A brief history of the species concept in virology and an opinion on the proposal to introduce Linnaean binomial virus species names.

The species concept used in virology is based on the logic of the Linnaean hierarchy, which views a species class as the lowest abstract category that is included in all the higher categories in the classification, such as genera and families. As a result of this class inclusion, the members of a species class are always less numerous than the members of higher classes, which become more numerous as one moves up in the hierarchy. Because species classes always have fewer members than any of the higher classes, logic requires that they need more qualifications for establishing membership than any of the higher classes. This invalidates the claim that a species could be defined by a single property present in all its members. Species were only accepted in virus classification in 1991, because virologists assumed that it would lead to the use of Latin species names, which they rejected. Anglicized binomial species names have been used by virologists for more the 40 years and are popular because they consist of a virus name followed by a genus name that most virologists are familiar with. The ICTV has proposed to introduce a new Latinized virus species binomial nomenclature using the genus name followed by a hard-to-remember Latinized species epithet that bears little resemblance to the name of the virus itself. However, the proposal did not clarify what the advantage is of having to learn hundreds of new unfamiliar virus species names. In 2013, the ICTV changed the definition of a virus species as an abstract class and defined it as a group of physical objects, which induced virologists to believe that a virus species could be defined by a few characteristics of the viral genome. In recent years, thousands of viral sequences have been discovered in metagenomic databases, and the ICTV has suggested that it should be possible to incorporate these sequences in the current ICTV virus classification. Unfortunately, the relational properties of these hypothetical viruses that result from their biological interactions with hosts and vectors remain in the vast majority of cases totally unknown. The absence of this information makes it in fact impossible to incorporate these metagenomic sequences in the current classification of virus species.

The metaphor that viruses are living is alive and well, but it is no more than a metaphor.

Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are larger and have a more complex genome than small bacteria has fostered the interpretation that viral factories, which are the compartments in virus-infected cells where the virus is being replicated, are able to transform themselves into a new type of living viral organism called a virocell. However, because of the widespread occurrence of horizontal gene transfer, endosymbiosis and hybridization in the evolution of viral genomes, it has not been possible to include metaphorical virocells in the so-called Tree of Life which itself is a metaphor. In the case of viruses that cause human diseases, the infection process is usually presented metaphorically as a war between host and virus and it is assumed that a virus such as the human immunodeficiency virus (HIV) is able to develop new strategies and mechanisms for escaping protective host immune responses. However, the ability of the virus to defeat the immune system is solely due to stochastic mutations arising from the error-prone activity of the viral enzyme reverse transcriptase. The following two types of metaphors will be distinguished: an intentionality metaphor commonly used for attributing goals and intentions to organisms and the living virus metaphor that considers viruses to be actually living organisms.

Virus species and virus identification: past and current controversies.

The basic concepts used in virus classification are analyzed. A clear distinction is drawn between viruses that are real, concrete objects studied by virologists and virus species that are man-made taxonomic constructions that exist only in the mind. Classical views regarding the nature of biological species are reviewed and the concept of species used in virology is explained. The use of pair-wise sequence comparisons between the members of a virus family for delineating species and genera is reviewed. The difference between the process of virus identification using one or a few diagnostic properties and the process of creating virus taxa using a combination of many properties is emphasized. The names of virus species in current use are discussed as well as a binomial system that may be introduced in the future.

Improving the quality of BIACORE-based affinity measurements.

Although the BIACORE technology has become the standard method for measuring the affinity of antigen-antibody interactions, many users of the technology do not apply the most advanced experimental design and data processing methods that are now available. In addition, many published reports fail to provide the experimental details that are necessary to assess the reliability of the affinity data that are presented. This review describes the experimental conditions that should be used to ensure that reliable biosensor data are collected. There is little justification for the belief that ELISA methods provide in principle more reliable affinity parameters than biosensor technology.

Analysing structure-function relationships with biosensors.

Elucidating the nature of the relationship between the structure and function of biomolecules remains one of the major challenges in biology. Biomolecules are dynamic entities that possess a variety of structures, and their functions at the molecular, cellular and organismic levels are quite different. Since there is no single causal link between structure and function, the search should be for correlations rather than causal relations. Biosensor instruments based on surface plasmon resonance are widely used for establishing correlations between the chemical structure of binding sites and their binding activity. Mutagenesis studies have shown that only a small percentage of the residues located in a binding site contribute to the binding energy. Since substitutions in residues located far away from the binding site are able to affect binding activity, this greatly complicates the rational design of proteins endowed with improved functions. However, biosensors can be used to determine and predict the influence of the chemical environment and of the structure of a ligand on binding kinetics.

Recognition of peptides by antibodies and investigations of affinity using biosensor technology.

The study of peptide-antibody interactions has many applications in biology and medicine. Synthetic peptides corresponding to single protein epitopes are used instead of intact proteins as reagents for the diagnosis of viral and autoimmune diseases. Furthermore, antibodies raised against peptides are useful reagents for isolating and characterizing gene products. In this review, methods for analysing the molecular basis of peptide-antibody interactions are described, such as amino acid replacement studies, X-ray crystallography of peptide-antibody complexes and biosensor technology based on surface plasmon resonance. The importance of peptide conformation in antibody recognition is discussed, and the antigenic reactivity of epitopes in synthetic peptides and in cognate, intact proteins is compared.

Differential recognition of epitopes present on monomeric and oligomeric forms of gp160 glycoprotein of human immunodeficiency virus type 1 by human monoclonal antibodies.

The mechanism of infectivity neutralization of human immunodeficiency virus type 1 (HIV-1) by Ig is poorly understood. Three human monoclonal antibodies (mAbs 1b12, 2G12 and 2F5) that are able to neutralize primary isolates of HIV-1 in vitro have been shown to act synergistically. In the present study this synergy was analyzed by measuring the epitope accessibility and binding kinetics for these three mAbs with respect to monomeric and oligomeric env protein gp160 IIIB using surface plasmon resonance. The results indicate that oligomerization of gp160 affects the accessibility of some of the epitopes recognized by the mAbs and provide some insight into the mechanism of synergy between different anti-(HIV-1) mAbs.

Pitfalls of reductionism in the design of peptide-based vaccines.

It is widely believed that all biological phenomena can be reduced to chemistry and physics. Such a reductionist view disregards the fact that complex biological systems have relational (also called emergent) properties that their constituents lack and that cannot be deduced or predicted from the properties of the isolated components. When the individual components of the immune system are studied in isolation, many interconnections are lost and it is not possible to understand how the system functions at the level of the organism as a whole. Our increasing knowledge of the antigenic structure of viral proteins has also been of little help for improving the immunogenicity of individual viral epitopes and for enhancing their capacity to elicit a protective immune response against viral infection. When molecular design principles are used to optimize the binding properties of a synthetic peptide epitope with respect to one neutralizing monoclonal antibody, this does not ensure that the peptide, when used as immunogen, will be able to induce neutralizing antibodies that protect against disease. A reductionist approach does not provide the information required for designing peptide immunogens that will elicit neutralizing rather than non-neutralizing antibody responses.

Predicting the kinetics of peptide-antibody interactions using a multivariate experimental design of sequence and chemical space.

A multivariate approach involving modifications in peptide sequence and chemical buffer medium was used as an attempt to predict the kinetics of peptide-antibody interactions. Using a BIACORE system the kinetic parameters of the interaction of Fab 57P with 18 peptide analogues of an epitope of tobacco mosaic virus protein were characterized in 20 buffers of various pH values and containing different chemical additives (NaCl, urea, EDTA, KSCN and DMSO). For multivariate peptide design, three amino acid positions were selected because their modification was known to moderately affect binding, without abolishing it entirely. Predictive mathematical models were developed which related kinetic parameters (k(a) or k(d)) measured in standard buffer to the amino acid sequence of the antigen. ZZ-scales and a helix-forming-tendency (HFT) scale were used as descriptors of the physico-chemical properties of amino acids in the peptide antigen. These mathematical models had good predictive power (Q(2) = 0.49 for k(a), Q(2) = 0.73 for k(d)). For the non-essential residues under study, HFT and charge were found to be the most important factors that influenced the activity. Experiments in 19 buffers were performed to assess the sensitivity of the interactions to buffer composition. The presence of urea, DMSO and NaCl in the buffer influenced binding properties, while change in pH and the presence of EDTA and KSCN had no effect. The chemical sensitivity fingerprints were different for the various peptides. The results indicate that multivariate experimental design and mathematical modeling can be applied to the prediction of interaction kinetics.

Antigenicity and immunogenicity of synthetic peptides.

The ability of a peptide to react specifically with the functional binding site of a complementary antibody is known as its antigenic reactivity or antigenicity. Our understanding of peptide antigenicity has improved considerably in recent years mainly through the X-ray crystallographic analysis of peptide-monoclonal antibody complexes. This knowledge is obtained along reductionist lines by turning the biological question of antigen recognition into the purely chemical phenomenon of protein-peptide interactions described in terms of atomic forces and non-covalent bonds. This makes it possible to improve the degree of steric complementarity between a peptide and a single monoclonal antibody and thus to improve the peptide's antigenicity following structure-based rational design principles. The situation is quite different with immunogenicity which is the ability of the peptide to induce an immune response in a competent host. Whereas antigenicity can be reduced to the level of chemistry, such a reduction is not achievable in the case of immunogenicity which depends on many complex interactions with various elements of the host immune system. These cellular and regulatory mechanisms cannot be controlled by adjusting the structure of the peptide in a predetermined manner. For this reason, it is not possible to develop a synthetic peptide vaccine using molecular design principles.