Small but mighty: Functional landscape of the versatile geminivirus-encoded C4 protein

The fast-paced evolution of viruses enables them to quickly adapt to the organisms they infect by constantly exploring the potential functional landscape of the proteins encoded in their genomes. Geminiviruses, DNA viruses infecting plants and causing devastating crop diseases worldwide, produce a limited number of multifunctional proteins that mediate the manipulation of the cellular environment to the virus’ advantage. Among the proteins produced by the members of this family, C4, the smallest one described to date, is emerging as a powerful viral effector with unexpected versatility. C4 is the only geminiviral protein consistently subjected to positive selection and displays a number of dynamic subcellular localizations, interacting partners, and functions, which can vary between viral species. In this review, we aim to summarize our current knowledge on this remarkable viral protein, encompassing the different aspects of its multilayered diversity, and discuss what it can teach us about geminivirus evolution, invasion requirements, and virulence strategies.

Clinically Relevant Influenza Virus Evolution Reconstituted in a Human Lung Airway-on-a-Chip

The rapid evolution of viruses, such as influenza viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is challenging the use and development of antivirals and vaccines. Studies of within-host viral evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape viral global evolution as well as development of better antivirals and vaccines.

Cruel Insensibility and an Ethics Without Authority

This article considers the phenomenon of being insensible to animal cruelty, and how such insensibility relates to human transgressions of the planet. I consider the visualization of animal culls that appeared upon the emergence of the coronavirus pandemic. The spectacular wasting of animal life, I argue, discloses the economic logic by which humanity secures itself as a sovereign species. Such a logic and its visuality are not only underpinned by a broader necropolitical paradigm, moreover, they co-constitute a primal scene that enables the liquidation of animal life to the point of extinction. Following the evolutionary biologist Rob Wallace, I consider animal culls in relation to the phenomenon of virus dumping, a systemic perturbation of forest ecologies preceded by the influx of capital in agricultural markets that results in the release and rapid evolution of viruses. I therefore recapitulate the relationship between animal cruelty and the economy of planet wasting that subtends it. In this vein, I consider how the visuality of animal cruelty is predicated on a banal violence. Yet, drawing from Hannah Arendt, I call for an ethics without authority, a version of the Sensus Communis by which we might witness cruelty from within the depths of planetary transgressions.

The human neuronal receptor NgR1 bridges reovirus capsid proteins to initiate infection

Human Nogo-66 receptor 1 (NgR1) is a receptor for mammalian orthoreoviruses (reoviruses), but the mechanism of virus-receptor engagement is unknown. NgR1 binds a variety of structurally dissimilar ligands in the adult central nervous system (CNS) to inhibit axon outgrowth. Disruption of ligand binding to NgR1 and subsequent signaling can improve neuron regrowth, making NgR1 an important therapeutic target for diverse conditions such as spinal crush injuries and Alzheimer disease. To elucidate how NgR1 mediates cell binding and entry of reovirus, we defined the affinity of interaction between virus and receptor, determined the structure of the virus-receptor complex, and identified residues in the receptor required for virus binding and infection. These studies revealed that NgR1 sequences in a central concave region of the molecule establish a bridge between two copies of the viral capsid protein, σ3. This unusual binding interface produces high-avidity interactions between virus and receptor and likely primes early entry steps. NgR1 sequences engaged by reovirus also are required for NgR1 binding to ligands expressed by neurons and oligodendrocytes. These studies redefine models of reovirus cell-attachment and highlight the evolution of viruses to engage multiple receptors using distinct capsid components.

Whole Genome or Single Genes? A Phylodynamic and Bibliometric Analysis of PRRSV

Diversity, ecology, and evolution of viruses are commonly determined through phylogenetics, an accurate tool for the identification and study of lineages with different pathological characteristics within the same species. In the case of PRRSV, evolutionary research has divided into two main branches based on the use of a specific gene (i.e., ORF5) or whole genome sequences as the input used to produce the phylogeny. In this study, we performed a review on PRRSV phylogenetic literature and characterized the spatiotemporal trends in research of single gene vs. whole genome evolutionary approaches. Finally, using publicly available data, we produced a Bayesian phylodynamic analysis following each research branch and compared the results to determine the pros and cons of each particular approach. This study provides an exploration of the two main phylogenetic research lines applied for PRRSV evolution, as well as an example of the differences found when both methods are applied to the same database. We expect that our results will serve as a guidance for future PRRSV phylogenetic research.

Arthropods and the evolution of RNA viruses

Many viruses of arthropods also infect other organisms including humans, sometimes with devastating consequences. Yet, for the vast diversity of arthropods, their associated viruses remain unexplored. Here, we mined meta-transcriptomes from 711 arthropod species, including insects, arachnids, myriapods, and crustaceans, and uncovered more than 1400 previously unknown RNA viruses, representing 822 novel evolutionary groups at a level between species and genus. These newly found viral groups fill major evolutionary gaps within the five branches of RNA viruses, bridging the evolution of viruses infecting early and later diverging eukaryotes. Additionally, co-phylogenetic analysis implies that RNA viruses of arthropods commonly co-evolved with their hosts. Our analyses indicate that arthropods have played a central role in the macroevolution of RNA viruses by serving as reservoirs in which viruses co-evolved with arthropods while being exchanged with a vast diversity of organisms.

COVID-19 PANDEMIC IN THE CONTEXT OF HUMAN SECURITY

The phenomenon of human security aims to combine security with human rights and freedoms as a product of the changing security perception of the West after the Cold War. The concept of human security has transformed security from the perception of “only the absence of threat” to a perception in which elements such as “fears and needs” are also taken into account. However, the new circumstance affected by COVID-19 and the measures taken to combat the pandemic have enforced us to experience a period in which human security is eroded, anxiety becomes the dominant emotion, dif􀏐iculties arise in meeting the existing needs as well as the new needs that are dif􀏐icult to meet. During the COVID-19 pandemic, the concept of human security has been abandoned and the classical protective-restrictive security approach has been adopted due to the wideness of the concept and its dif􀏐icult nature to de􀏐ine, which has criticised many times. In this process, sources such as the hierarchy of rights, the sociality of responsibility and the limit of freedom have constituted the legitimacy of the restrictive measures that had been taken. These extraordinary conditions, which are deemed appropriate for the limitation of rights and freedoms, are listed as a legitimate reason for the limitation of freedom in many legal texts. Another point that provides the legitimacy of struggle in extraordinary situations such as epidemic is the rarity of such cases. However, the world is faced with a problem that will destroy this source of legitimacy. While the world is changing rapidly, viruses that cause epidemics are not at a 􀏐ixed point. The rapid evolution of viruses and the spread of epidemics indicate the possibility of similar the outbreaks like the COVID-19 pandemic in the near future. For this reason, it will not be suf􀏐icient for concepts such as human security to be damaged in such extraordinary situations and to be amended again in the subsequent normalization processes. This study aims to analyze the human security phenomenon, the erosion that it has experienced during the COVID-19 pandemic, its underlying sources of legitimacy and the possible problems to be encountered.

Graphs in Molecular Epidemiology

Graphs and networks are used in molecular epidemiology to model the evolution of viruses and their spread during outbreaks and epidemics. They are instrumental at different stages of the computational pipelines. This includes the inference of transmission networks using viral sequences sampled from infected individuals, and studies of selection and accumulation of mutations in viral populations and their interactions with hosts' immune systems. This chapter describes some algorithmic and graph-theoretic problems associated with these stages to illustrate the relevance of the concepts of graph theory to molecular epidemiology of viral infections. The chapter will demonstrate how graph-theoretic methods combined with the machinery of differential equations, the Bayesian inference, and computational genomics uncover hidden biological and epidemiological patterns of virus evolution and transmission.

Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera

The Betacoronavirus genus of mammal-infecting viruses includes three subgenera (Sarbecovirus, Embecovirus, and Merbecovirus), in which most known human coronaviruses, including SARS-CoV-2, cluster. Coronaviruses are prone to host shifts, with recombination and positive selection possibly contributing to their high zoonotic potential. We analyzed the role of these two forces in the evolution of viruses belonging to the Betacoronavirus genus. The results showed that recombination has been pervasive during sarbecovirus evolution, and it is more widespread in this subgenus compared to the other two. In both sarbecoviruses and merbecoviruses, recombination hotspots are clearly observed. Conversely, positive selection was a less prominent force in sarbecoviruses compared to embecoviruses and merbecoviruses and targeted distinct genomic regions in the three subgenera, with S being the major target in sarbecoviruses alone. Overall, the results herein indicate that Betacoronavirus subgenera evolved along different trajectories, which might recapitulate their host preferences or reflect the origins of the presently available coronavirus sequences.