Viruses are self-replicating nucleoprotein complexes that have the ability to cause diseases; with only a few exceptions they are composed of, at least, a single copy of genetic material (either RNA or DNA) and a virally encoded protective shell. H.R. Gelderblom defined them as mobile genetic elements, most probably of cellular origin and characterized by a long co-evolution of virus and host. Viruses are infectious, obligate molecular parasites, do not produce their own energy (i.e., ATP), respire, grow or move. Most viruses are ~ 100 times smaller than a bacteria (0.5 – 5 µm) and their protective shell is called a capsid and when enclosing its genetic material, a nucleocapsid; some giant viruses can have several concentric shells. Capsids can be classified as symmetric (icosahedral or helical) and pleomorphic (not characterized by a single size or shape). Complex viruses also contain a host-derived lipid bilayer (envelope), spike proteins (glycoproteins), and host- and/or virally derived enzymes. Fig. 1 shows cryo-EM reconstructions of a double-stranded DNA (ds-DNA) bacterial virus (bacteriophage), a non-enveloped single-stranded RNA (ss-RNA) bacterial virus, an enveloped ss-RNA animal virus and a retrovirus. Viruses infect all of the life kingdoms and can retain their infectivity even outside their host and/or vector, even under very extreme conditions. All of these characteristics highlight the great diversity in the virus world, making generalizations almost impossible and opening the doors to novel biochemical processes and therefore creating new paradigms. Creative Biomart provides kinds of viral antigens such as H1N1 HA protein for research applications about viruses.
FIG 1. Cryo-EM reconstruction of four viruses.
A particular paradigm that has been challenged is the definition of life and inanimate objects. A. Rein recently proposed that a virus can be viewed as a rather regular, relatively simple physical object. Alternatively, it can be seen as a living organism, evolving in response to selective pressure. This duality concept is equivalent to that of light; depending on the measured property it behaves like a wave or like a particle. Viruses present such duality, like all “living organisms” they react to ecological and evolutionary pressures to ensure successful replication of their genes. On one hand, they have evolve to have a fast mutation rate to avoid been detected by the host immune response system (i.e., influenza) and/or incorporate genes from other viruses and/or hosts (horizontal gene transfer). On the other hand, they can “survive” outside of their host, they can be disassembled and further purified into their elemental constituents and then reassembled into infectious particles. They can be chemically modified and used for macromolecular assemblies in the absence of their genetic material, making them valuable tools for biotechnology.
Given the incredible diversity of virus composition, structure and biochemical properties, it is not possible to describe them by a taxonomic system equivalent to the one used for traditional life kingdoms, therefore a great deal of work has been done on trying to find a systematic way that better describes them. As a result several criteria have been proposed for the classification of viruses:
1) On the basis of their evolutionary relationships with other viruses: ICTV classification.
2) On the folding motifs of their main capsid protein.
3) By a combination of their nucleic acid, strandedness (double or single), sense and method replication: Baltimore classification.
4) Based on chemical and physical characters like nucleic acid, symmetry, presence of envelope, diameter of the capsid and number of capsomers: LHT system.
The ICTV classification (International Committee of Taxonomy of Viruses) shares many features with the classification system of cellular organisms and is based on the assumption that virus families have evolved from a common ancestor. David Baltimore’s classification system divides viruses into seven groups based on the way they go from their original genomic material to their messenger RNAs (see Fig. 2). The LHT system proposed in 1962 is based on a set of structural characteristics, which might be useful if one aims to understand the physical aspects of viruses. However, from the point of view of physical virology all of these classifications are far too complicated, making it almost impossible to find general rules that explain the assembly of viruses. Abrescia and co-workers proposed a simpler and elegant scheme by realizing that they could build a structured-based phylogenetic tree showing the four different lineages based on the folding motif of the viral capsid proteins (PRD1-, Picorna-, HK967- and BTV-like foldings). Unfortunately, this classification includes within the same viral lineage double- and single-stranded viruses. While all these classifications are extremely useful when looking at the structure of the capsids, evolution or biochemical properties they are either far too complicated or not appropriate when trying to understand virus assembly mechanisms.
FIG 2. The Baltimore classification is a system that places viruses into seven groups depending on how their replication method and the strandedness of the encapsidated viral genome in the mature infectious particle.
A very simple (and drastic) way to classify viruses from an assembly point of view is by grouping them whether on their genome is either single- or double-stranded during encapsidation. This extremely simple classification is independent of post-encapsidation processes in which the genome might go from single- to double-stranded encapsidation, i.e. Hepatitis B and HIV. Independent of the chemical nature of their nucleic acid (DNA or RNA) we can merge groups II, IV, V and VI from Baltimore’s classification into a single-stranded virus category and groups I, II and VII into a double-stranded one:
1) Double-stranded genome packaging involves the formation of empty capsids and subsequent translocation of the DNA or RNA into the capsid by a virally-encoded enzyme. The latter process requires chemical energy, i.e. ATP, and the performance of work.
2) Single-stranded genome capsid assembly and genome packaging are coupled to each other, and are spontaneous, not involving ATP.