Influenza virus antigens and ‘antigenic drift’

Influenza Viruses: Harnessing the Crucial Role of the M2 Ion-Channel and Neuraminidase toward Inhibitor Design

As a member of the Orthomyxoviridae family of viruses, influenza viruses (IVs) are known causative agents of respiratory infection in vertebrates. They remain a major global threat responsible for the most virulent diseases and global pandemics in humans. The virulence of IVs and the consequential high morbidity and mortality of IV infections are primarily attributed to the high mutation rates in the IVs' genome coupled with the numerous genomic segments, which give rise to antiviral resistant and vaccine evading strains. Current therapeutic options include vaccines and small molecule inhibitors, which therapeutically target various catalytic processes in IVs. However, the periodic emergence of new IV strains necessitates the continuous development of novel anti-influenza therapeutic options. The crux of this review highlights the recent studies on the biology of influenza viruses, focusing on the structure, function, and mechanism of action of the M2 channel and neuraminidase as therapeutic targets. We further provide an update on the development of new M2 channel and neuraminidase inhibitors as an alternative to existing anti-influenza therapy. We conclude by highlighting therapeutic strategies that could be explored further towards the design of novel anti-influenza inhibitors with the ability to inhibit resistant strains.

Conservation region finding for influenza A viruses by machine learning methods of N-linked glycosylation sites and B-cell epitopes

Influenza type A, a serious infectious disease of the human respiratory tract, poses an enormous threat to human health worldwide. It leads to high mortality rates in poultry, pigs, and humans. The primary target identity regions for the human immune system are hemagglutinin (HA) and neuraminidase (NA), two surface proteins of the influenza A virus. Research and development of vaccines is highly complex because the influenza A virus evolves rapidly. This study focused on three genetic features of viral surface proteins: ribonucleic acid (RNA) sequence conservation, linear B-cell epitopes, and N-linked glycosylation. On the basis of these three properties, we analyzed 12,832 HA and 9487 NA protein sequences, which we retrieved from the influenza virus database. We classified the viral surface protein sequences into the 18 HA and 11 NA subtypes that have been identified thus far. Using available analytic tools, we searched for the representative strain of each virus subtype. Furthermore, using machine learning methods, we looked for conservation regions with sequences showing linear B-cell epitopes and N-linked glycosylation. Compared to the prediction of the Immune Epitope Database (IEDB) antibody neutralization response (i.e., screening of antibody sequence regions), in this study, the virus sequence coverage was large and accurate and contained N-linked glycosylation sites. The results of this study proved that we can use the machine learning-based prediction method to solve the problem of vaccine invalidation that occurred during the rapid evolution of the influenza A virus and also as a prevaccine assessment. In addition, the screening fragments can be used as a universal influenza vaccine design reference in the future.

Fitness cost of reassortment in human influenza

Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10⁻² in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage.

The genome of the human influenza virus consists of 8 disjoint RNA polymer segments. These segments can undergo reassortment: when two viruses co-infect a host cell, they can produce viral offspring with a new combination of segments. In this paper, we show that reassortment within a given influenza lineage induces a fitness cost that increases in strength with increasing genetic distance of the parent viruses. Our finding suggests that evolution continuously produces viral proteins whose fitness depends on each other; reassortment reduces fitness by breaking up successful combinations of proteins. Thus, selection across proteins constrains viral evolution within a given lineage, and it may be an important factor in defining a viral species.

Predicting evolution from the shape of genealogical trees

Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of the sampled sequences and that this information can be used to predict successful strains. Our approach is based on the assumption that evolution proceeds by accumulation of small effect mutations, does not require species specific input and can be applied to any asexual population under persistent selection pressure. We demonstrate its performance using historical data on seasonal influenza A/H3N2 virus. We predict the progenitor lineage of the upcoming influenza season with near optimal performance in 30% of cases and make informative predictions in 16 out of 19 years. Beyond providing a tool for prediction, our ability to make informative predictions implies persistent fitness variation among circulating influenza A/H3N2 viruses.

DOI:http://dx.doi.org/10.7554/eLife.03568.001

When viruses multiply, they copy their genetic material to make clones of themselves. However, the genetic material in the clone is often slightly different from the genetic material in the original virus. These mutations can be caused by mistakes made during copying or by radiation or chemicals. Further mutations arise when the clones multiply, which means that, after many generations, there will be quite large differences in the genetic material carried by many members of the population. Most mutations have little or no effect on the ‘fitness’ of an individual - that is, on its ability to survive and multiply - but some mutations do have an influence.

Some viruses, like seasonal influenza (flu) viruses, can mutate so rapidly that the most common strains change from year to year. This is why new flu vaccines are needed every year. To date most attempts to predict the evolution of seasonal flu viruses have focused on identifying specific features within the genetic sequences that might indicate fitness. However, such approaches require lots of information about the viruses, and this information is often not available.

To address this problem, Neher, Russell and Shraiman have developed a more general method to predict fitness from virus genetic sequences. First, a ‘family tree’ for a virus population - which shows how each strain of the virus is related to other strains - was constructed by comparing the genetic sequences.

The next step was based on the observation that as long as differences in fitness arise from the accumulation of multiple mutations, the branching structure of this family tree will bear a visible imprint of the natural selection process as it unfolds. Using this insight and methods borrowed from statistical physics, Neher et al. then analyzed the shape and branching pattern of the tree to work out the fitness of the different strains relative to each other.

Neher et al. tested the method using historical influenza A virus data. In 16 of the 19 years studied, the family tree approach made meaningful predictions about which viruses were most likely to give rise to future epidemics. The ability to predict influenza virus evolution from tree shape alone suggests that influenza virus evolution may be more predictable than previously expected.

DOI:http://dx.doi.org/10.7554/eLife.03568.002

Antigenic and genetic evolution of equine influenza A (H3N8) virus from 1968 to 2007

Equine influenza virus is a major respiratory pathogen in horses, and outbreaks of disease often lead to substantial disruption to and economic losses for equestrian industries. The hemagglutinin (HA) protein is of key importance in the control of equine influenza because HA is the primary target of the protective immune response and the main component of currently licensed influenza vaccines. However, the influenza virus HA protein changes over time, a process called antigenic drift, and vaccine strains must be updated to remain effective. Antigenic drift is assessed primarily by the hemagglutination inhibition (HI) assay. We have generated HI assay data for equine influenza A (H3N8) viruses isolated between 1968 and 2007 and have used antigenic cartography to quantify antigenic differences among the isolates. The antigenic evolution of equine influenza viruses during this period was clustered: from 1968 to 1988, all isolates formed a single antigenic cluster, which then split into two cocirculating clusters in 1989, and then a third cocirculating cluster appeared in 2003. Viruses from all three clusters were isolated in 2007. In one of the three clusters, we show evidence of antigenic drift away from the vaccine strain over time. We determined that a single amino acid substitution was likely responsible for the antigenic differences among clusters.

A launch vector for the production of vaccine antigens in plants

Historically, most vaccines have been based on killed or live-attenuated infectious agents. Although very successful at immunizing populations against disease, both approaches raise safety concerns and often have limited production capacity. This has resulted in increased emphasis on the development of subunit vaccines. Several recombinant systems have been considered for subunit vaccine manufacture, including plants, which offer advantages both in cost and in scale of production. We have developed a plant expression system utilizing a 'launch vector', which combines the advantageous features of standard agrobacterial binary plasmids and plant viral vectors, to achieve high-level target antigen expression in plants. As an additional feature, to aid in target expression, stability and purification, we have engineered a thermostable carrier molecule to which antigens are fused. We have applied this launch vector/carrier system to engineer and express target antigens from various pathogens, including, influenza A/Vietnam/04 (H5N1) virus.

Vaccines for Pandemic Influenza. The History of our Current Vaccines, their Limitations and the Requirements to Deal with a Pandemic Threat

Fears of a potential pandemic due to A(H5N1) viruses have focussed new attention on our current vaccines, their shortcomings, and concerns regarding global vaccine supply in a pandemic. The bulk of current vaccines are inactivated split virus vaccines produced from egggrown virus and have only modest improvements compared with those first introduced over 60 years ago. Splitting, which was introduced some years ago to reduce reactogenicity, also reduces the immunogenicity of vaccines in immunologically naïve recipients. The A(H5N1) viruses have been found poorly immunogenic and present other challenges for vaccine producers which further exacerbate an already limited global production capacity. There have been some recent improvements in vaccine production methods and improvements to immunogenicity by the development of new adjuvants, however, these still fall short of providing timely supplies of vaccine for all in the face of a pandemic. New approaches to influenza vaccines which might fulfil the demands of a pandemic situation are under evaluation, however, these remain some distance from clinical reality and face significant regulatory hurdles. Key words: Adjuvant, Antigen, Cell-culture, Immune response, Immunogenicity, Influenza A(H5N1), Split vaccine

Epidemic dynamics and antigenic evolution in a single season of influenza A

We use a mathematical model to study the evolution of influenza A during the epidemic dynamics of a single season. Classifying strains by their distance from the epidemic-originating strain, we show that neutral mutation yields a constant rate of antigenic evolution, even in the presence of epidemic dynamics. We introduce host immunity and viral immune escape to construct a non-neutral model. Our population dynamics can then be framed naturally in the context of population genetics, and we show that departure from neutrality is governed by the covariance between a strain's fitness and its distance from the original epidemic strain. We quantify the amount of antigenic evolution that takes place in excess of what is expected under neutrality and find that this excess amount is largest under strong host immunity and long epidemics.

Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses

Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002–2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003–2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.

Evolution of the flu virus is analyzed via genomic phylogeny; humans are found to provide a reservoir of antigenic variability implicit in flu adaptation and virulence.

Reassortants in recent human influenza A and B isolates from South East Asia and Oceania

From 2000 to 2002, human influenza A and B viruses that were genetic reassortants of contemporary circulating human strains, were isolated in South East Asia and Oceania. Similar to reports from other regions, A(H1N2) isolates were found to be reassortants of circulating A(H3N2) viruses that had acquired only the haemagglutinin gene of an A(H1N1) virus. Some of these reassortants from Thailand and Singapore predate those previously recorded during the winter of 2001-2002 in Europe and the Middle East and may be precursors of these viruses. The B reassortants had a haemagglutinin similar to an earlier B strain, B/Shangdong/7/97 (B/Victoria/2/87-lineage) and a neuraminidase similar to the recently circulating B/Sichuan/379/99 virus (B/Yamagata/16/88-lineage). Despite the early occurrences of A(H1N2) reassortants and the extensive circulation of A(H1) viruses in South East Asia and Oceania during 2000-2001, these reassortant influenza A viruses have to date not been prominent unlike Europe and the Middle East where they were common in the 2001-2002 winter. In contrast the reassortant B viruses, which first emerged in this region in early 2002, rapidly became the predominant strains isolated from patients with influenza B in South East Asia and Oceania.