Investigating the Concept and Origin of Viruses

Abstract

The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks.

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

“…Since the availability of the first viral genome sequences, it has been discussed as to whether they carry any features of early replicons beyond those that can be inferred from cellular life forms or if they represent different stages of the “degeneration” of cellular life [ 221 ]. The jumbo phages on the bacterial side and the NCLDV on the eukaryotic side have been at the center of this discussion as their large genomes straddle the size range between the smallest cellular genomes and medium-sized viral genomes [ 2 , 3 ].…”

The Unique, the Known, and the Unknown of Spumaretrovirus Assembly

“…In order to address these functional and evolutionary questions in full detail, one has to take advantage of the constantly increasing wealth of sequencing data from different organisms leading to the identification of a growing number and diversity of retroid elements. Here, a combination of advanced tools and methods in molecular evolution and retroviral “paleontology” of endogenous sequences and functional molecular biology/virology concepts and studies may help us gain new insights into ancient viral evolution [ 121 , 122 ].…”

The essence of life revisited: how theories can shed light on it

“…Note that we (Cornish-Bowden and Cárdenas 2017, 2020) consider luca to have existed a very long time after the origin of life, as also implied by Fig. 1 of a recent article of Nasir et al (2020), and by their statement that "luca was not the first cell. It was the last population of cells that diversified into modern cells.…”