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Viruses: Evolution in the Suburbs

Despite the fact that viruses are among the simplest biological entities – consisting only of DNA or RNA encapsulated in a protein coat – they can have devastating consequences, as viruses such as influenza, human immunodeficiency virus (HIV), and Ebola have greatly affected Track. From human history. Since they generally lack the cellular mechanism needed for reproduction, they reproduce by hijacking the host cells, often at the expense of the host. While their status as a living organism may be questioned, there is no doubt that viruses are formed by evolutionary forces that affect their genomes, in addition to their reproduction, host range, phylum, and other characteristics. With the emergence of SARS-CoV-2, a virus that has closely affected nearly every aspect of human life over the past year, studying viral evolution may seem more in-depth and relevant than ever before. Genome Biology and EvolutionThe most recent hypothetical case is a set of thought-provoking research papers in the field of viral evolution from the past two years, providing new insight into the evolutionary mechanisms affecting viruses, their genomes, and their hosts, as well as showing their use in the study of evolution.

The rapid and variable mutation rates observed between viruses create challenges for viral genome evolution studies. A study by González et al. (2019) sought to investigate the balance between beneficial and harmful mutations by creating a tobacco catalyst virus mutant library containing every possible nucleotide substitute from the 6K2 gene and then infecting tobacco plants with the library. By evaluating the mutations remaining after intra-host competition, the study revealed that most of the observed mutations were associated with higher fit and milder symptom development, indicating a potential trade-off between intra-host accumulation and symptom severity in nature. A study by Willemsen et al. (2019) Research on the mutation origin and history of the E5 gene for papillomavirus, which is known to be associated with cancer development in the host. Surprisingly, the authors found that a long stretch of non-coding DNA arose at the current site of the E5 gene at least four times during the evolution of papillomaviruses, and evolved into at least three different open reading frames encoding new proteins associated with infection phenotypes. (Skin warts, genital warts, or anogenital cancers). This provides a mechanism for genetic novelties in viruses and explains their potential phenotypic effects. Finally, in their paper, Ou et al. (2020) hypothesizes that the metabolic background of RNA viruses – specifically the high demand for cytidine triphosphate (CTP) – leads to a mutagenic bias toward the replacement of cytosine with uracil, which might limit the evolutionary pathways of these viruses.

Since viruses use the host mechanism to replicate, they are restricted in using their own codon. Thus, another interesting area of ​​research involves comparing codon use patterns between viral genes and between viral and host genomes. Interestingly, the human hepatitis virus (HAV) exhibits a unique combination of codons, using codons that appear at a medium frequency in the host, rather than those that are rare or abundant in the host. To understand this unique feature, D’Andrea et al. (2019) conducted an experiment in which they tracked the evolution of the hepatitis C virus under the influence of artificially induced transcription discontinuation, which alters the available RNA pools of the virus. According to the resulting genotype phenotype maps, codon formation affected the robustness of translation and the viability of HAV evolution, with adaptation to transcription stopping involving mutations that significantly affected translation efficiency. In order to gain a better understanding of desirable codons in contexts and how combinations of tandem mutations affect viral growth, van Leuven et al. (2021) A study in which they systematically re-encoded the X174 phage with codons rarely used in the host Escherichia coli. The researchers found that although the additional mutations led to a decrease in viral fitness, the effects were not always linear or consistent across genes, confirming the need for further studies to reveal how selection affects viral codon use.

Another area of ​​study includes understanding the effects viruses have on host organisms. Fedorock et al. (2020) conducted a filamentous analysis of Pseudomonas aeruginosa, which is known to contribute to bacterial pathogenesis by promoting biofilm formation, suppression of phagocytosis by macrophages, and isolation of cationic antibacterial compounds. The study revealed two distinct phylogenetic strains of these phages, each with unique structural properties that may have differential effects on P. aeruginosa virulence and antimicrobial resistance. A study by Simons et al. (2019) investigated the effects of Simian Immunodeficiency Virus (SIV) in Ugandan Red Colobus and found no evidence of chronic immune activation, indicating that, unlike human immunodeficiency virus, SIV does not impair immunity in these primates.

The effects of the virus can also persist for a long time after the viral infection has cleared up. For example, viruses can leave traces in the host’s genome in the form of internal viral elements. Cheng et al. (2020) analyzed the genomes of insects and other arthropods and found evidence of naked virus-like genes in dozens of different taxa that were not previously known to be hosts of this viral strain, thus greatly expanding the host range of naked viruses. Gene transfer agents (GTAs) provide another example of the lasting effect of viruses on hosts. These sequences are so named because they allow the exchange of genetic material between bacteria, although it is believed that they were originally derived from viruses. In fact, according to a study by Kogay et al. (2019), these are often misinterpreted as viral proteins in genetic databases. Kojai and colleagues developed a machine learning algorithm to distinguish true GTAs from their viral homologs based on differences in amino acid composition between the two protein types. With this tool, they identified GTAs in more than half of the alphaproteobacterial genomes examined, expanding the known distribution of these sequences.

Together, these studies provide a deeper understanding of not only the viruses themselves but also the potential lasting effects on their hosts, which include nearly all cellular organisms across the tree of life. Genome Biology and Evolution It continues to provide a platform to post new insights and discuss new methods of investigating outstanding questions in the field of viral evolution.

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