Grapevine viruses in Mexico: studies and reports

Objective: To contribute to the knowledge of the diversity of viruses and the viral diseases reported in grapevines in Mexico to benefit producers and develop comprehensive viral disease control strategies. Design/methodology/approach: The literature search was conducted in databases such as Scopus, Google Scholar, and EBSCO host, using the following keywords alone or in combination: "virus", "plant", "grapevine", "Mexico". In addition, the INIFAP database was consulted alongside undergraduate and postgraduate dissertation theses. Results: Only one academic file was found published in an indexed international journal using the publication finder software; it corresponds to a grapevine virus report in Mexico. However, taking all the consulted sources, several viral diseases associated with nine grapevine viruses have been reported in Mexico. These species are grouped into seven genera and six families. The reports are from Aguascalientes (56%) and Baja California (44%). Three registered viral species are associated with the leafroll complex, three with rugose wood, one with fleck, one with infectious degeneration, and one with red blotch disease. Findings/conclusions: Several grapevine viruses associated with significant diseases have been reported in Mexico. Unfortunately, most of the reports lack detail and follow-up and are not of international access; therefore, the lack of knowledge in Mexico on this subject is significant. Monitoring the epidemiology of viral diseases in the grapevine is necessary, a national and international relevant crop.Objective: To contribute to the knowledge of the diversity of viruses and the viral diseases reported in grapevines in Mexico, in order to benefit producers and develop comprehensive viral disease control strategies. Design/methodology/approach: The literature search was conducted in databases such as Scopus, Google Scholar, and EBSCO host, using the following keywords alone or in combination: "virus", "plant", "grapevine", and "Mexico". In addition, the INIFAP database was consulted, alongside undergraduate and postgraduate dissertation theses. Results: Only one academic file was found published in an indexed international journal, using the publication finder software; the report corresponds to a grapevine virus present in Mexico. However, based on all the consulted sources, several viral diseases associated with nine grapevine viruses have been reported in Mexico. These species have been grouped into seven genera and six families. The reports come from Aguascalientes (56%) and Baja California (44%). Three registered viral species are associated with the leafroll complex, three with rugose wood, one with fleck, one with infectious degeneration, and one with red blotch disease. Findings/conclusions: Several grapevine viruses associated with major diseases have been reported in Mexico. Unfortunately, most of the reports lack detail and follow-up, and they are not readily available for international researchers; therefore, the lack of knowledge about this subject in Mexico is significant. Monitoring the epidemiology of viral diseases in the grapevine —a national and international relevant crop— is necessary

Conclusive Evidence of Replication of a Plant Virus in Honeybees Is Lacking

The recent article by Li et al. (1) lacks adequate evidence to support the authors’ assertion that a plant virus propagates or replicates in honeybees. Instead, it is possible that tobacco ringspot virus (TRSV) virions associate with the honeybee and parasitic Varroa mites in the absence of TRSV replication

Substitution of the premembrane and envelope protein genes of Modoc virus with the homologous sequences of West Nile virus generates a chimeric virus that replicates in vertebrate but not mosquito cells

Background: Most known flaviviruses, including West Nile virus (WNV), are maintained in natural transmission cycles between hematophagous arthropods and vertebrate hosts. Other flaviviruses such as Modoc virus (MODV) and Culex flavivirus (CxFV) have host ranges restricted to vertebrates and insects, respectively. The genetic elements that modulate the differential host ranges and transmission cycles of these viruses have not been identified. Methods: Fusion polymerase chain reaction (PCR) was used to replace the capsid (C), premembrane (prM) and envelope (E) genes and the prM-E genes of a full-length MODV infectious cDNA clone with the corresponding regions of WNV and CxFV. Fusion products were directly transfected into baby hamster kidney-derived cells that stably express T7 RNA polymerase. At 4 days post-transfection, aliquots of each supernatant were inoculated onto vertebrate (BHK-21 and Vero) and mosquito (C6/36) cells which were then assayed for evidence of viral infection by reverse transcription-PCR, Western blot and plaque assay. Results: Chimeric virus was recovered in cells transfected with the fusion product containing the prM-E genes of WNV. The virus could infect vertebrate but not mosquito cells. The in vitro replication kinetics and yields of the chimeric virus were similar to MODV but the chimeric virus produced larger plaques. Chimeric virus was not recovered in cells transfected with any of the other fusion products. Conclusions: Our data indicate that genetic elements outside of the prM-E gene region of MODV condition its vertebrate-specific phenotype

Repurposing Drugs as Potential Therapeutics for the SARS-Cov-2 Viral Infection: Automatizing a Blind Molecular Docking High-throughput Pipeline

In the context of the COVID-19 pandemic, scientists worldwide have been looking for ways to stop it using different approaches. One strategy is to look among drugs that have already proved safe for use in humans and tested for other illnesses. Several components from the virus and the infected cell are the potential therapeutic targets from a molecular perspective. We explain how we implemented a cavity-guided blind molecular docking algorithm into a high-throughput computational pipeline to automatically screen and analyze a large set of drugs over a group of SARS-CoV-2 and cell proteins involved in the infection process. We discuss the need to significantly extend the conformational space sampling to find an accurate target-ligand complex. Our results identify nine drugs with potential multi-target activity against COVID-19 at different stages of the infection and immune system evasion. These results are relevant in understanding the SARS-CoV-2 drug’s molecular mechanisms and further clinical treatment development. The code developed is available on GitHub [https://github.com/tripplab/HTVS]

VIPERdb2: an enhanced and web API enabled relational database for structural virology

VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ (Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids

Evolution of substrate specificity in a retained enzyme driven by gene loss.

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes