You probably had a common cold sometime in the last three months. Surely, you wondered which of your close contacts was the origin of the infection. I will give an answer, but I will start from the very beginning. In this article, I will discuss the evolution of viruses and how it differs from that of cellular life.
The first thing I want to say is that it is not the classical, well-known gradual mutations—and some occasional leaps—that accumulate over time, but a slightly different and mad model.
Viruses don’t just evolve; they restructure
Purifying Selection: The Quiet Sculptor of Cellular Genomes
In cellular lifeforms—bacteria, protists, plants, and animals—the dominant mode of genome evolution is gradualism. Genes are passed from one generation to the next vertically, and the vast majority of evolution proceeds through point mutations, small insertions or deletions, and occasional gene duplications. As these changes accumulate over long periods of time, they are subjected to filtering via natural selection. Beneficial mutations may spread as positive selection favors their propagation, while deleterious mutations are removed by purifying selection. Some other variations are neutral, as they have no or very mild deleterious effects, so they drift across generations. From time to time, leaps happen, such as in the case of horizontal gene transfer and domain shuffling.
Purifying selection, in particular, acts as the defender of essential genes. It maintains the integrity of protein-coding sequences and prevents harmful changes. This is the reason why certain genes, such as those for ribosomal proteins, are highly conserved across the tree of life.
Viral Evolution: A World of Genomic Reshuffling
Viruses, on the other hand, often have compact, fast-replicating, and highly modular genomes. They don’t always follow the same rules. Rather than accumulating small changes over extended periods of time, viruses evolve through episodic genome restructuring. They are natural genetic engineers. Events such as horizontal gene transfer and gene gain/loss, where they can pick up genes from the host, reshape the genome of the virus. Viruses can also swap functional gene cassettes in a process called modular recombination.
These events can radically alter viral genomes over short evolutionary timescales. A phage might acquire a new tail fiber gene, instantly expanding its host range. Or it might lose a regulatory gene, streamlining its replication. This mode of evolution is often described as saltational—evolutionary jumps rather than steps.
Furthermore, viruses have multiple origins, as different classes of viruses have different origins. This is different from the monophyletic origin of cellular life. Viruses most likely emerged independently multiple times, due to their ability to genetically engineer themselves and the presence of early replicators. This makes the evolutionary dynamics of viruses quite different from those of cellular life.
Do viruses experience purifying selection?
Yes, but not in the same way or to the same extent as cellular life. There is a group of proteins that are essential for a virus (e.g., capsid proteins, replication enzymes) that undergo some sort of purifying selection, as an RNA virus can’t simply lose or have a non-functional RNA polymerase. Yet, sometimes the high rates of mutation and recombination can blur the signals of traditional selection.
Applying classical population-genetic terms like “purifying selection” can be misleading. The population structures, mutation rates, and inheritance patterns of viruses are too dynamic and often violate key assumptions of these models.
In this sense, when you get a cold, blame these ultra-tiny yet innovative genetic engineers that have been propagating around and sometimes preying on cells for billions of years—not your friends.
Further Reads:
Shapiro, J. A. Evolution: A View from the 21st Century. (FT Press Science, 2011).
Koonin, E. V., Dolja, V. V. & Krupovic, M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 479–480, 2–25 (2015).
The image was generated using OpenAI’s Chatgpt 4
RNA Stuff 