 H3N2, referred as PAV, in maternal antibody positive pigs against an antigenic variant and a heterologous swine influenza virus challenge. Groups of three-week-old commercial-grade pigs were immunized intranasally with PAV or a commercial vaccine (CV) twice at 2 weeks intervals. Three weeks after the second immunization, pigs were challenged with the antigenic variant Swine/MN/08 H1N1 (MN08) and the heterologous Swine/NC/10 H1N2 (NC10) influenza virus. Antibodies in serum and respiratory tract, lung lesions, virus shedding in nasal secretions and virus load in lungs were assessed. Intranasal administration of PAV induced challenge viruses specific-hemagglutination inhibition- and IgG antibodies in the serum and IgA and IgG antibodies in the respiratory tract. Importantly, intranasal administration of PAV provided protection against the antigenic variant MN08 and the heterologous NC10 swine influenza viruses as evidenced by significant reductions in lung virus load, gross lung lesions and significantly reduced shedding of challenge viruses in nasal secretions. These results indicate that Poly I:C or its homologues may be effective as vaccine adjuvants capable of generating cross-protective immunity against antigenic variants/heterologous swine influenza viruses in pigs.     

Testing the vaccine potential of PilV, PilX and ComP, minor subunits of Neisseria meningitidis type IV pili

Because meningitis and septicaemia caused by Neisseria meningitidis are major public health problems worldwide, the design of a broadly protective vaccine remains a priority. Type IV pili (Tfp) are surface-exposed filaments playing a key role in pathogenesis in a variety of bacterial species, including N. meningitidis, that have demonstrated vaccine potential. Unfortunately, in the meningococcus, the major pilus subunit PilE usually undergoes extensive antigenic variation and is therefore not suitable as a vaccine component. However, we have recently shown that N. meningitidis Tfp contain low abundance subunits PilX, PilV and ComP, collectively called minor pilins, that are highly conserved and modulate Tfp-linked functions key to pathogenesis. This prompted us to examine the vaccine potential of these proteins by assessing whether sera directed against them have bactericidal properties and/or are able to interfere with Tfp-linked functions. Here we show that minor pilin proteins are recognized by sera of patients convalescent from meningococcal disease and that antibodies directed against some of them can selectively interfere with Tfp-linked functions. This shows that, despite their apparent inability to elicit bactericidal antibodies, minor pilins might have vaccine potential.     

Antigenic distance measurements for seasonal influenza vaccine selection

Influenza vaccination is one of the major options to counteract the effects of influenza diseases. Selection of an effective vaccine strain is the key to the success of an effective vaccination program since vaccine protection can only be achieved when the selected influenza vaccine strain matches the antigenic variants causing future outbreaks. Identification of an antigenic variant is the first step to determine whether vaccine strain needs to be updated. Antigenic distance derived from immunological assays, such as hemagglutination inhibition, is commonly used to measure the antigenic closeness between circulating strains and the current influenza vaccine strain. Thus, consensus on an explicit and robust antigenic distance measurement is critical in influenza surveillance. Based on the current seasonal influenza surveillance procedure, we propose and compare three antigenic distance measurements, including Average antigenic distance (A-distance), Mutual antigenic distance (M-distance), and Largest antigenic distance (L-distance). With the assistance of influenza antigenic cartography, our simulation results demonstrated that M-distance is a robust influenza antigenic distance measurement. Experimental results on both simulation and seasonal influenza surveillance data demonstrate that M-distance can be effectively utilized in influenza vaccine strain selection.     

TARV: Tree‐based Analysis of Rare Variants Identifying Risk Modifying Variants in CTNNA2 and CNTNAP2 for Alcohol Addiction

Since the development of next generation sequencing (NGS) technology, researchers have been extending their efforts on genome‐wide association studies (GWAS) from common variants to rare variants to find the missing inheritance. Although various statistical methods have been proposed to analyze rare variants data, they generally face difficulties for complex disease models involving multiple genes. In this paper, we propose a tree‐based analysis of rare variants (TARV) that adopts a nonparametric disease model and is capable of exploring gene–gene interactions. We found that TARV outperforms the sequence kernel association test (SKAT) in most of our simulation scenarios, and by notable margins in some cases. By applying TARV to the study of addiction: genetics and environment (SAGE) data, we successfully detected gene CTNNA2 and its 43 specific variants that increase the risk of alcoholism in women, with an odds ratio (OR) of 1.94. This gene has not been detected in the SAGE data. Post hoc literature search also supports the role of CTNNA2 as a likely risk gene for alcohol addiction. In addition, we also detected a plausible protective gene CNTNAP2, whose 97 rare variants can reduce the risk of alcoholism in women, with an OR of 0.55. These findings suggest that TARV can be effective in dissecting genetic variants for complex diseases using rare variants data.     

New Respiratory Enterovirus and Recombinant Rhinoviruses among Circulating Picornaviruses

Rhinoviruses and enteroviruses are leading causes of respiratory infections. To evaluate genotypic diversity and identify forces shaping picornavirus evolution, we screened persons with respiratory illnesses by using rhinovirus-specific or generic real-time PCR assays. We then sequenced the 5′ untranslated region, capsid protein VP1, and protease precursor 3CD regions of virus-positive samples. Subsequent phylogenetic analysis identified the large genotypic diversity of rhinoviruses circulating in humans. We identified and completed the genome sequence of a new enterovirus genotype associated with respiratory symptoms and acute otitis media, confirming the close relationship between rhinoviruses and enteroviruses and the need to detect both viruses in respiratory specimens. Finally, we identified recombinants among circulating rhinoviruses and mapped their recombination sites, thereby demonstrating that rhinoviruses can recombine in their natural host. This study clarifies the diversity and explains the reasons for evolution of these viruses.     

Epidemic mechanisms of type A influenza.

The antigenic varieties of influenza A virus isolated from 1968 to 1976 in a surveillance of a small, rather remote population were similar to those from England and Wales as a whole, despite frequent antigenic changes during the period. Household studies in the first two H3N2 influenza A epidemics found low attack rates within households, a high proportion (70%) of affected households with only one case of influenza, similar distributions of affected households in the two epidemics by the number of cases of influenza and similar distributions of the influenza cases by the day of their onset in the household outbreak. No serial interval could be demonstrated by cumulating household outbreaks. More than one minor variant was causing influenza contemporaneously in the same villages in several seasons, and different variants were on one occasion found on successive days in bedfellows. The regular occurrence of epidemics in winter was often accompanied by the disappearance of the epidemic variants and their replacement, after a virus-free interval, by new variants. These epidemiological findings seem best interpreted on the following tentative hypothesis. Influenza A sufferers do not transmit the virus during their illness; instead it rapidly becomes latent in their tissues so that they become symptomless carrier-hosts and develop specific immunity. Next season an extraneous seasonally mediated stimulus reactivates the latent virus residues so that the carrier-host becomes briefly infectious, though symptomless. Antigenic drift occurs because particles reconstituted to be identical with the progenitor virus cannot escape the specific immunity it has provoked in the carrier host. He can shed only mutants also determined by the progenitor virus. From the assortment of mutants shed by the carrier-host, his non-immune companions select that (those) which is best fitted to survive, and it rapidly causes influenzal illness. Epidemics consist largely or entirely of such persons sick with influenza caused by reactivated virus caught from symptomless carrier-hosts.     

Maintenance of foot and mouth disease viruses in buffalo (Syncerus caffer Sparrman, 1779) in southern Africa.

Using age-related infection rates derived from serological data in available deterministic and specially developed stochastic simulation models, it has been possible to establish that the basic reproductive rates for South African Territory (SAT) type foot and mouth disease virus in buffalo (Syncerus caffer) are high. The models predict that there is a periodicity of infection within herds and possibly the population as a whole. Thus, buffalo herds are likely to be more infectious at some times than at others. However, because most infections in buffalo are inapparent, such episodes are difficult to identify. There is wide intratypic variation within the SAT type virus populations circulating in buffalo. This was determined by sequencing part of the 1 D gene of buffalo isolates and establishing antigenic profiles with neutralising monoclonal antibodies and conventional antisera.     

Forecasting the epidemic potential of influenza virus variants based on their molecular properties

Sequence analysis of the influenza haemagglutinin, HA, (H1 and H3) suggests that many antigenic variants that are identified but which do not become predominant differ from contemporary epidemic strains in one or two amino acids, in the region 188–193. This information may assist in the optimum selection of vaccine strains when multiple variants are co-circulating. Genome analysis of H1N1 virus, from 1977 to 1983 (but not of H3N2 virus thus far) has identified two instances when large changes in total genome sequence was associated with major epidemic activity. The early detection of such gross genetic changes may provide a further indicator that can be used to forecast the likelihood of more widespread activity than normal.     

Antigenic sites of H1N1 influenza virus hemagglutinin revealed by natural isolates and inhibition assays

The antigenic sites of hemagglutinin (HA) are crucial for understanding antigenic drift and vaccine strain selection for influenza viruses. In 1982, 32 epitope residues (called laboratory epitope residues) were proposed for antigenic sites of H1N1 HA based on the monoclonal antibody-selected variants. Interestingly, these laboratory epitope residues only cover 28% (23/83) mutation positions for 9 H1N1 vaccine strain comparisons (from 1977 to 2009). Here, we propose the entropy and likelihood ratio to model amino acid diversity and antigenic variant score for inferring 41 H1N1 HA epitope residues (called natural epitope residues) with statistically significant scores according to 1572 HA sequences and 197 pairs of HA sequences with hemagglutination inhibition (HI) assays of natural isolates. By combining both natural and laboratory epitope residues, we identified 62 (11 overlapped) residues clustered into five antigenic sites (i.e., A-E) which are highly correlated to the antigenic sites of H3N2 HA. Our method recognizes sites A, B and C as critical sites for escaping from neutralizing antibodies in H1N1 virus. Experimental results show that the accuracies of our models are 81.2% and 82.2% using 41 and 62 epitope residues, respectively, for predicting antigenic variants on 197 paring HA sequences. In addition, our model can detect the emergence of epidemic strains and reflect the genetic diversity and antigenic variant between the vaccine and circulating strains. Finally, our model is theoretically consistent with the evolution rates of H3N2 and H1N1 viruses and is often consistent to WHO vaccine strain selections. We believe that our models and the inferred antigenic sites of HA are useful for understanding the antigenic drift and evolution of influenza A H1N1 virus.     

Broad vaccine protection against Neisseria meningitidis using factor H binding protein

Neisseria meningitidis, the causative agent of invasive meningococcal disease (IMD), is classified into different serogroups defined by their polysaccharide capsules. Meningococcal serogroups A, B, C, W, and Y are responsible for most IMD cases, with serogroup B (MenB) causing a substantial percentage of IMD cases in many regions. Vaccines using capsular polysaccharides conjugated to carrier proteins have been successfully developed for serogroups A, C, W, and Y. However, because the MenB capsular polysaccharide is poorly immunogenic, MenB vaccine development has focused on alternative antigens. The 2 currently available MenB vaccines (MenB-4C and MenB-FHbp) both include factor H binding protein (FHbp), a surface-exposed protein harboured by nearly all meningococcal isolates that is important for survival of the bacteria in human blood. MenB-4C contains a nonlipidated FHbp from subfamily B in addition to other antigens, including Neisserial Heparin Binding Antigen, Neisserial adhesin A, and outer membrane vesicles, whereas MenB-FHbp contains a lipidated FHbp from each subfamily (A and B). FHbp is highly immunogenic and a main target of bactericidal activity of antibodies elicited by both licensed MenB vaccines. FHbp is also an important vaccine component, in contrast to some other meningococcal antigens that may have limited cross-protection across strains, as FHbp-specific antibodies can provide broad cross-protection within each subfamily. Limited cross-protection between subfamilies necessitates the inclusion of FHbp variants from both subfamilies to achieve broad FHbp-based vaccine coverage. Additionally, immune responses to the lipidated form of FHbp have a superior cross-reactive profile to those elicited by the nonlipidated form. Taken together, the inclusion of lipidated FHbp variants from both FHbp subfamilies is expected to provide broad protection against the diverse disease-causing meningococcal strains expressing a wide range of FHbp sequence variants. This review describes the development of vaccines for MenB disease prevention, with a focus on the FHbp antigen.     

Within-host dynamics of antigenic variation.

Genomes of some parasites contain dozens of alternative and highly diverged surface antigens, of which only a single one is expressed in any cell. Individual cells occasionally change expression of their surface antigen, allowing them to escape immune surveillance. These switches appear to occur in a partly random way, creating a diverse set of antigenic variants. In spite of this diversity, the parasitemia develops as a series of outbreaks, in which each outbreak is dominated by relatively few antigenic types. Host-specific immunity eventually clears the dominant antigenic types, and a new outbreak follows from antigenic types that have apparently been present all along at low frequency. This pattern of sequential dominance by different antigenic types remains unexplained. We review the five most prominent theories, which have developed mainly from studies of the protozoans Trypanosoma and Plasmodium, and the bacterial spirochete Borrelia. The most promising theories depend on some combination of mechanisms to create favored connectivity pathways through the matrix of transitions between variants. Favored pathways may arise from biased switches at the molecular level of gene expression or from biases imposed by immune selection. We illustrate the concept of connectivity pathways by reanalysis of data on transitions between variants from Borrelia hermsii.     

Potentially conflicting selective forces that shape the vls antigenic variation system in Borrelia burgdorferi

Changing environmental conditions present an evolutionary challenge for all organisms. The environment of microbial pathogens, including the adaptive immune responses of the infected host, changes rapidly and is lethal to the pathogen lineages that cannot quickly adapt. The dynamic immune environment creates strong selective pressures favoring microbial pathogen lineages with antigenic variation systems that maximize the antigenic divergence among expressed antigenic variants. However, divergence among expressed antigens may be constrained by other molecular features such as the efficient expression of functional proteins. We computationally examined potential conflicting selection pressures on antigenic variation systems using the vls antigenic variation system in Borrelia burgdorferi as a model system. The vls system alters the sequence of the expressed antigen by recombining gene fragments from unexpressed but divergent ‘cassettes’ into the expression site, vlsE. The in silico analysis of natural and altered cassettes from seven lineages in the B. burgdorferi sensu lato species complex revealed that sites that are polymorphic among unexpressed cassettes, as well as the insertion/deletion mutations, are organized to maximize divergence among the expressed antigens within the constraints of translational ability and high translational efficiency. This study provides empirical evidence that conflicting selection pressures on antigenic variation systems can limit the potential antigenic divergence in order to maintain proper molecular function.     

Phylogenetic analyses of influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil

Pandemic influenza A H1N1 [A(H1N1)pdm09] was first detected in Brazil in May 2009, and spread extensively throughout the country causing a peak of infection during June to August 2009. Since then, it has continued to circulate with a seasonal pattern, causing high rates of morbidity and mortality. Over this period, the virus has continually evolved with the accumulation of new mutations. In this study we analyze the phylogenetic relationship in a collection of 220 A(H1N1)pdm09 hemagglutinin (HA) gene sequences collected during and after the pandemic period (2009 to 2014) in Brazil. In addition, we have looked for evidence of viral polymorphisms associated with severe disease and compared the range of viral variants with the vaccine strain (A/California/7/2009) used throughout this period.The phylogenetic analyses in this study revealed the circulation of at least eight genetic groups in Brazil. Two (G6-pdm and G7-pdm) co-circulated during the pandemic period, showing an early pattern of viral diversification with a low genetic distance from vaccine strain. Other phylogenetic groups, G5, G6 (including 6B, 6C and 6D subgroups), and G7 were found in the subsequent epidemic seasons from 2011 to 2014. These viruses exhibited more amino acid differences from the vaccine strain with several substitutions at the antigenic sites. This is associated with a theoretical decrease in the vaccine efficacy. Furthermore, we observed that the presence of any polymorphism at residue 222 of the HA gene was significantly associated with severe/fatal cases, reinforcing previous reports that described this residue as a potential virulence marker.This study provides new information about the circulation of some viral variants in Brazil, follows up potential genetic markers associated with virulence and allows infer if the efficacy of the current vaccine against more recent A(H1N1)pdm09 strains may be reduced.     

Antigenic and sequence variability of the human respiratory syncytial virus F glycoprotein compared to related viruses in a comprehensive dataset

A comprehensive analysis of sequence variation was carried out comparing the fusion (F) protein of human respiratory syncytial viruses (hRSV) from antigenic groups A and B with the prototype sequence of the A2 strain, also belonging to antigenic group A. The limited number of full bovine RSV F sequences available were included, as well as an extensive set of F sequences from the related human metapneumovirus (hMPV). The results were analysed in the context of the recently determined three dimensional F protein structures, with antigenic sites mapped to these. Although a high degree of sequence conservation in hRSV F exists, and sequence changes did not correlate with location of antigenic sites, preferential accumulation of amino acid changes in certain antigenic sites was noted. When the analysis was extended to hMPV F, a high number of changes was noticed, in agreement with the limited degree of sequence conservation. However, some conserved regions were noted, which may account for the limited number of cross-reactive monoclonal antibodies described between hRSV F and hMPV F. These results provide information about the degree of sequence and antigenic variation currently found in the F protein of circulating viruses. They highlight the importance of establishing a baseline dataset to monitor for future changes that might evolve should preventative immunological measures be made widely available.     

Population Genetics Identifies Challenges in Analyzing Rare Variants

Geneticists have, for years, understood the nature of genome‐wide association studies using common genomic variants. Recently, however, focus has shifted to the analysis of rare variants. This presents potential problems for researchers, as rare variants do not always behave in the same way common variants do, sometimes rendering decades of solid intuition moot. In this paper, we present examples of the differences between common and rare variants. We show why one must be significantly more careful about the origin of rare variants, and how failing to do so can lead to highly inflated type I error. We then explain how to best avoid such concerns with careful understanding and study design. Additionally, we demonstrate that a seemingly low error rate in next‐generation sequencing can dramatically impact the false‐positive rate for rare variants. This is due to the fact that rare variants are, by definition, seen infrequently, making it hard to distinguish between errors and real variants. Compounding this problem is the fact that the proportion of errors is likely to get worse, not better, with increasing sample size. One cannot simply scale their way up in order to solve this problem. Understanding these potential pitfalls is a key step in successfully identifying true associations between rare variants and diseases.     

Use of monoclonal anti-haemagglutinin antibodies for the “In vitro” selection of a sequential influenza virus antigenic variant

A sequential antigenic variant of the A/Texas/77 (H3N2) influenza virus was obtained in vitro using a monoclonal antibody against the haemagglutinin (HA) of the antigenic variant V18 previously selected in vitro from the parental Texas virus. The sequential antigenic variant, designated DV1, the V18 antigenic variant and the parental A/Texas/77 viruses were used to evaluate the frequency of anti-haemagglutinin antibodies in human sera in single radial haemolysis assays. Twenty six of 100 children's sera, which contained antibodies to the parental A/Texas/77 virus, failed to react with the V18 antigenic variant. A higher proportion of sera (42%) failed to react with the DV1 antigenic variant with alterations in two different antigenic determinants with respect to the parental virus. The results are discussed in relation to the mechanism of antigenic drift and to the in vivo reaction of antigenic variants selected in vitro.Corresponding author.     

Baculovirus surface display of E envelope glycoprotein of Japanese encephalitis virus and its immunogenicity of the displayed proteins in mouse and swine models

Japanese encephalitis virus (JEV), an important pathogen in humans and animals, is capable of causing febrile syndrome, encephalitis and death. The E glycoprotein of JEV is the main target for inducing neutralizing antibodies and protective immunity in the natural host. In this work, we have succeeded in construction of one recombinant baculovirus BacSC-E expressing His6-tagged E with the baculovirus envelope protein gp64 TM and CTD. After infection, E was expressed and anchored on the plasma membrane of Sf-9 cells, as demonstrated by Western blot and confocal microscopy. Immunogold electron microscopy demonstrated that the E glycoprotein was successfully displayed on the viral surface. Vaccination of mouse and swine with recombinant baculovirus BacSC-E successfully induced neutralizing antibody response and protective immunity toward a lethal challenge of the JEV. Taken all findings together, our results indicate that the recombinant baculovirus BacSC-E can be a potential vaccine against JEV infections. This finding provides valuable information for establishing subunit vaccines for JEV antigenic complex viruses. This is a fresh research demonstrating the potential of E-pseudotyped baculovirus as a JEV vaccine.