Introduction to Virus Origins and Their Role in Biological Evolution

Chapter Contents

1.1 Considerations on Biological Diversity

To approach the behavior of viruses acting as populations, we must first examine the diversity of the present-day biosphere, and the physical and biological context in which primitive viral forms might have arisen. Evolution pervades nature. Thanks to new theories and to the availability of powerful instruments and experimental procedures, which together constitute the very roots of scientific progress, we are aware that the physical and biological worlds are evolving constantly. Several classes of energy have gradually shaped matter and living entities, basically as the outcome of random events and Darwinian natural selection in its broadest sense. The identification of DNA as the genetic material, and the advent of genomics in the second half of the twentieth century unveiled an astonishing degree of diversity within the living world that derives mainly from combinations of four classes of nucleotides. Biodiversity, a term coined by O. Wilson in 1984, is a feature of all living beings, be multicellular differentiated organisms, single cell organisms, or subcellular genetic elements, among them the viruses. Next generation sequencing methods developed at the beginning of the twenty-first century, which allow thousands of sequences from the same biological sample (a microbial community, a tumor, or a viral population) to be determined, has further documented the presence of myriads of variants in a “single biological entity” or in “communities of biological entities.” Differences extend to individuals that belong to the same biological group, be it Homo sapiens, Droshophila melanogaster, Escherichia coli, or human immunodeficiency virus type 1 (HIV-1). No exceptions have been described.

During decades, in the first half of the twentieth century, population genetics had as one of its tenets that genetic variation due to mutation had for the most part been originated in a remote past. It was generally thought that the present-day diversity was essentially brought about by the reassortment of chromosomes during sexual reproduction. This view was weakened by the discovery of extensive genetic polymorphisms, first in Drosophila and humans, through indirect analyses of electrophoretic mobility of enzymes, detected by in situ activity assays to yield zymograms that were displayed as electromorphs. These early studies on allozymes were soon extended to other organisms. Assuming that no protein modifications had occurred specifically in some individuals, the results suggested the presence of several different (allelic) forms of a given gene among individuals of the same species, be humans, insects, or bacteria. In the absence of information on DNA nucleotide sequences, the first estimates of heterogeneity from the numbers of electromorphs were collated with the protein sequence information available. An excellent review of these developments (Selander, 1976) ended with the following premonitory sentence on the role of molecular biology in unveiling evolutionarily relevant information: “Considering the magnitude of this effect, we may not be overfanciful to think that future historians will see molecular biology more as the salvation for than, as it first seemed, the nemesis of evolutionary biology.”

The conceptual break was confirmed and accentuated when molecular cloning and nucleotide sequencing techniques produced genomic nucleotide sequences from multiple individuals of the same biological species. Variety has shaken our classification schemes, opening a debate on how to define and delimit biological “species” in the microbial world. From a medical perspective it has opened the way to “personalized” medicine, so different are the individual contexts in which disease processes (infectious or other) unfold. Diversity is a general feature of the biological world, with multiple implications for interactions in the environment, and also for human health and disease (Bernstein, 2014).

1.2 Some Questions of Current Virology and the Scope of This Book

Viruses (from the Latin “virus,” poison) are no exception regarding diversity. The number of different viruses and their dissimilarity in shape and behavior is astounding. Current estimates indicate that the total number of virus particles in our biosphere reaches 1032, exceeding by one order of magnitude the total number of cells. Viruses are found in surface and deep sea and lake waters, below the Earth surface, in any type of soil, in deserts, and in most environments designated as extreme regarding...