Biology subjects

Smith, D. B.

Publications and source records attributed to Smith, D. B..

4 recordsLinked to original sources

bioRxiv2026

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Members of the Orthoflavivirus genus in the family Flaviviridae are primarily vector-transmitted RNA viruses infecting humans, other mammals and birds, including major pathogens such as tick borne encephalitis, West Nile, Zika and dengue viruses. Vector-borne flaviviruses are assigned to the Euflavivirus subgenus of orthoflaviviruses, with more divergent largely unclassified insect-specific flaviviruses, including cell fusing agent virus assigned to the second subgenus, Fusivirus. The currently classified 57 orthoflavivirus species have traditionally been assigned descriptively on the basis of their genome and antigenic relatedness, ecology and host and vector tropisms, although many more orthoflavi-like viruses remain unassigned. To investigate whether species might be demarcated using a fixed genetic divergence threshold, we examined distributions of pairwise distances in NS5 and E genes (which encode the RNA-dependent RNA polymerase and envelope protein, respectively) of classified orthoflaviviruses. Demarcation thresholds of 0.1 in the two regions would be most parsimonious with current euflavivirus classification. Exceptions include species in the tick-borne encephalitis virus complex with divergences below the threshold, and dengue virus types currently assigned to a single species that are substantially above. Application of the proposed thresholds would provide the means to establish 25 new euflavivirus and 33 new fusivirus species and reconcile several anomalies and inconsistencies in the current species taxonomy. The use of a species demarcation threshold brings consistency with the classification of viruses in other families. A robust and evolutionarily consistent framework furthermore enables taxonomic assignments of the numerous currently unassigned orthoflaviviruses that lack the phenotypic descriptions required for the current species definition.

microbiology↗

bioRxiv2026

Comprehensive hallmark gene sequence, genomic and structural analysis of Picornavirales viruses clarifies new and existing taxa

The order Picornavirales is a group of highly diverse RNA viruses that includes many pathogens of significance to human and veterinary health, agriculture and the wider environment. However, the wide range of viruses assigned to the order, together with their genomic variability, and the recent description of numerous "picorna-like" viruses derived from metagenomic analyses of environmental samples, challenges the existing taxonomic classification of members of the order and the criteria for their classification. Here, we combine the existing gold standard, hallmark RNA-dependent RNA-polymerase (RdRp) gene sequence-based analysis with helicase sequence-based phylogeny, RdRp structural prediction through the use of ColabFold and Fold Tree, and analysis of coding complete genomes using GRAViTy-V2, to genetically classify 525 Picornavirales genomes and recently described "picorna-like" viruses. All analyses were conducted with a bespoke, fully automated pipeline for retrieval of genomes, domain classification and extraction, phylogenetic analysis, and output conditioning, which is available as open-source software. Our results reveal broad support for existing families as well as for six novel families, and 32 new genera. In instances where inconsistencies were found between classification methods, we demonstrate how examination of the pipelines output may be used to reconcile differences with respect to the genomic features quantified by the analysis. Automated multimodal taxonomic analysis may save significant resources over manual methods and better define demarcation criteria for families and genera.

microbiology↗

bioRxiv2025

Integrated analysis of protein sequence and structureredefines viral diversity and the taxonomy of the Flaviviridae

The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and flavi-like viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order, Amarillovirales, in three families (Flaviviridae, Pestiviridae, and Hepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.

microbiology↗

bioRxiv2019

Developmental exposure to pesticide contaminated food impedes bumblebee brain growth predisposing adults to become poorer learners

Understanding the risk to biodiversity from pesticide exposure is a global priority. For bees, an understudied step in evaluating pesticide risk is understanding how pesticide contaminated foraged food brought back to the colony can affect developing individuals. Provisioning bumblebee colonies with pesticide (neonicotinoid) treated food, we investigated how exposure during two key developmental phases (brood and/or early-adult), impacted brain growth and assessed the consequent effects on adult learning behaviour. Using micro-computed tomography ({micro}CT) scanning and 3D image analysis, we compared brain development for multiple neuropils in workers 3 and 12-days post-emergence. Mushroom body calyces were the neuropils most affected by exposure during either of the developmental phases, with both age cohorts showing smaller structural volumes. Critically, reduced calyces growth in pesticide exposed workers was associated with lower responsiveness to a sucrose reward and impaired learning performance. Furthermore, the impact from brood exposure appeared irrecoverable despite no exposure during adulthood.

ecology↗