RNA phage biology in a metagenomic era

The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies

Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive-sense RNA viruses have been classified in two genera (Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework

Guidance for creating individual and batch latinized binomial virus species names

The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages

Feline low-grade alimentary lymphoma: an emerging entity and a potential animal model for human disease

Background: Low-grade alimentary lymphoma (LGAL) is characterised by the infiltration of neoplastic T-lymphocytes, typically in the small intestine. The incidence of LGAL has increased over the last ten years and it is now the most frequent digestive neoplasia in cats and comprises 60 to 75% of gastrointestinal lymphoma cases. Given that LGAL shares common clinical, paraclinical and ultrasonographic features with inflammatory bowel diseases, establishing a diagnosis is challenging. A review was designed to summarise current knowledge of the pathogenesis, diagnosis, prognosis and treatment of feline LGAL. Electronic searches of PubMed and Science Direct were carried out without date or language restrictions. Results: A total of 176 peer-reviewed documents were identified and most of which were published in the last twenty years. 130 studies were found from the veterinary literature and 46 from the human medicine literature. Heterogeneity of study designs and outcome measures made meta-analysis inappropriate. The pathophysiology of feline LGAL still needs to be elucidated, not least the putative roles of infectious agents, environmental factors as well as genetic events. The most common therapeutic strategy is combination treatment with prednisolone and chlorambucil, and prolonged remission can often be achieved. Developments in immunohistochemical analysis and clonality testing have improved the confidence of clinicians in obtaining a correct diagnosis between LGAL and IBD. The condition shares similarities with some diseases in humans, especially human indolent T-cell lymphoproliferative disorder of the gastrointestinal tract. Conclusions: The pathophysiology of feline LGAL still needs to be elucidated and prospective studies as well as standardisation of therapeutic strategies are needed. A combination of conventional histopathology and immunohistochemistry remains the current gold-standard test, but clinicians should be cautious about reclassifying cats previously diagnosed with IBD to lymphoma on the basis of clonality testing. Importantly, feline LGAL could be considered to be a potential animal model for indolent digestive T-cell lymphoproliferative disorder, a rare condition in human medicine

RNA bacteriophages: diversity, abundance, and applications

We live in a world created by and dominated by microbes, yet we are only beginning to understand this complex and diverse realm. This vast collection of microorganisms (the microbiome) is composed of bacteria, viruses, fungi, archaea, protozoa, and algae, and is essential to every aspect of life and are involved in countless natural processes. While interest in the microbiome has exploded in recent years, studies regarding the viral fraction has lagged behind. This viral component (virome) is dominated by bacteriophages (phages) - viruses that target and infect prokaryotes. They are intrinsically linked to the bacterial community of every ecosystem and potentially dictate the bacterial composition, function, and dynamics through a series of complex interactions. Their roles across global environments, from human gut to marine and terrestrial settings, are only just beginning to be described. While gradual improvements in virome and phageome research have provided us with some insights into the function of these viruses, much more work is needed to gauge their full importance. Of the known phages, those that encode either a double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) genome have been more intensively studied than their RNA counterparts. The RNA phages are either positive-sense, single-stranded RNA (+ssRNA; Leviviricetes) or double-stranded RNA (dsRNA; Cystoviridae) and have been understudied and underrepresented in publicly available databases. This thesis tackled the limited knowledge of these phages, their lifecycles, and our current understandings of their taxonomy. It also explored the potential biases associated with isolating and extracting RNA phages from human faecal samples which may have contributed to their under-representation in many virome studies. Properly isolating and identifying RNA phage is crucial to better understand the diversity of the global microbiome. Given that only limited numbers of +ssRNA phages are present in databases, it was timely to explore their true abundance in different environments by exploiting advances in the science of bioinformatics. Our method, utilizing specific profile hidden Markov model (HMM) search tools, is described in detail. This work greatly expanded the numbers of +ssRNA phage genomes and resulted in the submission to and acceptance of an updated taxonomy by the International Committee on Taxonomy of Viruses (ICTV). The framework depicted in this thesis allows for the expected expansion of these phages in future work. It also offers an example for potential studies looking to combine both cultured and metagenomic-derived genomes in taxonomic updates. It is important that future studies not only optimize the bioinformatic approaches used but also target and improve the isolation and extraction methods applied to enhance the recovery of RNA phages. Since the biases associated with different extraction methodologies have been pinpointed as a crucial factor, three methods were examined and assessed for their efficacy using controls spiked with MS2 and Qbeta. This work was coupled with an in-house study that, using one of these alternative phage-extraction methods, isolated +ssRNA phages from a mammalian gut for the first time in our laboratory. Over the past year, the importance of studying RNA viruses has never been so apparent as a result of the global pandemic due to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its associated disease. However, given that this virus is classified as being extremely pathogenic and subject to high rates of mutation, the idea of using another virus as a safe surrogate has been previously suggested. One such candidate virus is phi6, a dsRNA phage of the Cystoviridae family. With its enveloped structure it offers a reliable model in the examination of different treatments and therapies in terms of their potential in combating SARS-CoV-2. A chapter of this thesis is dedicated to exploring phi6 as a surrogate in lipopeptide exposure and thermotolerance assays. Overall, this thesis investigated the realm of RNA phages. From examining the current literature on their basic biology to biases associated with their recovery from virome studies, the initial two chapters offer a foundation for the four subsequent chapters. In addition, RNA phage numbers were expanded, taxonomically restructured, tracked through different extraction methods, and assessed as a surrogate for SARS-CoV-2. In 1980, Norton Zinder wrote "as long as there are bacteria, there will be RNA phage" and it is suspected that we are just beginning to realize how accurate he was

Right frontal mass presenting as depression with dementia

Case report of a large right frontal mass that presented as a case of depression with a history of dementia without focal neurological signs in which structural imaging was initially not pursued, but subsequently proved essential in clarifying the diagnosis

Phage therapy targeting Escherichia coli - a story with no end?

Bacteriophages (phages) or bacterial viruses have long been proposed as an alternative therapy against antibiotic-resistant bacteria such as Escherichia coli. Even though poorly documented in the scientific literature, a long clinical history of phage therapy in countries such as Russia and Georgia suggests potential value in the use of phages as antibacterial agents. Escherichia coli is responsible for a wide range of diseases, intestinal (diarrhoea) and extraintestinal (UTI, septicaemia, pneumoniae, meningitis), making it an ideal target for phage therapy. This review discusses the latest research focusing on the potential of phage therapy to tackle E. coli-related illnesses. No intact phages are approved in EU or USA for human therapeutic use, but many successful in vitro and in vivo studies have been reported. However, additional research focused on in vivo multispecies models and human trials are required if phage therapy targeting E. coli pathotypes can be a story with happy end

Guidance for creating individual and batch latinized binomial virus species names

International audienceThe International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages

First-in-class thyrotropin-releasing hormone (TRH)-based compound binds to a pharmacologically distinct TRH receptor subtype in human brain and is effective in neurodegenerative models

JAK4D, a first-in-class thyrotropin-releasing hormone (TRH)-based compound, is a prospective therapeutic candidate offering a multifaceted approach to treating neurodegeneration and other CNS conditions. The purpose of these studies was to determine the ability of JAK4D to bind to TRH receptors in human brain and to evaluate its neuropharmacological effects in neurodegenerative animal models. Additionally, JAK4D brain permeation was examined in mouse, and initial toxicology was assessed in vivo and in vitro. We report that JAK4D bound selectively with nanomolar affinity to native TRH receptors in human hippocampal tissue and showed for the first time that these receptors are pharmacologically distinct from TRH receptors in human pituitary, thus revealing a new TRH receptor subtype which represents a promising neurotherapeutic target in human brain. Systemic administration of JAK4D elicited statistically significant and clinically-relevant neuroprotective effects in three established neurodegenerative animal models: JAK4D reduced cognitive deficits when administered post-insult in a kainate (KA)-induced rat model of neurodegeneration; it protected against free radical release and neuronal damage evoked by intrastriatal microdialysis of KA in rat; and it reduced motor decline, weight loss, and lumbar spinal cord neuronal loss in G93A-SOD1 transgenic Amyotrophic Lateral Sclerosis mice. Ability to cross the blood–brain barrier and a clean initial toxicology profile were also shown. In light of these findings, JAK4D is an important tool for investigating the hitherto-unidentified central TRH receptor subtype reported herein and an attractive therapeutic candidate for neurodegenerative disorders. •First-in-class TRH-based compound JAK4D detects new receptor subtype in human brain.•JAK4D elicits statistically significant effects in neurodegenerative animal models.•JAK4D crosses the blood–brain barrier and has a clean initial toxicology profile.•JAK4D is a tool to study central pharmacologically-distinct TRH receptor subtype.•JAK4D is an attractive therapeutic candidate for neurodegenerative diseases