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.