4′-Fluorouridine is an oral antiviral that blocks respiratory syncytial virus and SARS-CoV-2 replication

Preparing antiviral defenses Antiviral drugs are an important tool in the battle against COVID-19. Both remdesivir and molnupiravir, which target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase, were first developed against other RNA viruses. This highlights the importance of broad-spectrum antivirals that can be rapidly deployed against related emerging pathogens. Sourimant et al . used respiratory syncytial virus (RSV) as a primary indication in identifying further drugs that target the polymerase enzyme of RNA viruses. The authors explored derivatives of molnupiravir and identified 4′ fluorouridine (EIDD-2749) as an inhibitor of the polymerase of RSV and SARS-CoV-2. This drug can be delivered orally and was effective against RSV in mice and SARS-CoV-2 in ferrets. —VV

Insights from structural studies of the Cardiovirus 2A protein

Cardioviruses are single-stranded RNA viruses of the family Picornaviridae. In addition to being the first example of internal ribosome entry site utilization, cardioviruses also employ a series of alternative translation strategies, such as Stop-Go translation and programmed ribosome frameshifting. Here, we focus on cardiovirus 2A protein, which is not only a primary virulence factor, but also exerts crucial regulatory functions during translation, including activation of viral ribosome frameshifting and inhibition of host cap-dependent translation. Only recently, biochemical and structural studies have allowed us to close the gaps in our knowledge of how cardiovirus 2A is able to act in diverse translation-related processes as a novel RNA-binding protein. This review will summarize these findings, which ultimately may lead to the discovery of other RNA-mediated gene expression strategies across a broad range of RNA viruses.

DWV 3C protease uncovers the diverse catalytic triad in insect RNA viruses

Deformed wing virus (DWV) is the most prevalent Iflavirus that is infecting honey bees worldwide. However, the mechanisms of its infection and replication in host cells are poorly understood. In this study, we analyzed the structure and function of DWV 3C protease (3Cpro), which is necessary for the cleavage of the polyprotein to synthesize mature viral proteins. We found that the 3Cpros of DWV and picornaviruses share common enzymatic properties, including sensitivity to the same inhibitors, such as rupintrivir. The predicted structure of DWV 3Cpro by AlphaFold2, the predicted rupintrivir binding domain, and the protease activities of mutant proteins revealed that it has a Cys-His-Asn catalytic triad. Moreover, 3Cpros of other Iflaviruses and Dicistrovirus appear to contain Asn, Ser, Asp, or Glu as the third residue of the catalytic triad, suggesting diversity in insect RNA viruses. Both precursor 3Cpro with RNA-dependent RNA polymerase and mature 3Cpro are present in DWV-infected cells, suggesting that they may have different enzymatic properties and functions. DWV 3Cpro is the first 3Cpro characterized among insect RNA viruses, and our study uncovered both the common and unique characteristics among 3Cpros of Picornavirales. Furthermore, the specific inhibitors of DWV 3Cpro could be used to control DWV infection in honey bees.

Improvement of field-deployable metagenomic virus detection by a simple pretreatment method.

As both the current COVID-19 pandemic and earlier pandemics have shown, animals are the source for some of the deadliest viral pathogens, which can spread to humans. Therefore, early detection at the point of incidence is crucial to both prevent and understand the threats posed to human health from pathogens in animal reservoirs. Often, the exact genetic nature of these zoonotic pathogens is unknown and advanced laboratory facilities do not exist in most field settings and therefore the development of methods for unbiased metagenomic and point of incidence detection is crucial in order to identify novel viral pathogens in animals with zoonotic and pandemic potential. Here we addressed some of these issues by developing a metagenomic Nanopore next-generation sequencing (mNGS) method for nucleic acids extracted from clinical samples from patients with SARS-CoV-2. To reduce the non-RNA viral genetic components in the samples, we used DNase pretreatment in a syringe followed by filtration and found that these pretreatments increased the number of SARS-CoV2 reads by > 500-fold compared with no pretreatment. The simple protocol, described here, allows for fast (within 6 hours) metagenomic detection of RNA viruses in biological samples exemplified by SARS-CoV-2 detection in clinical throat swabs. This method could also be applied in field settings for point of incidence detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.

NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

RNA viruses are distributed in various environments, and most RNA viruses have been recently identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify their sequences. Therefore, this study generated a dataset of RNA-dependent RNA polymerase (RdRp) domains essential for all RNA viruses belonging to Orthornavirae. Also, the collected genes with RdRp domains from various RNA viruses were clustered by amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than five. Using the 1,467 HMM profiles, we detected RdRp domains in the RefSeq RNA virus sequences, combined the hit sequences with the RdRp domains, and reconstructed the HMM profiles. As a result, 2,234 HMM profiles were generated from 12,316 RdRp domain sequences, and the dataset was named NeoRdRp. Additionally, using the UniProt dataset, we confirmed that almost all NeoRdRp HMM profiles could specifically detect RdRps in Orthornavirae. Furthermore, we compared the NeoRdRp dataset with two previously reported RNA virus detection methods to detect RNA virus sequences from metatranscriptome sequencing data. Our methods can identify most of the RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. The NeoRdRp can be improved by repeatedly adding new RdRp sequences and can be expected to be widely applied as a system for detecting various RNA viruses from metatranscriptome data.

Covid-19: Systems Transdisciplinary Generalization, Technical and Technological Ideas, and Solutions

Aim/Purpose: The Covid-19 pandemic has created many adverse effects. It overloads the healthcare system, causes deaths, and angers some at anti-covid restrictions. This study examines the feasibility of using technical and technological ideas to overcome these effects. The solution is based on new knowledge about the virus, its nature, formation, and activation in the environment. Background: The rapid spread of a new coronavirus infection is taking place against the background of a lack of time required to create new treatment scenarios for the disease, development, production, and vaccine safety research. In such a situation, it became necessary to gain this time for organizing and conducting events that could reduce the burden on the healthcare system. Methodology: The science that studies the morphology, physiology, genetics, ecology, and evolution of viruses is virology. The modern development of virology is moving towards a more accurate and comprehensive description of the mechanisms of interaction of viruses with the host organism. This contributed to the emergence of genomics, transcriptomics, proteomics, and immunomics. However, in virology, there is no particular discipline that sets itself three fundamental goals: to substantiate a single concept of the emergence of viruses; to study the natural mechanisms of formation of virus molecules in the environment; to describe the natural mechanisms of activation of certain viruses in the environment that cause viral pandemics. As a result, there are many articles among the published scientific articles on viruses dealing with the mechanisms of interaction of viruses with the host organism. However, there are no articles on the natural mechanisms of formation and activation of certain viruses in the environment. In the absence of such specialized articles, we were forced to use the method of systems transdisciplinary generalization of disciplinary knowledge to achieve our article’s purpose. Generalization created new knowledge about the nature of viruses, about the mechanisms of their formation and activation in the environment and cells of biological organisms. It is logical to assume that to synchronize the state of biological objects of all functional ensembles on the planet, it is necessary to create and activate appropriate “technological tools.” We have suggested and proved that RNA viruses play the role of such tools. Piezoelectricity activates viruses. It occurs during the compression and stretching of sedimentary rocks and bases of continental plates in different territories. Contribution: The systems transdisciplinary generalization of the knowledge of scientific disciplines made it possible to edit the concept of viruses, to eliminate stereotypes that arose due to the use of unsuccessful analogies. As a result of this generalization, it was possible to prove that viruses are not intracellular parasites. The virus is a “technological tool” of the planetary organizing component. This “tool” aims to correct the genetic programs of organisms of all functional ensembles (plants, animals, people), which will maintain the state of organisms and the parameters of their metabolism in changing environmental conditions. Findings: The viruses that triggered pandemics in the 20th century and early 21st century are RNA viruses. RNA molecules play the role of “technological tools” that the planetary organizing component uses to carry out short-term and long-term adjustments and constant support of the genetic programs of biological organisms. Therefore, in such a situation, it is advisable to talk not about the fight against the virus but only about eliminating the negative manifestations of the Covid-19 pandemic: reducing the number of people in need of emergency hospitalization, eliminating cases of the acute course of the disease and deaths. It is proposed to use certain technical and technological ideas and solutions to eliminate these negative manifestations. Recommendation for Researchers: This paper recommends that researchers use new interdisciplinary and transdisciplinary approaches. They challenge assumptions and conclusions about the nature of viruses, and the mechanisms of their formation and activation in the environment can initiate. Such new research might describe the mechanisms that form and activate viruses in the environment and the body’s cells. They also might provide practical use of this knowledge to eliminate the multiple speculations and fears that arise against the background of reports of the likely appearance of more deadly viruses and viral infections. Future Research: The results of a systems transdisciplinary generalization of disciplinary knowledge about the nature and purpose of viruses are essential for expanding the horizon of the scientific worldview. Future fundamental research on the mechanisms of objective organizing constituents, a general description given in this article, will contribute to a deeper understanding of chemical and biological evolution mechanisms in which modern humanity is involved. In due time, such an understanding will allow a new look at the existing scenarios of the world socio-economic order, explore and describe new principles of sustainable development of society.