A critique of the use of species and below-species taxonomic terms for viruses—time for change?

The International Committee for the Taxonomy of Viruses (ICTV) regulates assignment and names of virus species and higher taxa through its taxonomy proposal and ratification process. Despite using similar taxonomic ranks to those used elsewhere in biology, the ICTV has maintained the principle that species and other taxa are strictly categories with a formal nomenclature, whereas the viruses as objects are referenced through a parallel inventory of community-assigned virus names. This is strikingly different from common and scientific name synonyms for species used elsewhere in biology. The recent introduction of binomial names for virus species resembling biological scientific names has intensified this confusion in terms within the virology community and beyond. The ICTV taxonomy furthermore does not engage with or regulate classification below species and consequently lacks taxonomic terms or descriptions for important viral pathogens such as polioviruses, severe acute respiratory syndrome coronavirus type 2, HIV-1, and avian influenza as examples. The consequent reliance on community-adopted virus names, genotypes, and other categories often lacks clarity for clinical, biocontainment, and other regulatory purposes. This article proposes a revision of rules and procedures for species and below-species level classification. It recasts virus and virus species names as ‘common’ and ‘scientific’ names that are used in other biology nomenclature codes, each with expanded reference to both object and taxon. It further advocates the creation of a formal below-species taxonomic rank to define a new inventory of approved taxa and specified nomenclature below species. Adoption of the proposed changes will realign virus taxonomy with other biological nomenclatural codes and provide greater transparency and clarity in virology, medical, and regulatory fields

A clash of ideas – the varying uses of the ‘species’ term in virology and their utility for classifying viruses in metagenomic datasets

Species definitions of viruses are frequently descriptive, with assignments often being based on their disease manifestations, host range, geographical distribution and transmission routes. This method of categorizing viruses has recently been challenged by technology advances, such as high-throughput sequencing. These have dramatically increased knowledge of viral diversity in the wider environment that dwarfs the current catalogue of viruses classified by the International Committee for the Taxonomy of Viruses (ICTV). However, because such viruses are known only from their sequences without phenotypic information, it is unclear how they might be classified consistently with much of the existing taxonomy framework. This difficulty exposes deeper incompatibilities in how species are conceptualized. The original species assignments based on disease or other biological attributes were primarily descriptive, similar to principles used elsewhere in biology for species taxonomies. In contrast, purely sequence-based classifications rely on genetic metrics such as divergence thresholds that include or exclude viruses in individual species categories. These different approaches bring different preconceptions about the nature of a virus species, the former being more easily conceptualized as a category with a part/whole relationship of individuals and species, while species defined by divergence thresholds or other genetic metrics are essentially logically defined groups with specific inclusion and exclusion criteria. While descriptive species definitions match our intuitive division of viruses into natural kinds, rules-based genetic classifications are required for viruses known from sequence alone, whose incorporation into the ICTV taxonomy is essential if it is to represent the true diversity of viruses in nature

The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication

Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1–1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-β, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host–pathogen interactions

Cetaceans and Marine Debris: The Great Unknown

Plastics and other marine debris have been found in the gastrointestinal tracts of cetaceans, including instances where large quantities of material have been found that are likely to cause impairment to digestive processes and other examples, where other morbidity and even death have resulted. In some instances, debris may have been ingested as a result of the stranding process and, in others, it may have been ingested when feeding. Those species that are suction or “ram” feeders may be most at risk. There is also evidence of entanglement of cetaceans in marine debris. However, it is usually difficult to distinguish entanglement in active fishing gear from that in lost or discarded gear. The overall significance of the threat from ingested plastics and other debris remains unclear for any population or species of cetaceans, although there are concerns for some taxa, including at the population level, and marine debris in the oceans continues to grow. Further research including the compilation of unpublished material and the investigation of important habitat areas is strongly recommended

Into the brains of whales

Abstract Whilst studies on cetaceans have focused on a few populations of just a few species, various complex behaviours and social structures that support the notion that cetaceans should be regarded as intelligent animals have been revealed. The evidence to support this is reviewed here and is best developed for some odontocete species, although recent studies on minke whales show that the behaviour of baleen whales may be more complex than previously thought. As one consequence of high intelligence, the potential impacts of whaling and other removals may be far greater than they appear and a new approach to the conservation of these species -which takes into account their intelligence, societies, culture and potential to suffer -is advocated.

Exercise therapy for the management of osteoarthritis of the hip joint: a systematic review

Introduction Recent guidelines pertaining to exercise for individuals with osteoarthritis have been released. These guidelines have been based primarily on studies of knee-joint osteoarthritis. The current study was focused on the hip joint, which has different biomechanical features and risk factors for osteoarthritis and has received much less attention in the literature. The purpose was to conduct a systematic review of the literature to evaluate the exercise programs used in intervention studies focused solely on hip-joint osteoarthritis, to decide whether their exercise regimens met the new guidelines, and to determine the level of support for exercise-therapy interventions in the management of hip-joint osteoarthritis. Methods A systematic literature search of 14 electronic databases was undertaken to identify interventions that used exercise therapy as a treatment modality for hip osteoarthritis. The quality of each article was critically appraised and graded according to standardized methodologic approaches. A 'pattern-of-evidence' approach was used to determine the overall level of evidence in support of exercise-therapy interventions for treating hip osteoarthritis. Results More than 4,000 articles were identified, of which 338 were considered suitable for abstract review. Of these, only 6 intervention studies met the inclusion criteria. Few well-designed studies specifically investigated the use of exercise-therapy management on hip-joint osteoarthritis. Insufficient evidence was found to suggest that exercise therapy can be an effective short-term management approach for reducing pain levels, improving joint function and the quality of life. Conclusions Limited information was available on which conclusions regarding the efficacy of exercise could be clearly based. No studies met the level of exercise recommended for individuals with osteoarthritis. High-quality trials are needed, and further consideration should be given to establishing the optimal exercises and exposure levels necessary for achieving long-term gains in the management of osteoarthritis of the hip

Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next?

Blood transfusion is a vital procedure, where transfusion-transmitted infection of hepatitis B virus (HBV) remains an important issue, especially from blood donors with occult hepatitis B virus infection (OBI). Occult hepatitis B virus infection is a complex entity to detect using surrogate blood biomarkers for intrahepatic viral transcriptional activity, requiring a continually refined battery of tests utilised for screening. This review aims to critically evaluate the latest advances in the current blood biomarkers to guide the identification of OBI donors and discuss novel HBV markers that could be introduced in future diagnostic practice. Challenges in detecting low HBV surface antigen levels, mutants, and complexes necessitate ultrasensitive multivalent dissociation assays, whilst HBV DNA testing requires improved sensitivity but worsens inaccessibility. Anti-core antibody assays defer almost all potentially infectious donations but have low specificity, and titres of anti-surface antibodies that prevent infectivity are poorly defined with suboptimal sensitivity. The challenges associated with these traditional blood HBV markers create an urgent need for alternative biomarkers that would help us better understand the OBI. Emerging viral biomarkers, such as pre-genomic RNA and HBV core-related antigen, immunological HBV biomarkers of T-cell reactivity and cytokine levels, and host biomarkers of microRNA and human leucocyte antigen molecules, present potential advances to gauge intrahepatic activity more accurately. Further studies on these markers may uncover an optimal diagnostic algorithm for OBI using quantification of various novel and traditional blood HBV markers. Addressing critical knowledge gaps identified in this review would decrease the residual risk of transfusion-transmitted HBV infection without compromising the sustainability of blood supplies

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